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Objectives • Distinguish between the term’s pharmaceutical, biopharmaceutical, biologic, generic, biosimilar, and drug • Identify the significant milestones in manufacturing a drug; R&D, pre-clinical studies, clinical studies and the application process for new products, & post-market surveillance • Differentiate between the different drug application review processes: NDA, ANDA, BLA, fast track, OTC, priority, and orphan • Explore exceptions to the drug review & patent process • Utilize FDA databases to look up drugs; orange book, clinical trials, drug database • Demonstrate knowledge of Prescription drug labeling and explain limitations to drug advertising This chapter provides an in-depth exploration of the regulations and submission requirements for a new drug. The process of bringing a drug out of development and onto the market is very rigorous, time-consuming, and expensive. By some estimates, the process can take upwards of 15 years, and a typical drug company may spend close to \$800 million to create a marketable new drug. The biggest hurdle a new drug must overcome is the testing required by the FDA. As previously discussed, prescription drugs are regulated under the Federal Food, Drug, and Cosmetic Act of 1938 (FD&C Act). Only about 1 in 5000 potential drugs successfully pass through the testing process to be approved by the FDA for patient use. The FDA has an extensive website outlining the drug development process. 06: The Drug Approval Process Terminology Before we begin diving into the regulation, it's important to understand standard pharmaceutical manufacturing terminology. Here are some relevant key terms. • A pharmaceutical product is a chemical agent that acts on the body to create a therapeutic effect. A therapeutic effect may include the treatment or prevention of symptoms of illnesses, injuries, or disorders in humans and animals. • The term drug applies to pharmaceuticals used in the diagnosis, cure, treatment, and prevention of disease and is substances, which are recognized by an official pharmacopeia or formulary. A new drug refers to drugs in which the safety and effectiveness of an application are not previously known. • A generic drug is the same as a brand-name drug in dosage, safety, strength, how it is taken, quality, performance, and intended use. A generic drug must contain identical amounts of the same active ingredient(s) as the brand name product. The generic drug product must have an equal therapeutic effect as the brand-name drug. • A New Molecular Entity (NME) is an active ingredient that has never been marketed in the United States in any form. • A therapeutic biological product is a protein derived from living material that can be used to treat or cure diseases, such as cells or tissues. • A biopharmaceutical is a specific type of drug created via genetic engineering of an organism. The term ‘biopharmaceutical agent' is synonymous with this kind of drug. • A biosimilar is a biological product, which is ‘biosimilar’ to an FDA-licensed biological product (e.g., Biopharmaceutical, biologic, vaccine, proteins, tissues). • A medical device definition is complicated. A medical device can range from a tongue depressor to a clinical testing kit, to a replacement hip. Due to the specialized complexity of devices and combination applications (for example, birth control implants), we will address device regulation in a later chapter. CDER The branch of the FDA that oversees drugs is the Center for Drug Evaluation and Research (CDER). This FDA Center evaluates a drug for both safety and effectiveness. It's important to note that they do not test the drug themselves but reviews the evidence the company sends them to ensure the drugs are safe and effective. The CDER team is constructed by physicians, chemists, pharmacologists, and other scientists.

textbooks/bio/Biotechnology/Quality_Assurance_and_Regulatory_Affairs_for_the_Biosciences/06%3A_The_Drug_Approval_Process/6.01%3A_Section_1-.txt

Overview New medicines can take upwards of 12 years and costs \$2.6 billion (Phrma, 2015). The first milestone for any new drug occurs during the research and discovery phase. Some form of experimentation in an R&D lab leads to the development of an active pharmaceutical ingredient (API) that may have therapeutic activity in the human body. If the active ingredient is believed to have real potential, the drug moves into the development stage. This early stage of development involves what is known as "preclinical testing," and is carried out in laboratories and animal testing facilities. This preclinical phase must be successful before testing can happen in humans. If the drug performs well during this stage, the company can file an Investigational New Drug Application (IND) with the FDA to request permission to begin testing on human subjects. There are three major phases a drug must pass through during human subject testing (clinical studies). If the drug passes through clinical studies successfully, the company can then submit a New Drug Application (NDA) to the FDA. If the FDA grants its approval, the company can finally begin selling the product, but its involvement does not end there. The FDA will continue to interact with the company to help ensure that the product is manufactured safely. It is important to note that the company that sponsors drug development may not be the company performing the tasks of the development. Contract Research Organizations (CROs) are frequently enlisted and paid to perform specific tasks of drug development. These tasks may include animal testing, human testing, and actual manufacturing. Explore! The FDA provides a simple overview of the drug review process here. Do over-the-counter medications go through the same approval process? Milestones in the Manufacture of a Drug Research and Development The earliest approaches to drug discovery involved identifying and isolating the active components of naturally occurring chemicals, such as those found in plants and other homeopathic remedies. In the modern laboratory, researchers also search for the causative agents of diseases (e.g., missing or over-active proteins) to guide drug research by understanding what problems must be targeted. High Throughput Screening (HTS) is another approach, which enables scientists to screen thousands of potential drugs all at once and allows for quick identification and targeting of potentially useful compounds. Preclinical Development Before testing a drug in humans, it must undergo nonclinical testing to obtain basic toxicity and pharmacological data. Nonclinical testing must include animal models and assays to explore pharmacology, toxicity, reproductive toxicity, and genotoxicity. Preclinical development can take anywhere from 1-4 years and may require further testing to be in conjunction (or in parallel) with clinical studies. The Objectives of Preclinical Development: 1. Identifying the physical and chemical properties of the candidate drug 2. Testing the candidate drug in vitro 3. Determining formulation for administration to test subjects and patients 4. Developing manufacturing methods for the candidate drug 5. Testing the candidate drug in cultured cells 6. Testing the candidate drug in animals for safety 7. Developing analytical assays 8. Securing intellectual property protection for the potential product, its uses, and its manufacture ADME For this potential drug to be useful, it must be stable, safe, and be manufactured practically. This stage is also dedicated to determining the drug's activity, chemical attributes, and solubility and outlining manufacturing schemes to ensure its potential as a drug. If the drug shows potential in the laboratory, the next step requires toxicity tests. These tests are also known as ADME (Absorption, Dissemination, Metabolic, and Excretion) studies. ADME studies are carried out on animals and help researchers determine: • How much of the drug is absorbed by the blood? • How is the substance metabolically altered in the body? • What are the toxicity effects of metabolic by-products? • How quickly will the drug and its by-products be excreted? Toxicity Safety assessment is done using toxicity studies. These studies are conducting using GLP guidelines for 30-90 days, in a minimum of two mammalian species, one of which must be non-rodent. The dosage, length of study, and complexity of study are related to the proposed clinical study; duration and complexity should be equal to or exceed what is proposed in humans. Additionally, if the new drug is also a New Chemical Entity (NCE) and has no long-term human data at all, the study may be required to exceed 12 months. • Reproductive Toxicity. Fertility and embryonic development are also studied extensively in human clinical trials. This includes early embryonic development, embryo-fetal development, as well as pre and post-natal development. • Genotoxicity. Genotoxicity, the propensity to damage genetic information, is also extensively studied in both in-vitro and in vivo. This assessment of mutagenicity is tested in both bacteria and mammalian cells. • Carcinogenicity. Carcinogenicity studies are not required before clinical studies begin and may not have to be done for some products. These studies may take upwards of 2 years to complete. Investigational New Drug Application (IND) If the drug candidate is promising in the preclinical testing, then the company compiles its data and submits a plan to test the drug on human subjects to the FDA, called the Investigational New Drug Application (IND). The IND contains information from animal studies, information relating to the composition and manufacture of the drug, and the investigational plan. The IND application includes a description of the product, the results of animal tests, and the plans for further testing. The FDA then decides whether the company’s materials are sufficiently complete that the company can begin testing the product in humans. The IND is not ‘approved'; rather, it becomes active within 30 days of the FDA receiving it. If deficiencies are discovered, the company is given an opportunity to correct it. If the issues are not addressed, the FDA will put the clinical studies on hold until they are. Some areas of concern for the FDA include unreasonable risk to human health, investigators without the appropriate credentials, and incomplete (or misleading) preclinical data. IND Amendments During the clinical development, the IND must be updated if any changes are made. These amendments may include changes to protocols, new toxicology data from animal studies that extended into the clinical studies, any adverse events, and any new findings that reveal this drug may cause a significant health risk for human volunteers. Clinical Development The government has an interest in protecting the public from defective products and drugs. Therefore, companies must demonstrate their effectiveness and safety before mass distribution. However, the only way they can actively do this is by having human subjects test out their products. As a refresher from the previous chapter on clinical studies, watch this video on clinical trials: youtu.be/pm1igf85uoA Clinical Trials Data Bank As previously discussed, all clinical data is published in the clinical trials data bank at clinicaltrials.gov, which is maintained by the National Institutes of Health (NIH). Companies are required to submit their Phase 2 and 3 clinical data. A company may request to withhold this data if they can prove that it will interfere substantially with a timely clinical study; however, this is up to the FDA.

textbooks/bio/Biotechnology/Quality_Assurance_and_Regulatory_Affairs_for_the_Biosciences/06%3A_The_Drug_Approval_Process/6.02%3A_Section_2-.txt

New Drug Application (NDA) If the drug passes all three phases of testing, the company may file a New Drug Application (NDA), which permits the FDA to ascertain that the new drug (or biologic) is safe, reliable, and effective for the indications on the labeling. The FDA employs expert reviewers who examine the test results and determine whether the new drug can be approved. Types of Drug Applications: 1. Traditional 505(b)(1) NDA – FD&C Act, Section 505(b)(1) 2. 505(b)(2) NDA 3. Abbreviated NDA (ANDA) 505(j) 4. Original BLA – PHS Act, Section 351(a) – for biologics discussed in the next chapter 5. Biosimilar BLA – PHS Act, Section 351(k) – for biosimilars discussed in the next chapter New Application of the Same Drug - Review Process Approval of a new application of the same drug: If a company wants to expand the use of their drug to a new application, previous safety studies are usually still applicable; however, new clinical studies will be required to test the efficacy of the drug for its new application. The 505(b) (1) NDA is the complete application with all the appropriate study information outlined in the CFR that will demonstrate the drug’s safety and effectiveness. The 505(b) (2) NDA can include drugs where safety and effectiveness have been established in previous studies (by other companies), allowing companies to develop treatments quicker with less clinical study volunteers. An example of an application would be instead of a ten-day treatment of the drug, the drug now has a slow-release capsule, so it has only 3-day treatment, but is slowly released over ten days. Abbreviated New Drug Application (ANDA) Interestingly, the term ‘generic drug' is not defined in FDA regulations. A generic drug must have the same active ingredient, same potency, and the same dosage to be sold without having to repeat the extensive clinical trials used in the development of the original, brand-name drugs. Generics must deliver the same amount of active ingredient into a patient's bloodstream over the same period as the brand name – this is referred to as bioequivalence. The rate and extent of absorption of a drug are called its bioavailability. If the bioavailability of the two is similar, the drugs are bioequivalent. An ANDA (505(j)), is an application for approval for a bioequivalent drug product. This application contains data submitted to FDA's Center for Drug Evaluation and Research, Office of Generic Drugs for their review for approval. Generic drug applications are called "abbreviated" because they frequently are not required to include any preclinical (animal) or clinical (human) data to show efficacy and safety. Instead, a generic applicant must scientifically demonstrate that its product has therapeutic equivalence. Therapeutic Equivalence means the drug must have the same clinical effect and safety (under the same labeling) as the non-generic drug and must have the identical active ingredient, with identical strength, quality, purity, and potency. It does not need to have the same inactive ingredients. Once approved, the company can then manufacture and market the generic drug product to provide a low-cost alternative to the brand-name drug. Biological License Application (BLA) A BLA is required for biological products submitted to CBER or CDER (characterized protein). The BLA must include all safety and efficacy information necessary for drug approval. A 351(a) application (Original BLA), contains all the information required and outlined in 21 CFR 601.2. A 351(k) application is an abbreviated BLA for a biosimilar. Although some biologics are overseen by CDER, the BLA process is further explored in the Biologics Regulatory Approval chapter. Expedited Reviews The FDA identifies four expedited approval processes: fast track, breakthrough therapy, priority review, and accelerated approval. These expedited processes can help drugs get to the hands of consumers faster based on their tangible needs, such as treating a serious illness with a new drug or one that is substantially improved over current therapies. Learn more here: www.fda.gov/patients/learnabout-drug-and-device-approvals/fast-track-breakthrough-therapy-accelerated-approval-priority-review 1. Fast Track is a process designed to facilitate the development and expedite the review of drugs to treat serious conditions and fill an unmet medical need to ensure vital new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. 2. Breakthrough Therapy Designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition, and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). 3. Priority Reviews These products represent significant improvements in the safety or efficacy of the treatment of a serious condition compared with currently marketed products. 4. Accelerated Approval This program ensures products for serious conditions are made available earlier in the development process by relying on a surrogate endpoint that may predict a clinical benefit, such as a tumor shrinkage may mean increased survival. Special Drug Incentive Program There are several sponsored programs to encourage the development of a drug that is in demand. The Orphan Drug Act and GAIN (Generating Antibiotic Incentives Now) and the Presidential Emergency Plan for AIDS Relief (PEPFAR) are three examples of special drug incentive programs available. GAIN is an incentive program to develop drugs that treat life-threatening bacterial infections. GAIN drugs get Fast Track and Priority review in addition to 5-year market exclusivity (7 yrs. for orphan drugs!). To learn more about the FDA Safety and Innovation Act visit: www.fda.gov/RegulatoryInformation/LawsEnforcedbyFDA/SignificantAmendmentstotheFDCAct/F DASIA/ucm20027187.htm The FDA does permit the approval of drugs and vaccines intended to counter biological, chemical, and nuclear terrorism without first proving their safety and worth in Phase II and III trials. It would be unethical to deliberately expose humans to harmful radiation or pathogens to test the effectiveness of treatment. For example, the FDA expedited approval of one new drug, Cipro®, an antibiotic that adequately treats those who are exposed to anthrax. The FDA also has a more streamlined process for approval of "orphan drugs" (drugs with small numbers of beneficiaries but with great benefit). Orphan Drugs The FDA administers a program that provides incentives to develop drugs for use in patient populations of rare diseases (200,000 or fewer cases), or if there is a reasonable expectation that the drug will not be developed without FDA assistance. To learn more about rare diseases, see the Office of Rare Diseases Research: http://rarediseases.info.nih.gov/. Companies manufacturing orphan drugs receive the following inducements: seven-year marketing exclusivity, a tax credit for the productassociated clinical research, research design assistance from FDA, and grants Test Your Knowledge! Download and read Case Study 1: Drug Approval: Bringing a New Drug to the Market. We will review this case study https://www.fda.gov/media/94428/download 1. In the case study, Dr. Green has hired regulatory affairs expert Dr. Robert’s, to guide the company’s development and FDA approval of Lowagliflozin, an NME to treat type 2 diabetes. What is an NME, and why does Lowagliflozin qualify as an NME? 2. Explain where Lowagliflozin is in the approval process and the remaining milestones to go. 3. Dr. Green asks the consultant if it is possible to do an expedited review for Lowagliflozin. What is an expedited review? What are the four expedited review programs that the FDA has? What do you think the chances are of obtaining expedited review? 4. Once Lowagliflozin gets FDA approval, is that the end of their interaction with the FDA? Explain. Over-The-Counter (OTC) Drug Review Process Over-the-counter (OTC) drug products are drugs that can be obtained and used without a prescription. More than 300,000 OTC drug products are available in the US. OTC drugs are still overseen by CDER to ensure they are appropriately labeled, and benefits to their use outweigh the risks. To be designated OTC, the drugs must be considered safe, benefits outweigh the risks, and have minimal potential for abuse. OTC drugs can still carry risks, in particular, risks of side effects, drug interactions, or overdose. One example is Tylenol (active ingredient acetaminophen), which most people assume is very safe. However, an overdose of this OTC drug results in over 44,000 individuals in the emergency room and over 400 die each year of liver failure. Learn more here! https://www.sciencedaily.com/releases/2015/06/150622124713.htm Behind the Counter Some OTC drugs are technically kept ‘behind the counter’ such as emergency contraceptive, and pseudoephedrine. Customers are intentionally prevented from direct access to these drugs due to their risk of unintentional or intentional misuse, as with some cold medicines that contain pseudoephedrine. Although a prescription is not required for pseudoephedrine, the pharmacist can dispense only with age and application verification. OTC Drug Development and Review Although many drugs are approved for OTC use through the new drug application (OTC NDA) review process, other OTC medicines are regulated under the OTC Monograph. This process relies on published monographs, which outline acceptable ingredients, doses, formulations, and consumer labeling for OTC drugs. Products that conform to a final monograph, and are generally recognized safe and effective (GRASE), may be marketed without prior FDA clearance. Drugs that are not GRASE may be subject to FDA pre-approval through an NDA either through a direct-to-OTC NDA or prescription-to-OTC designation change. A direct-to-OTC NDA will require the same drug approval process as a prescription drug, except it may need a wider clinical testing population. The cold-sore OTC drug Abreva (docosanol) is an example of a direct-to-OTC application. A more common route is the prescription-to-OTC switch after a patent expires. This route is popular because of the Hatch-Waxman Act, which qualifies companies for a 3-yr extension of patent exclusivity. A prescription-to-OTC route requires a demonstration that the need of doctor oversight is unnecessary; the patient can self-diagnose, and the product has low toxicity. In summary, all OTC drugs must comply with the same regulatory requirements and cGMP regulations for pharmaceuticals, as outlined in 21 CFR 210 and 211. Manufacturing sites must also register with the FDA, be subject to routine inspections, and be drug listed. However, OTC drugs undergo additional scrutiny to ensure they can be used safely and effectively by consumers without medical provider supervision.

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Post-Marketing Surveillance The drug can be manufactured, marketed, and sold once it has been approved. Manufacturing must follow current Good Manufacturing Practices (CGMP), to ensure the quality of the product. Postmarketing surveillance is used to determine the drug’s long-term safety, product quality, and advertising (including social media). Data is collected from patients and doctors, which includes adverse reactions and preventable medication errors. Adverse events (AE) are reported to the FDA by patients, healthcare providers, and facilities through the MedWatch program. Extreme cases of adverse reactions can cause a drug to be withdrawn from the market. The FDA checks for regulatory compliance by performing periodic inspections of production facilities (announced or unannounced) and by testing material samples either provided by the pharmaceutical company or acquired through retail channels. Post-Marketing 15-Day Alert Report Any adverse experience (serious and unexpected) must be reported within 15 days of being informed of the issue. For three years after marketing, the company must also submit a Periodic Adverse Experience Report (PAER), which demonstrates investigation and actions of adverse effects. Patents and Exclusivity Brand-name drug manufacturers have patent exclusivity for 20 years in the US. However, some drugs may qualify for patent & non-patent exclusivities, which can delay the market application of a generic drug. Drug patents are a complex issue in the US due to this specifically. Patent term extension can be given for exclusivity with antibiotic drugs, orphan drugs, pediatric drugs, and prescription-to-OTC designation change, to name a few. The Orange Book Once drugs are approved for the market, they are included in the Approved Drug Products with Therapeutic Equivalence Evaluations (commonly known as the Orange Book because the original had an orange cover). This list provides information for prescription and OTC drugs and biologics and includes therapeutic equivalence evaluations and patent and exclusivity rights. https://www.fda.gov/Drugs/InformationOnDrugs/ucm129662.htm Explore! Go to The Orange Book and search for any drug you currently use: www.accessdata.fda.gov/scripts/cder/ob/default.cfm Prescription Drug Labeling and Advertising The FDA also has authority over labeling and marketing of drugs. Labeling here is not only what is written on the container, but any material associated with the product, including package inserts, Medication Guides, marketing material (direct to consumer and promotional) even social media! 21 CFR 201.56 and 21 CFR 201.57 Guidance for Industry Labeling for Human Prescription Drug and Biological Products. There are specific requirements of labeling outlined in 21 CFR 201, some of which include appropriate placement and prominence of words on the label. All labeling, advertising, and promotional material must be submitted to the FDA for review before product approval. Here is a summary of a few of the guidance documents regarding labeling. 21 CFR 201.57(c)(1) Boxed Warnings & Precautions 21 CFR 201.57(c)(2) Indications & Usage 21 CFR 201.57(c)(3) Dosage & Administration 21 CFR 201.57(c)(4) Dosage forms & Strength 21 CFR 201.57(c)(6) Warnings 21 CFR 201.57(c)(7) Adverse Reactions 21 CFR 201.57(c)(8) Drug Interactions 21 CFR 201.57(c)(10) Drug Abuse & Dependence 21 CFR 201.57(c)(11) Over dosage 21 CFR 201.57(c)(17) Storage and handling Test Your Knowledge! 1. Decide on a drug that influences your life (positive or negative). Why did you choose this drug? 2. Look up your drug on the FDA database and write a one-paragraph summary including its name, who makes it, and what it is used for. https://www.accessdata.fda.gov/scripts/cder/daf/ 3. On the top left corner is the drug’s NDA APPLICATION NUMBER: ________________ 4. Look up the dates of when your drug was approved, and its patent expire date. Search by Application number! www.accessdata.fda.gov/scripts/cder/ob/default.cfm More Study Resources on CDER CDERLearn CDERLearn is an FDA website for training regulatory affairs professionals about drug approval. There are over ten chapters targeting specific areas of drug development. Quite a few significant ones can be found at CDERworld.

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Objectives • Define biologic • Outline the approval process for biologics • Distinguish the different product categories CBER has regulatory authority • Differentiate between a drug, biologic, generic drug, reference product, and biosimilar • 7.1: Introduction to Biologics Biologics are revolutionizing the biotechnology and health sector – and the most important biotechnology products of this century. Biologics include vaccines, tissue transplants, gene therapy, & stem cell treatment and may include biological molecules such as proteins, and nucleic acids, living tissues, and cells. Some biologics treat a disease or disorder, and some diagnose or prevent them. • 7.2: The Center for Biologics, Evaluation, and Research The Center for Biologics, Evaluation & Research (CBER) is the primary Center in the FDA, which oversees the regulation of biologic & related products. We will explore in this chapter the broad range of biological products CBER reviews. There are three main review offices in CBER; Office of Blood Research and Review (OBRR); Office of Cellular, Tissue and Gene Therapies (OCTGT); and the Office of Vaccine Research and Review (OVRR). • 7.3: Processes for Drug Approval The FDA regulates clinical studies in the US, and unapproved drugs and biologics must be conducted under an Investigational New Drug Application (IND). The IND is continually updated with new protocols, study data, and annual reports. The IND for a biologic must contain administrative information, preclinical research results, any previous human experience with the drug, and the clinical protocol. The IND is never approved; rather, it is pending, active, on hold, or partial hold. • 7.4: Office of Compliance & Biologics Quality (OCBQ) • 7.5: Labeling Labeling here is referring to the display of written or printed material on the container or an enclosed document. Labeling includes both FDA approved labelings such as container labels, professional labeling in the package insert (PI – prescribing information), patient labeling (PPI – patient package inserts), medication guides, and instructions for use. But also, any promotional material. 07: The Regulation of Biologics Biologics are revolutionizing the biotechnology and health sector – and the most important biotechnology products of this century. Biologics include vaccines, tissue transplants, gene therapy, & stem cell treatment and may include biological molecules such as proteins, and nucleic acids, living tissues, and cells. The official definition for a biologic – or a therapeutic biological product - is "any virus, therapeutic serum, toxin, antitoxin, vaccine, blood, blood component or derivative, allergenic product, or analogous product” (Public Health Services Act, 1944). Some biologics treat a disease or disorder, and some diagnose or prevent them. According to the Public Health Services Act (PHS Act) Section 351 (a) to manufacture and sell a biologic in the US, you must apply and receive a Biologics License (BLA). Since some biologics are considered drugs, they must comply with the FD&C Act Title 21 of the CFR pts 210 and 211 for CGMP and may be overseen by CDER. History of Biologics Regulation In 1902, the 57th United States Congress passed the Biologics Control Act in response to the death of children from contaminated vaccines in two separate incidences. This Act set a precedent to "regulate the sale of viruses, serums, toxins, and analogous products in the District of Columbia; to regulate interstate traffic in said articles, and for other purposes, and mandated producers of vaccines be licensed annually for the manufacture and sale of antitoxins, serum, and vaccines" (fda.gov). https://history.nih.gov/exhibits/history/docs/page_03.html In 1930 the National Institutes of Health was born and in 1937, created the Division of Biologics Control. It was not until 1972 that this division was transferred to the FDA and renamed the Bureau of Biologics, and in 1988, it was moved to the Center for Biologics, Evaluation & Research (CBER). CBER’s regulatory authority is derived from Section 351(a) of the PHS Act of 1944, which required Product License Applications. As you have probably noticed the definition of drug and biologic overlap and have resulted in confusion about which Center would oversee biologics that act like drugs. The FDA's stated policy is to review each product on a case-by-case basis to determine the Center of oversight, which is usually based on the drug's Primary Mode of Action (PMoA). In 1991, CBER & CDER executed an Intercenter Agreement (ICA) to attempt to clarify the regulation of biologics by outlining which of the Centers should regulate which products. They also clarified combination products in this agreement. Further, in 2003, the FDA transferred some of the therapeutic biological products (well-characterized proteins) from CBER to CDER, hoping to strengthen the product divisions. In 2009, the Biologics Price Competition and Innovation Act (BPCI Act) created an abbreviated approval pathway for biosimilars. Moreover, in 2014, the FDA released new draft guidance on market exclusivity for biological products approved under 351(a) of the PHS Act. Depending on the regulatory pathway, a product may have differing premarket submissions channels. It is important for a company to quickly establish the path to take since it affects not only the final approval, but approval on every step of the process, including pre-clinical, and clinical studies. Depending on the assigned Center the product may require a BLA or NDA, and in the case of some combination products, a PMA. More on approvals later in this chapter. The FDA has a review process to help clarify confusion, called the Request for Designation Process (RFD). The RFD helps establish a formal designation of which Center will oversee the regulatory process for combination products or for products where there is no clear jurisdiction. Jurisdictional updates are posted to the FDA website

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CBER Offices and Divisions The Center for Biologics, Evaluation & Research (CBER) is the primary Center in the FDA, which oversees the regulation of biologic & related products. We will explore in this chapter the broad range of biological products CBER reviews. There are three main review offices in CBER; Office of Blood Research and Review (OBRR); Office of Cellular, Tissue and Gene Therapies (OCTGT); and the Office of Vaccine Research and Review (OVRR). It is important to note here that CBER does oversee medical devices that are associated with the collection and testing of licensed blood and cellular products. CBER states its mission “To ensure the safety, purity, potency, and effectiveness of biological products including vaccines, blood and blood products, and cells, tissues, and gene therapies for the prevention, diagnosis, and treatment of human diseases, conditions, or injury. Through our mission, we also help to defend the public against the threats of emerging infectious diseases and bioterrorism.” (FDA, 2016) Biologics Product Categories 1. Allergenics are allergen extracts, allergen patch tests, and antigen skin tests 2. Blood & Blood Products Blood, Blood Components, Blood Bank Devices, Blood Donor Screening Tests 3. Cellular & Gene Therapy Products Gene-based Treatments, Cell-based Treatments, Cloning 4. Tissue & Tissue Products Bone, Skin, Corneas, Ligaments, Tendons, Stem Cells, Sperm, Heart Valves 5. Vaccines for Use in Children and Adults, Tuberculin Testing 6. Xenotransplantation Transplantation of Non-Human Cells, Tissues or Organs into a Human Allergenics "Allergen extracts are used for the diagnosis and treatment of allergic diseases. This may include general seasonal allergies such as hay fever, or more severe allergies such as bee venom or food allergy. Currently, there are two types of licensed allergen extracts; injectable extracts and sublingual extract tablets. You are probably most familiar with injectable allergen extracts that are used for both diagnosing allergies as well as treating them. These extracts are manufactured from natural substances such as insect venom, animal hair protein, and pollens. Sublingual allergen extract tables are used for treatment only of allergic reactions. Allergen Patch tests are diagnostic tests applied to the surface of the skin by healthcare providers to determine the cause of contact dermatitis. Antigen skin tests are diagnostic tests injected into the skin to aid in the diagnosis of infection with certain pathogens" (fda.gov). Blood & Blood Products "CBER regulates the collection of blood and blood components used for transfusion or the manufacture of pharmaceuticals derived from blood and blood components, such as clotting factors, and establishes standards for the products themselves. CBER also regulates related products such as cell separation devices, blood collection containers, and HIV screening tests that are used to prepare blood products or to ensure the safety of the blood supply. CBER develops and enforces quality standards, inspects blood establishments, and monitors reports of errors, accidents, and adverse clinical events" (fda.gov). Cellular & Gene Therapy Products "CBER regulates cellular therapy products, human gene therapy products, and certain devices related to cell and gene therapy. Cellular therapy products include cellular immunotherapies, which includes both adult and embryonic stem cells. Human gene therapy refers to products that introduce genetic material into a person’s DNA to replace faulty or missing genetic material, thus treating a disease or abnormal medical condition. Although some cellular therapy products have been approved, CBER has not yet approved any human gene therapy product for sale" (fda.gov). Explore! To learn more about how the FDA regulates Gene Therapy products, watch the following video. What regulations must companies follow for Gene Therapy products? Tissue & Tissue Products "Human cells or tissue intended for implantation, transplantation, infusion, or transfer into a human recipient is regulated as a human cell, tissue, and cellular and tissue-based product under 21 CFR Parts 1270 and 1271. Parts 1270 and 1271 require tissue establishments to screen and test donors, to prepare and follow written procedures for the prevention of the spread of communicable disease, and to maintain records. FDA has published three final rules to prevent the introduction, transmission, and spread of communicable disease; one final rule requires firms to register and list their HCT/Ps with FDA; the second rule requires tissue establishments to evaluate donors for infectious diseases; and the third final rule establishes current good tissue practices for HCT/Ps. It's important to note here that CBER does not regulate the transplantation of human organ transplants such as liver, kidney, or heart" (fda.gov) Vaccines "Vaccines, as with all products regulated by FDA, undergo a rigorous review of laboratory and clinical data to ensure the safety, efficacy, purity, and potency of these products. Vaccines approved for marketing may also be required to undergo additional studies to further evaluate the vaccine and often to address specific questions about the vaccine's safety, effectiveness, or possible side effects. According to the Centers for Disease Control and Prevention, vaccines have reduced preventable infectious diseases to an all-time low, and now few people experience the devastating effects of measles, pertussis, and other illnesses. Many of these are childhood vaccines that have contributed to a significant reduction of vaccine-preventable diseases" (fda.gov) Xenotransplantation According to the FDA, xenotransplantation is “any procedure that involves the transplantation, implantation or infusion into a human recipient of either (a) live cells, tissues, or organs from a nonhuman animal source, or (b) human body fluids, cells, tissues or organs that have had ex vivo contact with live nonhuman animal cells, tissues or organs” (FDA.gov). Organ transplant needs currently outpaces the supply, with over ten patients die each day waiting for an organ transplant, and xenotransplantation is one viable option.

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IND Process for Biologics - 21 CFR 312 The FDA regulates clinical studies in the US, and unapproved drugs and biologics must be conducted under an Investigational New Drug Application (IND). The IND is continually updated with new protocols, study data, and annual reports. The IND for a biologic must contain administrative information, preclinical research results, any previous human experience with the drug, and the clinical protocol. It’s important to reiterate the IND is never approved; rather, it is pending, active, on hold, or partial hold. To learn more about IND in biologics, the OCTGT has a website called OCTGT Learn. On the site, there are many videos and activities to find out more about the approval process for Biologics, including this video on IND approvals. Explore! Approved Biologics are listed at the FDA website here: Approved Biologics. Look around the site – are there any classes of biologics that surprise you that the CBER regulates? Click on “Biological Approvals by Year.” How many BLAs were approved in all of last year? Find a BLA from this list that interests you. Summarize the product information and supporting documents. Submitting a BLA Biologic license applications (BLAs) are the formal submissions of data when companies are seeking approval to market a biologic in the United States. BLAs for biologics are submitted to CBER, and BLAs for well-characterized proteins are submitted to CDER. BLAs are like an NDA in that they must provide the efficacy and safety information required for approval for use in humans; administrative information, CMC information, preclinical and clinical studies, and labeling. There are two different types of BLAs: full, stand-alone BLAs (351(a)) filed for approval of an originator biological product, and abbreviated BLAs (351(k)) filed for approval of a biosimilar product. The BLAs are regulated under 21 CFR Parts 600-680. BLAs must contain administrative information, the CMC, preclinical studies, clinical data, and labeling The Purple Book “In 2014, the FDA released the Purple Book, a listing of all biological products. The Purple Book will serve as a helpful resource to assist the pharmaceutical industry in determining the earliest date at which a biosimilar or interchangeable product could be licensed. Because biosimilar and interchangeable biological products will be listed under the corresponding reference product, users can also easily see if there is a biosimilar product or interchangeable biological product licensed” (FDA.gov). Explore the purple book, here: www.fda.gov/drugs/therapeutic-biologics-applications-bla/purple-book-lists-licensedbiological-products-reference-product-exclusivity-and-biosimilarity-or Biosimilars & BPCI Act In 2010, President Obama signed into law the Affordable Care Act, which included the Biologics Price Competition and Innovation Act (BPCI Act) - an amendment of the PHS Act - to create an abbreviated licensure pathway for products that are demonstrated to be ‘biosimilar.' Biosimilars are biotherapeutic products that are interchangeable (similar regarding efficacy, safety, and quality) with the FDA-licensed product. They are not ‘generic’ in that they are not exact copies; the complexity of biologics precludes the ability for them to be identical. The FDA has a Multi-Step Approach for Drug Approval for Biosimilars 1. Structural analysis 2. Functional assays (ex. Bioassays) 3. Animal data (ex. Toxicology) 4. Human Clinical Studies Approval of a biosimilar application may not occur until 12 years after the date on which the reference product was first licensed. Patents of biological products are started to expire by 2012, and we quickly saw approvals for biosimilars. “On March 6, 2015, Zarxio obtained the first approval of the FDA. [9] Sandoz's Zarxio is biosimilar to Amgen's Neupogen (filgrastim), which was originally licensed in 1991. This is the first product to be passed under the Biologics Price Competition and Innovation Act of 2009 (BPCI Act), which was passed as part of the Affordable Healthcare Act. However, Zarxio was approved as a biosimilar, not as an interchangeable product, the FDA notes. Moreover, under the BPCI Act, only a biologic that has been approved as an "interchangeable" may be substituted for the reference product without the intervention of the health care provider who prescribed the reference product. The FDA said its approval of Zarxio is based on a review of evidence that included structural and functional characterization, animal study data, human pharmacokinetic and pharmacodynamic data, clinical immunogenicity data and other clinical safety and effectiveness data that demonstrates Zarxio is biosimilar to Neupogen.” (Wikipedia, Biosimilar, 2017). US Approved Biosimilars https://en.Wikipedia.org/wiki/Biosimilar Date of Biosimilar Approval Biosimilar Product Original Product March 6, 2015 [20] filgrastim-sndz/Zarxio filgrastim/Neupogen April 5, 2016 [21] infliximab-dyyb/Inflectra infliximab/Remicade August 30, 2016 [22] etanercept-szzs/Erelzi etanercept/Enbrel September 23, 2016 [23] adalimumab-atto/Amjevita adalimumab/Humira April 21, 2017 [24] infliximab-abda/Renflexis infliximab/Remicade August 25, 2017 [25] adalimumab-adbm/Cyltezo adalimumab/Humira September 14, 2017 [26] bevacizumab-awwb/Mvasi bevacizumab/Avastin December 1, 2017 [27] trastuzumab-dkst/Ogivri trastuzumab/Herceptin December 13, 2017 [28] infliximab-qbtx/Ixifi infliximab/Remicade May 15, 2018 [29] epoetin alfa-epbx/Retacrit epoetin alfa/Procrit June 4, 2018 [30] pegfilgrastim-jmdb/Fulphila pegfilgrastim/Neulasta November 28, 2018 [1] rituximab-abbs/Truxima rituximab/Rituxan Biosimilar Products - Terminology To understand biosimilar products and their regulation, it is necessary to be clear on the terms used to describe these types of products. The FDA recently released a consumer update web page on Biosimilars. The following are definitions and explanations from the FDAs training website on biosimilars. • "A generic drug is bioequivalent to a brand name drug in dosage form, safety, and strength, route of administration, quality, performance characteristics, and intended use. Generic drugs are chemically identical to the brand-name drug. As a result, different manufacturers can produce what are essentially exact copies of the brand name product" (fda.gov). • "Biological products are medical products which are larger and more complex molecules than drugs, and therefore are harder to characterize. Many of these products are produced in a living system, such as a microorganism or plant or animal cell. The nature of biological products creates unique challenges that do not exist in small molecule drugs. There are many types of biological products." • "A reference product is a biological product approved by the FDA under the Public Health Service Act based on a full complement of product-specific data, including nonclinical and clinical data. A biosimilar product is approved based on a showing that it is highly similar and has no clinically meaningful differences regarding safety, purity, and potency (safety and effectiveness) from the reference product" (fda.gov). • "A biosimilar product is a biological product that is highly like the reference product with minor differences in clinically inactive components. It has no clinically meaningful differences in safety and effectiveness from the reference product. Biosimilar products will have some differences from the reference product because of the complexity and inherent variability of biological products. However, these differences must not result in clinically meaningful differences regarding safety, purity, and potency (safety and effectiveness) as compared to the reference product" (fda.gov). Test Your Knowledge! Review this FDA course on Biosimilars. You can click on the webinar link and also download the slides: https://www.accessdata.fda.gov/cder/bio/course/framework/index.html 1. In your own words, define a biosimilar and a reference product. 2. What is the difference between a generic drug and a biosimilar? 3. What year were biosimilars approved for marking in the US? 4. What is the BPCI Act, and why is it important for biosimilars? 5. True or False: To approve biosimilars, the FDA requires companies to independently establish safety and effectiveness for the biosimilar. 6. True/False: Slight differences between the biosimilar and reference products are okay and expected. Complexity of Biosimilar Manufacturing There is an inherent variability like biological products – and it is important to ensure lot-to-lot variation is minimal and has no effect on safety and efficacy. A small change in production may have a significant effect on the product. Therefore, it's important to understand this variability to maintain product quality, potency, safety, and efficacy. The degree of variability should be characterized and controlled within specifications to assure lot-to-lot consistency. This variability is limited by testing the in-process material and final product to ensure that the important quality attributes of the product are kept within an expected range. According to the FDA, Critical quality attributes are physical, chemical, biological, or microbiological properties or characteristics of a product that defines the product's function and may affect safety and efficacy. Here are some relevant specification terms to familiarize yourself with: 1. Acceptable Variability: Some degree of variability is acceptable if the intended use is unaffected by this variability. 2. Variability Controls: Variability is tightly controlled by understanding, monitoring, and validating the manufacturing process and assessed by lot release specifications. 3. Specification Defined: A specification is defined as a list of tests, references to analytical procedures, and appropriate acceptance criteria, which are numerical limits, ranges, or other criteria for the tests described (fda.gov). 4. Specification Criteria: Specifications establish the set of criteria to which a drug substance, drug product, or materials at other stages of the biological product's manufacturer should conform to be considered acceptable for its intended use. 5. Lot Release Specification: Lot release specifications are quality standards that are proposed and justified by the manufacturer and approved by the FDA as conditions of approval to ensure the product is safe and effective over its shelf life. Abbreviated Approval Pathway A biosimilar product can be approved based on existing knowledge about reference products – including safety and effectiveness of the reference product. The goal of approval is to demonstrate it to be biosimilar to a reference product and allows products are manufactured faster and at a lower cost than other biologicals without having to repeat clinical studies in humans. The important aspect of the abbreviated approval pathway is a robust analytical characterization of the product, which must demonstrate through structural and functional testing the product to be biosimilar to the reference product. All the general requirements in place for a biological product apply to a biosimilar product including a comprehensive CMC in addition to following CGMP regulations. Although this abbreviated pathway offers a shorter timeline for approval of the biosimilar product, this product must still meet the same manufacturing standards as a biological product. The FDA has a rigorous and science-based approach for the development and approval of biosimilar products. Characterization of a Biosimilar 1. Analytical Studies 2. Animal Studies 3. Clinical PK/PD studies 4. Clinical Immunogenicity assessment 5. Additional Clinical Studies There is one important point to note about any differences that arise. Residual uncertainty about biosimilarity is a concept related to differences observed between the proposed biosimilar product and the reference product, and whether those differences could affect safety, purity, or potency (safety and effectiveness). When differences are identified, they must be evaluated to determine the potential impact. Any potential impact of the differences in safety, purity or potency (safety and effectiveness) should be addressed and supported by appropriate data and information. If there is any uncertainty of biosimilarity of the product to the reference standard after completing analytical, animal, and PK/PD studies and immunogenicity assessment, the manufacturer may have to perform additional clinical data to address this uncertainty. The FDA uses the data in its entirety on a risk-based assessment to approve the product.

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Preapproval Inspections for Biologics Part of the BLA process includes a pre-license inspection, as outlined in the CFR. The inspector is looking for all the related operation facilities during all phases of manufacturing. These checks typically happen about halfway through the review cycle. The Division of Manufacturing and Product Quality in CBER's Office of Compliance and Biologics Quality (OCBQ) are responsible for the inspections of biologic drugs and devices. The Division of Blood Applications in CBERS OBRR is the lead for blood and blood product applicant inspections. Office of Compliance & Biologics Quality Activities The compliance activities related to biologics are customarily overseen by CBER's Office of Compliance & Biologics Quality (OCBQ). The OCBQ has many important activities within CBER and the approval of a biologic, including inspection and compliance activities, pre- and post-market approval activities, and compliance. It's important to note here that the FDA has limited recall authority – and recall of biologic products is voluntary. If CBER identifies areas of noncompliance it may issue a Regulatory Action Letter, revocate the BLA that has been published on that product (or even other products from the same company/facility), seizure, and injunction as well. More on FDA enforcement in a later chapter. Below is an overview of the compliance activities of the OCBQ. This excerpt is from the OCBQ website: https://www.fda.gov/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/ucm331317.htm OCBQ Inspection, Surveillance, and Compliance Activities • Ensures the quality of products regulated by CBER over their entire lifecycle through pre-market review and inspection, and post-market review, surveillance, inspection, outreach, and compliance. • Monitors the quality of marketed biological products through surveillance, inspections, and compliance programs; reviews, evaluates and takes appropriate compliance action • Reviews and evaluates all administrative action recommendations including suspension, revocation, denial of a license, disqualification of investigators, and recommended civil and criminal actions, including seizures, injunctions, and prosecution based on findings of inspections and investigations • Directs the biologic product shortages program for CBER-regulated products. • Directs the recall program for CBER-regulated products. • Directs CBER's bioresearch monitoring program, and takes appropriate compliance actions • Biological Product Deviation and Blood Collection and Transfusion Related Fatality Reports OCBQ Pre- and Post-Market Approval Activities • Leads pre-approval and pre-license inspections • Provides assessment of the compliance status of regulated establishments within CBER's purview • Evaluates proposed proprietary names to avoid potential medication errors related to look-alike and proprietary sound-alike names and mitigating other factors that contribute to medication errors • Provides consultative reviews of proposed product labeling • Plans and conducts tests on biological products and conducts research to develop and improve procedures to evaluate the safety, efficacy, and purity of biological products • In cooperation with other Center components, as appropriate, tests biological products submitted for release by manufacturers Compliance-Related Policy Activities • Advises the Center Director and other Agency officials on emerging and significant compliance issues for biological products and serves as CBER's focal point for surveillance and enforcement policy • Develops, with other CBER/Agency components, policies and compliance standards for biological products, including Current Good Manufacturing Practice (CGMP) regulations; ensures the uniform interpretation of standards and evaluates industry's conformance with CGMP in manufacturing biological products 7.05: Section 5- Labeling Labeling here is referring to the display of written or printed material on the container or an enclosed document. Labeling includes both FDA approved labelings such as container labels, professional labeling in the package insert (PI – prescribing information), patient labeling (PPI – patient package inserts), medication guides, and instructions for use. But also, any promotional material. Four Types of Prescription Drug Labeling 1. Professional Labeling: Also referred to as prescribing the information and package insert contains the necessary information for a safe and effective product for use by the healthcare provider (doctor). The Physician Labeling Rule (PLR) applies here and is covered by 21 CFR 201.56-57. This label has three sections: Full prescribing information, highlights of prescribing information, and the table of contents. 2. Patient Labeling: This includes PPI and medication guides for patients and is covered by 21 CFR 208.1(a) and (b). Medication guides are required when it could help prevent a severe adverse effect by providing the patient with information about a known serious side effect and how the patient should adhere to the directions of use when crucial to the effectiveness of the drug. 3. Container Label: The container or carton labels for biologicals are covered under 21 CFR 610.60- 61 and must contain the name of the product, the manufacturer's name and contact information, lot identifiable number, expiration date, recommended dose, for prescriptions must state ‘Rx only,' and must include the medication guide. In certain cases, this list may be expanded to include such things as storage conditions, preservatives, adjuvant, if present, and product source. 4. Structured Product Label (SPL): SPLs are posted publicly at labels.fda.gov/, an online label repository, which allows consumers to research labels and download information from this repository. The purpose of this site is to provide a single place where healthcare providers can access accurate and up to date information quickly. Advertising and Promotion The FDA distinguishes in its regulations between promotional and non-promotional activities. Product communications intended to be non-promotional must not make product claims, or they will be subject to FDA regulations. Regulated promotional materials may include advertisements on TV, in magazines, on the radio, and even on social media! For prescription advertising, the FDA has jurisdiction, and both CDER and CBER are responsible for promotional labeling for biologics. In CBER, APLB oversees labeling (OPDP in CDER). The bottom line for advertising is the labeling must be consistent with the FDA-approved labeling, must be backed by considerable evidence, and must not be misleading.

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Objectives • Understand how the FDA classifies a medical device • Describe how FDA regulates approvals: PMN, PMA, IDE, and IRB • Understand regulations that govern medical devices • Explore and apply CFR 82 • Differentiate between Class I, II, & III medical devices • Distinguish between IVD, IUO, RUO, LTD, GPR, & ASR • Understand ISO 13485 and why it is important in device regulation even though it is regulated by the FDA through CFR 820 • Provide examples of combination products 08: Medical Device and Combination Products Introduction to Medical Devices Defining what a medical device is can be a bit complex. A medical device can range from a Band-Aid to a tongue depressor, to a clinical testing kit, to a replacement hip. Due to the functional complexity of devices and combination applications (for example, birth control implants), the regulations can also be very complex and specialized as well. The Medical Device Product Classification database lists over 6,000 types of medical devices regulated by FDA's Center for Medical Devices and Radiological Health (CDRH) and the classification assigned to each type. Depending on the device classification, along with other factors, federal regulations (such as the Code of Federal Regulations, Title 21) define requirements that must be fulfilled for CDRH to approve or clear devices sold in the United States. In this chapter, we will look at a broad overview of medical device regulation, including different categories of devices, regulations that apply, and the approval process. As defined by 201(h) of the FD&C Act, a medical device is "an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or intended to affect the structure or any function of the body of man or other animals…" (fda.gov) Explore! Explore at the FDA website examples of medical devices: www.fda.gov/medicaldevices/device-approvals-denials-and-clearances/recently-approved-devices. What are some examples of items you didn't know are classified as devices? (look at the left-hand tabs) The FDA began regulating medical devices in 1938 under the FD&C Act. Under this act, the FDA focused on adulteration but not safety. It was not until the 1960s where the FDA began looking at areas of safety and effectiveness and was amended in 1976 to include setting standards and premarket approval. The Center for Devices and Radiological Health (CDRH) The Center for Devices and Radiological Health (CDRH) oversees the regulation of medical devices and radiation-emitting products. However, in 1991, the FDA created an inter-center agreement that gave the Center for Biologics Evaluation and Research (CBER) full responsibility to devices related to blood and cellular products. Later on, combination products. Medical devices must be registered and listed with the FDA. Even if they do not sell the device here in the US, they still must register with the FDA. The CDRH department has an entire website dedicated to medical device training called CDRHLearn. https://www.fda.gov/training-and-continuing-education/cdrh-learn Medical Device Registration (21 CFR 807) All medical devices (both domestic and foreign) must be registered and listed with the FDA. Explore! Go to CDRHLearn and Click on "Start here," click on "Overview of Regulatory Requirements" video, and watch this comprehensive 30min video on medical device regulation. Provide any interesting notes below Classification of a Medical Device (21 CFR 860) Medical devices are regulated based on the relative risk posed by the product and organized by class. A Class I device is the lowest risk device, Class II is an intermediate risk and, Class III are high-risk devices. • Class I: A Class I device is a relatively low-risk device with minimal safety considerations for the consumer; safety is assured through a general set of guidelines called "general controls." Examples of a Class I device include prescription sunglasses or elastic bandages. There are currently approximately 780 Class I devices on the market. General Controls include Adulteration/Misbranding, Electronic Establishment, Registration, Electronic Device Listing, Premarket Notification [510(k)], Quality Systems, Labeling, and Medical Device Reporting (MDR). • Class II: Most devices are classified as Class II, an intermediate-risk device that is subject to "special controls" to assure safety. The majority of Class II devices are subject to premarket review and clearance by FDA through the 510(k)-pre-market notification process and may have rigorous review requirements in-line with a Class III device. Examples include pregnancy tests and motorized wheelchairs. There are currently over 800 Class II devices on the market. • Class III: A Class III device is a high-risk device and includes devices that may be implanted or support life. Also, devices that are new in technology, and there is no substantially equivalent device currently available, must follow Class III regulations. Examples of a class III device include a pacemaker. Class III devices are subject to the most rigorous review process that includes general controls, special controls, and premarket approval. There are fewer than 120 Class III devices currently on the market. Explore! Learn More! Classify your medical device! Go into the Classification database and search for "wheelchair." What classification comes up? Search for a device you’re curious about. Medical Device Classification: 21 CFR 862-892 "Most medical devices can be classified by finding the matching description of the device in Title 21 of the CFR, Parts 862-892. FDA has classified and described over 1,700 distinct types of devices and organized them in the CFR into 16 medical specialty panels such as cardiovascular devices or in vitro diagnostics” 862 = Chemistry/Toxicology 864 = Hematology/Pathology 866 = Immunology/Microbiology 868 = Anesthesiology 870 = Cardiovascular 872 = Dental 874 = Ear, Nose and Throat 876 = Gastro/Urology 878 = General Plastic Surgery 880 = General Hospital 882 = Neurological 884 = Obstetrical/Gynecological 886 = Ophthalmic 888 = Orthopedic 890 = Physical Medicine 892 = Radiology Regulations For each of the devices classified, the CFR provides a description, which includes intended use, class the device belongs (i.e., Class I, II, or III), and marketing requirements.

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Premarket Notification (PMN) 510(k) In section 510(k) of the FD&C Act, device manufacturers are required to notify the FDA of their intent to market a medical device as a Premarket Notification (PMN) or 510(k). The purpose of a 510(k) is for a manufacturer to demonstrate that the device is as safe and effective (substantially equivalent) to a device already on the market. If FDA rules the device is "substantially equivalent," the manufacturer can market the device. Some Class I, most Class II, and a few Class III require a 510(k). https://www.fda.gov/medicaldevices/premarket-submissions/premarket-notification-510k What is Substantial Equivalence? A 510(k) requires a demonstration of substantial equivalence to another legally U.S. marketed device. Substantial equivalence means that the new device is at least as safe and effective as the predicate. A device is substantially equivalent if, in comparison to a predicate it: • has the same intended use as the predicate; and • has the same technological characteristics as the predicate; or • has the same intended use as the predicate; and • has different technological characteristics and does not raise different questions of safety and effectiveness; and • the information submitted to the FDA demonstrates that the device is at least as safe and effective as the legally marketed device. A claim of substantial equivalence does not mean the new and predicate devices must be identical. Substantial equivalence is established concerning the intended use, design, energy used or delivered, materials, chemical composition, manufacturing process, performance, safety, effectiveness, labeling, biocompatibility, standards, and other characteristics, as applicable. A device may not be marketed in the U.S. until the submitter receives a letter declaring the device substantially equivalent. If FDA determines that a device is not substantially equivalent, the applicant may: • resubmit another 510(k) with new data, • request a Class I or II designations through the De Novo Classification process • file a reclassification petition, or • submit a premarket approval application (PMA). Premarket Approval (PMA) 21 CFR 814 A Premarket Approval (PMA) application must be submitted if a manufacturer wants to market a new product that differs from products already on the market. PMA only applies to Class III devices! "A PMA is the most stringent of the submissions and must provide valid scientific evidence collected from human clinical trials showing the device is safe and effective for its intended use. If the device is life-sustaining or presents a potential, unreasonable risk of illness or injury, it may have special approval processes (under Class III)" (FDA.gov). www.fda.gov/medical-devices/premarket-submissions/premarket-approvalpma Devices Used in Blood Establishments The Center for Biologics, Evaluation, and Research (CBER) has expertise in blood, blood products, and cellular therapies as well as the integral association of certain medical devices with these biological products. To utilize this expertise, marketing, and investigational device submissions (Premarket Notification, Premarket Approval, an Investigational Device Exemption) for medical devices associated with the blood collection and processing procedures as well as those associated with cellular therapies are reviewed by CBER. Although these products are reviewed by CBER, the medical device laws and regulations still apply. Class I/II Exemptions Certain Class I and Class II devices are exempt from premarket notification [510(k)] requirements as well as the Medical Device Good Manufacturing Practices (GMPs), also referred to as the Quality System (QS) Regulation. A Class I or Class II device that is exempt from 510(k) requirements must still comply with other requirements (known as regulatory controls) unless the device is explicitly exempt from those requirements, as indicated in the regulation for that device type. Anyone can determine whether a device is exempt from 510(k) or GMP requirements by searching the FDA’s Product Classification database. https://www.fda.gov/medical-devices/classify-your-medical-device/class-i-ii-exemptions 510(k) Exemptions Most Class I and some Class II devices are exempt from 510(k) requirements, subject to certain limitations (see sections 510(l) and 510(m) of the Federal Food, Drug & Cosmetic Act). A device may be exempt from 510(k) requirements if the FDA determines that a 510(k) is not required to provide reasonable assurance of safety and effectiveness for the device. Devices which may be exempt from 510(k) requirements are: 1. Preamendments devices; and 2. Class I and Class II devices specifically exempted by the FDA The term “preamendments device” refers to a device legally marketed in the U.S. before the enactment of the Medical Device Amendments on May 28, 1976, and that has not been significantly changed or modified since then; and for which the FDA has not determined a Premarket Approval (PMA) application is needed to provide reasonable assurance of the device’s safety and effectiveness. Humanitarian Device Exemption Through the Orphan Drug Act (ODA) of 1984, a rare disease is defined as a disease or condition that affects fewer than 200,000 people in the United States. Currently, in the United States, only a portion of the 7,000 known rare diseases have approved treatments. By definition, rare diseases or conditions occur in a small number of patients. As a result, it has been difficult to gather enough clinical evidence to meet the FDA standard of reasonable assurance of safety and effectiveness. To address this challenge, Congress included a provision in the Safe Medical Devices Act of 1990 to create a new regulatory pathway for products intended for diseases or conditions that affect small (rare) populations. This is the Humanitarian Device Exemption (HDE) Program. Definitions: • Humanitarian Use Device (HUD): a medical device intended to benefit patients in the treatment or diagnosis of a disease or condition that affects or is manifested in not more than 8,000 individuals in the United States per year (Section 3052 of the 21st Century Cures Act (Pub. L. No. 114-255). • Humanitarian Device Exemption (HDE): a marketing application for a HUD (Section 520(m) of the Federal Food, Drug, and Cosmetic Act (FD&C Act)). An HDE is exempt from the effectiveness requirements of Sections 514 and 515 of the FD&C Act and is subject to certain profit and use restrictions. Prohibition on Profit The Food and Drug Administration Amendments Act of 2007 (FDAAA) contained incentives to facilitate the development of medical devices for pediatric populations (defined as patients who are younger than 22 years of age). Under section 520(m)(6)(A)(i) of the FD&C Act, an HUD is only eligible to be sold for profit after receiving an HDE approval if the device is intended for the treatment or diagnosis of a disease or condition that either (1) occurs in pediatric patients or a pediatric subpopulation, and such device is labeled for use in pediatric patients or in a pediatric subpopulation in which the disease or condition occurs; or (2) occurs in adult patients and does not occur in pediatric patients or occurs in pediatric patients in such numbers that the development of the device for such patients is impossible, highly impracticable, or unsafe. HDE applicants whose devices meet one of the eligibility criteria and wish to sell their HUD for profit should provide adequate supporting documentation to FDA in the original HDE application. HDE holders who wish to sell their devices for profit and who did not submit the request in the original HDE application may submit a supplement and provide adequate supporting documentation to demonstrate that the HUD meets the eligibility criteria. Other Exemptions: Investigational Device Exemption (IDE) 21 CFR 812 An investigational device exemption (IDE) allows the investigational device to be used in a clinical study to collect safety and effectiveness data. Clinical studies are most often conducted to support a PMA. Only a small percentage of 510(k)s require clinical data to support the application. Investigational use also includes clinical evaluation of certain modifications or new intended uses of legally marketed devices. All clinical evaluations of investigational devices require an approved IDE. Depending on the class of device (Class I, II, or III), the application may take a different regulatory route. For example, a Class III device requires a Pre-Market Application (PMA) and clinical studies, a Class II may not require clinical studies, and Class I do not need FDA approval to market the product (but it must be registered with FDA). More on devices in a later chapter! www.fda.gov/medical-devices/howstudy-and-market-your-device/device-advice-investigational-device-exemption-ide Institutional Review Board (IRB) Device clinical studies are monitored by the Institutional Review Boards (IRB) located at the clinical studies site. Recall the IRB's purpose is to ensure ethical practices such as informed consent and patient selection criteria. If the IRB determines that a device is a significant risk to the patient, they must submit an IDE application to the FDA. The FDA must approve the application before the applicant enrolling patients in the clinical study. If the IRB determines that the device is not a significant risk, they may enroll patients without submitting an IDE. The clinical study will be monitored by the IRB under the IDE regulations in 21 CFR 812.2(b). Confidentiality requirements ensure the FDA will not disclose the existence of an IDE. This review process is not only rigorous, but it is also expensive. The FDA reported, in 2013, the PMA process fee was \$248,000, and the 510(k)-processing fee was an additional \$4,900. Test Your Knowledge! Decorative Contact Lenses – A Case Study: Explore this webpage and watch the accompanying video on decorative contact lenses. https://www.fda.gov/forconsumers/consumerupdates/ucm275069.htm and consumer information here: https://www.fda.gov/medicaldevices/productsandmedicalprocedures/homehealthandconsumer/consumerproducts/contactlenses/ucm270953.htm 1. Why are decorative contact lenses considered devices? 2. What are the risks of decorative contact lenses? 3. Imagine you are a company wanting to sell a decorative contact lens. Map out your application process, consider: 1. What class of device? 2. What Center will you contact? 3. Will you require PMN, PMA, IDE, or IRB?

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In Vitro Diagnostics (IVDs) In vitro diagnostics are tests done on samples such as blood or tissue that have been taken from the human body. In vitro diagnostics can detect diseases or other conditions and can be used to monitor a person’s overall health to help cure, treat, or prevent diseases. In vitro diagnostics may also be used in precision medicine to identify patients who are likely to benefit from specific treatments or therapies. These in vitro diagnostics can include next-generation sequencing tests, which scan a person’s DNA to detect genomic variations. Some tests are used in laboratory or other health professional settings and other tests are for consumers to use at home. IVD Oversight Under the inter-center agreement, both CDRH and CBER oversee IVDs. The Office of Blood Research and Review (OBRR) within CBER manages the pre-market review and post-market surveillance for IVDs assigned to CBER, whereas the Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD) within CDRH administers the pre-market review and post-market surveillance for IVDs assigned to CDRH. OIVD is also responsible for CLIA waivers (see below). Manufacturers apply for the CLIA determination during the pre-market review process. IVD Classification IVDs can be classified I, II, or III depending on their application, diagnosis, monitoring, patient population, type of specimen, and the consequence of a false test result. For example, if the false test results in the amputation of a leg due to suspected cancer, this would be classified as a Class III IVD. Approximately 8% of IVDs on the market are Class III. This classification determines the regulatory pathway for the device. www.fda.gov/medical-devices/ivd-regulatory-assistance/overview-ivdregulation There are 11 types of IVDs listed on the FDA website. Click here and explore them (panel on the left side): https://www.fda.gov/medical-devices/products-and-medical-procedures/vitro-diagnostics. Here are five interesting and relevant ones: 1. Companion Diagnostics: A companion diagnostic is a medical device, often an in vitro device, which provides information that is essential for the safe and effective use of a corresponding drug or biological product. The test helps a health care professional determine whether a therapeutic product's benefits to patients will outweigh any potentially serious side effects or risks. If the diagnostic test is inaccurate, then the treatment decision based on that test may not be optimal. https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm407297.htm Companion diagnostics can: • Identify patients who are most likely to benefit from a therapeutic product; • identify patients likely to be at increased risk for serious side effects as a result of treatment with a therapeutic product, or • monitor response to treatment with a particular therapeutic product for the purpose of adjusting treatment to achieve improved safety or effectiveness" (FDA.gov) 2. Direct-To-Consumer: In vitro diagnostics (IVDs) that are marketed directly to consumers without the involvement of a health care provider are called direct-to-consumer tests (also referred to as DTC). These tests generally request the consumer collect a specimen, such as a saliva or urine, and send it to the company for testing and analysis. www.fda.gov/medical-devices/vitrodiagnostics/direct-consumer-tests Companion diagnostics can: • Direct-to-consumer testing is expanding the number of people who can get genetic testing of their DNA (or genome). Some variants have clinical significance and may give consumers insight into monitoring their health, or about potential disease or conditions. • Not all direct-to-consumer tests are genetic tests, though the majority on the market today are. Some measure other things, such as types of bacterial flora (referred to as a "microbiome"). • Direct-to-consumer tests have varying levels of evidence that support their claims. Some direct-to-consumer tests have a lot of scientific and clinical data to support the information they are providing, while other tests do not have as much supporting data 3. Nucleic-Acid Based Tests: tests analyze variations in the sequence, structure, or expression of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) to diagnose disease or medical conditions, infection with an identifiable pathogen, or determine genetic carrier status. https://www.fda.gov/medical-devices/vitro-diagnostics/nucleic-acid-based-tests 4. Laboratory Developed Test (LDT): A laboratory-developed test (LDT) is a type of in vitro diagnostic test designed, manufactured, and used within a single laboratory. LDTs can be used to measure or detect a wide variety of analytes (substances such as proteins, chemical compounds like glucose or cholesterol, or DNA), in a sample taken from a human body" (FDA.gov). https://www.fda.gov/medical-devices/vitro-diagnostics/laboratory-developed-tests 5. Precision Medicine: Most medical treatments are designed for the "average patient" as a one-size-fits-all-approach, which may be successful for some patients but not for others. Precision medicine, sometimes known as "personalized medicine," is an innovative approach to tailoring disease prevention and treatment that considers differences in people's genes, environments, and lifestyles. The goal of precision medicine is to target the right treatments to the right patients at the right time. https://www.fda.gov/medical-devices/vitro-diagnostics/precision-medicine Advances in precision medicine have already led to powerful discoveries and FDA-approved treatments that are tailored to specific characteristics of individuals, such as a person's genetic makeup, or the genetic profile of an individual's tumor. Patients with a variety of cancers routinely undergo molecular testing as part of patient care, enabling physicians to select treatments that improve chances of survival and reduce exposure to adverse effects. Next-Generation Sequencing (NGS) Tests Precision care will only be as good as the tests that guide diagnosis and treatment. Next-Generation Sequencing (NGS) tests are capable of rapidly identifying or 'sequencing' large sections of a person's genome and are important advances in the clinical applications of precision medicine. Patients, physicians, and researchers can use these tests to find genetic variants that help them diagnose, treat, and understand more about human disease. FDA's Bioinformatics Platform The FDA created https://precision.fda.gov/, cloud-based community research, and development portal that engages users across the world to share data and tools to test, pilot, and validate existing and new bioinformatics approach NGS processing. Individuals and organizations in the genomics community can find more information and sign up to participate at http://precision.fda.gov. Research Use Only (RUO) & Investigational Use Only (IUO) Both IVDs are considered to be pre-commercial since they are not used for diagnostic purposes and do not have to follow the strict labeling requirements that apply to commercial diagnostic IVDs. The labeling needs of these are found in 21 CFR 809.10. The difference between RUO and IUO is that RUO is for research only, but IUO may be pre-shipped and may be evaluated for future use as an IVD. General Purpose Reagents (GPR) & Analyte Specific Reagents (ASR) GPR has a general laboratory application and is a Class I device. As such, Class I devices are exempt from PMN. ASR is a little more complicated in that it can be used as a Class I, II, or III device depending on its application. ASR devices can range from antibodies to nucleic acid binding proteins used for diagnostics in blood banking samples (class II) to a test for Ebola (Class III). Clinical Laboratory Improvement Amendments (CLIA) Diagnostic testing helps health care providers screen for or monitor specific diseases or conditions. It also helps assess patient health to make clinical decisions for patient care. The Clinical Laboratory Improvement Amendments (CLIA) regulate laboratory testing and require clinical laboratories to be certificated by their state as well as the Center for Medicare and Medicaid Services (CMS) before they can accept human samples for diagnostic testing. Laboratories can obtain multiple types of CLIA certificates, based on the kinds of diagnostic tests they conduct. www.fda.gov/medical-devices/ivd-regulatoryassistance/clinical-laboratory-improvement-amendments-clia In 1988, the Clinical Laboratory Improvement Amendments (CLIA) was established to define quality standards for all laboratory testing to ensure accuracy, reliability, and timeliness of patient test results regardless of where the test was performed. Final regulations were established in 1992. Three federal agencies are responsible for CLIA: The Food and Drug Administration (FDA), Center for Medicaid Services (CMS), and the Center for Disease Control (CDC). Each agency has a unique role in assuring quality laboratory testing. www.cms.gov/Regulations-andGuidance/Legislation/CLIA/Program_Descriptions_Projects.html CLIA AND THE FDA, CMS, CDC Three federal agencies are responsible for CLIA: The Food and Drug Administration (FDA), Center for Medicaid Services (CMS), and the Center for Disease Control (CDC). Each agency has a unique role in assuring quality laboratory testing. CLIA Categorizations The FDA categorizes diagnostic tests by their complexity—from the least to the most complex: waived tests, moderate complexity tests, and high complexity tests. Diagnostic tests are categorized as waived based on the premise that they are simple to use, and there is little chance the test will provide wrong information or cause harm if it is done incorrectly. Tests that are cleared by the FDA for home or over-the-counter use are automatically assigned a waived categorization. CLIA categorization is determined after the FDA has cleared or approved a marketing submission. The FDA determines the test’s complexity by reviewing the package insert test instructions and using a criteria “scorecard” to categorize a test as moderate or high complexity. Each test is graded for level of complexity by assigning scores of 1, 2, or 3 for each of the seven criteria on the scorecard. A score of 1 indicates the lowest level of complexity, and the score of 3 indicates the highest level. The 7 scores are added together and the tests with a score of 12 or less are categorized as moderate complexity, and those with a score above 12 are categorized as high complexity. The FDA will notify the sponsor—usually within two weeks of the marketing clearance or approval of their CLIA categorization. CLIA Waiver Application Under CLIA, FDA categorizes in vitro diagnostic (IVD) tests by their degree of complexity: waived, moderate complexity, and high complexity. Tests that are waived by regulation under 42 CFR 493.15(c), or cleared or approved for home use or for over-the-counter use, are automatically categorized as waived following clearance or approval. Otherwise, following clearance or approval, tests may be categorized either as moderate or high complexity according to the CLIA categorization criteria listed in 42 CFR 493.17. The statute states that: The examinations and procedures that may be performed by a laboratory with a Certificate of Waiver are laboratory examinations and procedures that have been approved by the Food and Drug Administration for home use or that are simple laboratory examinations and procedures that have an insignificant risk of an erroneous result, including those that — (A) employ methodologies that are so simple and accurate as to render the likelihood of erroneous results by the user negligible, or (B) the Secretary has determined pose no unreasonable risk of harm to the patient if performed incorrectly. Explore! There are three ways to find out what categorization a laboratory test has received. Take a look at these three databases. 1. CLIA Database 2. Waived Analytes 3. Over the Counter Database

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Medical Device Labeling Any label or written material on the device or material that accompanies the device. Labeling must provide adequate directions for use unless exempt and labeling must not be false or misleading. Labeling must have adequate directions for use, proper operating instructions, and warnings where the device's use may be dangerous. The FDA recognizes three types of labeling for devices. A. FDA-approved labeling. B. FDA-promotional labeling and C. Package-insert labeling. The basic outline for labeling specific to medical devices includes the manufacturer, Device Name, Description, Indication, Contraindications, Warnings, and Precautions, Use in Specific Populations, Prescription device statement, Adverse reactions, and Date of issue. To learn more about device labeling: https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/Overview/DeviceLabeling/default.htm Labeling Enforcement FDA can enforce labeling violations through Notices of Violation (NOVs), Warning Letters, or judicial action (consent decrees, injunctions, and seizures). The FDA looks at a company's website, videos, commercials, brochures, bulk mailings, and press releases to determine if there is any misrepresentation of labeling a device. The FDA responds to violations with the least stringent action depending on the potential to jeopardize public health. Misbranding Section 502 of the FFDCA contains provisions on misbranding and false or misleading labeling. A device is considered misbranded if it is false or misleading in any way and if it does not include adequate directions for use. Other examples of misbranding from the FDA website: • It is in package form, and its label fails to contain the name and place of business of the manufacturer, packer, or distributor; and an accurate statement of the contents regarding weight, measure, or numerical count; • Any required wording is not prominently displayed as compared with other wording on the device, or is not clearly stated; • It is dangerous to health when used in the dosage or manner or with the frequency or duration prescribed, recommended or suggested in the labeling; • If the device's established name, its name in an official compendium or any common or usual name is not prominently printed in type at least half as large as that used for any proprietary name; • If the establishment is not registered with FDA as per Section 510, has no device listed as per section 510(j), or obtained applicable premarket notification clearance as per Section 510(k); • If the device is subject to a performance standard and it does not bear the labeling prescribed in that standard" (FDA.gov). Quality System (QS) Regulation - CFR 820 "CFR 820 covers the design and manufacture of devices sold in the US and is like ISO 13485. Part of this regulation states manufacturing facilities will be inspected by the FDA. The quality system regulation includes requirements related to the methods used in and the facilities and controls used for designing, purchasing, manufacturing, packaging, labeling, storing, installing, and servicing of medical devices. Manufacturing facilities undergo FDA inspections to ensure compliance with the QS requirements. www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/PostmarketRequirements/QualitySy stemsRegulations/default.htm Code of Federal Regulations (CFR) Citations • 21 CFR Parts 50, 56, 812: Clinical Studies • 21 CFR Part 807 • Establishment Registration and Listing • Premarket Notification [510(k)] • 21 CFR Part 814: Premarket Approval (PMA) • 21 CFR Part 812: Investigational Device Exemptions • 21 CFR Parts 801, 809, 812, 820 • Medical Device Labeling • 21 CFR Part 820: Quality System Regulation • 21 CFR Part 821: Tracking Requirements • 21 CFR Part 803: Medical Device Reporting The Flexibility of the QS Regulation "The QS regulation for devices embraces the same "umbrella'' approach to the CGMP regulation of drugs. Because the regulation must apply to so many different types of devices, the regulation does not prescribe in detail how a manufacturer must produce a specific device. Rather, the regulation provides the framework that all manufacturers must follow by requiring that manufacturers develop and follow procedures and fill in the details that are appropriate to a given device according to the current state-of-the-art manufacturing for that specific device. Manufacturers should use good judgment when developing their quality system and apply those sections of the QS regulation that apply to their specific products and operations, 21 CFR 820.5 of the QS regulation. Operating within this flexibility, it is the responsibility of each manufacturer to establish requirements for each type or family of devices that will result in devices that are safe and effective. The responsibility for meeting these needs and for having objective evidence of meeting these requirements may not be delegated. Because the QS regulation covers a broad spectrum of devices, production processes, etc., it allows some leeway in the details of quality system elements. It is left to manufacturers to determine the necessity for, or extent of, some quality features and to develop and implement specific procedures tailored to their particular processes and devices" (FDA.gov). International Harmonization The FDA has been a strong advocate for international harmonization of regulations. They worked in collaboration with the Global Harmonization Taskforce (GHTF) to develop QSR that promotes incorporation of international harmonization. In 2011, the GHTF re-organized to become the International Medical Device Regulators Forum (IMDRF), which includes representatives from the US, Canada, Australia, Brazil, Japan, and Europe. More information can be found here: http://www.imdrf.org/ ISO Device Regulations - ISO 13485 ISO 13485 is the standard for a quality management system for the design and manufacture of medical devices. Although ISO 13485 is a stand-alone document, it is harmonized with ISO 9001 with a few important exceptions: It does not need to demonstrate continual improvement, and it does not have customer satisfaction requirements. What it does have, is a focus on risk management and design control, which is essential for device manufacturing. ISO 3485 also includes inspection and traceability requirements for implantable devices. It promotes awareness of regulatory requirements but also in-line with IMDRF Post-Marketing Activities The FDA requires medical device manufacturers to participate in many post-market activities, maintaining a quality system, inspections, post-market surveillance studies, tracking, reporting device malfunctions and injury, and death. • Medical Device Reporting (MDR) 21 CFR 803: If a device causes death or serious injury, it must be reported. There are also instances where malfunctions must also be reported and allows the FDA to monitor problems. The report must be made within 30 days, and there is a form and a website called Med Watch. • Medical Device Recall: A medical device recall is an action that takes place to address a problem with a medical device that may be in violation of an FDA law. Recalls occur when the device is defective; it causes a risk to health or both. A recall does not necessarily mean the product must be returned, sometimes it just needs to be adjusted, or clarification safety instructions provided. 21 CFR 7 provides guidance so that responsible firms may conduct an active voluntary recall. Examples of the types of actions that may be considered recalls: • Inspecting the device for problems • Repairing the device • Adjusting settings on the device • Re-labeling the device • Destroying device • Notifying patients of a problem • Monitoring patients for health issues A recall is either a correction or removal of a product. A Correction addresses a problem with a medical device where it is used or sold; a Removal addresses a problem with a medical device by removing it from where it is used or sold. In most cases, a company voluntarily recalls a device on its own. When the company has violated an FDA law, the company must recall the device (correction or removal) and notify the FDA. Legally, the FDA can require a company to recall a device if a company refuses to do so under 21 CFR 810, Medical Device Recall Authority. 21 CFR 810 describes the procedures the FDA follows in exercising its medical device recall authority under section 518(e) of the FD&C Act. It is important to note that a recall does not include a market withdrawal or a stock recovery. When there is a minor infraction not subject to legal action, the FDA may approve a market withdrawal. In the end, almost all recalls are conducted on a voluntary basis by the manufacturer. A list of recalls by date, https://www.fda.gov/Safety/Recalls/, and a comprehensive searchable recall device database www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfRES/res.cfm Device recalls following the same general recall procedure as previously discussed for drugs, which includes classification of recall (I, II or III), developing a recall strategy, and providing the FDA with recall status reports. To learn more about Device Recalls, visit the FDA device recall web page, and watch the FDA Video: http://fda.yorkcast.com/webcast/Play/1b95461f64be40ecbe3415195cb394911d

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Combination Products are therapeutic and diagnostic products that combine drugs, devices, and/or biological products. One of the more challenging regulated products is combination products. Combination products are therapeutic and diagnostic products that combine drugs, devices, and biological products. Although each has clearly defined regulatory guidance's in place, a combination of one or more of these create a new product with a unique regulatory pathway. An asthma inhaler is an example of a combination device; it includes both the asthma drug and the device to get the drug to the lungs. FDA expects to receive large numbers of combination products for review as technological advances continue to merge product types and blur the historical lines of separation between FDA’s medical product centers, which are made up of the Center for Biologics Evaluation and Research (CBER), the Center for Drug Evaluation and Research (CDER), and the Center for Devices and Radiological Health (CDRH). Because combination products involve components that would normally be regulated under different types of regulatory authorities, and frequently by different FDA Centers, they raise challenging regulatory, policy, and review management challenges. Differences in regulatory pathways for each component can impact the regulatory processes for all aspects of product development and management, including preclinical testing, clinical investigation, marketing applications, manufacturing and quality control, adverse event reporting, promotion and advertising, and post-approval modifications. www.fda.gov/combination-products/aboutcombination-products Types of Combination Products Combination products are defined in 21 CFR 3.2(e). The term combination product includes: 1. A product comprised of two or more regulated components, i.e., drug/device, biologic/device, drug/biologic, or drug/device/biologic, that are physically, chemically, or otherwise combined or mixed and produced as a single entity; 2. Two or more separate products packaged together in a single package or as a unit and comprised of drug and device products, device and biological products, or biological and drug products; 3. A drug, device, or biological product packaged separately that according to its investigational plan or proposed labeling is intended for use only with an approved individually specified drug, device, or biological product where both are required to achieve the intended use, indication, or effect and whereupon approval of the proposed product the labeling of the approved product would need to be changed, e.g., to reflect a change in intended use, dosage form, strength, route of administration, or significant change in dose; or 4. Any investigational drug, device, or biological product packaged separately that according to its proposed labeling is for use only with another individually specified investigational drug, device, or biological product where both are required to achieve the intended use, indication, or effect. The table below has been created to identify and describe the nine different types for a combination product. A package that contains only devices is not a combination product. Additionally, a product that is a combination of only drugs is not a combination product. Type Description 1 Convenience Kit or Co-Package. Drug and device are provided as individual constituent parts within the same package 2 Prefilled Drug Delivery Device/ System. The drug is filled into or otherwise combined with the device, AND the sole purpose of the device is to deliver drug 3 Prefilled Biologic Delivery Device/ System. Biological product is filled into or otherwise combined with the device, and sole purpose of the device is to deliver biological product 4 Device Coated/ Impregnated/ Otherwise Combined with Drug. Device has an additional function in addition to delivering the drug 5 Device Coated or Otherwise Combined with Biologic. Device has an additional function in addition to delivering the drug 6 Drug/Biologic Combination. 7 Separate Products Requiring Cross Labeling. 8 Possible Combination Based on Cross Labeling of Separate Products. 9 Other Type of Part 3 Combination Product. Regulatory History Combination product regulations were first provided in 1990 by the Safe Medical Device Act (SMDA). A provision was added (Section 503(g)) of the FD&C Act, requiring "combination products be assigned to a lead agency based on its Primary Mode of Action (PMOA)." In Title 21 of the Code of Federal Regulation (CFR) part, 3 established a Request for Designation (RFD) process, which allows the FDA to provide guidance on which Center to be assigned to a product without a clear (or disputed) pathway. In 2002, the FDA (through the Medical Device User Fee and Modernization Act (MDUFMA)), amended Section 503(g) mandated the FDA to establish an Office of Combination Products (OCP). The OCP was set up to work with FDA centers to develop guidelines and regulations to clarify combination product regulatory pathway. Office of Combination Products (OCP) The OCP is responsible for combination product assignment, coordinating premarket review with the Centers involved, and ensure consistent post-market regulation. Also, they examine and revise Guidance’s and practices unique to combination products. The bottom line – they serve as a facilitator of clearing combination product issues – but do not review the products themselves. What is a Combination Product? - 21 CFR 3.2(e) A combination product is defined in 21 CFR 3.2(e) as two or more regulated products; chemically or physically combined (21 CFR 3.2(e) (1)), or co-packaged (21 CFR 3.2(e)(2)), or cross-labeled but separately packaged (21 CFR 3.2(e)(3)). Explore! Explore at the FDA website for combination products examples of each of these products: 1. Physically or chemically combined: 2. Co-packaged: 3. Cross-labeled: 8.06: Section 6- Primary Mode of Action (PMOA) Regulations are based on the primary mode of action (PMOA) of that combination product (drug, device, or biologic), which in turn dictates which center primarily oversees this approval (CDER, CBER, or CDRH) in combination with all interested centers by committee. If there is not a clearly defined determination, the device manufacturer may file a Request for Designation (RFD) with the FDA. An RFD compels the FDA to classify the product and indicate the primary review group. The FDA has established an algorithm for assigning combination products when a PMOA is not set up with "reasonable certainty." The FDA defines PMOA as "the single-mode (or greatest contribution) of action of a combination product that provides the most important therapeutic action of the combination product" (FDA.gov). For example, if a device is used to deliver a therapeutic drug, the PMOA would be the drug, and the Center assigned would be CDER. When a single, clear, mode of action is not established, the FDA utilizes an ‘assignment algorithm' to assign the Center to oversee the combination product. The FDA will consider the historical duties as well as the Center that may have the most expertise with similar products. Request for Designation It is highly recommended the manufacturer (sponsor) of the combination product seek assignment early in the process as this has a dramatic effect on regulatory strategy. When the PMOA is "clear," the sponsor may contact the OCP informally (phone or email) to seek advice – this process is not binding and is subject to change. The formal designation is made through a Request for Designation (RFD) – which is a written application for designation submitted to the OCP. In this formal written request, the sponsor must clearly state the product description, ingredients, and components. If any of these changes, the designation is no longer binding (and you may need to reapply for an RFD. In the RFD, you must also provide all known mode of action (MOA), the sponsor's identification of the PMOA, and a description of any related products with their regulatory status. The sponsor is also required to provide a recommendation of assignment with reasons why you recommend that assignment. Premarket Review Although the assigned Center is responsible for the review, other centers may also be involved in the review depending on the product. The FDA has created a streamlined Standard Operating Procedures (SOP) for the Intercenter Consultative and Collaborative Review Process to assist FDA staff in handling combination product submissions. The lead center typically applies its regulatory pathway – however, some situations require multiple applications – especially those combination products where the goods are separate products themselves.

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Objectives • Understand the FDA’s regulatory authority over food • Describe the regulatory functions of CFSAN, CVM, and CVB • Understand how the FDA, EPA, and USDA together regulate GMOs and their focus • Explore the FSMA, and the five main elemental changes brought about in food safety including recall authority in food • Understand what Medical foods are and how they are regulated • Identify several veterinary products and how and why the FDA regulates them • Explore how the FDA regulates cosmetics and why they regulate them • 9.1: Food Safety FDA authority over food comes from the FD&C Act, which defines food as "articles used for food or drink for man or another animal, chewing gum and articles used for components of any such article.". The FDA is responsible for the safety of all food, including individual components of food, animal and pet food, and food ingredients. Their mission is to prevent food adulteration and ensure foods are safe, wholesome, and sanitary in addition to providing accurately labeled food. • 9.2: Regulation of Plant GMOs • 9.3: Regulation of Animal GMOs and Medical Foods • 9.4: Regulation of Veterinary Products • 9.5: Regulation of Cosmetics You might be surprised to learn that the FDA has regulatory oversight over cosmetics. You may be even more surprised to know that this oversight is largely self-regulated! The FDA acts with hazardous products – but the remainder of the control is by the companies themselves. The other area the FDA does scrutinize heavily is misbranding. Many companies have recently moved to market their cosmetics with drug language – such as "anti-aging cream." 09: Regulation of Food and Other Products The Regulation of Food FDA authority over food comes from the FD&C Act, which defines food as "articles used for food or drink for man or another animal, chewing gum and articles used for components of any such article." (Federal Food, Drug and Cosmetic Act, 1938). The FDA is responsible for the safety of all food, including individual components of food, animal and pet food, and food ingredients. Their mission is to prevent food adulteration and ensure foods are safe, wholesome, and sanitary in addition to providing accurately labeled food. (FDA, FDA.gov, 2016) https://www.fda.gov/food Center for Food Safety and Applied Nutrition (CFSAN) The regulatory Center for food in the FDA is the Center for Food Safety and Applied Nutrition (CFSAN), which oversees food safety and purity. It has the power to regulate all domestic and imported food except for meat, poultry, and eggs (those are regulated by USDA). They oversee the safety of food ingredients developed through biotechnology, dietary supplements, food additives, and proper labeling of food. CFSAN is also concerned with food contamination, such as biological pathogens and naturally occurring toxins. They are also responsible for the regulation and safety of cosmetics ingredients and finished products. Collaboration With Other Regulatory Bodies FDA regulates food and cosmetic products sold in interstate commerce. However, products made and sold entirely within a state are governed by that state. This means, the FDA maintains close communications and interagency agreements with other regulatory bodies including the U.S. Department of Commerce's National Marine Fisheries Service, the Centers for Disease Control and Prevention (CDC), the U.S. Department of Treasury's U.S. Customs and Border Protection, the Federal Trade Commission (FTC), the U.S. Department of Transportation (DoT), the Consumer Product Safety Commission (CPSC), and the U.S. Department of Justice (DoJ) (FDA.gov). Collaboration With Academia and Industry CFSAN is actively involved in several academic projects through its Centers of Excellence (COE) program. CFSAN has four COEs: 1. the National Center for Food Safety and Technology (NCFST) with the Illinois Institute of Technology 2. the Joint Institute for Food Safety and Applied Nutrition (JIFSAN) at the University of Maryland 3. the FDA COE for Botanical Dietary Supplement Research at the National Center for Natural Products Research (NCNPR), University of Mississippi 4. the Western Center for Food Safety (WCFS) with the University of California at UC, Davis USDA The FDA is not responsible for meat, poultry, and eggs, that purview belongs to the United States Department of Agriculture (USDA) (www.usda.gov). The USDA also contributes to nutrition research and public health education. A division of the USDA, the Animal and Plant Health Inspection Service (APHIS), regulates genetically engineered food plants. EPA The Environmental Protection Agency (EPA) (www.epa.gov) regulates pesticides and their use on food crops. It sets tolerance limits for pesticide residues in foods (which the FDA enforces), publishes “safe use” directives, and establishes quality standards for drinking water. The EPA also has some regulatory authority over the release of genetically modified organisms into the environment. Maintaining a Safe Food Supply Although the U.S. food supply is among the world's safest, we do not have to go too far back in the news to realize our supply is not fallible. (FDA Food Recall, 2016). See the many FDA publications on Listeria outbreaks in food just in the last year! Read more here on the Listeria outbreak in Texas's favorite Blue Bell ice-cream. The food industry and manufacturing practices are widely varied, and therefore the possible potential areas of contamination are many, including pre-harvest, processing, packaging, and storage! Check out the FDA’s Bad Bug Book to learn more! www.fda.gov/food/foodbornepathogens/bad-bug-book-second-edition Some of CFSAN's current areas of food safety concern are: • pathogens such as bacteria and viruses • naturally occurring toxins such as mycotoxins • dietary supplements • pesticide residues • toxic metals including lead • particulate matter • food allergens including wheat, nuts, and dairy • added nutrient concerns • dietary components and labeling • Transmissible Spongiform Encephalopathy-type diseases • product tampering Food Safety There are three major issues related to food safety that are the most common causes of regulatory enforcement actions, which are the most closely monitored: 1. Contamination by pathogens (e.g., E. coli, Listeria monocytogenes). 2. Adverse effects of additives such as food coloring and sweeteners. 3. Unintentional additives (e.g. pesticide residues). The FDA has the authority to inspect any facility where food is manufactured, packaged, or handled in any way. Contamination by pathogens is one of the most significant problems faced in the United States according to the Centers for Disease Control (CDC). It is estimated that foodborne illnesses affect 1 out of every 6 Americans at some point in their lives. Forty-Eight million people become sick due to foodborne pathogens each year, of which approximately 128,000 are hospitalized, and 3,000 died (FDA.gov). The USDA and FDA have active consumer education programs targeted towards preventing such illnesses by teaching consumers about safe handling and preparation of foods, the shelf life of various kinds of food, and other common-sense tips. Explore! Explore these resources on foodborne statistics in the US. What germ is responsible for most foodborne illnesses? Deaths? Why? Legislative Acts That Regulate Food and Agriculture The FD&C Act sets out broad regulations of both the food and drug industries. There are additional, specific acts that regulate food beyond the FD&C Act, which includes: • The Federal Insecticide, Fungicide, Rodenticide Act (FIFRA) of 1910 • The Federal Import Milk Act (1927) • The Public Health Service Act (1944) • Federal Meat Inspection Act and the Poultry Products Inspection Act of 1957 • The Federal Plant Act (FPPA) • The Fair Packaging and Labeling Act (1966) • Toxic Substances Control Act (TSCA) of 1976 • The Infant Formula Act of 1980, as amended • The Nutrition Labeling and Education Act of 1990 • The Dietary Supplement Health and Education Act of 1994 • Food Allergen Labeling and Consumer Protection Act of 2004 • Food and Drug Administration Amendments Act of 2007 • Food Safety Modernization Act (FSMA) of 2011 Food Safety Modernization Act Food Safety Modernization Act (FSMA), which was signed into law by President Obama on January 4, 2011, enables FDA to better protect public health by strengthening food safety measures. Under the new law, FDA now has much more effective enforcement tools to protect the food supply, including the authority to issue a mandatory recall order. To learn more about FSMA regulatory implications, see the FSMA Q&A factsheet. www.fda.gov/food/food-safety-modernization-act-fsma/frequently-askedquestions-fsma In short, here are the main elements of FSMA: 1. Preventive controls - Provides FDA legislative mandate to require comprehensive, preventionbased controls across the food supply to minimize the likelihood of contamination occurring. 2. Inspection and Compliance – Allows FDA to enforce compliance through inspection. 3. Imported Food Safety - Importers must verify that their suppliers have adequate preventive controls in place to ensure the safety of imported food products. 4. Response - FDA is given mandatory recall authority for all food products as well as expanded administrative detention of products that are potentially in violation of the law, and suspension of a food facility’s registration. 5. Enhanced Partnerships - The legislation encourages strengthening the existing collaboration among all food safety agencies. Food Defense Food Defense is an effort to protect food from acts of intentional adulteration. In May 2016, FDA issued the final rule on Mitigation Strategies to Protect Food Against Intentional Adulteration with requirements for covered facilities to prepare and implement food defense plans. FDA works with the private sector and other government agencies on activities related to food defense, including conducting research and analysis, developing and delivering training and outreach, and conducting exercises. Also, FDA has developed several tools and resources to help food facilities prevent, prepare for, respond to, and recover from acts of intentional adulteration of the food supply. Explore! To read more about Food Defense Guidelines: 1. www.fda.gov/food/guidance-documents-regulatory-information-topic-food-anddietary-supplements/food-defense-guidance-documents-regulatory-information 2. www.fda.gov/food/food-safety-modernization-act-fsma/fsma-final-rulemitigation-strategies-protect-food-against-intentional-adulteration 3. What’s new in FSMA: www.fda.gov/food/food-safety...whats-new-fsma

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Food Ingredients Although the FDA has little regulatory control over food before it goes to the market, what it does have control over is food ingredients, such as food additives. Food additives include intentional components added to food as well as unintentional additives from the manufacturing process. All food additives are approved before use – a list of approved food additives can be found on the FDA website. Any substance that the FDA considers ‘Generally Recognized as Safe (GRAS)’ does not need to be approved before use. https://www.fda.gov/Food/IngredientsPackagingLabeling/FoodAdditivesIngredients/ucm091048.htm "GRAS" is an acronym for the phrase Generally Recognized As Safe. Under sections 201(s) and 409 of the Federal Food, Drug, and Cosmetic Act (the Act), any substance that is intentionally added to food is a food additive, that is subject to premarket review and approval by FDA, unless the substance is generally recognized, among qualified experts, as having been adequately shown to be safe under the conditions of its intended use, or unless the use of the substance is otherwise excepted from the definition of a food additive. https://www.fda.gov/food/food-ingredients-packaging/generally-recognized-safe-gras Regulation of Agricultural Biotechnology FDA regulates the safety of food for humans and animals, including foods produced from genetically engineered (GE) plants. Foods from GE plants must meet the same food safety requirements as foods derived from traditionally bred plants. While genetic engineering is sometimes referred to as “genetic modification” producing “genetically modified organisms (GMOs),” FDA considers “genetic engineering” to be the more precise term. www.fda.gov/food/food-new-plantvarieties/consumer-info-about-food-geneticallyengineered-plants What are Genetically Engineered (GE) Organisms? Crop improvement happens all the time, and genetic engineering is just one form of it. We use the term “genetic engineering” to refer to genetic modification practices that utilize modern biotechnology. In this process, scientists make targeted changes to a plant’s genetic makeup to give the plant a new desirable trait. For example, two new apple varieties have been genetically engineered to resist browning associated with cuts and bruises by reducing levels of enzymes that can cause browning. Humans have been modifying crops for thousands of years through selective breeding. Early farmers developed cross-breeding methods to grow numerous corn varieties with a range of colors, sizes, and uses. For example, the garden strawberries that consumers buy today resulted from a cross between a strawberry species native to North America and a strawberry species native to South America. Why Genetically Engineer Plants? Developers genetically engineer plants for many of the same reasons that traditional breeding is used. They may want to create plants with better flavor, higher crop yield (output), greater resistance to insect damage, and immunity to plant diseases. Traditional breeding involves repeatedly cross-pollinating plants until the breeder identifies offspring with the desired combination of traits. The breeding process introduces many genes into the plant. These genes may include the gene responsible for the desired trait, as well as genes responsible for unwanted characteristics. Genetic engineering isolates the gene for the desired trait, adds it to a single plant cell in a laboratory, and generates a new plant from that cell. By narrowing the introduction to only one desired gene from the donor organism, scientists can eliminate unwanted characteristics from the donor’s other genes. Genetic engineering is often used in conjunction with traditional breeding to produce the genetically engineered plant varieties on the market today. Am I Eating Food from Genetically Engineered Plants? The planting of genetically engineered (GE) crops was allowed for the first time in the United States in 1995. Today, it is estimated that over 90% of soy, and over 80% of cotton and canola products come from genetically modified crops. Genetically modified crops were created to improve productivity and cut costs by improving insect resistance, virus resistance, herbicide tolerance, and similar issues that affect commercial crops. The majority of GE plants are used to make ingredients that are used in other food products. Such ingredients include corn starch in soups and sauces, corn syrup used as a sweetener, corn oil, canola oil, and soybean oil in mayonnaise, salad dressings, bread, and snack foods. Voluntary Pre-Market Engagement for New Plant Varieties In the 1992 policy on new plant varieties, FDA recommended that developers consult with FDA about bioengineered foods under development; since the issuance of the 1992 policy, developers have routinely done so. To date, FDA's interactions with developers have taken three forms: biotechnology final consultations, new protein consultations, and rarely, the establishment of a food master file or submission of a food additive petition. In the Federal Register of January 18, 2001 (the premarket notification proposal; 66 FR 4706, available as text and 193 KB PDF), FDA proposed a rule that would require that developers submit a scientific and regulatory assessment of the bioengineered food 120 days before the bioengineered food is marketed. In the premarket notification proposal, FDA recommended that developers continue the practice of consulting with the agency before submitting a premarket notice. A developer who intends to commercialize a bioengineered food may meet with the FDA to identify and discuss relevant safety, nutritional, or other regulatory issues regarding the bioengineered food in an initial consultation. With or without an initial consultation, a developer may submit to FDA a summary of its scientific and regulatory assessment of the food (the final consultation). Submissions to the agency under the 1997 guidance are designated biotechnology notification files (BNF). FDA evaluates the submission and responds to the developer by letter. FDA maintains an inventory of Biotechnology Consultations on Food from GE Plant Varieties, which includes the agency's response to the developer and the text of the agency's final memorandum regarding the submission. 1. Biotechnology Consultations: www.fda.gov/food/submissions...-consultations 2. New Protein Consultations: https://www.fda.gov/food/submissions...-consultations 3. Food Additive Petitions: www.fda.gov/food/submissions-bioengineered-new-plantvarieties/food-master-files-food-additive-petitions Regulatory Agencies for GE Crops The FDA regulates human, and animal food from genetically engineered (GE) plants the same way they regulate all food. The existing FDA safety requirements impose a clear legal duty on everyone in the farm to table continuum to market safe foods to consumers, regardless of the process by which such foods are created. It is unlawful to produce, process, store, ship, or sells to consumers unsafe foods. Three federal agencies evaluate new crop varieties developed using genetic engineering: the FDA, the USDA, and the EPA. www.fda.gov/food/food-new-plant-varieties/how-fda-regulates-foodgenetically-engineered-plants 1. FDA: Evaluates food and feed safety. The FDA’s Center for Food Safety and Nutrition (CFSAN) and the Center for Veterinary Medicine (CVM) evaluate new GE crops. They look for increased allergens, toxins, and changes in nutrition or composition. The FDA's main concerns here are threats to human health through food and threats to animal health through feed. What the FDA is comparing these genetically modified products is their unmodified counterpart. The FDA may then issue a statement about the modified food's substantial equivalence but does not approve the food as "safe," per se. 2. USDA: Ensures agricultural and environmental safety. The USDA, through the Biotechnology Regulatory Service (BRS) office of the Animal and Plant Health Inspection Service (APHIS), regulates all GE crops before commercial release. The USDA's primary concern is whether the new plant will harm agriculture or the environment. The USDA's authority over these matters is derived from the Plant Protection Act of 2000. 3. EPA: Evaluates food safety and environmental issues associated with new pesticides. The EPA regulates GM crops that have altered pesticide characteristics. Bt GM corn is an example of a product that the EPA would evaluate. Bt corn is genetically modified to contain what’s known as a “Plant Incorporated Protectant” (PIP). In other words, the Bt corn produces its insecticide. The EPA evaluates this type of product for its impact on the environment and human health. Test Your Knowledge! Visit the EPA website: http://www.epa.gov/ The EPA is currently responsible for regulating GE plants. Why do you think the EPA is concerned about GE plants? What is the Food Quality Protection Act?

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FDA, EPA, or USDA: Animals with Intentional Genomic Alterations On January 19, 2017, the FDA released for public comment draft revised Guidance for Industry (GFI) #187, “Regulation of Intentionally Altered Genomic DNA in Animals.” This draft revised guidance expands the scope of the existing GFI #187 to address animals with intentionally altered genomic DNA developed through the use of genome editing technologies, as well as techniques such as rDNA in genetic engineering. AquAdvantage Salmon: First Approved AquAdvantage Salmon has been genetically engineered to reach a growth marker important to the aquaculture industry more rapidly than its non-GE farm-raised Atlantic salmon counterpart. It does so because it contains an rDNA construct that is composed of the growth hormone gene from Chinook salmon under the control of a promoter (a sequence of DNA that turns on the expression of a gene) from another type of fish called an ocean pout. Is it Safe? Based on a comprehensive analysis of the scientific evidence, as required by the Federal Food, Drug, and Cosmetic Act (FD&C Act), the FDA determined that AquAdvantage Salmon meets the statutory requirements for safety and effectiveness under the FD&C Act. As part of its evaluation, the FDA examined data comparing three groups of fish: non-GE farm-raised Atlantic salmon from both the sponsor’s farm and from a different commercial farm, and AquAdvantage Salmon. This study compared key hormones (including estradiol, testosterone, 11-ketotestosterone, T3, T4, and insulin-like growth factor 1 (IGF1)) and found no biologically relevant differences. The salmon are safe to eat and has a comparable nutritional profile to that of the non-GE farm-raised Atlantic salmon. The introduced DNA is safe for the fish itself, and the salmon meets the sponsor’s claim about faster growth. The FDA also analyzed the potential environmental impact that approval of the original AquAdvantage Salmon application and a supplemental application would have on the quality of the human environment in the United States and issued its Environmental Assessments and Findings of No Significant Impact. https://www.fda.gov/media/93823/download Containment Under the approval and subsequent supplements to the original approval, AquAdvantage Salmon are subject to stringent conditions to prevent the possibility of escape into the wild. The salmon cannot be raised in ocean net pens: instead, the approval allows for them to be grown only at specific land-based facilities: one in Canada, where the breeding stock is kept, and Indiana, where the fish for market will be grown out using eggs from the Canada facility. Both the Canada and Indiana facilities have multiple and redundant physical barriers to prevent eggs and fish from escaping, including metal screens on tank bottoms, standpipes, and incubator trays to prevent the escape of eggs and fish during hatching or rearing. Read more here: www.fda.gov/animal-veterinary/animals-intentional-genomicalterations/aquadvantage-salmon-fact-sheet FDA, EPA, or USDA: Oxitec Mosquito Oxitec mosquito is a type of “living pesticide,” genetically engineered to carry a gene that prevents female offspring from surviving but allowing male progeny to survive. The male offspring, in turn, half will carry this self-limiting gene. Resulting in the decline of the target mosquito population – the Zika and yellow-fever mosquito vector Aedes aegypti. Learn more about the company and its technology, here, www.oxitec.com/our-technology. On October 5, 2017, FDA issued final Guidance for Industry (GFI) #236 –Clarification of FDA and EPA Jurisdiction over Mosquito-Related Products, which clarifies that mosquito-related products intended to function as pesticides by preventing, destroying, repelling, or mitigating mosquitoes for population control purposes, and that are not intended to cure, mitigate, treat or prevent a disease are not “drugs” under the FD&C Act, and will be regulated by the EPA under the Federal Insecticide, Fungicide, and Rodenticide Act. The FDA will continue to have jurisdiction over mosquito-related products that are intended to prevent, treat, mitigate, or cure a disease. With the issuance of final guidance #236, Oxitec Ltd’s genetically engineered mosquito, with its proposed claim to control the population of wild-type Aedes aegypti mosquitoes, now falls under EPA’s regulatory authority and all related regulatory questions should be directed to the EPA. www.fda.gov/animal-veterinary/animals-intentional-genomicalterations/oxitec-mosquito. Findings, no significant impact: https://www.fda.gov/media/99731/download Labeling and Intentionally Altered Food National Bioengineered Food Disclosure Standard was announced on December 20, 2018. The National Bioengineered Food Disclosure Law, passed by Congress in July of 2016, directed USDA to establish this national mandatory standard for disclosing foods that are or may be bioengineered. The Standard defines bioengineered foods as those that contain detectable genetic material that has been modified through certain lab techniques and cannot be created through conventional breeding or found in nature. https://www.ams.usda.gov/rules-regulations/be The Standard requires food manufacturers, importers, and certain retailers to ensure the disclosure of bioengineered foods. Regulated entities have several disclosure options: text, symbol, electronic or digital link, and text message. Additional options such as a phone number or web address are available to small food manufacturers or for small and very small packages. Watch this video to learn more: youtu.be/08FHkS-pwHw, List of bioengineered foods: https://www.ams.usda.gov/rules-regulations/be/bioengineered-foods-list Medical Food Food can be more than meeting basic nutritional and safety standards – it can be used to reduce the risk of disease. Medical foods are distinguished from other foods in their formulation – specifically to treat a disease or disorder. They are intended for the specific management of a disease or disorder for which distinctive nutritional requirements exist based on scientific evidence. They are not the same as nutritional supplements. Medical foods are a distinct class of food because they are not classified as food nor medicine. However, this is food that the FDA intends to be used under medical supervision by a patient requiring medical care. Foods such as these, for "special dietary uses," were first brought up in regulation in 1941, and added to the FD&C Act in 1976. In 1988 Congress amended the Orphan Drug Act to include a statutory definition of "medical food." The term medical food, as defined in section 5(b) of the Orphan Drug Act (21 U.S.C. 360ee (b) (3)) is: "…a food which is formulated to be consumed or administered enterally under the supervision of a physician and which is intended for the specific dietary management of a disease or condition for which distinctive nutritional requirements, based on recognized scientific principles, are established by medical evaluation." Medical foods are food, and therefore are regulated the same as foods. However, they cannot be marketed for a condition that can be managed or treated solely by a regular diet. That being said, any ingredient added to a medical food must be recognized as safe (GRAS). Medical foods do not need to be registered with the FDA, but the manufacturing facilities do for inspection purposes. Although they are not drugs, they still must meet the requirements for the manufacture and labeling of foods, which include CGMP regulations in manufacturing, packaging, and handling of human food. There is a particular compliance program for medical foods. Test Your Knowledge! Go to FDA’s Medical Food Guidance’s Q&A and answer the following questions 1. Does FDA regulation medical foods as drugs? Why/why not? 2. Do medical foods require clinical studies or premarket review (PMA)? 3. What labeling requirements apply to medical foods? 4. What is the purpose of FDA’s compliance program for medical foods? 5. Does medical food require a prescription? Why/Why not?

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The FDA has regulatory oversight over Animal & Veterinary Products. Veterinary products are a diverse area of regulation by the FDA and include: 1. Animal Drugs 2. Animal Food & Feeds (which includes pet food) 3. Animal Medical Devices Because of this, the regulations and marketing approval that apply depending on the product itself. In this chapter, we briefly touch on some of the more prominent areas of veterinary products. For more information, see the Center for Veterinary Medicine (CVM) as well as the USDA and EPA, all of which oversee the regulations of veterinary products. Center for Veterinary Medicine, and (CVM) The CVM oversees the regulation of food, food additives, drugs, and biologics used on animals. They also conduct research that helps the FDA ensure the safety of animal drugs, food for animals, and food products made from animals. Test Your Knowledge! Explore the CVM FAQ website: www.fda.gov/animal-veterinary/safety-health/frequentlyasked-questions-about-animal-drugs Does the FDA oversee vaccination regulations for animals? Why or why not? Drugs for Animal Use The CVM regulates veterinary drugs under the authority of the Animal Drug Amendments to the FD&C Act (in 1968) in which provisions were added to ensure animal drugs, as well as human drugs, were safe and effective. Animal drugs must be produced under CGMP conditions outlined in 21 CFR 211. There are several central regulatory pathways for animal drugs; Investigational New Animal Drug (INAD), New Animal Drug Application (NADA), and Abbreviated New Animal Drug Application (ANADA). New animal drugs are reviewed and approved through a pathway like human drugs. They first must get approval for clinical studies in animals through the INAD. To manufacture and sell a drug for use in animals, the company must seek approval through a NADA. This application shows the drug has been tested in animal clinical studies and provides data demonstrating its safety and effectiveness. For generic animal drugs, again, the process is like in humans, and the company must apply for an abbreviated application – ANADA – before marketing. Regulation of Pet Food There is no requirement that pet food products have pre-market approval by the FDA. However, the FDA ensures that the ingredients used in pet food are safe and have an appropriate function (nutrition) in the pet food. Many ingredients, such as meat, poultry, and grains, are considered safe and do not require pre-market approval. https://www.fda.gov/animal-veterinary/animal-food-feeds/pet-food Other substances such as sources of minerals, vitamins, or other nutrients, flavorings, preservatives, or processing aids may be generally recognized as safe (GRAS) for intended use or must have approval as food additives. For more information about pet foods and marketing pet food, see FDA’s Regulation of Pet Food. https://www.fda.gov/animal-veterinary/animal-health-literacy/fdas-regulation-pet-food Medicated pet foods, however, do require a regulatory pathway depending on the class of medicated feed. Class A requires NADA (or ANADA), and Class B/C follows a unique route – Veterinary Feed Directive (VFD). VFD foods are available only under veterinarian supervision. Other Categories • Grooming devices are not regulated unless they show claims of therapeutic treatment. Medical devices for an animal are subject to regulation. • Veterinary biologics are licensed through the USDA and Center for Veterinary Biologics (CVB) and are defined in the Virus-Serum-Toxin-Act (VSTA). These biologics follow the same regulatory and approval pathway as other animal drugs and must be safe and effective for the diagnosis, prevention, and treatment of animal diseases. • Pesticides for pets are regulated by EPA under FIRFA and includes topical flea treatments and insecticide dips – which intend to prevent, destroy, or repel pets externally. It is important to note that products for internal pests are treated as drugs. Pesticide regulation mainly focuses on safety to humans that handle the pets through or after treatment with pesticides, including disposal.

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You might be surprised to learn that the FDA has regulatory oversight over cosmetics. You may be even more surprised to know that this oversight is largely self-regulated! The FDA acts with hazardous products – but the remainder of the control is by the companies themselves. The other area the FDA does scrutinize heavily is misbranding. Many companies have recently moved to market their cosmetics with drug language – such as "anti-aging cream." https://www.fda.gov/cosmetics Some of the areas the FDA looks at when considering cosmetics is: • regulations and policy governing the safety of cosmetic ingredients and finished products • regulations, policy, and other activities dealing with proper labeling of cosmetics • regulatory and research programs to address possible health risks associated with chemical or biological contaminants • post-market surveillance and related compliance activities ✓ industry outreach and consumer education As with foods, the complexity of the cosmetic industry and the technologies and ingredients used in the production of cosmetics is overwhelming. A global cosmetics industry has increased the calls for safety oversight since products and components enter the U.S. from many countries with different regulatory and safety standards. Some of the current areas of focus for cosmetics include: 1. microbiological contaminants 2. chemical contaminants 3. drug vs. cosmetic products 4. use of nanoscale materials as ingredients 5. botanical ingredients 6. alternatives to animal testing What is a Cosmetic? The Federal Food, Drug, and Cosmetic Act (FD&C Act) define cosmetics as "articles intended to be rubbed, poured, sprinkled, or sprayed on, introduced into, or otherwise applied to the human body...for cleansing, beautifying, promoting attractiveness, or altering the appearance" (FDA.gov). Lipstick, nail polish, moisturizers all are examples of cosmetics that would meet this definition. The FDA excludes “soap” as a cosmetic – but this is a complicated and tricky topic. Soaps that are composed of fat and alkali (ex. Vegetable oil and lye) are not regulated at all by the FDA – but rather are under the purview of the Consumer Product Safety Commission. Soap that is advertised to cleanse, or beautify in any way, is regulated as a cosmetic. Moreover, soap that has a treatment claim, such as an anti-bacterial soap, is a drug! Whew! Is it a Cosmetic, Drug, or Both? One of the biggest issues with cosmetics is determining Is It a Cosmetic, a Drug, or Both? (Or Is It Soap?) Whether a product is a cosmetic or drug primarily depends on its intended use. Different laws (above) come into play, depending on the use of the product. A product can be considered both a cosmetic and a drug when it is used to diagnose or treat a disease or disorder and to beautify. An excellent example of this would be dandruff shampoo – it is used to both clean the hair as well as treat a disorder. Ultimately, which regulations apply to depend on labeling and marketing. Law & Regulations of Cosmetics Many laws and regulations on the regulations of cosmetics. To learn more, click on the law below! Good Manufacturing Practice for Cosmetics The FDA provides CGMPs for cosmetic products – however, there are no requirements in the FD&C Act for cosmetic products to be manufactured under CGMPs. Many legislative attempts have been made to change this, but so far, none has passed. The industry does provide many of its manufacturing guidelines; some follow the international Guidance’s provided in ISO 22716. Adulteration of Cosmetics One of the FDA enforcement areas is of facility and product inspection. Specifically, the FDA is looking for: 1. A poisonous or deleterious substance that may injure the customer under regular use 2. Filthy, putrid or decomposed substance (including microorganism contamination) 3. Packaging under unsanitary conditions 4. The container is composed of a poisonous or deleterious substance 5. The product contains an unsafe (or unapproved) color additive 6. Any outlawed ingredient (ex. Mercury, lead, zirconium, chlorofluorocarbons) 7. Prohibited cattle material (brain, skull, spinal cord) FDA's Enforcement Tools for Food and Cosmetic Products For food and cosmetics, the FDA focuses on: • inspection of establishments • collection and analysis of samples • monitoring of imports • monitoring of adverse event reports and consumer complaints • premarket review (e.g., food and color additives) • notification programs (e.g., food contact substances, infant formula) • regulations/agreements (e.g., memoranda of understanding) • determine the health effects of food and cosmetic contaminants • determine the effects of processing on food composition and allergenicity • determine the health effects of dietary factors • determine skin penetration of cosmetic ingredients and contaminants

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Objectives • Identify FDA monitoring & enforcement practices • Understand enforcement terminologies such as misbranding, adulteration, recall, inspection, injunction, and debarment • Explore the civil and criminal enforcement tools and relative harshness: seizure, injunction, warning letters, 483, recall, debarment, civil penalty, criminal enforcement • Understand FDA recall authority • Apply an understanding of class I, II, & III recalls • 10.1: FDA Monitoring and Enforcement Over the last few chapters, you have explored the FDA organization, the Centers overseeing different products, and dove into some of the product areas themselves. Next, we will examine the regulations that govern this process and how the FDA inspects and enforces laws in this area to protect public health. • 10.2: Enforcement Terminologies • 10.3: Enforcement Activities Regulations must be enforceable to be effective, and the FDA has plenty of tools to encourage compliance. The key to the FDA is product public health and safety. Enforcement proceedings usually take place after an inspection has been deemed OAI. The inspections, through appropriate centers, can be either every two years or as indicated by an issue the FDA has been made aware of. There are two broad categories of enforcement activities; civil and criminal. • 10.4: Recalls A recall is the voluntary removal of a product by a manufacturer or at the request of the FDA. Recalls are almost always voluntary. The FDA can only issue a recall when they have the mandated power to do so. The FDA cannot recall a drug, or biologic, but can recall a medical device, some cosmetics, and food. When they do have recall authority, they can only do so when there is a substantial public health and safety risk. 10: FDA Enforcement Over the last few chapters, you have explored the FDA organization, the Centers overseeing different products, and dove into some of the product areas themselves. Next, we will examine the regulations that govern this process and how the FDA inspects and enforces laws in this area to protect public health. The FDA is mandated by the FD&C Act to protect public health from adulterated and misbranded regulated products and has significant and broad enforcement power to do so. The FD&C Act is the basic food and drug law of the U.S. With numerous amendments, it is the most extensive law of its kind in the world. The law is intended to assure the consumer that foods are pure and wholesome, safe to eat, and produced under sanitary conditions; that drugs and devices are safe and effective for their intended uses; that cosmetics are safe and made from appropriate ingredients; and that all labeling and packaging is truthful, informative, and not deceptive. Companies are highly encouraged to engage the FDA in all forms of communication as these communication methods serve as prior notice of a lawsuit. However, aside from lawsuits, or regulations where the FDA has recall authority, most communication responses from the company are voluntary. Explore! Go to the following website and read the statement by the acting commissioner, Dr. Ned Sharples, regarding global enforcement strategies. Consider, why do we care about global enforcement? https://www.fda.gov/news-events/fda-voices-perspectives-fda-leadership-and-experts/expanding-criminal-enforcement-operations-globally-protect-public-health Inspections, Compliance, Enforcement, and Criminal Investigations As FDA’s criminal law enforcement arm, the Office of Criminal Investigations (OCI) protects the American public by conducting criminal investigations of illegal activities involving FDA-regulated products, arresting those responsible, and bringing them before the Department of Justice for prosecution. https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/criminal-investigations Since 1993, OCI has investigated thousands of criminal schemes involving a broad range of criminal conduct, including the distribution of foreign counterfeit, unapproved, and misbranded medical products and clinical investigators and health fraud involving FDA-regulated drugs and medical devices. Explore! Explore some of the examples of the types of criminal investigations OCI investigates. Did you discover anything interesting? • Cyber Crime • Prescription Drugs • Foods, Dietary Supplements • Medical Devices • Tobacco • Veterinary Drugs • Most Wanted Fugitives Compliance Programs: www.fda.gov/inspections-compliance-enforcement-and-criminalinvestigations/compliance-manuals/compliance-program-guidance-manual-cpgm Compliance Activities: www.fda.gov/inspections-compliance-enforcement-and-criminalinvestigations/compliance-actions-and-activities Inspection Activities: www.fda.gov/inspections-compliance-enforcement-and-criminalinvestigations/inspection-references FD&C Act Section 331 The list of prohibited acts in which the FDA may pursue action against a company for is outlined in the FD&C Act Section 331. These all apply if the product is regulated by the FDA; biologics, drugs, devices, cosmetics. Below are some key areas as they relate to enforcement. You will notice that it makes companies responsible for adulteration, even for outside third-party vendors. Common Violations of the FD&C Act 1. Adulterated or misbranded regulated product 2. Receiving or delivering an adulterated or misbranded product 3. Refusal for inspection 4. Counterfeiting product 5. Altering a product label 6. Not registering a product 7. Refusal to provide required documents Code of Federal Regulations for IND, NDA, ANDA, and BLA Explore! FDA has the authority to not only enforce the laws enacted by the U.S. Congress but also communicate regulations in the Code of Federal Regulations under Title 21. The following Code of Federal Regulations(CFR) sections provide regulations for INDs, NDAs, and BLAs. All parts of section 21 of the Code of Federal Regulations are also available. To view the most current CFRs, go to https://www.ecfr.gov, and select Title 21 in the pull-down and GO. Use the “simple search” to complete the table below. CFR Sections BLA Part 600-Biological Products: General Part 601-Licensing Part 610-General Biological Products Standards IND NDA ANDA IND

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Legal Terminology Before we continue on the discussion of FDA enforcement, it is important to understand some key terms in this area. The FD&C Act frequently refers to interstate commerce, adulteration, and misbranding. Interstate Commerce applies to all steps in the manufacture, packaging, and distribution of a product. It is common that some of the ingredients or packaging most likely originate from out of state or even out of the country and even will leave the state. What Makes a Product Adulterated? From the FDA (FDA, 2016). Note that regarding adulteration, the law addresses the composition of the product, the conditions under which the product is manufactured, shipped, and stored, the product's container. A product shall be deemed to be adulterated if: 1. If it bears or contains any poisonous or deleterious substance which may render it injurious to users under the conditions of use prescribed in the labeling 2. If it consists of any filthy, putrid, or decomposed substance 3. If it has been prepared, packed, or held under insanitary conditions whereby it may have become contaminated with filth, or whereby it may have been rendered injurious to health 4. If its container is composed of any poisonous or deleterious substance which may render the contents injurious to health 5. If it contains an unapproved color (or other) ingredient What makes a product Misbranded? Section 602 of the FD&C Act [21 U.S.C. 362] describes what causes a product to be considered misbranded. It includes not only what the label says but also what it fails to say! Note that under the FD&C Act, the term "misbranding" applies to false, misleading, or missing information or packaging. A product shall be deemed to be misbranded: 1. . If its’ labeling is false or misleading 2. If the label is missing (1) the name and place of business of the manufacturer, packer, or distributor; and (2) an accurate statement of the quantity of the contents in terms of weight, measure, or numerical count 3. If any word, statement, or other information required is not prominently placed 4. If its container is filled as to be misleading Monitoring Bioresearch Monitoring (BIMO) The overarching goals of the FDA's bioresearch monitoring (BIMO) program are to defend the rights, safety, and welfare of subjects involved in FDA-regulated clinical trials (fda.gov). Additionally, the BIMO serves to determine the accuracy and reliability of clinical trial data submitted to the FDA and to assess compliance with the FDA's regulations governing the conduct of clinical trials. The BIMO program performs on-site inspections of both clinical and nonclinical studies carried out to support research and marketing applications/submissions to the agency. To learn more about the research monitoring program: https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/compliance-actions-and-activities/fda-bioresearch-monitoring-information The FDA Tests Products How do quality issues come to the attention of the FDA? The FDA can purchase and test products on its own. The FDA can also inspect production facilities. If a product is found to be defective (or an inspection facility to be out of compliance), there are several options the FDA may pursue: 1. warn the public, 2. seize products from the market, and 3. bring a seizure or injunction case in court, to name a few.

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Civil Enforcement Regulations must be enforceable to be effective, and the FDA has plenty of tools to encourage compliance. The key to the FDA is product public health and safety. Enforcement proceedings usually take place after an inspection has been deemed OAI. The inspections, through appropriate centers, can be either every two years or as indicated by an issue the FDA has been made aware of. There are two broad categories of enforcement activities; civil and criminal. The guidelines to the enforcement actions the FDA takes can be found at the Inspections, Compliance, Enforcement, and Criminal Investigation (ICECI) webpage. The FDA publishes enforcement activities in annual reports to its website. Look around and see what kinds of enforcement activities are most prominent. The 2017 statistics can be found here: https://www.fda.gov/downloads/ICECI/EnforcementActions/UCM592790.pdf Inspections The FDA has the legal authority to inspect pharmaceutical companies, and it can do so unannounced. The guidelines for the inspections are posted to the Inspections, Compliance, Enforcement, and Criminal Investigation (ICECI) webpage. Different inspection guidelines govern different product types. https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/inspection-references 1. Inspections Operations Manual: www.fda.gov/inspections-compliance-enforcement-andcriminal-investigations/inspection-references/investigations-operations-manual 2. Inspection Guides: www.fda.gov/inspections-compliance-enforcement-and-criminalinvestigations/inspection-references/inspection-guides 3. Foreign Inspection Guides: www.fda.gov/inspections-compliance-enforcement-andcriminal-investigations/inspection-references/foreign-inspections The FDA performs routine (every two years) inspections for compliance with CGMP, GLP, GCP, and Quality System Regulations. They also perform targeted inspections based on other enforcement events such as follow-ups on recall events or warning letters. When the FDA enters a facility for inspection, they provide the inspection request document (FDA 482) as well as provide identification. If they are refused entry, the FDA can obtain a search warrant from a federal court. The scope of the inspection is primarily based on the reason for the visit and the history of the facility. The only limits the FDA has in inspections relate to financial information, sales data (not related to shipping), personnel data (not related to training), and research data (not related to the approval of products). During inspections, the FDA looks at seven systems to determine if they are ‘in control’: 1. Management responsibility 2. Design control 3. Corrective and preventative action (CAPA) 4. Production and process controls 5. Records and document change controls 6. Material controls 7. Facilities and equipment controls Inspection Classification After an inspection, the FDA determines if the areas evaluated are in compliance with applicable laws and regulations. FDA and the Inspection Classification Database classifies the inspection by each project area with one of three classifications. The Inspection Classification Database only shows inspections conducted by FDA. www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/inspection-references/inspection-classification-database The FDA conducts careful inspections of facilities that perform nonclinical laboratory studies to determine compliance with Part 58 (Good Laboratory Practice for Nonclinical Laboratory Studies) of Title 21 of the CFR. Nonclinical laboratory studies are experiments in which test articles are studied prospectively in test systems, such as animals, plants, microorganisms under laboratory conditions to determine their safety. Learn more here: https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/inspection-references/nonclinical-laboratories-inspected-under-good-laboratory-practices The three Inspection Classifications displayed are: 1. No Action Indicated (NAI) which means no objectionable conditions or practices were found during the inspection (or the objectionable conditions found do not justify further regulatory action), 2. Voluntary Action Indicated (VAI) which means objectionable conditions or practices were found, but the agency is not prepared to take or recommend any administrative or regulatory action, or 3. Official Action Indicated (OAI), which means regulatory or administrative actions will be recommended. Inspections & Form 483 Adulteration and misbranding are the two most common violations found during an inspection. Pharmaceutical facilities and biotechnology companies are periodically inspected by the FDA. Any CGMP violations the inspectors find are noted on forms, called “483’s,” and if no response to the regulatory compliance issues, an official Warning Letter is sent to the company. A 483 is a result of an inspection and notice of regulatory non-compliance. It is a list of specific items seen at the end of the inspection and is issued by the investigator. After an inspection, the inspector meets with the facilities manager to address as many of the problems before the 483 is written. The inspector offers an opportunity to remedy a situation immediately after the inspection and document compliance and remedies, or future solutions and agreements. After the letter is written and received by the company, the company then has 15 working days to voluntarily respond to the 483 in writing with an action plan. If the 483 issued is not remedied quickly, the FDA can then respond with a warning letter (see below). It should be noted that the issuance of form 483 does not automatically mean that a firm is not in GMP compliance. Additionally, the length of the form is not a reliable indicator of the seriousness of any observed violations. The form should be viewed critically, and companies that feel they have received a 483 containing questionable observations of GMP deviations should discuss the issue with the inspector, district director, regional director, or even the center of issuance if necessary. Companies are not required to respond to a 483. However, their response is recommended. If a company receives too many 483s and is not providing the FDA with adequate responses to these forms, they are subjected to a warning letter or more punitive measures as outlined below. Establishment of Inspection Reports After the FDA closes an inspection, they release an Establishment of Inspection Report (EIR). It is a formal written report summarizing the findings with supporting evidence. In this report, the FDA classifies the inspection as No Action Indicated (NAI), Voluntary Action Indication (VAI), or Official Action Indicated (OAI). If an OAI is noted, enforcement activities may be listed or be scheduled to come. Inspection Reports and Data: https://datadashboard.fda.gov/ora/cd/inspections.htm Inspections & Warning Letters When FDA finds that a manufacturer has significantly violated FDA regulations, the FDA notifies the manufacturer, most often, in the form of a Warning Letter. The Warning Letter identifies the violation and makes clear that the company must correct the problem and provides directions and a timeframe for the company to inform the FDA of its plans for correction. FDA then checks to ensure that the company’s corrections are adequate. Matters described in FDA warning letters may have been subject to subsequent interaction between the FDA and the recipient of the letter that may have changed the regulatory status of the issues discussed in the letter. A warning letter issued by the FDA is a voluntary informal advisory communication and offers a company the opportunity to remedy the regulatory situation. The overall goal of a warning letter is to encourage voluntary compliance. If the issue does not put the public in immediate danger, a warning letter may be written before other punitive measures. An important aspect of a warning letter is to establish a record of ‘prior notice’ during legal proceedings. However, when issued, a warning letter is published immediately on the FDA website and is shared across regulatory agencies. 1. View general FDA warning letters: www.fda.gov/inspections-compliance-enforcementand-criminal-investigations/compliance-actions-and-activities/warning-letters 2. View tobacco FDA warning letters: www.fda.gov/inspections-compliance-enforcementand-criminal-investigations/warning-letters/tobacco-retailer-warning-letters 3. View drug marketing and advertising warning letters: www.fda.gov/drugs/enforcementactivities-fda/warning-letters-and-notice-violation-letters-pharmaceutical-companies Warning Letter Closeouts FDA may issue a Warning Letter close-out letter once they have completed an evaluation and determined that corrective actions were undertaken by a firm in response to a Warning Letter. The corrective actions must have been made and verified by the FDA, usually through a follow-up inspection. If the Warning Letter contains violations that by their nature are not correctable, then no close-out letter will be issued. Future FDA inspections and regulatory activities may further assess the adequacy and sustainability of these corrections. Should violations be observed during a subsequent inspection or through other means, enforcement action may be taken without further notice. Inspections & Untitled Letters Untitled letters are the least harsh form of communication with the FDA. Like Warning Letters, the untitled letters can notify a company of a violation that may not reach the threshold of a regulatory issue. Unlike a warning letter, an untitled letter does not include a statement that warns the individual or firm that failure to promptly correct the violation may result in enforcement action. F However, companies are encouraged to address any issues as this does constitute ‘prior notification' and is why you should respond. https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/compliance-actions-and-activities/issuance-untitled-letters. For more information on warning and untitled letters: https://www.fda.gov/media/71878/download Inspections & Press Releases The FDA can also issue unfavorable press releases or federal register notices. In the event of an egregious defect, the FDA can criminally prosecute, seize materials, and perform injunctions against a company and individuals. (fda.gov). Current press releases: www.fda.gov/inspections-compliance-enforcementand-criminal-investigations/criminal-investigations/press-releases Seizures If a company refuses to recall, the FDA can bring a seizure or injunction case against it to address violations even if the products are not defective. Then, they can petition the court for an order that allows federal officials to take possession of “adulterated” drugs and destroy them. This process enables the FDA to immediately prevent a company from distributing defective and potentially harmful drugs to consumers. Both seizure and injunction cases frequently result in court orders that require companies to take many steps to correct violations. These steps may include hiring outside experts to help resolve the problem, writing new procedures, and training employees. In some cases, violations may become criminal cases, allowing the FDA to seek fines and jail time. Injunctions If a company violates the FD&C Act, the FDA may file an injunction against the company. This injunction is a civil judicial proceeding and is typically used when a significant health hazard is identified with a product. This FDA may seek a temporary restraining order, a temporary injunction, or permanent injunction. The key here is for the FDA to be able to act quickly to get a product to stop from reaching the customers short of a recall (which the FDA does not have authority in some cases). The FDA also uses this enforcement method if the company has ignored repeated warning letters. If the company addresses the issues, the temporary restraining order can be lifted. Civil Money Penalties The FD&C Act, as well as the PHSA, have civil money penalty provisions. Guidance on CMP is provided in 21 CFR 17.2. Look up the CFR on the FDA website, and notice the CMPs are quite harsh! Some penalties exceed a million dollars for aggregate offenses. Disqualification of Clinical Investigators FDA regulates scientific studies that are designed to develop evidence to support the safety and effectiveness of investigational drugs (human and animal), biological products, and medical devices. Physicians and other qualified experts ("clinical investigators") who conduct these studies are required to comply with applicable statutes and regulations intended to ensure the integrity of clinical data on which product approvals are based and, for research involving human subjects, to help protect the rights, safety, and welfare of those subjects. In certain situations, in which the FDA alleges a clinical investigator has violated applicable regulations, the FDA can disqualify a clinical investigator and prevent them from providing any clinical data for any product submission. Typically, information on clinical investigators is obtained through the BIMO inspection. https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/compliance-actions-and-activities/clinical-investigators-disqualification-proceedings Debarment The FDA has the debarment authority of individuals or companies from the drug industry. Debarment means they can no longer manufacturing an approved drug. Debarred companies can no longer manufacture, nor submit any further drug applications. In 2018, the FDA debarred a corporate entity for the first time. Read more here: https://www.federalregister.gov/documents/2018/03/01/2018-04195/meunerie-sawyerville-inc-denial-of-hearing-final-debarment-order. Debarred people can also be subject to civil money penalties, as well. See a list of debarments on the FDA website. You will notice it is a shockingly long list! https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/compliance-actions-and-activities/fda-debarment-list-drug-product-applications Criminal Enforcement Criminal investigations are made by the Office of Criminal Investigations (OCI). It is important to remember when we are discussing FDA regulations on Food & Drugs, we are referring to laws. Breaking laws have many penalties, which can range from fines to jail time. Check out the FDA’s most wanted fugitives here: https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/criminal-investigations/office-criminal-investigations-most-wanted-fugitives Consent Decree Companies that repeatedly violate CGMP requirements may be forced to make changes via the issuance of a consent decree. The consent decree is signed by the company’s top official, the U.S. Attorney, and the U.S. District Court. The decree is then filed with the court and is later submitted to the FDA. Enforced by the Federal courts, consent decrees typically involve fines, reimbursements to the government for inspection costs, and penalties for noncompliance. Consent decrees can be permanent. However, if a company has complied, it can petition the court to remove the decree. Test Your Knowledge! Read here a featured story on the OCI website: "April 4, 2016: Former Carlsbad Resident Jailed for Sale of Unapproved "Energy Wave" Medical Devices." 1. What is David Perez accused of doing? 2. Why is this against the law? Can you reference the law? 3. How long of a sentence did he receive? If he did not receive a plea deal and was found guilty in a court of law, how long would his maximum sentence have been? 4. Do you agree with the charge and his sentence? Explain.

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Recalls - Drugs, Biologics, Devices, & Food A recall is the voluntary removal of a product by a manufacturer or at the request of the FDA. Recalls are almost always voluntary. The FDA can only issue a recall when they have the mandated power to do so. The FDA cannot recall a drug, or biologic, but can recall a medical device, some cosmetics, and food. When they do have recall authority, they can only do so when there is a substantial public health and safety risk. https://www.fda.gov/consumers/consumer-updates/fda-101-product-recalls Recall Resources: https://www.fda.gov/safety/recalls-m...call-resources Food The FDA can issue a food recall. In 2011, the FDA gained increased authority in regulating and responding to food product contamination via the new Food Safety Modernization Act (FSMA). The FSMA allows the FDA to suspend the services and production of food distributors if contamination is suspected. There need not be any proof of the source of the contamination. For more information on the FSMA: http://www.foodsafety.gov/news/fsma.html Medical Device The FDA can issue a device recall. In 2012, the US Food and Drug Administration (FDA) announced that it was seeking to implement medical device recall authority under § 518(e) of the FD&C Act and Chapter 21, Section 810 of the CFR. Recall authority for medical devices would permit the FDA to order manufacturers to cease the distribution of a device and notify health professionals if FDA finds a reasonable probability that the device would cause serious adverse health reactions or death (fda.gov). A recall does not necessarily mean the product must be returned, sometimes it just needs to be adjusted, or clarification safety instructions provided. 21 CFR 7 provides Guidance for conducting an efficient voluntary recall. Examples of the types of actions that may be considered device recalls: 1. Inspecting the device for problems 2. Repairing the device 3. Adjusting settings on the device 4. Re-labeling the device 5. Destroying device 6. Notifying patients of a problem 7. Monitoring patients for health issues A medical device recall is either a correction or removal. A Correction addresses a problem with a medical device in the place where it is sold. A Removal approaches the problem by removing the device from where it is sold. In most cases, a company voluntarily recalls a device on its own. When the company has violated an FDA law, the company must recall the device (correction or removal) and notify the FDA. Legally, the FDA can require a company to recall a device if an organization refuses to do so under 21 CFR 810, Medical Device Recall Authority. 21 CFR 810 describes the procedures the FDA follows in exercising its medical device recall authority under section 518(e) of the FD&C Act. A recall does not include a market withdrawal or a stock recovery. A market withdrawal is a firm's removal or correction of a distributed product which involves a minor violation that would not be subject to legal action by the FDA or which involves no violation, e.g., normal stock rotation practices, routine equipment adjustments, and repairs (fda.gov). In the end, almost all recalls are conducted voluntarily by the manufacturer. https://www.fda.gov/safety/recalls-market-withdrawals-safety-alerts Explore! A comprehensive, searchable recall medical device recall database: www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfRES/res.cfm To learn more about Device Recalls, visit the FDA device recall web page https://www.fda.gov/medicaldevices/safety/listofrecalls/ and also, watch the FDA Video here. http://fda.yorkcast.com/webcast/Play/1b95461f64be40ecbe3415195cb394911d Device recalls following the same general recall procedure, as previously discussed for drugs. This includes classification of recall (I, II, or III) developing a recall strategy and providing the FDA with recall status reports. Medical device safety alert: issued in situations where a medical device may present an unreasonable risk of substantial harm. In some cases, these situations also are considered recalls (fda.gov) Market withdrawal occurs when a product has a minor violation that would not be subject to FDA legal action. The firm removes the product from the market or corrects the violation. For example, a product removed from the market due to tampering, without evidence of manufacturing or distribution problems would be a market withdrawal. (fda.gov) Drug Safety and Availability The FDA offers many websites that address specifically drug safety and availability to communicate with customers. Here are a few you may want to explore. https://www.fda.gov/drugs/drug-safety-and-availability 1. Drug Safety Communications: https://www.fda.gov/drugs/drug-safety-and-availability/drug-safety-communications 2. Post-Market Drug Safety: https://www.fda.gov/drugs/drug-safety-and-availability/postmarket-drug-safety-information-patients-and-providers 3. What’s New – Human Drugs: https://www.fda.gov/drugs/news-events-human-drugs 4. Adverse Event Reporting: https://www.fda.gov/drugs/surveillance/questions-and-answers-fdas-adverse-event-reporting-system-faers Drug Recall A drug recall is a voluntary action taken by a company. www.fda.gov/drugs/drug-recalls/fdas-roledrug-recalls. Not all recalls are announced on FDA.gov or in the news media. Public notification is generally issued when a product that has been widely distributed or poses a serious health hazard is recalled. However, if a company does not issue public notification of a recall, FDA may do so if the agency determines it is necessary to protect patients. FDA evaluates the effectiveness of a recall by evaluating a company’s efforts to properly notify customers and remove the defective product from the market. If a recall is determined to be ineffective FDA will request the company take additional actions. Class I, II & III Recalls • Class I Recall: "A reasonable probability that the use of or exposure to a violative product will cause serious adverse health consequences or death." (fda.gov) • Class II Recall: "use of or exposure to a violative product may cause temporary or medically reversible adverse health consequences or where the probability of serious adverse health consequences is remote." (fda.gov) • Class III Recall: "use of or exposure to a violative product is not likely to cause adverse health consequences." (fda.gov) Test Your Knowledge! Read the article and watch the video “FDA 101: Product Recalls - From First Alert to Effectiveness Checks” and read FDA FAQs: 1. How does the FDA first learn about a problem with a product? 2. How does the FDA alert the product about a product recall? 3. Discuss an example of a recall, and state what class of recall it is and why. Explore! The FDA Drug Safety Podcasts are produced by FDA's CDER and provide emerging safety information about drugs in conjunction with the release of Public Health Advisories and other drug safety issues. (fda.gov).

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The Domains of Life As of the 1970's, life has been classified into three domains: Bacteria, Archaea, and Eukarya (shown in Figure \(1\) as Eukaryota). All known life on Earth is thought to have descended from a single common ancestor: LUCA (last universal common ancestor). The relationship between the three domains of life is depicted in the phylogenetic tree below. This diagram represents Archaea and Eukarya as sister taxa, more closely related than either group is to Domain Bacteria. Depicting Relationships Branching tree diagrams (like the phylogenies shown above) are used to communicate a hypothesis for how organisms are related. In Figure \(3\) and Figure \(4\), some example trees are drawn to show how this works. 2.01: Cyanobacteria The earliest cells on Earth were prokaryotic (pro- meaning before, karyo- referring to the nucleus). As is implied by the name, prokaryotic cells lack a nucleus, as well as any membrane bound organelles. Prokaryotes have been divided into two domains: Bacteria and Archaea. Alongside domain Eukarya, these three domains compose the tree of life, as we currently understand it. Cell Structure In their simplest form, these unicellular organisms possess a cell wall, cell membrane, cytosol, ribosomes, and DNA. As the vast diversity of life on Earth is prokaryotic, you can imagine that there is a great diversity of forms and many exceptions to these general guidelines. The DNA in prokaryotic cells is a single chromosome in the form of a loop, often bundled into a condensed region called a nucleoid. There may be small loops of DNA present called plasmids. These small loops of DNA can be exchanged between prokaryotes and the environment and are frequently the location of antibiotic resistance genes. On the exterior, prokaryotes have a cell wall. They may also have flagella (sing. flagellum) for movement and/or pili (sing. pilus) for interacting with other organisms. Reproduction There is no nucleus in a prokaryotic cell, so they cannot undergo mitosis or meiosis. Instead, prokaryotes replicate by a process called binary fission (bi- meaning two, fission meaning to split apart). Endosymbiosis Endosymbiosis (endo- meaning inside, symbiosis meaning shared life) is a process by which several organelles were acquired by lineages of eukaryotic organisms, including mitochondria and plastids. Primary Endosymbiosis Both mitochondria and the chloroplasts in plants were acquired through a process called primary endosymbiosis. In the primary endosymbiosis that resulted in chloroplasts, a photosynthetic prokaryote similar to modern day cyanobacteria was engulfed by a heterotrophic eukaryote (a method of eating called phagocytosis). Something went wrong during this process and the prokaryotic cell was not digested. Instead, it was trapped within the eukaryotic cell. It continued to photosynthesize, producing sugars that resulted in increased fitness for its host. Over a long period of time, genes were eventually transferred between the prokaryote and the eukaryotic nucleus and an organelle was formed: the chloroplast. Secondary Endosymbiosis Many unrelated groups of photosynthetic organisms obtained the ability to photosynthesize by a process called secondary endosymbiosis. This is similar to primary endosymbiosis, except the organism that gets engulfed is a photosynthetic eukaryote (whose chloroplasts were the result of primary endosymbiosis somewhere in their evolutionary history). For example, brown algae and diatoms are both the result of a secondary endosymbiotic event in which a heterotrophic heterokont (see Chapter 5.2 Water Molds) engulfed a red alga. • 2.1: Cyanobacteria Cyanobacteria are a group within Domain Bacteria that perform oxygenic photosynthesis are related to the chloroplasts in plants. They are often found in mutualistic relationships fixing nitrogen. • 2.2: Root Nodules Root nodules are a form of mutualism between bacteria and plant roots 02: Prokaryotes Stromatolites The earliest fossils are interpreted to be unicellular organisms similar to modern day cyanobacteria, sometimes referred to as blue green algae. The most widely accepted of these fossils dates back to 3.4 billion years ago from the Strelley Pool Formation in Western Australia. These particular fossils are called stromatolites and are composed of alternating layers of fossilized cells and calcium carbonate. We can use evidence from modern day stromatolite formation in Western Australia to infer that these fossilized cells were doing a process called photosynthesis, using dissolved CO2 in the water to form sugar molecules. This causes calcium to precipitate out of the seawater, forming hardened layers of calcium carbonate on top of the colony of organisms. Because they need access to light to continue photosynthesizing, living cells begin forming a new layer on top of the calcium carbonate. This process continues, making a ringed pattern as the formation grows, much like we see in trees and corals. Modern Cyanobacteria Free-Living Cyanobacteria can be found in a vast diversity of places, from floating in the ocean to living in cryptobiotic crusts in the desert. Nostoc is a type of cyanobacteria that can often be found living in gelatinous colonies in wet, terrestrial environments. The colony secretes a mucilaginous sheath that provides a protective barrier and allows for the exchange of materials between cells in the colony. Mutualists Many cyanobacteria that you'll see in botany will be in mutualistic relationships. Anabaena is a genus of colonial cyanobacteria that can be found within the leaves of the water fern Azolla, fixing nitrogen in the fern's relatively nutrient-poor aquatic environment. Nostoc is another genus of colonial cyanobacteria capable of fixing nitrogen. It can be found free-living in gelatinous colonies shown above or, as you are likely to see it in your botany course, in compartments of a hornwort thallus. Cyanobacteria can also be found in a mutualistic relationship with fungi in cyanolichens (Figure \(5\)). Looking at Cyanobacteria in Water Ferns If you were to chop up a sample of the water fern Azolla and look at it under the microscope, you'd see what looked like strings of green beads. Each bead is an individual cyanobacterium of the genus Anabaena. However, even though each one is an individual, some cells will specialize to provide a service for the colony, as a whole. • Heterocysts are thick-walled, chlorophyll-free cells that are fixing atmospheric nitrogen into bioavailable forms using the enzyme nitrogenase. Heterocysts cannot do photosynthesis, as that process produces oxygen and nitrogenase cannot function in the presence of oxygen. • Akinetes are individuals that still perform photosynthesis, but also function as a sort of failsafe. Akinetes store large amounts of lipids and carbohydrates so that they have enough energy to begin a new colony if conditions become too cold or too dry for survival. Their formation is triggered by these conditions (dry or cold), so you may not see them from a fresh water fern leaf, as this is a relatively stable, comfortable environment. 2.02: Root Nodules Several different groups of prokaryotes form mutualistic relationships with plant roots. Nitrogen is an essential nutrient for plants, yet it is difficult to obtain in many ecosystems. Though it is abundant in our atmosphere, this form a nitrogen (N2) is triple-bonded to itself, a bond which most organisms cannot break. However, certain bacteria have an enzyme called nitrogenase that can break the triple bond and convert nitrogen into usable forms for plants, such as ammonia (NH3). These bacteria can be found free-living in the environment or in mutualistic relationships with certain plants. A common relationship between plants and these nitrogen-fixing bacteria is the formation of root nodules--swellings in the plant roots that connect to the vascular tissue, allowing for the exchange of sugars and nutrients between the two different organisms. Root Nodules in Legumes Plants in the bean family (Fabaceae) form mutualistic relationships in the form of root nodules with nitrogen-fixing bacteria in the order Rhizobiales. Root Nodules in Alder Frankia is a genus of bacteria that grows filamentously, called an actinomycete. Root nodules present on alder and few other groups of woody plants contain Frankia.

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• 3.1: Kingdom Fungi An overview of the general characteristics and diversity of Kingdom Fungi. • 3.2: Aquatic Fungi (Chytrids) Like many of the earlier fungal lineages, this group has been divided into several distinct lineages. Once all classified as Chytridiomycota, these early, aquatic fungi are now grouped into Blastocladiomycota, Chytridiomycota, and Neocallimastigomycota. • 3.3: Zygospore-forming Fungi Zygospore-forming fungi were classified into the Zygomycota. This group has since been split into several lineages. However, some shared characteristics and life cycle features that are covered here. • 3.4: Glomeromycota (Endomycorrhizal Fungi) Glomeromycota are a group of fungi known for the endomycorrhizal relationships they form with the majority of plant species. • 3.5: Ascomycota (Sac Fungi) Ascomycota includes fungi that have simple septations in their hyphae and produce spores within a sac-like structure called an ascus. Most form ascocarps (apothecia, perithecia, or cleistothecia), while others produce naked asci or reproduce asexually with conidia. • 3.6: Basidiomycota (Club Fungi) Basidiomycota produce complex septations with clamp connections and form spores externally on basidia. This group includes three major lineages: the Agaricomycotina (mushroom-forming fungi are found here), Ustilaginomycotina (the smuts), and Pucciniomycotina (the rusts). • 3.7: Lichens Lichens are a symbiotic relationship, generally classified as a mutualism, between at least one fungal partner (the mycobiont) and at least one photosynthetic partner (the photobiont). 03: Fungi and Lichens The Mycelium The growth form for most fungi is a network of thread-like cells called hyphae (sing. hypha). En masse, the network of hyphae is called a mycelium. Spores Fungi reproduce by making haploid spores. Spores can be formed through asexual or sexual reproduction. The method by which fungi produce spores via sexual reproduction is a useful characteristic for grouping them into different phyla. The shape, size, number, color, and texture of spores are all often useful characteristics in identifying fungi to a more specific level. Molds "Molds" are filamentous fungi producing spores (usually asexually). Many different groups of fungi produce molds, including many of the former Zygomycota, Ascomycota, and Basidiomycota. Video \(1\): In this epic digital rendering (cue electric guitar on synthesizer), a fungus in the genus Aspergillus is producing tall, lollipop-like conidiophores. From these, chains of conidia are formed. As the conidiophores sway and bump into each other, the conidia are dispersed into the air. Yeasts Normally, fungi have a filamentous form. However, many groups within Kingdom Fungi produce yeasts. Yeasts are unicellular fungi. Though some yeasts can reproduce sexually, they are usually found reproducing asexually via a process called budding. In budding, the parent yeast cell replicates its nucleus by mitosis. A small protrusion forms in the cell wall and the new nucleus and cytoplasm are pushed into this protrusion or "bud". A wall forms between the bud and the parent cell, leaving a bud scar on the parent cell. The new yeast cell can then grow to a mature size. 3.02: Aquatic Fungi (Chytrids) Like many of the earlier fungal lineages, this group has been divided into several distinct lineages. Once all classified as Chytridiomycota, these early, aquatic fungi are now grouped into Blastocladiomycota, Chytridiomycota, and Neocallimastigomycota. Though likely not directly related, these fungi share a few characteristics: • Primarily aquatic, though some are parasites of terrestrial plants • Swimming spores (zoospores) with a single whiplash flagellum 3.03: Zygospore-forming Fungi These organisms were formerly classified in a group called the Zygomycota because they sexually reproduce by forming a structure called a zygospore. However, they have since been broken into several different lineages. Zygospore Formation When the mycelium of one fungus encounters another fungus of the same species and a complementary mating type, it can start to produce compounds to interact with the new fungus. Through a series of chemical exchanges, the two fungi each begin to extend toward each other. When they touch, they wall off an area of that extension by creating a septum. This area, filled with haploid nuclei, is called a gametangium (see Figure \(3\)). The walls between the gametangia of each fungus dissolve and the two fungi combine cytoplasm (plasmogamy) and then fuse the nuclei together (karyogamy) to form many diploid nuclei. As this happens, a thick, orange, ornamented wall forms around the nuclei. This is the zygosporangium. Rhizopus stolonifer Life Cycle The life cycle below shows both sexual and asexual reproduction in Rhizopus stolonifer. Both sexual and asexual reproduction result in the production of haploid spores that can germinate and grow into a haploid mycelium. However, the spores produced by the mitosporangia will all be genetically identical, while the spores produced by the sporangia emerging from the zygosporangium will be genetically distinct. Watch the video below to see the microscopic structures involved in the asexual portion of the life cycle of Rhizopus stolonifer. • 0:50 The video starts, showing coenocytic hyphae growing • 1:25 Mitosporangium formation (asexual reproduction) • 2:00 Mitospores, haploid spores produced via mitosis, are shown • 2:30 Video ends Video \(1\): Asexual structures of Rhizopus stolonifer. Sourced from YouTube. Examples of Zygospore-forming Fungal Lineages These groups of fungi can be found in your daily life, if you know what to look for. Molds on fruits and bread are often (but certainly not always) from the Mucorales, as well as molds that form on dog poop (specifically, a genus called Phycomyces). You can also find a diverse assortment of former "Zygomycota" members parasitizing other fungi and insects.

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Glomeromycota represent the endomycorrhizal fungi. These fungi form a mutualistic relationship with plant roots, forming hyphal structures within the plant cell walls. Thus, these images contain primarily plant roots. They are a mysterious bunch, though well-studied for their importance in crop production. 3.5.02: Types of Ascocarps • 3.5.1: Characteristics Shared characteristics found in Ascomycota • 3.5.2: Types of Ascocarps Fruiting bodies formed by sexual reproduction in Ascomycota are called ascocarps. There are three main types: apothecium, perithecium, and cleistothecium. • 3.5.3: Life Cycle Ascomycetes have a haplontic life cycle that produces dikaryotic hyphae. These hyphae will produce asci, where both karyogamy and meiosis take place. 3.05: Ascomycota (Sac Fungi) Apothecium Apothecia are cup-shaped with the hymenium fully exposed (lining the interior of the cup), though this can be inverted and take on strange shapes (see Figure \(3\)). Perithecium A flask-shaped fruiting structures, often microscopic and/or embedded within either the substrate it is fruiting in or a fungal structure called a stroma. Cleistothecium A cleistothecium is a fully-enclosed fruiting structure. These typically have bag-like asci. Some split open to release their spores and are called chasmothecia. 3.6.01: Characteristics • 3.6.1: Characteristics Characteristics shared by members of the Basidiomycota. • 3.6.2: Types of Basidiocarps Basidiomycetes in the Agaricomycotina sexually reproduce within fruiting structures called basidiocarps. These can take many forms. • 3.6.3: Life Cycles of Basidiomycetes For each of the three major lineages of Basidiomycota, there is a different model life cycle. The common element between the three is that both karyogamy and meiosis take place within the basidium. There is often an extended dikaryotic stage. • 3.6.4: Rusts and Smuts Rusts and smuts are the other two lineages of Basidiomycota. These are primarily known as plant pathogens, but many smuts are also saprotrophs and/or commensal organisms. 3.06: Basidiomycota (Club Fungi) Fungi with the following structures can be placed in the Basidiomycota*: *It is important to note that these features may look different or not be present at all in some groups of Basidiomycota, such as the rusts (Pucciniomycotina) and smuts (Ustilagomycotina). However, there are many physiological and genetic similarities that support grouping these organisms together in the Basidiomycota. Basidia and Basidiospores Both karyogamy and meiosis occur within a cell called the basidium. Haploid basidiospores from atop projections on the basidum called sterigmata (sing. sterigma). There are generally four spores, as shown in the image below, though the number of spores produced can vary by species. For example, the mushroom you are likely most familiar with, Agaricus bisporus (though you probably know it as a crimini or button mushroom at its immature stage and portobello at maturity), only produces two spores on each basidium (bi- meaning two). Clamp Connections Basidiomycetes maintain their dikaryotic (n+n) state in each hyphal compartment by making structures called clamp connections. These are not always present, but provide a helpful identification feature when they are! 3.6.02: Types of Basidiocarps The fruiting body of a basidiomycete is called a basidiocarp. These structures produce haploid spores by meiosis and come in an incredible variety of shapes and sizes. General Mushroom Anatomy Though only a subset of basidiocarps look this way, they are the model for how we describe "mushrooms". In mycology, this type of basidiocarp is called "agaricoid" or "agaric" because it is the general form we see in the genus Agaricus. A more complex version of the agaric mushroom is seen in the genus Amanita, which is shown below. Other Basidiocarps There are a vast diversity of basidiocarp forms out there. Below are a few examples of the more common ones you might run into. Clubs & Corals Figure \(10\): On the left are the club-shaped fruiting bodies of Clavariadelphus occidentale. On the right, is the branched, antler-like fruiting body. The branching-forms are generally referred to as corals. Spores can be produced on both clubs and corals on any exterior surface. Photos by Maria Morrow, CC-BY-NC. 3.6.03: Life Cycles of Basidiomycetes Agaricomycotina The fungi covered so far in this chapter have all been in the subdivision Agaricomycotina. These fungi follow some version of the life cycle in Figure \(1\) below. Pucciniomycotina Rust fungi are in the Pucciniomycotina. These fungi have complex life cycles that can have a variety of different spore stages that require different plant hosts. A macrocyclic life cycle (containing all of the five spore stages) of Puccinia gramminis is represented in Figure \(2\). Ustilaginomycotina Smut fungi are in the Ustilaginomycotina. These fungi often have a saptrotrophic phase where they form yeasts and a biotrophic phase during which they act as parasites. The life cycle of the corn smut fungus Ustilago maydis is shown in Figure \(3\). 3.6.04: Rusts and Smuts Rusts (Pucciniomycotina) Rusts are plant pathogens in the subphylum Pucciniomycotina that infect one or more host species. Rusts have amazing and complex life cycles (as you saw in chapter 3.6.3) potentially involving multiple hosts and as many as five different spore stages! Autoecious rusts continue to infect the same host species, while heteroecious rusts must use multiple species of plant hosts to complete their life cycle. Rusts that form all five different types of propagules during their life cycle are called macrocyclic, while rusts that lack one or more of these spore stages are called microcyclic. Smuts (Ustilaginomycotina) Smuts are the third subphylum within Basidiomycota. These fungi form saprotrophic yeasts and can have a variety of ecological roles, but are most famous for their plant pathogens and perhaps the smut fungus (Malassezia) that lives on the oils produced on human skin, sometimes causing the formation of dandruff on your scalp. 3.07: Lichens Biology Lichens are not individual organisms, but a single body formed from multiple symbiotic organisms. Lichens contain a fungal partner (the mycobiont) that forms the majority of the lichen body (called a thallus) and one or more photosynthetic partners (the photobiont) that are typically found in a thin layer or in isolated pockets. The mycobiont is typically an ascoymycete, but can very rarely be a basidiomycete (basidiolichen). The photobiont is usually green algae, but can also be cyanobacteria (cyanolichen) or both green algae and cyanobacteria (tripartite lichen). The mycobiont is responsible for maintenance of the lichen thallus, while the photobiont is responsible for producing food for both partners through photosynthesis. A cyanobacterial partner might also be fixing nitrogen for the lichen. As the study of lichens progresses, we are uncovering more partners with as yet unknown roles, such as basidiomycete yeasts and bacteria. Forms Lichens can generally be classified into three general forms: crustose, foliose, and fruticose. However, there are some lichens that don't really fit into these categories as nicely, such as the "dustose" lichens that form powdery crusts. Crustose Figure \(10\): This image shows several different crustose lichens (and one foliose lichen) on the bark of a young pear tree. The crustose lichen closest to the camera is in the genus Graphis. It looks as though it has been painted onto the tree bark, but has small raised black lines running through it, giving it the common name "script lichen". These lines are the elongated apothecia. Photo by Maria Morrow, CC-BY. Foliose Foliose lichens have a distinct upper and lower surface, much like a leaf. Sometimes these can grow appressed to a substrate, but unlike crustose lichens, they can usually be separated from it (with some effort).

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/03%3A_Fungi_and_Lichens/3.04%3A_Glomeromycota_%28Endomycorrhizal_Fungi%29.txt

Protists are not a phylogenetically related group of organisms. In the very recent past--and still in many textbooks today--eukaryotic organisms were lumped into four groups: Animals, Plants, Fungi (only separated from plants since around the same time we figured out how to get to THE MOON), and Protists. Organisms were classified as belonging to Kingdom Protista by saying "Well, it isn't an animal, plant, or fungus," so it isn't surprising to find out that these organisms are not actually genetically related to each other. Protists encompass an incredibly diverse group of organisms that span many evolutionary lineages. Below are a few supergroups discussed in Pawlowski (2013) that include groups you'll find in the "Protists" chapter of this book: • Stramenopiles: Includes the water molds, brown algae, and diatoms • Archaeplastida: Includes the red and green algae (and plants!) • Amoebozoa: Includes the slime molds • 4.1: Slime Molds Slime molds encompass organisms from several lineages. Here, we look at two major types. Cellular slime molds are groups of unicellular amoebae that collaborate to form fruiting structures to disperse spores. This group includes Dictyostelids and Acrasids. Plasmodial slime molds (classified under Myxogastria or Myxomycetes) form a large, multinucleate amoeba with no cell wall that will eventually wall off individual nuclei to form spores. • 4.2: Water Molds Water molds belong to the phylum Oomycota. These fungus-like organisms have cellulose cell walls, a diplontic life cycle, and zoospores with one whiplash and one tinsel flagellum. They are more closely related to brown algae and diatoms (in a group called the Heterokonts) than to Kingdom Fungi. • 4.3: Brown Algae Brown algae are a lineage of primarily marine, multicellular heterokonts. Rockweeds and kelps belong to this group. • 4.4: Diatoms Diatoms are another photosynthetic lineage of heterokonts. They are unicellular organisms surrounded by a silica frustule. Diatoms are an incredibly diverse group of unicellular organisms containing anywhere from 20,000 to 2 million species. • 4.5: Red Algae The red and green algae are descendents of the primary endosymbiosis event that resulted in the first chloroplast. Red algae are primarily marine and can be unicellular or multicellular. They have a complex alternation of generations life cycle with an extra diploid phase. • 4.6: Green Algae The nature of the evolutionary relationships between the green algae are still up for debate. As of 2019, genetic data supports splitting the green algae into two major lineages: chlorophytes and streptophytes. The streptophytes include several lineages of green algae and all land plants. Streptophytes and chlorophytes represent a monophyletic group called Viridiplantae (literally “green plants”). 04: Protists Slime molds encompass organisms from several lineages. Here, we look at three main groups. Cellular slime molds (dictyostelids) are groups of unicellular amoebae that collaborate to form fruiting structures to disperse spores. Protostelids make small fruiting bodies that have cellular stalks. Plasmodial slime molds (classified under Myxogastria or Myxomycetes) form a large, multinucleate amoeba with no cell wall that will eventually wall off individual nuclei to form spores. Cellular Slime Molds Video \(1\) : A video showing the cellular slime mold Dictyostelium, both as individual amoebae and collaborating to form fruiting structures. Link to the YouTube video. Protostelids The examples shown here are Ceratiomyxa fruticulosa. This organism may not actually be a protostelid, but the small, stalked fruiting bodies with a single sporangium produced on the external surfaces are similar to what would be seen in a protostelid. Plasmodial Slime Molds Plasmodial slime molds represent a vast diversity of morphologies. While still a plasmodium (see Figure \(5\)), they can be difficult to distinguish. However, once they have formed into a fruiting structure, they can form distinct, varied, and amazing shapes (see Figure \(\PageIndex{6-9}\))! Other Features In addition to having interesting macroscopic morphologies, they also have interesting microscopic features! Ornamentation and size of the spores, as well as the appearance of the capillitial threads, can be necessary for identification.

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Water molds belong to the phylum Oomycota in the Stramenopile supergroup. Oomycetes are also fungus-like organisms with cell walls made of cellulose. Similar to myxomycetes, they have motile spores with 2 flagella. However, one of these flagella is "normal"-looking (called a whiplash flagellum) and the other is ornamented. This strange characteristic puts organisms into a group called the heterokonts (meaning "different flagella"). Many oomycetes, such as Saprolegnia, are important decomposers in aquatic ecosystems, while others -- namely those in the genus Phytophthora -- have adapted to life on land and are some of the most destructive plant pathogens. Saprolegnia This organism reproduces asexually by producing zoospores (zoospores are spores that swim, zoo- meaning ‘to live’) inside of an elongated sac called a zoosporangium (-angium meaning vessel, so a zoosporangium is what zoospores are produced inside of). These zoospores grow by mitosis into a diploid thallus, an undifferentiated body. Saprolegnia's sexual reproducing structures include the globose oogonium and smaller, pad-like antheridia (singular, antheridium) that attach to the oogonium. Because these structures produce gametes--much like spores are produced in sporangia--the oogonia and antheridia are also referred to as gametangia (gametangium singular). The oogonium produces haploid eggs via meiosis. These eggs are fertilized by the haploid male nuclei produced by meiosis within the antheridium, creating a diploid, thick-walled zygote called an oospore. The oospore will be released and grow by mitosis to create a new multicellular thallus, completing the diplontic life cycle. Phytophthora Phytophthora is a genus of water molds that parasitize plants. They have specialized zoosporangia that detach, allowing zoospores to be transported terrestrially and await germination until moisture is present. Some notable Phytophthoras are P. ramorum (causal agent of sudden oak death, see Figure \(5\)) and P. infestans (causal agent of late blight of potato and the Irish potato famine, see Figure \(6\)). 4.03: Brown Algae Secondary Endosymbiosis in Heterokonts Brown algae are a photosynthetic lineage of heterokonts. They derived their golden brown chloroplasts from secondary endosymbiosis. In this event, an ancestral oomycete engulfed a red alga. As in primary endosymbiosis, instead of being digested, overtime the red alga degenerated into a chloroplast, this time with 4 membranes -- the engulfing membrane from the oomycete, the red alga’s plasma membrane, and the two membranes of the original chloroplast within the red alga. In many groups derived from secondary endosymbiosis, the chloroplast has lost one of these membranes. Brown Algae, Phylum Phaeophyta Brown algae are brown due to the large amounts of carotenoids they produce, primarily one called fucoxanthin. These organisms are exclusively multicellular and can get so large that they require special conductive cells to transport photosynthates from their blades down to the rest of their tissues. These conductive cells are called trumpet hyphae and have sieve plates and resemble sieve tubes found in flowering plants. Much like Saprolegnia, the body of an alga is termed a thallus because it is not differentiated into specialized tissues. The general morphology of a brown alga includes a holdfast, stipe, gas bladder(s), and blade(s). Kelp Figure \(4\): A piece of feather boa kelp with several small gas bladders. The four gas bladders shown all attach to the edge of the stipe. If the full thallus were visible, gas bladders would be attached down the entire length of both sides of the flattened stipe. Do you see any blades present? Photo by Maria Morrow, CC-BY-NC. Fucus A model organism for the Phaeophyta life cycle is Fucus (rockweed), which, like its relative Saprolegnia, has a diplontic life cycle. The Fucus thallus has dichotomous branching (forking into two equal branches) and swollen, heart-shaped reproductive tips of the branches. These swollen branch tips are called receptacles. The receptacles are covered in small bumps, each with a pore at the center of the bump called an ostiole. The bumps are conceptacles, chambers that house the male and female gametangia.

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Diatoms, Phylum Bacillariophyta Diatoms are another photosynthetic lineage of heterokonts that was derived from the secondary endosymbiosis of the red alga. Diatoms are an incredibly diverse group of unicellular organisms containing anywhere from 20,000 to 2 million species. These organisms are unicellular and surrounded by a frustule, a silica shell made from two distinct valves that enclose the plasma membrane. Frustules are amazingly intricate, covered with small pores in an arrangement specially adapted for capturing sunlight (Figure \(1\)). They have golden chloroplasts due to the carotenoid pigment fucoxanthin (Figure \(2\)). Morphology We are still trying to figure out how to determine what a diatom "species" is and, so far, they have been classified based on the morphology of their frustules. Using this classification, historically there were two major groups of diatoms: centric (have radial symmetry) and pennate (have bilateral symmetry). These classifications have improved and increased in complexity, so here we will cover just the broad strokes. For a more in-depth look at current diatom morphological classification and fantastic images, check out this great website. Ecology In addition to morphology, diatoms can also be classified by where they occur. Free-floating diatoms are planktonic. Diatoms attached to other organisms (like giant kelp) are epiphytic. Benthic diatoms tend to dwell toward the bottom of a body of water. Reproduction Diatoms primarily reproduce asexually by binary fission, similar to prokaryotes. During binary fission, the two valves of the frustule are separated and each new cell forms a new valve inside the old one. However, the new valve is always smaller. If diatoms only reproduce in this way, it results in a continual decrease in average size. When some minimal size is reached, this can trigger sexual reproduction. When diatoms sexually reproduce, they have a diplontic life cycle and produce a very large auxospore. Diversity Video \(1\): This video shows some of the incredible diversity of diatom shapes and the amazing art Klaus Kemp makes with them. Sourced from YouTube. 4.05: Red Algae The red and green algae are descendents of the primary endosymbiosis event that resulted in the first chloroplast. Their plastids have two membranes, an inner membrane that was the cyanobacterial cell wall and an outer membrane from the organism that first engulfed it. The story of these algal groups is the evolutionary history of all plants. Red Algae, Phylum Rhodophyta Morphology Red algae have a diverse range of morphologies. They can be unicellular or multicellular. Unicellular forms may live solitarily or as colonies. Multicellular forms can be filamentous, leafy, sheet-like, coralloid, or even crust-like (some examples in Figure \(2\) and Figure \(3\)). Polysiphonia Life Cycle Red algae have an alternation of generations life cycle that has an extra diploid stage: the carposporophyte. Polysiphonia is the model organism for Rhodophyta. The gametophytes of Polysiphonia are isomorphic (iso- meaning same, morph- meaning form), meaning they have the same basic morphology. Male Gametophyte The male gametophyte has elongated structures that emerge from the tips of the thallus branches. These are spermatangia, where spermatia are produced by mitosis. Female Gametophyte and Carposporophyte The female gametophyte produces an egg that is contained within a structure called the carpogonium. This structure has a long, thin projection called a trichogyne (trich- meaning hair, -gyne meaning female). During fertilization, a spermatium fuses with the trichogyne and the nucleus of the spermatium travels down the tube to the egg. When the nucleus of the spermatium fuses with the egg, a zygote is produced. This zygote is retained and nourished by the female gametophyte as it grows. The globose structures you see growing from the female gametophyte thallus are called cystocarps. A cystocarp is composed of both female gametophyte tissue (n) and carposporophyte tissue (2n). The outer layer of the cystocarp, the pericarp (peri- meaning around) is derived from the female gametophyte and is haploid. The interior of the cystocarp consists of the carposporophyte, which is diploid, and produces structures called carposporangia, inside of which it produces carpospores by mitosis. All of these--carposporophyte, carposporangia, and carpospores--are diploid. Tetrasporophyte The diploid carpospores are released into the ocean waters, where they will be carried on currents to another location. If a carpospore lands in an appropriate environment, it will grow by mitosis into a tetrasporophyte (2n). The tetrasporophyte produces tetrasporangia (2n) within the branches of the thallus. Each tetrasporangium produces four unique, haploid tetraspores by meiosis. Tetraspores (n) are released and will grow by mitosis into either male or female gametophytes, completing the life cycle.

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/04%3A_Protists/4.04%3A_Diatoms.txt

The nature of the evolutionary relationships between the green algae are still up for debate. As of 2019, genetic data supports splitting the green algae into two major lineages: chlorophytes and streptophytes. The streptophytes include several lineages of green algae and all land plants. Streptophytes and chlorophytes represent a monophyletic group called Viridiplantae (literally “green plants”). Some green algal lineages have adapted to life on land, either inside of lichens or free-living (see Figure \(1\)). General Morphology Similar to red algae, green algae can be unicellular or multicellular. Many unicellular species form colonies. Unicellular Unicellular species will have two whiplash flagella. Video \(1\): This video shows how sexual reproduction occurs in the colonial green alga Volvox. Sourced from YouTube. Multicellular Oedogonium is a genus of filamentous green algae. Some species of Oedogonium are nannandrous. In nannandrous species, the antheridia are small, elongate filaments, usually produced on a different filament than the oogonium. Other species are macrandrous and the antheridia are produced as stacked cells within the same filament as the oogonium. Figure \(10\): A close up of the sexual structures of a nannandrous Oedogonium sp. The oogonium is located at the end of the filament and, in this case, is almost lemon-shaped. It is unfertilized, still appearing evenly granular throughout. Many small antheridia are reaching up to try to fuse with the oogonium to fertilize it. These can be seen on the sides of the filament below the oogonium and look like upside down blue bowling pins. Photo by Maria Morrow, CC BY-NC. Spirogyra Life Cycle Though green algae display a diversity of life cycles, many have a haplontic life cycle. A model organism for the green algae is Spirogyra. Spirogyra is a unicellular green algae that grows in long, filamentous colonies, making it appear to be a multicellular organism. Even though it is technically unicellular, its colonial nature allows us to classify its life cycle as haplontic. In the haploid vegetative cells of the colony, the chloroplasts are arranged in spirals, containing darkened regions called pyrenoids where carbon fixation happens. Each haploid cell in the filament is an individual, which makes sexual reproduction between colonies an interesting process. When two colonies of Spirogyra meet that are of a complementary mating type (+/-), sexual reproduction occurs. The two colonies align, each cell across from a complementary cell on the other filament. A conjugation tube extends from each cell in one colony, inducing formation of a tube on the cells in the other colony. The conjugation tubes from each colony fuse together. Figure \(13\): Spirogyra conjugation tubes meet. These two colonies are both forming conjugation tubes toward each other. Two sets of cells near the top of the image have successfully fused conjugation tubes, forming a connection between the two different organisms. Photo by Maria Morrow, CC BY-NC. The contents of one cell will move through the conjugation tube and fuse with the contents of the complementary cell, resulting in a diploid zygote. Figure \(14\): Movement of the cytoplasm from one colony to another in Spirogyra. The cytoplasm from one of the cells in the colony on the right has almost completely transferred through the conjugation tube and into the colony on the left. Photo by Maria Morrow, CC BY-NC. Figure \(15\): Cells in various stages of conjugation. Of the cells that have formed conjugation tubes and connected, the one farthest to the left has just recently finished the transfer and fusion of its cytoplasm, but the zygote hasn't fully formed yet. In the cell on the far right, there is a fully formed zygote. It is dark in color and has thick walls. The chloroplasts are not individually distinguishable within it. Photo by Maria Morrow, CC BY-NC. The zygote appears as a large, egg-like structure contained within the complementary cell. It has a thick wall that provides resistance to desiccation and cold, allowing colonies of Spirogyra to overwinter, when needed. The other colony is now a filament of empty cells that will be broken down by some decomposer. When conditions are right, the zygote undergoes meiosis to produce another vegetative colony of haploid cells. 5.02: Liverworts Bryophytes arose in a period of Earth’s history before soils had formed. The terrestrial surface was rocky and consisted primarily of crusts (microbial mats) composed of assemblages of prokaryotes. The exposure to sunlight would have been intense relative to the buffer provided by water. In addition, being surrounded by water would provide regulation of surrounding temperature and structural support. As green algae began to colonize the terrestrial surface, at least one of these lineages accumulated adaptations that were favorable to living on land--a waxy cuticle to prevent water loss, desiccation-resistant dispersal propagules called spores, and retention and feeding of the developing zygote. This lineage of green algae evolved into the ancestor of the bryophytes. This evolutionary group includes liverworts, mosses, and hornworts. These plants do not have true roots to absorb water, nor do they have vascular tissue to transport that water to other regions of the plant. Because of this, bryophytes tend to grow prostrate (close to the surface they are growing on) and stay quite small. They do not have roots, but they have projections to anchor them to the surface, called rhizoids. They also tend to grow in moist areas where there is access to water and are reliant on water for the dispersal of gametes and fertilization. There are approximately 23,000 described species of bryophytes, most of them belonging to the mosses. • 5.1: Hornworts Hornworts, phylum Anthocerotophyta, are have thalloid gametophytes with monoplastidic cells. Their sporophytes are composed of a long, thing sporangium that grows from a basal meristem. • 5.2: Liverworts Liverworts, phylum Marchantiophyta, have gametophytes that are either leafy or thalloid. Leafy gametophytes have leaves without costae that form in a single plane across from each other. Smaller leaves called underleaves line the underside of the thallus. • 5.3: Mosses Mosses, phylum Bryophyta, have leafy gametophytes with spirally arranged leaves. Many mosses will have leaves with costae. Their sporophytes can be complex, though like the other bryophytes, each only forms one sporangium. 05: Bryophytes Thalloid liverworts have no leaves and their gametophytes look more similar to hornwort gametophytes. Another similarity to hornworts is the presence of simple pores for gas exchange (no guard cells, meaning pores are permanently open). Unlike hornworts, liverwort cells have multiple chloroplasts. Many liverwort gametophytes produce asexual clones called gemmae. Attribution Content by Maria Morrow, CC-BY-NC. 5.03: Mosses Mosses, Phylum Bryophyta Gametophyte Generation Mosses produce only leafy gametophytes. You can differentiate them from leafy liverworts because the leaves are arranged in a spiral and usually have a midrib-like struture called a costa. Like the other two groups of bryophytes, simple pores on the gametophyte allow for gas exchange (no guard cells, meaning pores are permanently open).

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/04%3A_Protists/4.06%3A_Green_Algae.txt

As bryophytes began to colonize the terrestrial surface, they produced organic acids during metabolism that aided in the breakdown of the rocky substrate. When they died, their organic matter mixed with the weathered rock, forming the Earth’s earliest soils. Formerly abundant to the first photosynthesizers to become terrestrial, access to sunlight became competitive as bryophytes expanded. This led to selection for individuals that could lift themselves higher and transport water throughout their tissues. Eventually, this selection resulted in the evolution of vascular tissue -- pipes that could bring water up from the ground so that parts of the plant could be raised upward, and those parts raised upward could transport their photosynthates down to the lower parts of the plant. The cells in the xylem (water-transporting vascular tissue) contained lignin, the tough, decay-resistant compound that wood is made out of. This rigid molecule in the vascular tissue allowed for structural support, allowing plants to grow taller -- some over 100 feet! The vascular system also allowed for the specialization of organs: roots for water absorption, leaves for photosynthesis, and stems for structural support. Seedless vascular plants (SVPs) also began to rely more on the sporophyte stage. The sporophyte became the larger, nutritionally independent stage of the life cycle. Branching sporophytes offered more sites for meiosis to occur, resulting in increased opportunities for variation, which could be interpreted as more options in an increasingly competitive environment. There are approximately 20,000 known extant species, most of which are ferns. • 6.1: Lycophytes Lycophytes are seedless vascular plants with sporophytes that have microphylls and branch dichotomously. Sporangia are produced in strobili. Some are homosporous (e.g. Lycopodium), while others are heterosporous (e.g. Selaginella). • 6.2: Ferns and Horsetails Ferns and horsetails are homosporous seedless vascular plants that produce megaphylls. Taxonomy has been in flux for this group, most recently classified as either phylum Monilophyta or class Polypodiopsida. • 6.3: Extinct SVPs During the Carboniferous period, seedless vascular plants dominated the landscape in tree-like forms. 06: Seedless Vascular Plants • Microphylls. Leaves have a single, unbranched vein of vascular tissue. Note: The term microphyll, confusingly, is not an indication of the size of the leaf. • Rhizomes. Asexual propogation of the sporophyte through underground stems. • Homosporous or heterosporous. Haploid spores grow into bisexual gametophytes in Lycopodium. In Selaginella, microspores develop into microgametophytes that produce sperm and megaspores develop into megagametophytes that produce eggs. Extinct lycophytes like Lepidodendron and Sigillaria grew into tall trees, branching dichotomously and producing a moss-like canopy of microphylls. Some of these microphylls were several feet long! Lycophytes first appear in the fossil record over 400 million years ago. By the Carboniferous period (around 300 mya), the landscape was covered with lycophyte forests and shallow swamps. Much of the fossil fuels we use today are derived from these extinct arboreal lycophytes falling into swamps, slowing decomposition and creating layers of carbon-rich material that we now find as coal seams. Extant lycophytes (those species still alive today) are represented by creeping forms, such as Lycopodium and Selaginella. Observe fresh specimens and prepared slides of Selaginella and/or Lycopodium. Draw and describe the important characteristics that differentiate these plants from bryophytes, including stem and leaf structure, below ground parts, and where spores are produced. 6.01: Lycophytes Gametophyte Morphology In seedless vascular plants, the sporophyte is the longer-lived, larger, leafy generation. This trend of sporophyte dominance throughout the evolutionary timeline of plants leads to continually smaller, less complex gametophytes. Gametophytes of this group are seldom seen. They are small and thalloid. In Lycopodium, the gametophyte grows from a homospore and is bisexual, producing both antheridia and archegonia. Sporophyte Morphology Sporophytes branch dichotomously and have true roots and leaves due to the presence of lignified vascular tissue. The leaves, called microphylls, have a single, unbranched vein of vascular tissue. Note: The term microphyll, confusingly, is not an indication of the size of the leaf. Figure \(2\): A Lycopodium sporophyte grows across a bed of feather mosses on the forest floor. Many branches stick upright and may develop strobili. Photo by Maria Morrow, CC-BY 4.0. Asexual propogation can occur via an underground stem called a rhizome. Homospores are produced in a structure called a strobilus that is produced at the end of a branch. A single plant can have many strobili.

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/06%3A_Seedless_Vascular_Plants/6.1.01%3A_Lycopodium.txt

Members of the genus Selaginella are heterosporous, meaning they produce two different types of spores. 6.2.01: Horsetails Characteristics of Ferns and Horsetails • Megaphylls. Leaves have branching veins of vascular tissue. • Rhizomes. Asexual propogation of the sporophyte through underground stems. • Homospory. Haploid spores grow into bisexual gametophytes that produce both antheridia and archegonia. Note: There is an order of aquatic ferns (Salviniales, to which the water fern genus Azolla belongs) that are heterosporous. 6.02: Ferns and Horsetails Horsetails are one of the most ancient lineages of plants and are relatively unchanged from the fossil record. If you look closely at the nodes of a green vegetative shoot, you will see that branches and leaves have not only switched roles, they have also switched places, with the photosynthetic branches emerging below the papery, non-photosynthetic leaves. The stems of horsetails are covered in silica, giving them the common name scouring rush, as they were formerly used to clean pots due to the abrasive nature of silicate granules. This is what gives the epidermis of the shoot its rough texture. Gametophyte Morphology Horsetail gametophytes are reduced and thalloid. Bisexual gametophytes grow from homospores and produce both antheridia and archegonia. Sporophyte Morphology Vegetative Shoots On the sporophyte, the leaves are dark, papery and non-photosynthetic. Branches are photosynthetic and produced in whorls on the vegetative shoot. Shoots contain silica, which has an abrasive texture. Reproductive Shoots Sporangia are produced in a terminal strobilus on the reproductive shoot. In some species, this reproductive shoot lacks chlorophyll and is instead fed through the rhizome of connected vegetative shoots. Spores are photosynthetic and have four hygroscopic arms called elaters. Video \(1\): This video shows how the elaters of Equisetum spores respond to changes in humidity. Retrieved from YouTube. 6.2.02: Ferns Gametophyte Morphology Fern gametophytes are reduced, thalloid, and heart-shaped. They are often referred to as a prothallus or prothallium. Sporophyte Morphology Fern sporophytes are composed of megaphylls, often pinnately compound fronds that emerging as fiddleheads in the spring. Sporangia are produced in clusters called sori (sorus, singular) on the fronds. Circinate Vernation Circinate vernation is a term used to describe the development of the fern fiddlehead into a frond. Because plants grow apically, it is important to protect the apical meristems in growing organs (as we have seen in both axillary and terminal buds with the evolution of bud scales). The fiddlehead is essentially a structure that tucks away the growing tips of the fronds. As the frond develops, it gradually unfurls, releasing the tips last. Sori A sorus (plural, sori) is a cluster of sporangia, often protected by an umbrella-like structure called the indusium as the spores mature. Each sporangium is lined by an inflated strip of cells called an annulus. When the spores have matured, the cells in the annulus begin to dry out, causing the cells to collapse and pull the sporangium open, releasing the spores. Full Life Cycle Diagram Note: Images by Jon Houseman are licensed in Wikimedia as CC BY-SA. In an email with Maria Morrow, he agreed that we could use the CC BY-NC license for these images.

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/06%3A_Seedless_Vascular_Plants/6.1.02%3A_Selaginella.txt

The plants that would become the gymnosperms evolved xerophytic leaves to prevent desiccation in the dry air. Some would have the ability to grow wider (and thus taller) via the production of a new layer of secondary xylem (wood) each year. These plants could also produce exterior layers of dead cells, unlike the living epidermis, called bark. Together, the production of bark and wood are part of a process called secondary growth. To increase the chances of fertilization in the absence of water, gametes began to be dispersed aerially via pollen. Perhaps most importantly, the zygote and female gametophyte were surrounded in a protective coating and dispersed as seeds. Both seeds and pollen develop within structures called cones (strobili). The fossil record shows gymnosperms diversifying in a dry period called the Permian that followed the swampy Carboniferous period. Extant groups of gymnosperms include conifers, cycads (somewhat similar in appearance to palms), gnetophytes, and a single species from the ginkgophytes, Ginkgo biloba. Of the approximately 1,000 species of gymnosperms alive today, about 600 of these are conifers. • 7.1: Cycads Cycads often look fern-like, with large pinnately compound leaves. However, their leaves are xerophytic and tough. Seeds are produced in strobili that grow at the base of the vegetative leaves. Plants are dioecious, either producing a megastrobilus or microstrobilus. • 7.2: Ginkgos Ginkgos are represented by a single extant species: Ginkgo biloba, a living fossil. Ginkgos have fan-shaped, deciduous leaves. Plants are dioecious, producing either paired ovules with fruit-like fleshy coverings or microstrobili. • 7.3: Gnetophytes Gnetophytes are a group of strange angiosperm-like plants that are most likely derived from conifers. They have opposite leaves and produce fruit-like strobili. Plants are dioecious, producing microstrobili and megastrobili on different individuals. Similar to angiosperms, they produce vessel elements and undergo double fertilization. • 7.4: Conifers Conifers are the largest group of gymnosperms. They are monoecious, producing megastrobili (seed cones) and microstrobili (pollen cones) on the same plant. They generally produce small needle- or scale-like leaves with a thick, waxy cuticle. 07: Gymnosperms Cycads are one of the more ancient gymnosperm lineages, appearing in the fossil record around 300 million years ago. Currently, many extant species are in danger of extinction in the wild. However, during the Jurassic period, these plants would have dominated the landscape. Though their large, compound leaves make them appear to be ferns at first glance, cycads can be classified as gymnosperms by the production of seeds instead of spores and xerophytic leaves. These plants share the following features: 7.02: Ginkgos As of 2019, the most recent genetic studies have placed Ginkgos as the oldest of the extant gymnosperms. This does not mean that it was the first gymnosperm. From the fossil record, it seems that most early gymnosperms went extinct. The sole remaining species in this group, Ginkgo biloba, is a living fossil virtually unchanged from its fossilized ancestors. It is possible that this species was only kept alive due to cultivation efforts by Buddhist monks for its medicinal properties. This species is also long-lived, a single tree can live for thousands of years, and resistant to most pests. Ginkgo biloba can be recognized by the following features: 7.03: Gnetophytes Gnetophytes represent an anatomically and genetically difficult group to classify. They have several traits in common with angiosperms, such as vessel elements in the xylem, double fertilization, and a covering over their seeds. Even their leaves are angiosperm-like, with netted venation. However, these traits are convergently evolved, meaning that angiosperms and gnetophytes each evolved these traits separately. Genetically, recent studies have placed the gnetophytes as a sister group to the Pinaceae (pine family) within the conifers. This would mean that pines, firs, and spruces are more closely related to strange gnetophytes like Ephedra than they are to other conifers like redwoods, cedars, and Pacific yew. However, the true nature of this evolutionary relationship remains murky and contentious. Notable Gnetophytes Welwitschia mirabilis This strange plant grows in the desert of Namibia. It has two large leaves that grow from a basal meristem.

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/07%3A_Gymnosperms/7.01%3A_Cycads.txt

Conifers Conifers are the most species-rich lineage of gymnosperms. From the fossil record, we think there were over 20,000 species of conifers. However, their diversity declined with the dinosaurs. Currently, there are around 600 extant species. These amazing plants represent some of the oldest, tallest, and most massive organisms on the planet. Though currently low in diversity, these amazing plants make up 30% of Earth’s forests. Conifers share the following characteristics: Note: The Pinaceae is currently the largest family of conifers, so many of our examples for this group of gymnosperms will be from the type genus Pinus (pines). Seeds & Pollen Seed Cones The megastrobilus, or seed cone, contains diploid megasporocytes that are produced within a megasporangium. Each megasporocyte (also called a megaspore mother cell) undergoes meiosis. Only one of the four cells produced will survive to develop into a megagametophyte and the other three will die. The megagametophyte is part of the ovule and contains archegonia, each with an egg cell inside. The megagametophyte is retained within the megasporangium, which becomes the nucellus. Surrounding the nucellus is the integument, which is initially continuous with the ovuliferous scale and has a small opening called a micropyle. A grain of pollen will be transported on the wind and, if lucky, it will land on a seed cone. The seed cone has a drop of sugary liquid that it secretes, then retracts, pulling the pollen in toward the ovule. This stimulates the tube cell to germinate a pollen tube, while the generative cell divides by mitosis to produce two sperm. These sperm travel down the pollen tube, through the micropyle, and into an archegonium where one will fertilize an egg. When fertilization occurs, the micropyle closes and the integument becomes the seed coat. The zygote will grow and develop as an embryo, nourished by the megagametophyte tissue, as well as the nucellus. If you look in a long section of a pine seed, you can see the embryo’s RAM and SAM. The seed will be dispersed by wind or animals and germinate to grow into a diploid pine tree once again. Pollen Cones The microgametophyte in gymnosperms is the four-celled, "winged" pollen grain. Within the pollen grain, you can distinguish the generative cell and the tube cell nucleus. The two prothallial cells are not apparent under the microscope. On either side of the pollen grain, two ear-like structures emerge. These air sacs may help orient the pollen grain toward the ovule. Xerophytic Leaves Xerophytic leaves are adapted to withstand drought conditions. In conifers, we see a wide range of xerophytic leaves with different morphologies that can be shaped by their local environment. Consider the leaves of the coast redwood and the giant sequoia, shown below. Though these two trees belong to different genera--Sequoia and Sequoiadendron, respectively--they are sister taxa. However, the coast redwood has adapted to life on the coast, where the giant sequoia has evolved in inland, higher elevation forests with much more extreme climatic conditions. How can this be seen in the structure of their leaves? 7.04: Conifers This video is an extremely helpful narrated animation of the pine life cycle. I recommend watching this video or some other walkthrough of the pine life cycle before attempting to interpret the complex diagram below. Video \(1\): A narrated video of the pine life cycle, sourced from YouTube.

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/07%3A_Gymnosperms/7.04%3A_Conifers/7.4.01%3A_Pine_Life_Cycle.txt

The exact timing of the emergence of angiosperms is unknown, so it is difficult to relate their evolution to specific climatic conditions or other circumstances. However, there is relatively new fossil evidence of flowering plants as early as the Jurassic period, 174 mya. This was the age of the dinosaurs and coincides with the emergence of the first feathered dinosaurs -- birds! Angiosperms represent a single origin of related organisms, the phylum Anthophyta, that experienced an exceptional radiation in species. As of 2019, there are approximately 370,000 known extant species. Most of the plants that you see, eat, and otherwise interact with in your daily life are likely to be in this group. Angiosperms can be distinguished from other plant groups by the production of flowers. These collections of modified leaves allowed angiosperms to attract pollinators and increase the chances of successful fertilization. Over time, angiosperms evolved different flower morphologies, smells, and colors that corresponded to their particular pollinators. These sets of characteristics, called pollination syndromes, allow scientists to predict the pollinators for different plants. Once pollinated, the fertilized seeds are encased in a protective ovary whose structure can be specialized for different methods of dispersal, such as animal ingestion, animal attachment, flotation, or wind dispersal. This protective ovary and the encased seed(s) are more commonly called a fruit. Inside the developing seeds, angiosperms provide an additional food source to the developing zygote, the endosperm. In the xylem, this group of plants evolved large diameter conducting cells for rapid water uptake called vessel elements, though this made them vulnerable to freezing conditions. In the phloem, sieve cells evolved into sieve tube elements with their associated companion cells, increasingly specialized for transportation of photosynthates. • 8.1: Flower Anatomy Flowers are reproductive structures composed of whorls of highly modified leaves. • 8.2: Flower Morphology The symmetry, number of parts, and arrangement of parts within a flower are used for identification of angiosperms. • 8.3: Monocots vs. Eudicots Monocots and eudicots are to major lineages within the angiosperms. There are several ways to differentiate between these evolutionary groups, including the number of cotyledons, number of floral parts, leaf venation, and internal anatomy. • 8.4: Inflorescence Types Instead of producing single flowers, some angiosperms produce inflorescences. These take the place of a single flower, developmentally, so each flower in an inflorescence is called a floret. The formation and arrangement of florets determines the inflorescence type. • 8.5: Fruits Fruits are swollen ovaries that have evolved to specialize in seed dispersal. Fruits can be fleshy or dry. Fleshy fruits are generally classified by layers of the pericarp. Dry fruits can be dehiscent or indehiscent. • 8.6: Life Cycle The angiosperm life cycle is complex, much of it taking place within the flower, which then becomes the fruit. Within the ovule, both the egg and the polar nuclei are fertilized. Lilies are often used as models for the angiosperm life cycle. 08: Angiosperms Flowers are composed of many distinct components: sepals, petals, stamens, and carpels. These components are arranged in whorls and attach to an area called the receptacle, which is at the end of the stem that leads to the flower. This stem is called the peduncle. In the case of an inflorescence, where multiple florets are produced in place of a single flower, the stems leading to the florets are called pedicels. Whorls Flowers are composed of sets of highly modified leaves arranged in whorls. The outermost whorl of a flower is called the calyx and is composed of sepals. Inside the calyx is the corolla, which is composed of petals. The sepals are often smaller and less colorful than the petals, but this general rule can be misleading. For example, lilies often have identical sepals and petals. The only way you can distinguish between them is by location: Which whorl is on the outside? Together, the calyx and corolla are called the perianth (peri- meaning around, anth- meaning flower). Reproductive Parts: Androecium and Gynoecium Inside the perianth is the androecium (house of man), a whorl composed of stamens. Each stamen has a long filament holding up pollen sacs called anthers. Inside the androecium is the gynoecium (house of woman), which is composed of carpels. Each carpel has an ovary at the base where ovules are housed. The style emerges from the ovary and is topped by the stigma. Pollen grains land on the stigma and must grow a tube down the style to reach the ovule and complete fertilization. 8.02: Flower Morphology Flowers are sets of highly modified leaves that function to attract a pollinator or, if no animal pollinator is used, to optimize spore dispersal in some way. Over the course of evolutionary history and coevolution, this has lead to an incredible diversity of shape, size, color, smell, and just about any other characteristic you can think of. Because most plants are angiosperms and because flowers are often so diverse, learning the terminology to describe flowers is a major step in learning to identify plants. Floral Symmetry Flowers that have multiple lines of symmetry (like a starfish) are radially symmetrical, also called actinomorphic. Flowers with only a single line of symmetry (like you) are bilaterally symmetrical, also called zygomorphic. Whorls Most flowers are composed of four whorls. If all whorls are present, a flower is said to be both complete and perfect. If any whorl is missing, the flower is incomplete. If one of those missing whorls is either the androecium (pollen-producing) or gynoecium (seed-producing), the flower is also imperfect. Ovary Position We can use the location of the ovary to further distinguish between flowers. If the other whorls of the flower meet below the ovary (the ovary or ovaries look a bit like an egg or eggs in a nest), the ovary is superior (on top of the rest of the flower). This means that the rest of the flower parts are below the gynoecium, so we can also call this flower hypogynous (below the gynoecium). The two terms both describe the same situation, but superior refers only to the ovary while hypogynous refers to the flower, in general. Inferior Ovary (Epigynous Flowers) In the opposite situation, the other floral whorls join at a point above the ovary. In this case, the ovary is inferior and the flower is epigynous (on top of the gynoecium). Semi-inferior Ovary (Perigynous Flowers) As always, there are less clear situations. In some flowers, as in the rose family, the floral whorls join together and fuse at a point above the ovary, then travel down, around, and below the ovary as a fused unit. This fused unit is called a hypanthium. The ovary is termed semi-inferior, as it is located below the unfused parts of the floral whorls. Because the floral whorls travel around the ovary as the hypanthium, the flower is perigynous (peri- meaning around). 8.06: Life Cycle Watch Video \(1\) to help untangle this complex life cycle. Video \(1\): A digital, narrated rendition of the angiosperm life cycle. https://youtu.be/0UEpq1W9C_E

textbooks/bio/Botany/A_Photographic_Atlas_for_Botany_(Morrow)/08%3A_Angiosperms/8.01%3A_Flower_Anatomy.txt

Viewing microscopic structures is an integral part of the study of botany. Many life cycle features or anatomical characteristics used to differentiate between lineages of organisms can only be distinguished through a microscope. However, this affords you the opportunity to view that which most will never see! The study of microscopic features of tissues is called histology. This study involves a variety of techniques for specimen preparation, including thin sections, squash mounts, heat treatments, and staining. Many tissues are colorless, making distinguishing features difficult. Stains can allow you to distinguish your specimen from the background (such as Congo Red for fungal hyphae, which stains the cytoplasm) or might have different chemical reactions with cellular compounds (such as Toluidine Blue for plant cells, which stains the primary wall purple and the secondary wall light blue). Some stains are carcinogenic, caustic, or are in some way hazardous, so be sure to follow the safety protocols when using them. Always avoid getting stains on yourself or your clothing (even when they are harmless, they still stain). Microscopy is a skill that must be practiced. Like most skills, you might struggle with it at first--making good thin sections is particularly difficult. The more opportunities you have to practice, the better you'll get, and the more you'll be able to see in your specimens. Knowing how to apply stains and which are best for different types of specimens will dramatically improve your results. Keep notes! This resource makes for an excellent additional companion for your adventures into histology. • 9.1: Using Microscopes This section describes the parts of both the compound and dissecting microscopes. It also covers some slide making skills, including wet mounts, thin sections, and staining. 09: Introduction to Microscopy The Microscope Dissecting Microscope A dissecting microscope generally has lower magnification and uses incident light, meaning the light shines onto (not through) the specimen to view it. Compound Microscope A compound microscope is used for viewing small samples or pieces of a larger specimen at higher magnification. This type of microscope uses transmitted light, where the light must pass through the specimen to view it. Making and Staining Slides There are many ways to make a slide. Preparation method and technique will vary, depending on your specimen and what you need to see. Below are some basic guidelines, but you should experiment with what works best for you and your specimen. With compound microscopes, the light must pass through the specimen. For this to work, your prepared sample must be quite thin. Many prepared slides are made using a machine called a microtome to achieve the extremely thin, even sections needed to see many anatomical features. As a human trying to perform this process, you'll need as much practice as possible to get a good thin section. Video \(1\): This video provides a demonstration of making thin cross-sections by hand for plant material such as stems and roots; includes a demonstration of staining the material using TBO (toluidine blue O), a metachromatic stain useful for many plant materials. [See Episode 6 for how to prepare TBO.] Sourced from YouTube. Focusing with a Compound Microscope Video \(2\): Dr. Patrick demonstrates the steps in focusing a compound light microscope from 10X to 100X. She shows you how the field of view changes with each lens. The use of immersion oil for the 100X lens is specifically shown. Sourced from YouTube.

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• 10.1: Plant Cell Structure and Components Plant cells are different from animal cells. They have a cell wall and a large central vacuole that help contribute to the plant's structure, and chloroplasts, which are responsible for photosynthesis. • 10.2: Types of Plant Cells This section covers three types of plant cells: parenchyma, collenchyma, and sclerenchyma. • 10.3: Cell Division Plant cells can multiply for growth, repair, or asexual reproduction via mitosis or produce gametes via meiosis. 10: Cells and Tissues Plant Cell Components Cell Wall, Plasma Membrane, and Middle Lamella Plasmodesmata are channels through the cell wall and middle lamella where the plasma membrane of adjacent cells (and therefore the cytoplasm) is connected. Plastids Plastids are organelles that are the result of an endosymbiotic event in the evolutionary history of plants. In plants, plastids have two membranes. Chloroplasts Chloroplasts are plastids that contain green pigments called chlorophylls. Chromoplasts Chromoplasts are plastids that do not contain chlorophyll, but do contain other pigments, such as carotenoids. Carotenoid pigments reflect colors like yellow, orange, and red. Leucoplasts Leucoplasts are plastids that do not contain pigments. The main function of leucoplasts is to store starches and oils. Leucoplasts that store starch are called amyloplasts (as in amylose). The Central Vacuole The central vacuole is a large organelle that often fills most of the plant cell. It is filled with liquid and surrounded by a membrane called the tonoplast. Plants can alter the solute concentration in the central vacuole to influence cell structure and movement of water. It is also a place to store pigments, such as anthocyanins, or other secondary metabolites, such as phytotoxins. 10.2.01: The -enchymas Plants have three primary cell types and these cell types compose tissues within the plant. These cells, as well as specialized cells formed from these general types, will be described in the pages of this chapter. 10.02: Types of Plant Cells There are three major cell types in plants that we can distinguish by differences in their cell walls. These three cell types are parenchyma, collenchyma, and sclerenchyma. Parenchyma Parenchyma cells are characterized by an even, relatively thin primary wall. Collenchyma Collenchyma cells are characterized by an uneven, relatively thick primary wall. Sclerenchyma Sclerenchyma cells are characterized by the formation of a secondary wall composed of lignin. This secondary wall forms within the primary wall and eventually leads to the death of the cell. Sclerenchyma cells are dead at functional maturity. 10.2.02: Specialized Cells Specialized Cells From the Protoderm Guard Cells Stomata are pores (holes) in the epidermis of plants. Guard cells are the pairs of cells, shaped a bit like parentheses or two sides of a donut, that flank the stoma. The guard cells regulate when the stoma is open or closed, which in turn regulates gas exchange with the environment and the rate of transpiration. Trichomes Trichomes are hairs composed of cells on the epidermis of a plant. Specialized Cells From the Ground Meristem Two types of specialized sclerenchyma cells that can be produced by the ground meristem are sclereids and fibers. Specialized Cells From the Procambium Tracheids and Vessel Elements Tracheids and vessel elements are cells in the xylem that transport water. They have secondary walls with lignin and are dead at functional maturity. 10.3.01: Interphase Mitosis and Cytokinesis Interphase Cells spend most of their time in a stage called interphase. During this phase, the nuclear envelope surrounds the nucleus. There may be one or more nucleoli (dark, condensed regions) visible within the nucleus. The material around the nucleoli, contained within the nuclear envelope is DNA in the form of chromatin. This will not pick up a stain well and so will not appear as distinct shapes within the nucleus. Find these indicators of interphase in cell A in the image below. In contrast, when a cell begins the process of division, the chromatin condenses into visible chromosomes that will pick up a stain and look like dark strings within the nuclear envelope, as seen in cell B in the image above. In order to begin dividing, the cell needs to go through several processes that take place during interphase, including replicating the DNA (occurs in S-phase) and all of the cell contents. Mitosis Mitosis is the process of dividing the nucleus. To see cells in meiosis, we look in areas of a plant that would be actively growing. These areas where cells are actively dividing are called meristems, such as the root apical meristem.

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The root system of a plant serves two primary functions: water absorption and anchorage. Roots with a higher surface area will be better adapted to absorbing water because they have more area to interact with the soil environment. Increased interaction with the soil environment can also contribute to increased anchorage, but there are always trade-offs. If roots become too fine, they will be easily broken and lose the anchorage function. Additionally, finer roots can also lose more water if the soil environment becomes dry. Alternatively, roots with more volume are able to store more water, starches, or other materials belowground. The balancing of these trade-offs with localized environments has resulted in a great diversity of root types and morphologies. • 11.1: Primary Growth All plant roots begin in primary growth, which is a lengthening of plant organs. Primary growth involves the root apical meristem, primary meristems, and primary tissues. • 11.2: Secondary Growth In secondary growth, primary tissues and residual meristematic tissues produce secondary meristems, which then produce secondary tissues. Whereas primary tissues allow for vertical growth, secondary tissues allow for lateral growth. • 11.3: Root Systems Plants tend to have either a netted root system (typical of monocots) or a taproot system (typical of eudicots). Some plants can also produce roots from stem tissue (adventitious roots) or for a specialized function (e.g. prop roots and pneumatophores). 11: Roots All plant roots begin in primary growth, which is a lengthening of plant organs. Primary growth involves the root apical meristem, primary meristems, and primary tissues. Video \(1\): This video by Ben Montgomery provides a walkthrough of the internal structures and organization of plant roots, including lateral root formation. Sourced from YouTube. 11.01: Primary Growth Figure \(2\): A diagram of a growing root tip. The tip of the root is covered by a cap of cells (C). Most of the root is covered by small projections (root hairs). The region of the root with hairs is labeled E. Between the area covered with hairs and the area covered by the cap, the root is labeled D. A=Root hair, B=Root cap, C=Zone of Division, D=Zone of Elongation, E=Zone of Maturation. Image from the public domain with labels added by Maria Morrow. 11.1.02: Monocot Roots Zea mays Zea mays (corn) is often used as a model organism for monocot anatomy. Smilax The organization of tissues in a Smilax root is similar to that in a corn root. 11.1.03: Eudicot Root Cross Section (Ranunculus) Ranunculus Figure \(1\): A cross section of a young Ranunculus root. The epidermis and cortex are in a similar arrangement as in monocots. However, the vascular cylinder has no internal pith region. Instead, it is composed entirely of vascular tissue with xylem at the center in a Y-shape and phloem filling the regions between the arms of the Y. Photo by Melissa Ha, CC BY-NC with labels added. 11.02: Secondary Growth In secondary growth, primary tissues and residual meristematic tissues produce secondary meristems, which then produce secondary tissues. Whereas primary tissues allow for vertical growth, secondary tissues allow for lateral growth: they allow stems and roots to become wider by producing wood. In addition to growing wider, secondary growth exchanges the living epidermis for a thick layer of dead, waterproofed cells called cork. The cork and a few other layers of tissue comprise something called the periderm, or perhaps more familiarly called bark. This type of growth first evolved in gymnosperms. It is also present in many angiosperms. As a general rule, monocots do not undergo secondary growth (though some, like bamboo, have an analogous process). 11.03: Root Systems Netted Roots Figure \(3\): The netted root system of Zea mays. There are many roots of approximately the same diameter that then branch off into smaller roots. There is, distinctly, no one larger root. This is a netted root system. Photo by Maria Morrow, CC-BY 4.0.

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The shoot of a plant is responsible for two major functions: photosynthesis and reproduction. In most plants, the leaves carry out photosynthesis, while the stems provide stability to elevate those leaves above potential competition. In annual plants, whose entire life cycle from germinate to death is completed in a single year, the epidermis on the stem is often photosynthetic, as well. All stems undergo primary growth. In gymnosperms and many angiosperms, stems will transition into secondary growth to form woody tissues. • 12.1: Primary Growth Tissues in the shoot are derived from the shoot apical meristem (SAM). The SAM produces three primary meristems, which produce the primary tissues. • 12.2: Secondary Growth Gymnosperms and some eudicots are capable of secondary growth. This type of growth occurs by the production of secondary meristems and secondary tissues, which result in lateral growth, and the formation of wood and bark. • 12.3: Woody Shoot Structures Woody shoots have several different types of scars, which can be used to make inferences about the plant's age and identity. • 12.4: Modified Shoots Some stems and leaves have adapted for a function other than what is typical. 12: Stems Tissues in the shoot are derived from the shoot apical meristem (SAM). Just like in the root, the SAM produces three primary meristems, which produce the primary tissues: These primary tissues will then either differentiate into specialized cells or, as is the case in many eudicots, become meristematic and produce secondary tissues. Coleus Stem Tip Though it looks a bit alien, this is a section through a growing tip of a plant. In the center, where the alien’s head might be, is a region of small, densely packed cells. This is the SAM of the apical bud. On either side of the SAM, like two upraised arms, are the leaf primordia. These are the early stages of developing leaves. Through the center of these leaf primordia is a darker region of small cells. This is the procambium, which will develop into the vascular tissue. Lining the outer edge of the SAM and the youngest portions of the leaf primordia is the protoderm. As the protoderm matures into the epidermis, it produces hair-like projections called trichomes. Between the protoderm and the procambium is the ground meristem. On either side of the growing tip are two other darkened lumps of densely packed cells. These bud primordia will develop into axillary buds, producing either branches or flowers. Each bud primordium has its own SAM. Monocots Figure \(3\): A cross section of a Zea mays stem. The organization of tissues differs from the Zea mays root. Most notably, the vascular tissue is arranged in bundles, rather than a central cylinder. These bundles are densely packed toward the outside of the stem, then occur less frequently toward the inside. Because there is no distinct delineation of the tissues produced by the ground meristem, it is now called ground tissue (as opposed to cortex and/or pith). Photo by Maria Morrow, CC BY-NC. 12.03: Woody Shoot Structures Figure \(1\): A woody shoot and labeled scars. The most prominent scar on this shoot is the v-shaped leaf scar, which is lined with circular vascular bundle scars. Above the leaf scar, in the crotch of the v it forms, is a round axillary bud scar. Covering the bark are many small, circular scars. These are lenticels. Photo by Maria Morrow, CC BY-NC.

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Leaves are specialized organs for performing photosynthesis. A leaf is often a relatively large, flat surface used to optimize sunlight capture. However, surfaces are areas that water can evaporate from, so a large amount of surface area exposed to sunlight results in increased transpiration. The anatomy of a leaf has everything to do with achieving the balance between photosynthesis and transpiration in the environment in which the plant grows. Plants that grow in moist areas can grow large, flat leaves to absorb sunlight like solar panels because sunlight is likely more limiting than water. Plants in dry areas must prevent water loss and adapt a variety of leaf shapes and orientations to accomplish the duel tasks of water retention and sunlight absorption. In general, leaves adapted to dry environments are small and thick with a much lower surface area to volume ratio. 13: Leaves In angiosperm anatomy, a leaf can be identified by where it emerges from the node. In a node, a leaf emerges below the axillary bud. Leaf Parts Leaves are generally composed of a few main parts: the blade and the petiole. Figure \(2\): A leaf is usually composed of a blade and a petiole. The blade is most frequently the flat, photosynthetic part. The petiole is a stem that attaches the leaf blade to the main stem of the plant. As plants have radiated, diversified, and adapted to different environments, you'll see that there are many variations on this theme. The photo on the left is a palmate leaf, the diagram on the right is a pinnate leaf. Photo by Maria Morrow, CC-BY 4.0. Diagram on the right from Chapter 3.4.2, Botany, by Algiers, Ha, and Morrow. The Leaf Blade and Vascular Arrangement The leaf blade is (usually) the flat, photosynthetic part of the blade. In eudicots, the leaf will have a central midvein (also called the midrib), with smaller veins branching off from there. This type of vein organization is called netted venation. The edge of the blade is the margin. In monocots, the veins may be all approximately the same size or there may be a larger midvein, but the veins run parallel to each other. This is called parallel venation. The Petiole Most leaves have a stem that attaches the blade of the leaf to the rest of the plant. This is the petiole. However, in some plants, the leaves do not have a petiole and the blade is directly attached to the plant stem. These leaves are sessile (lacking a petiole). Stipules Some plants will have paired appendages found at the base of the leaf. These are called stipules. Stipules can look leaf-like or take on other forms (e.g. spines or tendrils). Compound Leaves A compound leaf looks like a branch with leaves emerging from it. However, these leaves are not accompanied by axillary buds (i.e. they do not emerge from a node). This branch is in fact a compound leaf composed of leaflets. Though there are no buds at the base of the leaflets, there will be a bud at the base of the compound leaf's petiole. A compound leaf can be palmate or pinnate. In a pinnate compound leaf, the leaflets are attached to a central stem called a rachis. The leaflets can be sessile or may be attached to the rachis by petiolules. Compound leaves can be even more complex by being compounded multiple times. Leaf Arrangement In angiosperms, leaf arrangement is determined by how many leaves emerge per node. Alternate Leaf Arrangement In alternate leaf arrangement, one leaf emerges per node, giving the appearance of alternating leaves. Opposite Leaf Arrangement In opposite leaf arrangement, two leaves emerge per node. Think of this as how your arms are opposite each other on your torso. Whorled Leaf Arrangement In whorled leaf arrangement, three or more leaves emerge per node. I try to remember this as "around the whorled (world)", because the leaves often encircle the stem.

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Macroscopic Features Monocot leaves tend to have parallel venation, as opposed to the branching patterns seen in eudicots. Microscopic Features The model organism for monocots in botany is usually corn (Zea mays). Below, you'll see examples of corn leaf cross sections to demonstrate monocot leaf anatomy. Note that there are approximately the same number of stomata on either side of the leaf, that the vascular bundles are all facing you in cross section (because they run parallel to each other), and that the mesophyll is not divided into two distinct types. Note: There are exceptions. Many monocots will have a more specialized mesophyll arrangement. Bulliform Cells The bulliform cells present in the upper epidermis are not common to all monocots. This is an adaptation you can find in many grasses that are adapted to hot or dry environments. To avoid water loss, the bulliform cells can contract, causing the leaf to roll up and reduce surface area. In the image below, you can see a leaf from the beach grass Ammophila rolled in on itself. Can you find the bulliform cells? Vascular Bundles In the vascular bundle, the xylem will be on the top (adaxial side) and the phloem will be on the bottom (abaxial side). If you think about the way a leaf emerges from the plant, this matches the way the xylem and phloem are oriented in the stem, with the xylem toward the center of the stem and the phloem closer to the outside/epidermis. The vascular bundle is often surrounded by inflated parenchyma cells that form a structure called a bundle sheath. In C4 plants, like corn, this is where the Calvin Cycle would take place. Below is an image of a vascular bundle in another monocot, Yucca. This vascular bundle has large groups of sclerenchyma cells within it, a smaller group above the xylem and a much larger group below the phloem. How might you distinguish the sclerenchyma cells from the parenchyma cells? Consider the thickness of the cell wall(s) and how each cell type reacts to stains. 13.3.01: Adaptations to Water Availability Macroscopic Features Eudicot leaves tend to have netted venation, with a larger central vein (the midrib or midvein) that branches off into a network of smaller veins. In the image below, you can see this branching pattern in a skeletal leaf. Microscopic Features Eudicot leaves can usually be distinguished by netted venation at the macroscopic level, but they also differ at the microscopic level. Note the difference in organization between the tissues in the leaf below and the leaves shown in the monocot section. Cuticle You will often see a waxy cuticle coating the surface of most plant tissues. In leaves, the location and thickness of the cuticle can give you clues about the environment that the plant has adapted to. Vascular Bundles Seeing vascular bundles of eudicots in cross sections can be confusing. The organization of tissues in the much larger midrib vascular bundle is often spread out into a semicircle, still with xylem on the top and phloem on the bottom, but they can be difficult to distinguish. In addition to this, the smaller veins are not oriented in the same direction, as they are in monocots. In the image below, the vascular bundle just to the left of the midrib is coming more or less straight at us, so it is easy to distinguish the tissues. In contrast, the vascular bundle to the right of the midrib was moving diagonally and so was caught in an oblique section and looks more like a smear. Often with these oblique sections, you can distinguish the xylem cells by their strange secondary wall thickenings -- they look a bit like coiled springs. 13.03: Eudicot Leaves The morphology and anatomy of a leaf can allow you to predict the conditions that the plant is adapted to. In particular, what is the water availability in that plant's environment? Mesophytic Leaves A leaf in "normal" conditions is called mesophytic (meso- means middle), meaning it is not particularly adapted for either high or low water conditions. Hydrophytic Leaves Hydrophytes (literally "water plants") are adapted to living in aquatic conditions. Below is an image of another hydrophytic leaf. This one is from a monocot, Potamogeton. Note the similarity to the Nymphaea leaf and the distinct differentiation between regions of mesophyll. A good example of convergent evolution to similar environmental pressures! Location of Stomata Because Nymphaea is aquatic and sits on top of the water, the stomata are located only in the upper epidermis. You can locate them in the cross section by finding the gaps (stomatal pits) in the palisade mesophyll. Why wouldn't there be stomata in the lower epidermis? Other Features If you see strange branching structures within your Nymphaea leaf cross section, you may be looking at an astrosclereid (astro- meaning star). This is a branching sclerenchyma cell with a thick secondary wall. What function might these cells have? Xerophytic Leaves Xerophytes (literally "dry plants") are adapted to living in dry conditions with low water availability. Cuticle Thickness The image below shows the cuticle of the Nerium leaf. Notice how thick it is on the upper (adaxial) surface of the leaf and how it changes in thickness as it transitions to the lower (abaxial) surface. Location of Stomata In xerophytic leaves, stomata tend to be located on the lower (abaxial) surface. This side of the leaf is usually cooler, as the upper (adaxial) surface is facing the sun. In extremely dry conditions, stomata might be further protected from the desiccating outer air by being located in stomatal crypts. Gymnosperms: The Original Xerophytes Though pines are not angiosperms, they have xerophytic leaves (needles). Note the features this pine needle has in common with the Nerium leaf.

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The structure and function of a leaf can be modified over the course of evolution as a plant adapts to a particular environment. Some leaves may be converted to storage structures below ground (as with a bulb) or into plant defense structures (as with a spine). When function of the leaf blade is no longer primarily photosynthesis, some other plant part is usually modified to take its place. A phyllode is a petiole that has become flat and photosynthetic, looking much like a leaf blade. 14.01: Pollination Syndromes Ecology is the study of the relationships among living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. • 14.1: Pollination Syndromes Flowers have coevolved with their pollinators. The shape, color, smell, and many other features of a floral phenotype are adapted to their method of pollen delivery. This set of characteristics is called a pollination syndrome. • 14.2: Dispersal Mechanisms Fruits are specialized for seed dispersal. Characteristics of fruits can allow us to determine the likely dispersal mechanism, usually animals, wind, water, or self-propelled (ballistic). 14: Ecology Flowers have coevolved with their pollinators. The shape, color, smell, and many other features of a floral phenotype are adapted to their method of pollen dispersal. This set of characteristics is called a pollination syndrome and allows scientists to make inferences about the pollinator of a particular flower. Some of these are more obvious, while others, more cryptic. For example, humans do not see ultraviolet (UV) light, but many insects can (like bees). Flowers might be communicating with UV light in a way that might not be apparent to humans until you shine a UV light on them. In the Malva assurgentiflora flower (Figure \(1\)), the pollen has UV fluorescence. Pollination Syndromes and Vectors Though flower phenotypes can also correlate to other environmental factors (e.g. Peach et al. 2020), we can connect pollination syndromes to pollen vectors, both biotic and abiotic (see Table \(1\)). Table \(1\): Pollination Syndromes (adapted from the US Forest Service). Pollination Syndrome Color Structure Scent Nectar or Pollen Wind Dull, perianth often absent or reduced Large feathery stigmas, large anthers None No nectar, large amounts of pollen Birds Reds and pinks Often tubular or cupped None Lots of hidden nectar, moderate pollen Bees Purples, blues, yellows, white, UV Flat and shallow or tubular, with landing area Sweet, fresh, mild Pollen often sticky and scented, nectar usually present Bats White, dull green, or purple Often bowl-shaped or pendant, anthers protruding Musty or fruity, strong, emitted at night Lots of hidden nectar Moths White, pale pink or purple Often tubular or cupped, no landing pad Strong and sweet, emitted at night Lots of hidden nectar, limited pollen Butterflies Bright colors Tubular, with wide landing pad Faint, fresh Lots of hidden nectar, limited pollen Flies Dark red, purple, brown Shallow, funnel, or trap-like Putrid, rotting No nectar, moderate pollen 14.02: Dispersal Mechanisms Ballistic Video \(1\): Watch this fun video of different plants utilizing ballistic seed dispersal. Sourced from YouTube. Water Video \(2\): Watch this clip to see more water-dispersed seeds and fruits. Sourced from YouTube.

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Biology is the scientific study of living organisms and their interactions with one another and their environments. This is a very broad definition because the scope of biology is vast. Biologists may study small organisms, such as the microscopic blue-green algae that give us clues about the evolution of plants, or biomes such as the Mojave desert, shown here with a Joshua Tree in the foreground (Figure \(1\)). Plant biology is the study of plants and their interactions with their environment. Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge of the physical or natural world through observation or experimentation. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning. Biologists study the living world by posing questions about it and seeking science-based responses. The scientific method is a method of research with defined steps that include experiments and careful observation. Attribution Curated and authored by Kammy Algiers using 1.2 (The Process of Science) from Biology 2e by OpenStax (licensed CC-BY). • 1.1.1: The Scientific Method In simple terms, biology is the study of living organisms and their interactions with one another and their environments. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet. • 1.1.2: Organisms Studied in Botany Plants are so vitally important to the world. Plants start the majority of food and energy chains, they provide us with oxygen, food and medicine. Most plants are what you typically think of: multicellular eukaryotic organisms that are ancestrally terrestrial and photosynthesize. In addition to plants, fungi, photosynthetic prokaryotes, algae, and some heterotrophic "protists" are typically included in the study of botany. • 1.1.3: Intro to Evolution The history of life on Earth goes back more than three and a half billion years. A unifying theme throughout this course is the theory of evolution. Evolution explains both the diversity and unity of life. Natural selection, the most dominant evolutionary force, is a main mechanisms that is responsible for the diversity of species on Earth today. • 1.1.4: Life Cycles Plants display an alternations of generations life cycle. The haploid multicellular life stage is called the gametophyte as it produces gametes, which, after fertilization, develop into a mature diploid sporophyte. The sporophyte produces spores by meiosis, and the spores eventually develop into mature multicellular gametophytes. • 1.1.5: Subfields and Applications in Plant Biology Botany, or plant biology, is the study of plants. However, the discipline can further be divided into many subdisciplines. These subdisciplines can blend with other disciplines such as agriculture, chemistry, genetics, molecular biology, physiology, systematics, paleontology, and various branches of ecology. • 1.1.6: Chapter Summary Thumbnail: Malva assurgentiflora under UV light. Photo by Alan Rockefeller, CC-BY-NC 1.01: Introduction Learning Objectives • Identify the shared characteristics of the natural sciences. • Summarize the steps of the scientific method. • Compare inductive reasoning with deductive reasoning. • Describe the goals of basic science and applied science. The Process of Science Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure \(1\)). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Natural sciences could be categorized as astronomy, biology, chemistry, earth science, and physics. One can divide natural sciences further into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Natural sciences are sometimes referred to as “hard science” because they rely on the use of quantitative data; social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings. Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals. Scientific Reasoning One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning. Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (numeric), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Deductive reasoning, or deduction, is the type of logic used in hypothesis-based science. In deductive reason, the pattern of thinking moves in the opposite direction as compared to inductive reasoning; that is, specific results are predicted from a general premise. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change. These predictions have been made and tested, and many such changes have been found, such as the modification of arable areas for agriculture, with change based on temperature averages. Inductive and deductive reasoning are often used in tandem to advance scientific knowledge (Example \(1\)). Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science, which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that one can test. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. Example \(1\) Here is an example of how the two types of reasoning might be used in similar situations. In inductive reasoning, where a conclusion is drawn from a number of observations, one might observe that members of a species are not all the same, individuals compete for resources, and species are generally adapted to their environment. This observation could then lead to the conclusion that individuals most adapted to their environment are more likely to survive and pass their traits to the next generation. In deductive reasoning, which uses a general premise to predict a specific result, one might start with that conclusion as a general premise, then predict the results. For example, from that premise, one might predict that if the average temperature in an ecosystem increases due to climate change, individuals better adapted to warmer temperatures will outcompete those that are not. A scientist could then design a study to test this prediction. The Scientific Method Biologists study the living world by posing questions about it and seeking science-based responses. The scientific method is a method of research with defined steps that include experiments and careful observation. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626; Figure \(2\)), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost all fields of study as a logical, rational problem-solving method. It is important to note that even though there are specific steps to the scientific method, the process of science is often more fluid, with scientists going back and forth between steps until they reach their conclusions. Observation and Question Scientists are good observers. In the field of biology, naturalists will often will make an observation that leads to a question. A naturalist is a person who studies nature. Naturalists often describe structures, processes, and behavior, either with their eyes or with the use of a tool such as a microscope. A naturalist may not conduct experiments, but they may ask many good questions that can lead to experimentation. Scientists are also very curious. They will research for known answers to their questions or run experiments to learn the answer to their questions. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?” Proposing a Hypothesis A hypothesis is an educated guess or a suggested explanation for an event, which can be tested. Sometimes, more than one hypothesis may be proposed. Once a hypothesis has been selected, the student can make a prediction. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .”. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” However, there could be other responses to the question, and therefore one may propose other hypotheses. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.” In this case, you would have to test both hypotheses to see if either one could be supported with data. A hypothesis may become a verified theory. This can happen if it has been repeatedly tested and confirmed, is general, and has inspired many other hypotheses, facts, and experimentations. Not all hypotheses will become theories. Testing a Hypothesis A valid hypothesis must be testable. It should also be falsifiable, meaning that it can be disproven by experimental results. Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. The control group contains every feature of the experimental group except that it was not manipulated. Therefore, if the results of the experimental group differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and this hypothesis should be rejected. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure, and this hypothesis should be rejected. Each hypothesis should be tested by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure \(3\)). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected. While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis. The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. Notice, too, that the scientific method can be applied to solving problems that aren’t necessarily scientific in nature (Example \(2\)). Example \(2\) In the example below, the scientific method is used to solve an everyday problem. Match the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses. Steps of the Scientific Method 1. Observation 2. Question 3. Hypothesis (answer) 4. Prediction 5. Experiment 6. Result Process of Solving an Everyday Problem 1. There is something wrong with the electrical outlet. 2. If something is wrong with the outlet, my coffee maker also won’t work when plugged into it. 3. My toaster doesn’t toast my bread. 4. I plug my coffee maker into the outlet. 5. My coffee maker works. 6. Why doesn’t my toaster work? Two Types of Science: Basic Science and Applied Science The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science. Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that, in the end, it may not result in a practical application. In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield or find a cure for a particular disease. In applied science, the problem is usually defined for the researcher. Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the wide knowledge foundation generated through basic science. One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, DNA makes new copies of itself, shortly before a cell divides. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist. Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is their genome.) Other less complex organisms have also been studied as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project (Figure \(4\)) relied on basic research carried out with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases. While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs. Reporting Scientific Work Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—are all important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference (Figure \(5\)), but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists. A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments. The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This structure is sometimes called the “IMRaD” format, an acronym for Introduction, Method, Results, and Discussion. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published; for example, some review papers require an outline. The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work; it justifies the work carried out and also briefly mentions the end of the paper, where the hypothesis or research question driving the research will be presented. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is considered plagiarism. The materials and methods section includes a complete and accurate description of the substances used, and the method and techniques used by the researchers to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how measurements were made and what types of calculations and statistical analyses were used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them. Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow the combination of both sections, the results section simply narrates the findings without any further interpretation. The results are presented by means of tables or graphs, but no duplicate information should be presented. In the discussion section, the researcher will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, proper citations are included in this section as well. Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answered one or more scientific questions that were stated, any good research should lead to more questions. Therefore, a well-done scientific paper leaves doors open for the researcher and others to continue and expand on the findings. Review articles do not follow the IMRaD format because they do not present original scientific findings (they are not primary literature); instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections. Attributions Curated and authored by Kammy Algiers using 1.2 (The Process of Science) from Biology 2e by OpenStax (licensed CC-BY).

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/01%3A_Introduction_to_Botany/1.1.01%3A_The_Scientific_Method.txt

Learning Objectives Describe the importance of plants in the study of botany and list other organisms that typically included in the study of botany. Botany is the scientific study of plants and organisms that were historically considered plantlike. It helps us understand why plants are so vitally important to the world. Plants start the majority of food and energy chains, they provide us with oxygen, food and medicine. Most plants are what you typically think of: multicellular eukaryotic organisms that are ancestrally terrestrial and photosynthesize. In the process of photosynthesis, these organisms produce their own food, using sunlight, carbon dioxide, and water into organic molecules, or food. However, some organisms ecologically are considered plant-like due ot their role in nature. For example, green slugs, Elysia chlorotica (see Figure \(1\)) collect chloroplasts from algae and use them for their entire life as food producers. Therefore, green slugs, while technically classified as animals, have plantlike characteristics. Plants are in the domain Eukarya and in the kingdom Plantae. There are about 320,000 species of plants that have been named so far. They fill our terrestrial ecosystem and provide food and shelter for animals. Plants cells contain chloroplasts, which conduct photosynthesis. They are thus autotrophic, synthesizing their own organic carbon. In addition, most of the plant cell is filled with a large membrane-bound structure, the central vacuole, which functions in store. Plant cells are surrounded by rigid cell walls containing cellulose. Plants are multicellular, composed of like cells that function as tissue. Their leaves, stems, and roots function as organs. Plants can be small like duckweed or large like the giant sequoia (Figure \(2\)). While fungi are neither closely related to plants, nor do they share key characteristics (like photosynthesis), they are sometimes included in the study of botany. Perhaps this is because the fruiting bodies that some fungi use for reproduction (such as mushrooms) may seem plantlike in the sense that they a stationary structures emerging from the soil. Fungi are heterotrophic, meaning that they feed on other organisms to obtain organic carbon. Unlike animals, which ingest their food, fungi secrete digestive enzymes to breakdown large molecules surrounding them. They then absorb the smaller molecules. Fungal cells are surrounded by rigid cell walls that contain the polysaccharide chitin. Some fungi are unicellular while other are multicellular. Although fungi and plants are not closely related, their are intertwined ecologically. For example, mycorrhizae are fungi that grow in or on plant roots and assist with nutrient absorption. Additionally, fungi often decompose dead plant material, releasing nutrients back into the soil and promoting further plant growth. Other organisms studied in botany are "protists", which have complex, eukaryotic cells but are not plants, animals, or fungi. Some "protists", like slime molds, resembling fungi in the sense that they are heterotrophic. Other "protists" superficially resemble plants in that they conduct photosynthesis and are autotrophic. These are collectively called algae, but they arise from many different groups, and some are not closely related to plants at all. Multicellular algae are sometimes called seaweeds. Most algae have cell walls, which may or may not contain cellulose. Photosynthetic prokaryotes, which have simple cells, are sometimes studied in botany as well. For example, cyanobacteria, are commonly called blue-green algae, but this is a misnomer because true algae are eukaryotes. Instead, cyanobacteria are photosynthetic bacteria, that often form filaments of cells. Bacteria that are pathogens of plants may also be included in the study of botany. Viruses, which are infectious particles that contain protein and nucleic acid, can also infect plant cells. Unlike plants, fungi, "protists", and prokaryotes, viruses are not technically considered organisms because they are not composed of cells. Attribution Curated and authored by Kammy Algiers and Melissa Ha using 1.1 Plants, Botany, and Kingdoms from Introduction to Botany by Alexey Shipunov (public domain)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/01%3A_Introduction_to_Botany/1.1.02%3A_Organisms_Studied_in_Botany.txt

Learning Objectives • Describe the role of evolution in the history of life. • Describe the role of natural selection in evolution. The history of life on Earth goes back more than three and a half billion years. This past serves as a key to understanding the diversity of life. A unifying theme that can be employed throughout this course to boost biology from an overwhelming sea of facts to a coherent study of life is the theory of evolution. Evolution explains both the diversity and unity of life. Through time, some species evolved adaptations that increased their ability to survive and reproduce in their environment. This gave them an evolutionary advantage to other species. Natural selection, the most dominant evolutionary force, is a main mechanism that is responsible for the diversity of species on Earth today. Yet, it is through evolution that we also understand the unity of all life. All living organisms today can be followed back to a common ancestor. Scientific evidence from this is extensive and includes data from fossils, genetics, cell biology, and molecular biology, just to name a few. Through descent with modification, our common ancestors gave rise to the species we see on Earth today. Evolution Evolution can be defined as the change in the genetic make up of a population over time (or, for short, change over time). It is important to note that the change happens from one generation to the next. Thus, an individual cannot evolve because their genes do not change throughout their lifetime. However, a population, a community, or an ecosystem can change over time, as can a species or a group of species. The time it takes for evolution to occur is better described as generation time. This can be very short (minutes for a bacterium), or very long (a century or more for a sea turtle). It is the time it takes for one generation of individuals to reproduce and pass their genes down to the next generation. Charles Darwin's book "On the Origin of Species" published in 1859 described and popularized the theory of evolution and proposed a mechanism for evolution he called natural selection. Independently, Alfred Russell Wallace also introduced the concept of natural selection. Natural Selection There are many forces or mechanisms that cause evolution. However, natural selection is a key mechanism as it is the one that produces adaptive traits. For natural selection to occur, several conditions must be met: 1. The population must contain genetic variation in the trait. This means the differences in the traits of the individuals within the population. 2. The trait must be heritable. This means the individual receives the genetic information for the specific trait from their parent(s). 3. There must be variation in fitness as a result of the trait. This means that some traits result in the individuals with higher reproductive success (they have more offspring) than others. If these three criteria are met, individuals with the most adaptive trait for the current environment will have more offspring, and thus the adaptive traits will accumulate in the environment.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/01%3A_Introduction_to_Botany/1.1.03%3A_Intro_to_Evolution.txt

Learning Objectives • Describe the role of ploidy in the haplodiplontic (alternation of generations) life cycle of plants. • Compare and contrast gametophyte and sporophyte generations. Organisms or cells that contain two copies of each chromosome are considered diploid, or 2n (they contain homologous chromosomes in pairs that were acquired from their parents). Organisms or cells that contain one set of chromosomes are considered haploid, or n, meaning they only contain one of each chromosome, either material or paternal. Your body cells are diploid and contain pairs of chromosomes. Your gametes (egg and sperm cell) are haploid and contain unpaired chromosomes. For more on ploidy, see Biology 2e 11.1 Meiosis. Plants have a haplodiplontic (alternations of generations) life cycle. In plants, there are two distinct generations that alternate: the gametophyte and the sporophyte generation. The gametophyte begins as a single-celled spore that germinate into a multicellular life stage. This mature gametophyte life stage is haploid and by mitosis (division of cells with identical genetic information) produces gametes. These gametes are either egg or sperm cells. Often cross fertilization occurs where the sperm cell of one plant individual fertilizes the egg cell of another plant individual. The results is a fertilized egg, or zygote, which is diploid. This begins the sporophyte generation in plants. The sporophyte then divides into a multicellular life stage (division occurs by mitosis). This mature sporophyte will now produce spores by meiosis, a type of cell division that reduces chromosome numbers to half. The sporophyte is diploid, but the spores are haploid. The spores disperse and germinate into new gametophytes, repeating the process (see Figure \(1\)). Note that both the gametophyte and sporophyte are mature plants. However, they reproduce in different ways and have different chromosome counts. The gametophyte generation produces gametes by mitosis that are fertilized, undergoing sexual reproduction. The sporophyte generation produces spores by meiosis that are dispersed. Both gametophyte and sporophytes grow by mitosis. Contributors and Attributions Curated and authored by Kammy Algiers using 11.2 Sexual Reproduction from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org. 1.1.05: Subfields and Applications in Plant Biology Learning Objective Describe the various subdisciplines of plant biology. Branches of Plant Biology The scope of biology is broad and therefore contains many branches and subdisciplines. The branch of plant biology can further be divided into many subdisciplines as well. Botanists may pursue one of those subdisciplines and work in a more focused field. Botany's origins come from ancient studies of herbal medicine. Even today, ethnobotany focuses on the traditional knowledge and practical uses of plants in medicine, religion, food, etc. An agronomist or agricultural scientist, is a scientist who studies crops. Their focus may include crop quality, growth, nutrition, or disease. George Washington Carver (1860-1943) was an American agricultural scientists who revolutionized crop rotation (Figure \(1\)). He found that by planting different crops in the same location, the nutrients such as nitrogen in the soil are replenished. He promoted planting peanuts as part of the rotation. Phytochemists are plant biochemists who study chemical substances of plants. This is a field that incorporates chemistry as well as biology. These compounds can be studied for medicine, culinary purposes, or as dyes and building material. Some botanists study plant hormones so they can understand the mechanisms of plant growth and regulation. A plant geneticist would study plant genes, often working to create new varieties of plants or crops. Molecular biology biological processes at the molecular, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. A plant molecular biologist would be interested in these aspects of plants. A plant physiologist would study the internal chemical and physical activities of plants and plant metabolism. Plant anatomy would focus on the structures of plants. A systematic botanist studies the diversity of plants and their evolutionary relationships. Paleobotanists study plant fossils and are interested in understanding past environments and ancient plant types. This can also aid in our understanding of the evolution of modern plants. Plant ecologists are scientists that study the interaction of plants with their environments. Plant ecologists can focus on populations, communities, or ecosystem interactions. Restoration ecologists and conservation biologists focus on the the negative impacts of the environment. The restoration ecologist works to reverse environmental impacts caused by human disturbance. Conservation biologists focus on preserving and maintaining existing habitat. There is often a focus on policy change. In many circumstances these two fields overlap with one another and overlap with other disciplines. Many government employees who focus on the environment are involved in restoration, conservation, and promote education, public engagement, and awareness of the environment. Contributors and Attributions Curated and authored by Kammy Algiers using 1.2 Themes and Concepts of Biology from Biology2e by OpenStax (licensed CC-BY)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/01%3A_Introduction_to_Botany/1.1.04%3A_Life_Cycles.txt

Biology is the science that studies living organisms and their interactions with one another and their environments. Plant biology is the study of plants and their interactions with their environment. Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge of the physical or natural world through observation or experimentation. Science attempts to describe and understand the nature of the universe in whole or in part by rational means. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning. Inductive reasoning uses particular results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method, a step-based process that consists of making observations, defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied science, however, is to solve practical problems. A scientific research paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion. Review papers summarize the research done in a particular field over a period of time. Plants are vitally important to the world. Plants start the majority of food and energy chains, they provide us with oxygen, food and medicine. Most plants are what you typically think of: multicellular eukaryotic organisms that are ancestrally terrestrial and photosynthesize. They have a haplodiplontic life cycle, which alternates between two multicellular life stages: the haploid gametophyte and the diploid sporophyte. Fungi, photosynthetic prokaryotes, algae, and some heterotrophic "protists" are also commonly studied as part of botany. The history of life on Earth goes back more than three and a half billion years. A unifying theme that can be employed throughout this course to boost biology from an overwhelming sea of facts to a coherent study of life is the theory of evolution. Evolution explains both the diversity and unity of life. Through time, some species evolved adaptations that increased their ability to survive and reproduce in their environment. This gave them an evolutionary advantage to other species. Natural selection, the most dominant evolutionary force, is a main mechanisms that is responsible for the diversity of species on Earth today. A few examples of subfields of plant biology are ethnobotanyagriculture sciencephytochemistry, systematic botany, and plant ecology. After completing this chapter, you should be able to... • Identify the shared characteristics of the natural sciences. • Summarize the steps of the scientific method. • Compare inductive reasoning with deductive reasoning. • Describe the goals of basic science and applied science. • Describe the importance of plants in the study of botany and list other organisms that typically included in the study of botany. • Describe the role of evolution in the history of life. • Describe the role of natural selection in evolution. • Describe the role of ploidy in the haplodiplontic (alternation of generations) life cycle of plants. • Compare and contrast gametophyte and sporophyte generations. • Describe the various subdisciplines of plant biology.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/01%3A_Introduction_to_Botany/1.1.06%3A_Chapter_Summary.txt

Biodiversity refers to the diversity of living organisms. Botany, rather than strictly plant biology, includes the study of many different groups of organisms. This section begins by discussing the organization (classification) and naming (taxonomy) of these groups based on their evolutionary history and genetic relatedness. The following chapters explore the wealth of diversity, beginning with the unicellular prokaryotes and acellular viruses. The other chapters cover eukaryotic groups that are often distinguished based on life cycles, morphology, nutritional mode, and cellular composition. Fungi, officially classified in the same group as plants until 1969, are heterotrophic eukaryotes more closely related to animals. Other heterotrophic organisms once thought to be fungi, including the slime molds and water molds, are discussed in the Protists chapter. Protists include an unrelated assemblage of eukaryotes that simply don't fit in as plants, fungi, or animals. Some of these lineages engulfed photosynthetic organisms and gained chloroplasts. These include the brown algae and diatoms from one engulfing event, and the red algae and green aglae from another. The red and green algae share their ancestors with land plants. These terrestrial, multicellular organisms can be divided into four major groups based on important evolutionary adaptations: bryophytes, seedless vascular plants, gymnosperms, and angiosperms. The angiosperms are the most diverse and most recent lineage, containing nearly 90% of all plant species. Unlike other plants, angiosperms make flowers and fruits. • 2.1: Systematics By following pathways of similarities and changes—both visible and genetic—scientists seek to map the evolutionary past of how life developed from single-celled organisms to the tremendous collection of creatures that have germinated, crawled, floated, swam, flown, and walked on this planet. • 2.2: Prokaryotes and Viruses Most organisms on Earth, and in fact most of the cells in your body, are prokaryotic. These unicellular organisms are ubiquitous across ecosystems and organisms, involved in every aspect of ecology. Prokaryotes can be divided into two major groups: Bacteria and Archaea. Unlike prokaryotes, viruses are acellular, and so are not considered living. However, they are distinct biological entities with important roles in evolutionary history and the life histories of organisms. • 2.3: Fungi Kingdom Fungi includes an enormous variety of living organisms. While scientists have identified about 150,000 species of fungi, this is only a fraction of the several million species of fungi likely present on Earth. Organisms in this group are heterotrophic eukaryotes that eat by external digestion, then absorption. Fungi can be unicellular (yeasts) or composed of filamentous cells called hyphae, which taken together form a thallus called the mycelium. • 2.4: "Protists" Protists are an artificial group of eukaryotes that are neither animals, fungi, nor plants. They represent the vast diversity of eukaryotic organisms, and thus span the breadth of possibilities with regard to life history traits. They can be heterotrophs or autotrophs, unicellular to massively multicellular (though rarely with any specialized tissue organization), and can be found across ecosystems worldwide. Photosynthesis within protists is the result of multiple separate endosymbiotic events. • 2.5: Early Land Plants Bryophytes were the first group of plants to evolve on land, followed by the seedless vascular plants. These early plants, accompanied by their fungal mutualists and other microbes, transformed the rocky terrestrial landscape into an ecosystem with stratified soils and complex biotic communities. Synapomorphies of bryophytes derive from the challenges of life on land, while those of seedless vascular plants relate to increases in height and opportunities for meiosis (i.e. competition). • 2.6: Seed Plants Seeds represent one of the most important innovations in plant evolution: a protected, nutrient-supplied embryo with the ability to await appropriate conditions for germination. Seeds and pollen allowed plants to limit their reliance on water for completion of their life cycle. The first plants to evolve seeds were the gymnosperms, which grew wider and taller with secondary growth. Angiosperms then improved upon seed dispersal and pollination strategies with the evolution of fruits and flowers. • 2.7: Angiosperm Diversity It is likely that most plants you see are angiosperms. Of the nearly 400,000 species of land plants described, nearly 90% are angiosperms. Angiosperms can be divided into two major groups: monocots and dicots. Dicots can be further divided into basal angiosperm lineages (magnoliids and ANA grades) and eudicots. Monocots produce one cotyledon, while dicots produce two. However, there are other characteristics that can be used to differentiate between these groups. Attribution Content by Maria Morrow, CC BY-NC 02: Biodiversity (Organismal Groups) • 2.1.1: Introduction All life on Earth is related. This section explores how we determine and depict those relationships. • 2.1.2: Organizing Life on Earth In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. • 2.1.3: Determining Evolutionary Relationships Scientists must collect accurate information that allows them to make evolutionary connections among organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic. • 2.1.4: Perspectives on the Phylogenetic Tree The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community. • 2.1.5: Chapter Summary A brief summary of the concepts covered in Chapter 2.1 Contributors and Attributions • Chapter thumbnail by Pengo, Public domain, via Wikimedia Commons. 2.01: Systematics The history of life on earth goes back more than 3.5 billion years, with all life evolving from a common ancestor and diversifying to what we currently see on earth today. The evolutionary history of a group of species is referred to as a phylogeny. The process of reconstructing a phylogeny is part of the science of systematics (the scientific study of biological diversity and its classification). Taxonomy is the science of classification (categorizing) and nomenclature (naming). Biologists prefer a system of classification that indicates evolutionary relationships among organisms. Cladistics is a method of classification in which organisms are categorized in groups (or clades) based on the most recent common ancestor. This methodology produces a phylogenetic tree that is a testable representation of the theoretical true phylogeny. Cladistics differs from historical methods of classification by relying on shared derived characters (a character shared by closely related organisms because they inherited it from their closest ancestor and which is not present in more distant ancestors) rather than overall similarity.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.01%3A_Systematics/2.1.01%3A_Introduction.txt

Learning Objectives • Discuss the components and purpose of a phylogenetic tree. • Interpret relationships between organisms using a phylogenetic tree. • Correctly order the different levels of taxonomic classification. • Discuss the benefits of having a comprehensive classification system. The evolutionary history of a group of species is referred to as a phylogeny. Phylogeny describes the relationships of the group within the context of related organisms. Though phylogenetic relationships provide information on shared ancestry, they don't necessarily address how organisms are similar or different. Phylogenetic Trees Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure \(1\)). Unlike a taxonomic classification diagram, a phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (indicated with a "you are here" star in Figure \(1\)) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t predict a common ancestor but do show relationships among species. In a rooted tree, the branching indicates evolutionary relationships (see Figure \(2\)). The point where a split occurs, called a branch point or node, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called a basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other. The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. By starting with a single species and tracing back towards the "trunk" of the tree, one can discover that species' ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms. Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other. Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned. Examples of Simple Trees In Figure \(3\) and Figure \(4\), some example trees are drawn to show how to interpret the structure of a phylogenetic tree. The Levels of Classification Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. As you saw in Figure \(1\), scientists divide organisms into three large categories called domains: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. Each domain might encompass many kingdoms. For example, kingdom Plantae, kingdom Animalia, and kingdom Fungi represent three of the many kingdoms contained within domain Eukarya. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species (Figure \(5\)). The kingdom Plantae stems from the Eukarya domain. For the shore pine (Pinus contorta var. contorta), the classification levels would be as shown in Figure \(6\). Therefore, the full name of an organism technically has multiple terms associated. For the shore pine, it is: Eukarya, Plantae, Pinophyta, Pinopsida, Pinales, Pinaceae, Pinus, Pinus contorta, and var. contorta. Notice that each name is capitalized except for the specific epithet (contorta), and the genus and species names are italicized. Notice also the underlined endings of the words. In plant taxonomy, the underlined portion is always used for those taxonomic levels: phyla end in -phyta, classes end in -opsida, orders end in -ales, and families end in -aceae. The scientific name for an organism usually refers to the species name, a two-word scientific name that includes the genus name (e.g. Pinus) and specific epithet (e.g. contorta). This two word naming system is called binomial nomenclature. The name at each level is also called a taxon. In other words, pines are in order Pinales. Pinales is the name of the taxon at the order level; Pinaceae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, shore pine. Note that the shore pine is additionally a subspecies or variety: the second “contorta” in Pinus contorta var. contorta. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors. Shore pines are coastal (hence the common name) and tend to grow in scraggly, twisted shapes (hence the scientific name). Lodgepole pines (Pinus contorta var. latifolia) typically have a straight trunk and grow in the mountains. Figure \(6\) shows how the levels move toward specificity with other organisms. Notice how the shore pine (leftmost image) shares a domain with the widest diversity of organisms, including plants, fungi, algae, and animals. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists grouped similar organisms using characteristics, but as DNA technology developed, more precise relationships have been determined. Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale. Summary Scientists continually gain new information that helps understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships. Contributors and Attributions Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.01%3A_Systematics/2.1.02%3A_Organizing_Life_on_Earth.txt

Learning Objectives • Compare homologous and analogous traits. • Discuss the purpose of cladistics. • Describe the concept of maximum parsimony. Scientists must collect accurate information that allows them to make evolutionary connections among organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogenies, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic. Two Options for Similarities In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures and stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures (Figure \(1\)), as do the leaves of monocots and eudicots (Figure \(2\)). Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more likely any kind of overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms. In plants, we see similar trends. An example of a homologous structure in plants is the leaf. Groups of vascular plants have evolved from a shared common ancestor that formed leaves. In particular, we could look at leaves formed by flowering plants (Angiosperms), the most recent major clade within kingdom Plantae. The developmental pathway and internal anatomy of these leaves have similarities due to shared ancestry, though they may appear outwardly different. Misleading Appearances Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very much alike. This usually happens because both organisms were in common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures (Figure \(3\) and Figure \(4\)). Similar traits can be either homologous or analogous. Homologous traits are shared due to common ancestry; analogous traits have a similar function but are not similar due to common ancestory. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm, though one is specialized for swimming and the other climbing. These structures are not analogous. The wings of a bee and the wings of a bird are analogous but not homologous, both specialized for flying but of completely different biological arrangement. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous, both used for flight and both with a similar biological arrangement. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied. Link to Learning: This website has several examples to show how appearances can be misleading in understanding the phylogenetic relationships of organisms. Analogous structures are often caused by convergent evolution of structures used for similar functions. For example, there are many different groups of unrelated organisms that photosynthesize. Plants are one lineage of photosynthetic organisms, whose ancestors are shared with the green and red algae. The brown algae have a completely different evolutionary history and do not share a common ancestor with plants (they are more closely related to water molds). However, many brown algae form flat, leaf-like structures similar to plants, as both groups use these structures for photosynthesis. Many brown algae, such as the kelps, also form stem- and root-like structures (see Figure \(4\)). Molecular Comparisons With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated. Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny. Why does phylogeny matter? Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. Think of all the ways humans use plants—food, medicine, and clothing are a few examples. If a plant contains a compound that is effective in treating cancer, scientists might want to examine all of the relatives of that plant for other useful drugs. A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) and worked to identify which species had this segment (Figure \(6\)). After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify whether a newly discovered plant was in this family and assess its potential medicinal properties. Building Phylogenetic Trees How do scientists construct phylogenetic trees? After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics. This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in Figure \(7\), all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include all of the descendants from a branch point. Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship. Figure \(8\) shows various examples of clades. Notice how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point. Phylogenetic trees can be constructed by scoring similarities and differences between the taxa of interest (check out this supplementary video to see how it is done). These traits can be morphological or developmental features (Figure \(7\)) or genetic traits called single nucleotide polymorphisms (SNPs, or snips, for short). Taxa with the most similarities are placed into the same clade. Shared Characteristics Organisms evolve from common ancestors and then diversify. Scientists use the phrase “descent with modification” because even though related organisms have many of the same characteristics and genetic codes, changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life: 1. A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group. 2. Many organisms descend from this point and have this trait. 3. New variations continue to arise: some are adaptive and persist, leading to new traits. 4. With new traits, a new branch point is determined (go back to step 1 and repeat). If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate in Figure \(7\) is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in Figure \(7\) have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree. The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. Returning to Figure \(8\), note that the amniotic egg is a shared ancestral character for the Amniota clade, while having hair is a shared derived character for some organisms in this group. These terms help scientists distinguish between clades in the building of phylogenetic trees. Choosing the Right Relationships Imagine being the person responsible for organizing all of the items in a department store properly—an overwhelming task. Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms. Trying to decipher the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections. To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony. Maximum parsimony is a principles that assumes the fewest evolutionary events occurred in a given phylogeny. This is also called Ockham's razer - that we should also select the simplest hypothesis that explains the data. Maximum likelihood, another principle used when constructing phylogenies, suggests that the most likely sequence of evolutionary events most likely occured. For example, if you saw a friend who was wearing a blue shirt, then saw them again in the evening and they were still wearing that blue shirt, you'd probably assume that they had been wearing that same blue shirt all day. However, it is possible that they went home, changed, and changed back or changed into a shirt that looks very similar. It is just less likely, and so we often assume the former. For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits. These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth. Summary To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). Newer technologies can be used to help distinguish homologies from analogies. After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the principles of maximum parsimony and maximum likelihood, which state that the order of events probably occurred in the most obvious and simple way with the least amount of steps and that the the most likely sequence of evolutionary events probably occured. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence. Contributors and Attributions Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.01%3A_Systematics/2.1.03%3A_Determining_Evolutionary_Relationships.txt

Learning Objectives • Describe horizontal gene transfer. • Illustrate how prokaryotes and eukaryotes transfer genes horizontally. • Describe the process of endosymbiosis and explain how this can produce membrane-bound organelles. • Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept. The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community. Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure \(1\)a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (\(\PageIndex{a}\)b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community. Limitations to the Classic Model Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonaly. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships. The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence. Horizontal Gene Transfer Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table \(1\)). Table \(1\): Summary of Mechanisms of Prokaryotic and Eukaryotic HGT. Mechanism Mode of Transmission Example Prokaryotes transformation DNA uptake many prokaryotes transduction bacteriophage (virus) bacteria conjugation pilus many prokaryotes gene transfer agents phage-like particles purple non-sulfur bacteria Eukaryotes from food organisms unknown aphid jumping genes transposons rice and millet plants epiphytes/parasites unknown yew tree fungi from viral infections HGT in Prokaryotes The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiotic Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species. The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms: 1. Transformation: naked DNA is taken up by a bacteria 2. Transduction: genes are transferred using a virus 3. Conjugation: the use a hollow tube called a pilus to transfer genes between organisms More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages (viruses that infect bacteria) that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 1013 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution. As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution. HGT in Eukaryotes Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future. In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or “jumping genes” have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived from the bark, have acquired the ability to make taxol themselves, a clear example of gene transfer. In animals, a particularly interesting example of HGT occurs within the aphid species (Figure \(2\)). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure \(2\)). Endosymbiosis, Genome Fusion, and the Evolution of Eukaryotes Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species (see Figure \(3\)), which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Mitochondrial DNA is usually inherited from the mother only. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg. However, recent studies suggest fathers also occasionally contribute their mitochondrial DNA to their offspring as well (See this Nature Article). Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure \(4\)a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis. More recent work by Lake (\(4\)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes. The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (\(5\)a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host (\(5\)b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (\(5\)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data. Web and Network Models The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in Figure \(6\)a, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree (Figure \(6\)b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT. Ring of Life Models Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” (Figure \(7\)); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model. In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal. This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed. Summary The phylogenetic tree, first used by Darwin, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings. Contributors and Attributions Curated and authored by Maria Morrow using the following sources: 2.1.05: Chapter Summary All organisms on Earth are related at some point in evolutionary history. In western science, a taxonomic classification system is used to nest organisms into related groups of increasing specificity. Domain is the least specific (most inclusive) level of classification, followed by kingdom, phylum, class, order, family, genus, and finally, species. Organisms placed together in more specific levels of classification (such as family or genus) are thought to be more closely related, sharing a more recent common ancestor than they do with organisms outside those groups. One way to depict evolutionary relationships between organisms is by using phylogenetic trees. Every phylogenetic tree is a hypothesis based on traits. Traits can be morphological, anatomical, or molecular. Visible characteristics such as morphology and anatomy were originally used to form many of these hypotheses. Included amongst these similar traits are homologous structures and analogous structures. Homologous structures are similar due to evolutionary relatedness, though sometimes they can look quite different due to divergent evolution from different selective pressures. Analogous structures look similar due to similar selective pressures, but have evolved convergently from different lineages. Genetic information offers a relatively new wealth of molecular traits (single nucleotide polymorphisms) to consider and has upended and reorganized many of the previous hypotheses on evolutionary relationships. However, genetic information can be exchanged between groups of organisms through horizontal gene transfer and endosymbiotic events, rather than vertically through direct evolutionary decent. This complicates the traditional phylogenetic tree representation of evolutionary descent. Other models, such as the web of life and ring of life, have been proposed as alternatives that account for horizontal gene transfer. Deciphering the relatedness of organisms is a complex task that requires considering a variety of information. The phylogenetic tree of life, like any hypothesis, is subject to change as new information emerges. After completing this chapter, you should be able to... • Discuss the components and purpose of a phylogenetic tree. • Interpret relationships between organisms using a phylogenetic tree. • Correctly order the different levels of taxonomic classification. • Discuss the benefits of having a comprehensive classification system. • Compare homologous and analogous traits. • Discuss the purpose of cladistics. • Describe the concept of maximum parsimony. • Describe horizontal gene transfer. • Illustrate how prokaryotes and eukaryotes transfer genes horizontally. • Describe the process of endosymbiosis and explain how this can produce membrane-bound organelles. • Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept. Attribution • Content authored by Maria Morrow, CC-BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.01%3A_Systematics/2.1.04%3A_Perspectives_on_the_Phylogenetic_Tree.txt

Most organisms on Earth, and in fact most of the cells in your body, are prokaryotic. These unicellular organisms are ubiquitous across ecosystems and organisms, involved in every aspect of ecology. Prokaryotes can be divided into two major groups: Bacteria and Archaea. Unlike prokaryotes, viruses are acellular, and so are not considered living. However, they are distinct biological entities with important roles in evolutionary history and the life histories of organisms. • 2.2.1: Prokaryotes This chapter will examine the diversity, structure, and function of prokaryotes. Prokaryotes have an important role in changing, shaping, and sustaining the entire biosphere. They can produce proteins and other substances used by molecular biologists in basic research and in medicine and industry • 2.2.2: Viruses Viruses are generally ultramicroscopic, typically from 20 nm to 900 nm in length, though some larger viruses have been found. Viruses are acellular and consist of a nucleic acid, DNA or RNA, but not both, surrounded by a protein capsid. There may also be a phospholipid membrane surrounding the capsid. Viruses are obligate intracellular parasites. • 2.2.3: Chapter Summary A summary of the chapter concepts. Attributions Chapter thumbnail artwork by Nikki Harris CC BY-NC 2.02: Prokaryotes and Viruses Scientists have studied prokaryotes for centuries, but it wasn’t until 1977 that Carl Woese discovered two distinct lineages within the prokaryotes: Bacteria and Archaea. Prokaryotes have an important role in changing, shaping, and sustaining the entire biosphere. They can produce proteins and other substances used by molecular biologists in basic research and in medicine and industry. For example, the bacterium Shewanella lives in the deep sea, where oxygen is scarce. It grows long appendages, which have special sensors used to seek the limited oxygen in its environment. It can also digest toxic waste and generate electricity. Other species of prokaryotes can produce more oxygen than the entire Amazon rainforest, while still others supply plants, animals, and humans with usable forms of nitrogen; and inhabit our body, protecting us from harmful microorganisms and producing some vitally important substances. Prokaryotes are everywhere, playing important roles in the transformation and exchange of nutrients in every ecosystem. In 1966, scientist Thomas Brock discovered that certain bacteria can live in boiling water. This led many to wonder whether prokaryotes may also live in other extreme environments, such as at the bottom of the ocean, at high altitudes, or inside volcanoes, or even on other planets. This chapter will examine some of the diversity, structure, and function of prokaryotes. • 2.2.1.1: Cell Structure Prokaryotic cells differ from eukaryotic cells in that their genetic material is a single, circular chromosome contained in a nucleoid rather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles. Prokaryotic cells of the same species typically share a similar cell morphology and cellular arrangement. Most prokaryotic cells have a cell wall that helps the organism maintain cellular morphology. • 2.2.1.2: Archaea When these microscopic organisms were first discovered (in 1977), they were considered bacteria. However, when their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and were, in fact, more closely related to the eukaryotes (including ourselves!) For a time they were referred to as archaebacteria, but now to emphasize their distinctness, we call them Archaea. • 2.2.1.3: Bacteria Bacteria are a diverse group of organisms, ubiquitous on planet Earth. These prokaryotes have many important ecological roles, diverse metabolic strategies, and symbiotic relationships with plants. Bacteria were the biosphere's first photosynthesizers. Attribution Content from OpenStax modified by Maria Morrow, CC-BY-NC 2.2.01: Prokaryotes Learning Objectives • Explain the distinguishing characteristics of prokaryotic cells • Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology • Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function • Compare the distinguishing characteristics of bacterial and archaean cells Cell theory states that the cell is the fundamental unit of life. However, cells vary significantly in size, shape, structure, and function. At the simplest level of construction, all cells possess a few fundamental components. These include cytosol (a gel-like substance composed of water and dissolved chemicals needed for growth), which is contained within a plasma membrane (also called a cell membrane or cytoplasmic membrane); one or more chromosomes (condensed DNA and proteins), which contain the genetic blueprints of the cell; and ribosomes, organelles used for the synthesis of proteins. Beyond these basic components, cells can vary greatly between organisms, and even within the same multicellular organism. The two largest categories of cells—prokaryotic cells and eukaryotic cells—are defined by major differences in several cell structures. Prokaryotic cells (Figure \(1\)) lack a nucleus surrounded by a complex nuclear membrane and generally have a single, circular chromosome located in a nucleoid. Prokaryotic microorganisms are classified within the domains Archaea and Bacteria. The structures inside a cell are analogous to the organs inside a human body, with unique structures suited to specific functions. Some of the structures found in prokaryotic cells are similar to those found in some eukaryotic cells; others are unique to prokaryotes. Although there are some exceptions, eukaryotic cells tend to be larger than prokaryotic cells. The comparatively larger size of eukaryotic cells dictates the need to compartmentalize various chemical processes within different areas of the cell, using complex membrane-bound organelles. In contrast, prokaryotic cells generally lack membrane-bound organelles; however, they often contain inclusions that compartmentalize their cytoplasm. Figure \(1\) illustrates structures typically associated with prokaryotic cells. These structures are described in more detail in the next section. Common Cell Morphologies and Arrangements Individual cells of a particular prokaryotic organism are typically similar in shape, or cell morphology. Although thousands of prokaryotic organisms have been identified, only a handful of cell morphologies are commonly seen microscopically. Figure \(2\) names and illustrates cell morphologies commonly found in prokaryotic cells. In addition to cellular shape, prokaryotic cells of the same species may group together in certain distinctive arrangements depending on the plane of cell division. Some common arrangements are shown in Figure \(3\). Prokaryotic Cell Structures The Nucleoid All cellular life has a DNA genome organized into one or more chromosomes. Prokaryotic chromosomes are typically circular, haploid (unpaired), and not bound by a complex nuclear membrane. Prokaryotic DNA and DNA-associated proteins are concentrated within the nucleoid region of the cell (Figure \(4\)). In general, prokaryotic DNA interacts with nucleoid-associated proteins (NAPs) that assist in the organization and packaging of the chromosome. In bacteria, NAPs function similar to histones, which are the DNA-organizing proteins found in eukaryotic cells. In archaea, the nucleoid is organized by either NAPs or histone-like DNA organizing proteins. Plasmids Prokaryotic cells may also contain extrachromosomal DNA, or DNA that is not part of the chromosome. This extrachromosomal DNA is found in plasmids, which are small, circular, double-stranded DNA molecules. Cells that have plasmids often have hundreds of them within a single cell. Plasmids are more commonly found in bacteria; however, plasmids have been found in archaea and eukaryotic organisms. Plasmids often carry genes that confer advantageous traits such as antibiotic resistance; thus, they are important to the survival of the organism. Ribosomes All cellular life synthesizes proteins, and organisms in all three domains of life possess ribosomes, structures responsible protein synthesis. However, ribosomes in each of the three domains are structurally different. Ribosomes, themselves, are constructed from proteins, along with ribosomal RNA (rRNA). Prokaryotic ribosomes are found in the cytoplasm. They are called 70S ribosomes because they have a size of 70S (Figure \(5\)), whereas eukaryotic cytoplasmic ribosomes have a size of 80S. (The S stands for Svedberg unit, a measure of sedimentation in an ultracentrifuge, which is based on size, shape, and surface qualities of the structure being analyzed). Although they are the same size, bacterial and archaeal ribosomes have different proteins and rRNA molecules, and the archaeal versions are more similar to their eukaryotic counterparts than to those found in bacteria. Plasma Membrane Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the cell envelope. In prokaryotic cells, the structures of the cell envelope vary depending on the type of cell and organism. All cells (prokaryotic and eukaryotic) have a plasma membrane (also called cytoplasmic membrane or cell membrane) that exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others. The structure of the plasma membrane is often described in terms of the fluid mosaic model, which refers to the ability of membrane components to move fluidly within the plane of the membrane, as well as the mosaic-like composition of the components, which include a diverse array of lipid and protein components (Figure \(6\)). The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. These phospholipids and proteins have the ability to move laterally within the plane of the membranes as well as between the two phospholipid layers. Archaeal membranes are fundamentally different from bacterial and eukaryotic membranes in a few significant ways. First, archaeal membrane phospholipids are formed with ether linkages, in contrast to the ester linkages found in bacterial or eukaryotic cell membranes. Second, archaeal phospholipids have branched chains, whereas those of bacterial and eukaryotic cells are straight chained. Finally, although some archaeal membranes can be formed of bilayers like those found in bacteria and eukaryotes, other archaeal plasma membranes are lipid monolayers. Proteins on the cell’s surface are important for a variety of functions, including cell-to-cell communication, and sensing environmental conditions and pathogenic virulence factors. Membrane proteins and phospholipids may have carbohydrates (sugars) associated with them and are called glycoproteins or glycolipids, respectively. These glycoprotein and glycolipid complexes extend out from the surface of the cell, allowing the cell to interact with the external environment (Figure \(6\)). Glycoproteins and glycolipids in the plasma membrane can vary considerably in chemical composition among archaea, bacteria, and eukaryotes, allowing scientists to use them to characterize unique species. Plasma membranes from different cells types also contain unique phospholipids, which contain fatty acids. Phospholipid-derived fatty acid analysis (PLFA) profiles can be used to identify unique types of cells based on differences in fatty acids. Archaea, bacteria, and eukaryotes each have a unique PFLA profile. Photosynthetic Membrane Structures Some prokaryotic cells, namely cyanobacteria, have membrane structures that enable them to perform photosynthesis. These structures consist of an infolding of the plasma membrane that encloses photosynthetic pigments such as green chlorophylls and bacteriochlorophylls. In cyanobacteria, these membrane structures are called thylakoids; in other photosynthetic bacteria, they are called chromatophores, lamellae, or chlorosomes. Cell Wall The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. Most (but not all) prokaryotic cells have a cell wall, but the makeup of this cell wall varies. The major component of bacterial cell walls is called peptidoglycan (or murein); it is only found in bacteria. Structurally, peptidoglycan resembles a layer of meshwork or fabric. Since peptidoglycan is unique to bacteria, many antibiotic drugs are designed to interfere with peptidoglycan synthesis, weakening the cell wall and making bacterial cells more susceptible to the effects of osmotic pressure. In addition, certain cells of the human immune system are able to “recognize” bacterial pathogens by detecting peptidoglycan on the surface of a bacterial cell; these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which breaks down and digests the peptidoglycan in their cell walls. Filamentous Appendages Many bacterial cells have protein appendages embedded within their cell envelopes that extend outward, allowing interaction with the environment. These appendages can attach to other surfaces, transfer DNA, or provide movement. Filamentous appendages include fimbriae, pili, and flagella. Fimbriae and Pili Fimbriae and pili are structurally similar and, because differentiation between the two is problematic, these terms are often used interchangeably. The term fimbriae commonly refers to short bristle-like proteins projecting from the cell surface by the hundreds. Fimbriae enable a cell to attach to surfaces and to other cells. For pathogenic bacteria, adherence to host cells is important for colonization, infectivity, and virulence. Adherence to surfaces is also important in biofilm formation. The term pili (singular: pilus) commonly refers to longer, less numerous protein appendages that aid in attachment to surfaces (Figure \(7\)). A specific type of pilus, called the F pilus or sex pilus, is important in the transfer of DNA between bacterial cells, which occurs between members of the same generation when two cells physically transfer or exchange parts of their respective genomes (see How Asexual Prokaryotes Achieve Genetic Diversity). Flagella Flagella are structures used by cells to move in aqueous environments. Bacterial flagella act like propellers. They are stiff spiral filaments composed of flagellin protein subunits that extend outward from the cell and spin in solution. Different types of motile bacteria exhibit different arrangements of flagella (Figure \(8\)). Summary • Prokaryotic cells differ from eukaryotic cells in that their genetic material is contained in a nucleoid rather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles. • Prokaryotic cells of the same species typically share a similar cell morphology and cellular arrangement. • Most prokaryotic cells have a cell wall that helps the organism maintain cellular morphology and protects it against changes in osmotic pressure. • Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA in plasmids. • Prokaryotic ribosomes that are found in the cytoplasm have a size of 70S. • Bacterial membranes are composed of phospholipids with integral or peripheral proteins. The fatty acid components of these phospholipids are ester-linked and are often used to identify specific types of bacteria. The proteins serve a variety of functions, including transport, cell-to-cell communication, and sensing environmental conditions. Archaeal membranes are distinct in that they are composed of fatty acids that are ether-linked to phospholipids. • Prokaryotic cell walls may be composed of peptidoglycan (bacteria) or pseudopeptidoglycan (archaea). • Some prokaryotic cells have fimbriae or pili, filamentous appendages that aid in attachment to surfaces. Pili are also used in the transfer of genetic material between cells. • Some prokaryotic cells use one or more flagella to move through water. Attribution Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.02%3A_Prokaryotes_and_Viruses/2.2.01%3A_Prokaryotes/2.2.1.01%3A_Cell_Structure.txt

Learning Objectives • Describe why the Archaea have been difficult to place on the tree of life • Explain what it means to be an extremophile When these microscopic organisms were first separated from bacteria in 1977. When their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and seemed to be more closely related to the eukaryotes. For a time they were referred to as archaebacteria, but to emphasize their distinctness, we now call them Archaea. Diversity of Archaea Though archaeans are involved in many important ecological processes and present across Earth's ecosystems, they are most known for being extremophiles, existing in conditions that prevent most organisms from functioning: • thermophiles live at high temperatures • hyperthermophiles live at really high temperatures (present record is 121°C!) • psychrophiles (also called cryophiles) like it cold (one in the Antarctic grows best at 4°C) • halophiles live in very saline environments (like the Dead Sea) • acidophiles live at low pH (as low as pH 1 and who die at pH 7!) • alkaliphiles thrive at a high pH. Methanogens Methanogens are chemoautotrophs that use hydrogen as a source of electrons for reducing carbon dioxide to food. This process produces methane ("marsh gas", CH4) as a byproduct. These are found living in such anaerobic environments as: • the muck of swamps and marshes • the rumen of cattle (where they live on the hydrogen and CO2 produced by other microbes living along with them) • our colon (large intestine) • sewage sludge • the gut of termites Two methanogens that have had their complete genomes sequenced are Methanocaldococcus jannaschii and Methanothermobacter thermoautotrophicus. Crenarchaeota The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One can grow at 121°C (the same temperature in the autoclaves used to sterilize culture media, surgical instruments, etc.). Many like it acidic as well as hot and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO2). Aeropyrum pernix is one member of the group that has had its genome completely sequenced. Other members of this group seem to make up a large fraction of the plankton in cool, marine waters and the microbes in both soil and the ocean that convert ammonia into nitrites (nitrification). Evolutionary Position of the Archaea The Archaea have a curious mix of traits characteristic of bacteria as well as traits found in eukaryotes (discussed in Chapter 2.1). Table \(1\) summarizes some of them. Table \(1\): Traits that the Archaea have in common with Eukarya (left) and Bacteria (right). Eukaryotic Traits Bacterial Traits • DNA replication machinery • Histones • Nucleosome-like structures • Transcription machinery • RNA polymerase • TFIIB • TATA-binding protein (TBP) • Translation machinery • initiation factors • ribosomal proteins • elongation factors • poisoned by diphtheria toxin • Single, circular chromosome • Operons • No introns • Bacterial-type membrane transport channels • Many metabolic processes • energy production • nitrogen-fixation • polysaccharide synthesis Economic Importance of the Archaea Because they have enzymes that can function at high temperatures, considerable effort is being made to exploit the Archaea for commercial processes such as providing enzymes to be added to detergents (maintain their activity at high temperatures and pH) and an enzyme to covert corn starch into dextrins. Archaea may also be enlisted to aid in cleaning up contaminated sites, e.g., petroleum spills. There are no known pathogenic Archaea. Summary Archaea are a group of prokaryotes that were distinguished from Bacteria in the late 1970s. These organisms often exist in extreme environments and have diverse metabolic processes, including anaerobes that produce methane. Archaea are difficult to place in the phylogenetic tree of life. Though they share many prokaryotic traits with Bacteria, they seem to be genetically closer to Eukarya, including the processes used to replicate DNA and synthesize proteins. Attribution Content authored and curated by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.02%3A_Prokaryotes_and_Viruses/2.2.01%3A_Prokaryotes/2.2.1.02%3A_Archaea.txt

Learning Objectives • Describe some of the important ecological roles performed by bacteria • Explain a few ways bacteria interact with plants • Differentiate between oxygenic and anoxygenic photosynthesis Bacteria are prokaryotes that, along with several other distinctions, have peptidoglycan in their cell wall. These unicellular organisms are incredibly diverse and involved in all ecological processes across every ecosystem. Though most are too small to see with the naked eye and thus easily overlooked, some bacteria, such as the myxobacteria (in the order Myxococcales), collaborate to produce multicellular structures (see Figure \(1\)). This section will address some select bacterial taxa relevant to botany. Phototrophic Bacteria The phototrophic bacteria are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis. One large group of phototrophic bacteria includes the purple or green bacteria that perform photosynthesis with the help of bacteriochlorophylls, which are green, purple, or blue pigments similar to chlorophyll in plants. Some of these bacteria have a varying amount of red or orange pigments called carotenoids. Their color varies from orange to red to purple to green (Figure \(2\)), and they are able to absorb light of various wavelengths. Some green sulfur bacteria are able to photosynthesize at the bottom of the ocean using the light wavelengths emitted from geothermally heated rocks around hydrothermal vents!1 Traditionally, photosynthetic bacteria are classified into sulfur and nonsulfur bacteria; they are further differentiated by color (e.g. purple sulfur bacteria). The sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria use organic substrates, such as succinate and malate, as donors of electrons. The purple sulfur bacteria oxidize hydrogen sulfide into elemental sulfur and sulfuric acid and get their purple color from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus Chromatium are purple sulfur Gammaproteobacteria. These microorganisms are strict anaerobes and live in water. They use carbon dioxide as their only source of carbon, but their survival and growth are possible only in the presence of sulfites, which they use as electron donors. Chromatium has been used as a model for studies of bacterial photosynthesis since the 1950s. The green sulfur bacteria use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. The genus Chlorobium is a green sulfur bacterium that is implicated in climate change because it produces methane, a greenhouse gas. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes. Purple nonsulfur bacteria are similar to purple sulfur bacteria, except that they use hydrogen rather than hydrogen sulfide for oxidation. Among the purple nonsulfur bacteria is the genus Rhodospirillum. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize (“fix”) nitrogen. They may be valuable in the field of biotechnology because of their potential ability to produce biological plastic and hydrogen fuel. The green nonsulfur bacteria are similar to green sulfur bacteria but they use substrates other than sulfides for oxidation. Chloroflexus is an example of a green nonsulfur bacterium. It often has an orange color when it grows in the dark, but it becomes green when it grows in sunlight. It stores bacteriochlorophyll in chlorosomes, similar to Chlorobium, and performs anoxygenic photosynthesis, using organic sulfites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available. Chloroflexus does not have flagella but can glide, like Cytophaga. It grows at a wide range of temperatures, from 35 °C to 70 °C, thus can be thermophilic. Another large, diverse group of phototrophic bacteria compose the phylum Cyanobacteria; they get their blue-green color from the chlorophyll contained in their cells (Figure \(3\)). Species of this group perform oxygenic photosynthesis, producing megatons of gaseous oxygen. Scientists hypothesize that cyanobacteria played a critical role in the change of our planet’s anoxic atmosphere 1–2 billion years ago to the oxygen-rich environment we have today. This group is discussed further in 3.1.3.1. Table \(2\) summarizes the characteristics of some important groups of phototrophic bacteria. Table \(2\): Characteristics of Phototrophic Bacteria. Phylum Class Example Genus or Species Common Name Oxygenic or Anoxygenic Sulfur Deposition Cyanobacteria Cyanophyceae Microcystisaeruginosa Blue-green bacteria Oxygenic None Chlorobi Chlorobia Chlorobium Green sulfur bacteria Anoxygenic Outside the cell Chloroflexi (Division) Chloroflexi Chloroflexus Green nonsulfur bacteria Anoxygenic None Proteobacteria Alphaproteobacteria Rhodospirillum Purple nonsulfur bacteria Anoxygenic None Betaproteobacteria Rhodocyclus Purple nonsulfur bacteria Anoxygenic None Gammaproteobacteria Chromatium Purple sulfur bacteria Anoxygenic Inside the cell Bacteria and Plants Some important plant diseases are caused by pathogenic bacteria. For example, members of the genus Agrobacterium infect a variety of plants. Much like viruses, these bacteria insert part of their own genome into their host, causing the infected plant to produce a large gall (Figure \(4\)). This genus is particularly famous for its use in the genetic engineering of plants. Scientists can insert a gene into the Agrobacterium genome, which will then be inserted into the plant after infection. Other pathogenic bacteria can cause rot, blight, and even death of some host species. Species like Pseudomonas syringae and Erwinia herbicola are capable of inducing the formation of ice (ice nucleation), injuring plant tissues. In addition to diseases, many bacteria live within plant tissues, either freely or within endophytic fungi that live between the plant cells. These endophytic and/or endohyphal bacteria may play important roles in plant physiology, defense, and other aspects of plant biology by the production of a wide array of chemical compounds. Some bacteria are capable of nitrogen-fixation, converting atmospheric nitrogen into plant available forms. Plants in the bean family and alders have a mutualistic relationship with nitrogen-fixing bacteria and form structures called root nodules (see 3.1.3.2). Summary • Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green. • Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons. • Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms. • Cyanobacteria are oxygen-producing bacteria thought to have played a critical role in the forming of the earth’s atmosphere. • Plants have complex symbiotic relationships with bacteria, including parasites, commensalists, and mutualists. Attribution Content authored and curated by Maria Morrow, using the following source: • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at https://openstax.org/books/microbiology/pages/1-introduction) 2.2.1.03: Bacteria Learning Objectives • Explain the role of Cyanobacteria in changing Earth's atmosphere • Describe a few mutualistic relationships formed with Cyanobacteria • Distinguish between different Cyanobacterial cell types and describe their functions Stromatolites The earliest fossils are interpreted to be unicellular organisms similar to modern day cyanobacteria, sometimes referred to as blue green algae. The most widely accepted of these fossils dates back to 3.4 billion years ago from the Strelley Pool Formation in Western Australia. These particular fossils are called stromatolites and are composed of alternating layers of fossilized cells and calcium carbonate (Figure \(1\)). We can use evidence from modern day stromatolite formation in Western Australia to infer that these fossilized cells were doing a process called photosynthesis, using dissolved CO2 in the water to form sugar molecules. This causes calcium to precipitate out of the seawater, forming hardened layers of calcium carbonate on top of the colony of organisms. Because they need access to light to continue photosynthesizing, living cells begin forming a new layer on top of the calcium carbonate. This process continues, making a ringed pattern as the formation grows, much like we see in trees and corals. Cyanobacteria perform oxygenic photosynthesis. The ancestors of modern day cyanobacteria are responsible for the initial production of our oxygen-rich atmosphere. In addition to these initial inputs, cyanobacteria are the origin of chloroplasts in all eukaryotic phototrophs, including plants. In an event called primary endosymbiosis, a cyanobacterium was engulfed by a heterotrophic eukaryote. Instead of being digested, the prokaryote lived within the larger cell. Over time, genes were exchanged between the prokaryote and the eukaryote, eventually resulting in the first chloroplasts. Modern Cyanobacteria Cyanobacteria can be found free-living, often in colonies, or living in symbiotic relationships with other organisms, such as fungi and plants. Free-Living Cyanobacteria can be found in a vast diversity of places, from floating in the ocean to living in cryptobiotic crusts in the desert. Nostoc is a type of cyanobacteria that can often be found living in gelatinous colonies in wet, terrestrial environments. The colony secretes a mucilaginous sheath that provides a protective barrier and allows for the exchange of materials between cells in the colony. Mutualists Many cyanobacteria that you'll see in botany will be in mutualistic relationships. Anabaena is a colonial cyanobacterium that lives within the water fern Azolla, fixing nitrogen in the fern's relatively nutrient-poor aquatic environment. Nostoc is another colonial cyanobacterium capable of fixing nitrogen. It can be found free-living in gelatinous colonies shown above or, as you are likely to see it in your botany course, in compartments of a hornwort thallus. Cyanobacteria can also be found in a mutualistic relationship with fungi in cyanolichens. Anabaena If you were to chop up a sample of Azolla and look at it under the microscope, you'd see what looked like strings of green beads. Each bead is an individual cyanobacterium of the genus Anabaena. However, even though each one is an individual, some cells will specialize to provide a service for the colony, as a whole. • Heterocysts are thick-walled, chlorophyll-free cells that are fixing atmospheric nitrogen into bioavailable forms using the enzyme nitrogenase. Heterocysts cannot do photosynthesis, as that process produces oxygen and nitrogenase cannot function in the presence of oxygen. • Akinetes are individuals that still perform photosynthesis, but also function as a sort of failsafe. Akinetes store large amounts of lipids and carbohydrates so that they have enough energy to begin a new colony if conditions become too cold or too dry for survival. Their formation is triggered by these conditions (dry or cold), so you may not see them from a fresh water fern leaf, as this is a relatively stable, comfortable environment. Summary Cyanobacteria are a group of bacteria that perform oxygenic photosynthesis. The ancestors of modern cyanobacteria were responsible for the initial input of large amounts of oxygen into Earth's atmosphere. Evidence of these early cyanobacteria can be found in fossilized structures called stromatolites, which are still formed in some regions of the world. Cyanobacteria can be found free-living or as mutualists within the tissues of other organisms. Colonies of individuals are often encased within a protective mucilage. Within a colony, individual cells might specialize to fix nitrogen (heterocysts) or to survive cold and/or dry conditions (akinetes). Attribution Content by Maria Morrow, CC BY-NC 2.2.1.3.02: Root Nodules Learning Objectives • Describe the root nodule symbiosis between plants and bacteria • Explain why plants cannot get nitrogen from the nitrogen-rich atmosphere Several different groups of prokaryotes form mutualistic relationships with plant roots. Nitrogen is an essential nutrient for plants, yet it is difficult to obtain in many ecosystems. Though it is abundant in our atmosphere, this form a nitrogen (N2) is triple-bonded to itself, a bond which most organisms cannot break. However, certain bacteria have an enzyme called nitrogenase that can break the triple bond and convert nitrogen into usable forms for plants, such as ammonia (NH3). These bacteria can be found free-living in the environment or in mutualistic relationships with certain plants. A common relationship between plants and these nitrogen-fixing bacteria is the formation of root nodules--swellings in the plant roots that connect to the vascular tissue, allowing for the exchange of sugars and nutrients between the two different organisms. Rhizobiales and Legumes Plants in the bean family (Fabaceae) form mutualistic relationships in the form of root nodules with nitrogen-fixing bacteria in the order Rhizobiales. Frankia and Alder Frankia is a genus of bacteria that grows filamentously, called an actinomycete. Root nodules present on alder and few other groups of woody plants contain Frankia. Summary Some plants form a mutualistic relationship with bacteria for access to nitrogen. The bacteria infect the root hairs of the plant, forming a nodule. Within the nodule, the bacteria converts atmospheric nitrogen to a plant-available form. In return, the plant supplies the bacteria in the nodule with sugars. Attribution Content by Maria Morrow, CC BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.02%3A_Prokaryotes_and_Viruses/2.2.01%3A_Prokaryotes/2.2.1.03%3A_Bacteria/2.2.1.3.01%3A_Cyanobacteria.txt

Learning Objectives • Describe the general characteristics of viruses • Describe the range of effects viral infections can have on plants Viruses are microscopic (see Figure \(1\) for scale), acellular, and contain nucleic acids. Despite their small size, which prevented them from being seen with light microscopes, the discovery of a filterable component smaller than a bacterium that causes tobacco mosaic disease (TMD) dates back to 1892.1 At that time, Dmitri Ivanovski, a Russian botanist, discovered the source of TMD by using a porcelain filtering device first invented by Charles Chamberland and Louis Pasteur in Paris in 1884. Porcelain Chamberland filters have a pore size of 0.1 µm, which is small enough to remove all bacteria ≥0.2 µm from any liquids passed through the device. An extract obtained from TMD-infected tobacco plants was made to determine the cause of the disease. Initially, the source of the disease was thought to be bacterial. It was surprising to everyone when Ivanovski, using a Chamberland filter, found that the cause of TMD was not removed after passing the extract through the porcelain filter. So if a bacterium was not the cause of TMD, what could be causing the disease? Ivanovski concluded the cause of TMD must be an extremely small bacterium or bacterial spore. Other scientists, including Martinus Beijerinck, continued investigating the cause of TMD. It was Beijerinck, in 1899, who eventually concluded the causative agent was not a bacterium but, instead, possibly a chemical, like a biological poison we would describe today as a toxin. As a result, the word virus, Latin for poison, was used to describe the cause of TMD a few years after Ivanovski’s initial discovery. Even though he was not able to see the virus that caused TMD, and did not realize the cause was not a bacterium, Ivanovski is credited as the original discoverer of viruses and a founder of the field of virology. Today, we can see viruses using electron microscopes (Figure \(2\)) and we know much more about them. Viruses are distinct biological entities; however, their evolutionary origin is still a matter of speculation. In terms of taxonomy, they are not included in the tree of life because they are acellular (not consisting of cells). In order to survive and reproduce, viruses must infect a cellular host, making them obligate intracellular parasites. The genome of a virus enters a host cell and directs the production of the viral components, proteins and nucleic acids, needed to form new virus particles called virions. New virions are made in the host cell by assembly of viral components. The new virions transport the viral genome to another host cell to carry out another round of infection. Table \(1\) summarizes the properties of viruses. Table \(1\): Properties of viruses. Characteristics of Viruses Infectious, acellular pathogens Obligate intracellular parasites with host and cell-type specificity DNA or RNA genome (never both) Genome is surrounded by a protein capsid and, in some cases, a phospholipid membrane studded with viral glycoproteins Lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce Viruses and Plants Viruses can infect every type of host cell, including those of plants, animals, fungi, protists, bacteria, and archaea. Most viruses will only be able to infect the cells of one or a few species of organism. This is called the host range. However, having a wide host range is not common and viruses will typically only infect specific hosts and only specific cell types within those hosts. The viruses that infect bacteria are called bacteriophages, or simply phages. The word phage comes from the Greek word for devour. Other viruses are just identified by their host group, such as fungal or plant viruses. Once a cell is infected, the effects of the virus can vary depending on the type of virus. Viruses may cause abnormal growth of the cell or cell death, alter the cell’s genome, or cause little noticeable effect in the cell. Some viruses, like TMV, cause disease and inhibit plant growth (Figure \(2\)). In other cases, scientists are finding that viruses can confer adaptive traits to their hosts, such as heat tolerance in the grass geyser's Panicum (see Figure \(3\)). Viruses can be transmitted through direct contact, indirect contact with contaminated materials, or through a vector: an animal that transmits a pathogen from one host to another. Arthropods such as mosquitoes, ticks, and flies, are typical vectors for viral diseases, and they may act as mechanical vectors or biological vectors. Mechanical transmission occurs when the arthropod carries a viral pathogen on the outside of its body and transmits it to a new host by physical contact. Biological transmission occurs when the arthropod carries the viral pathogen inside its body and transmits it to the new host through biting. Most plant viruses are transmitted by aphids (see Figure \(4\)). Summary Viruses are acellular, obligate intracellular parasites. They are composed of a nucleic acid (either DNA or RNA), a protein coat, and occasionally lipids. Viruses are not considered living because they are not composed of cells. However, viruses have important impacts on the life histories of organisms. As agents of disease, viruses contribute to top-down population control. They can also influence host biology in positive ways, such as thermal tolerance in panic grasses. Viruses can be spread from host to host by vectors. Sucking insects like aphids are important viral vectors for plants, as they transmit viruses into the vascular system. Footnotes 1 H. Lecoq. “[Discovery of the First Virus, the Tobacco Mosaic Virus: 1892 or 1898?].” Comptes Rendus de l’Academie des Sciences – Serie III – Sciences de la Vie 324, no. 10 (2001): 929–933. 2 L.M. Marquez, R.S. Redman, R.J. Rodriguez, and M.J. Roossinck. (2007) A virus in a fungus in a plant: Three-way symbiosis required for thermal tolerance. Science. Vol 315. DOI: 10.1126/science.1137195 Attribution Content authored and curated by Maria Morrow, using the following source: • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at https://openstax.org/books/microbiology/pages/1-introduction) 2.2.03: Chapter Summary Prokaryotes are unicellular organisms with circular DNA that lack a nucleus or other membrane-bound organelles. These organisms can be divided into two distinct evolutionary lineages: Bacteria and Archaea. Though Bacteria and Archaea share many traits, Archaea are considered more closely related to eukaryotes due to their cellular processes. Both groups of prokaryotes have complex and essential roles in ecosystems across the globe. With regard to plants, Bacteria are particularly important for their role in converting atmospheric nitrogen into plant-available forms. Some of these nitrogen-fixing bacteria can be found in root nodules or other specialized compartments (e.g. cephalodia), while others are free-living. Additionally, without the original endosymbiotic event of a photosynthetic bacterial ancestor, "plants" would not exist! Viruses are biological entities that are not classified as organisms because they are not composed of cells. They have an obligate intracellular relationship with their hosts. Most viruses that we are aware of are disease-causing, such as the Tobacco Mosaic Virus. However, as we learn more about virology, other outcomes are emerging, such as the heat tolerance observed in some grasses. After completing this chapter, you should be able to... • Explain the distinguishing characteristics of prokaryotic cells • Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology • Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function • Compare the distinguishing characteristics of bacterial and archaean cells • Describe why the Archaea have been difficult to place on the tree of life • Explain what it means to be an extremophile • Describe some of the important ecological roles performed by bacteria • Explain a few ways bacteria interact with plants • Differentiate between oxygenic and anoxygenic photosynthesis • Explain the role of Cyanobacteria in changing Earth's atmosphere • Describe a few mutualistic relationships formed with Cyanobacteria • Distinguish between different Cyanobacterial cell types and describe their functions • Describe the root nodule symbiosis between plants and bacteria • Explain why plants cannot get nitrogen from the nitrogen-rich atmosphere • Describe the general characteristics of viruses • Describe the range of effects viral infections can have on plants Attribution Content by Maria Morrow, CC-BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.02%3A_Prokaryotes_and_Viruses/2.2.02%3A_Viruses.txt

Kingdom Fungi includes an enormous variety of living organisms. While scientists have identified about 150,000 species of fungi, this is only a fraction of the several million species of fungi likely present on Earth. Organisms in this group are heterotrophic eukaryotes that eat by external digestion, then absorption. Fungi can be unicellular (yeasts) or composed of filamentous cells called hyphae, which taken together form a thallus called the mycelium. • 2.3.1: Introduction to Fungi The word fungus is from the Latin word for mushroom, which is also similar to the Greek word for sponge. Indeed, the familiar mushroom is a reproductive structure used by only some of the fungi. There are many fungal species that don't produce mushrooms at all. The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi. • 2.3.2: Characteristics of Fungi What features do we use to classify organisms into Kingdom Fungi? This section considers the life cycle, morphology, cellular make up, and nutritional modes of fungi. • 2.3.3: Ecology of Fungi Where are fungi found, what roles do they have in nutrient cycling, and how do they interact with other organisms? • 2.3.4: Microfungi The term microfungi encompasses the more ancestral lineages of fungi that form microscopic fruiting bodies, including chytrids, zygospore-forming lineages, and the glomeromycetes. Yeasts and molds from the Ascomycota and Basidiomycota are commonly grouped with the microfungi. • 2.3.5: Macrofungi The term macrofungi refers to the fungal lineages that make macroscopic fruiting bodies: Ascomycota and Basidiomycota. These groups are sister taxa and are commonly referred to as higher fungi, as they are more recently diverged in the fungal phylogeny. There are molds, yeasts, and other fungi contained within these groups (such as the rusts and smuts) that do not form macroscopic fruiting structures. • 2.3.6: Importance of Fungi in Human Life Although people often associate fungi with disease and food spoilage, fungi are important to human life on many levels. They form important symbiotic relationships that influence ecosystem services. Humans use fungi directly for food, medicine, bioremediation, construction of goods (e.g. packaging, fungus leather), and spiritual purposes. • 2.3.7: Chapter Summary A summary of broad chapter concepts. 2.03: Fungi The word fungus is from the Latin word for mushroom, which is also similar to the Greek word for sponge. Indeed, the familiar mushroom is a reproductive structure used by only some of the fungi. There are many fungal species that don't produce mushrooms at all. The kingdom Fungi includes an enormous variety of living organisms collectively referred to as Eucomycota, or true Fungi. While scientists have identified almost 150,000 species of fungi as of 2020,1 this is only a fraction of the millions of fungal species likely present on Earth. Though understudied, kingdom Fungi is filled with fascinating organisms. An individual Armillaria ostoyae fungus in Oregon is one of the oldest and largest organisms on Earth, spreading across almost 10 km2 of forest, with a mass anywhere from 6,800 to 30,000 metric tons and an estimated age between 1,900 to 8,500 years old, depending on estimates of growth rate. The fungus Pilobolus can shoot its spores twice as fast as a rifle bullet, many fungal species glow in the dark, others control the minds of insects, and still others negotiate the distribution of carbon, nitrogen, phosphorus, and other materials between trees in the world's forests. Fungi were once considered plant-like organisms and so are studied under the umbrella of botany. Though they are more closely related to animals than plants, fungi were not moved into their own kingdom until 1969, the same year we landed on the moon. Fungi are not capable of photosynthesis: they are heterotrophic, using complex organic compounds as sources of energy and carbon. These sources of carbon are digested externally, then absorbed. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual reproduction. Most fungi produce a large number of spores, which are haploid cells that can undergo mitosis to form multicellular, haploid individuals. Like bacteria, fungi participate in nearly every role in an ecosystem. They are often decomposers and participate in the cycling of nutrients by breaking down organic materials to simple molecules. Fungi are frequently found in symbiotic relationships with other organisms. For example, most terrestrial plants form a mutualistic symbiosis with fungi; the roots of the plant connect with the underground parts of the fungus forming mycorrhizae. Through mycorrhizae, the fungus and plant exchange nutrients and water, greatly aiding the survival of both species. Lichens are another association between a fungus and a photosynthetic partner (usually an alga), where they form a single body that might contain two to many different organisms. Fungi also cause serious infections in plants and animals. For example, Dutch elm disease, which is caused by the fungus Ophiostoma ulmi, is a particularly devastating type of fungal infection that destroys many native species of elm (Ulmus sp.) by infecting the tree’s vascular system. The elm bark beetle acts as a vector, transmitting the disease from tree to tree. Accidentally introduced in the 1900s, the fungus decimated elm trees across the continent. Many European and Asiatic elms are less susceptible to Dutch elm disease than American elms. The close evolutionary relationship between fungi and animals makes fungal infections in humans a challenging to treat. Unlike bacteria, fungi do not respond to traditional antibiotic therapy because they are eukaryotes. Fungal infections may prove deadly for individuals with compromised immune systems. Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and wine making. Cheeses and cured meats are products of fungal metabolism. Many industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes, as well s the main source of citric acid production. Fungi are important to the health industry. Antibiotics were originally discovered in the fungus Penicillium notatum and many current medications, such as some antibiotics or the immunosuppressant Cyclosporine, are derived from fungi. What is a mycologist? Mycologists are biologists who study fungi. Many mycologists start their careers with a degree in botany, microbiology, or even ecology. To become a lab mycologist, a bachelor's degree in a biological science (preferably majoring in microbiology) and a master's degree in mycology are often necessary. Mycologists can specialize in taxonomy and fungal genomics, molecular and cellular biology, plant pathology, fungal ecology, biotechnology, or biochemistry. Some medical microbiologists concentrate on the study of infectious diseases caused by fungi (mycoses). Mycologists collaborate with zoologists and plant pathologists to identify and control difficult fungal infections, such as the devastating chestnut blight, the mysterious decline in frog populations in many areas of the world, or the deadly epidemic called white nose syndrome, which is decimating bats in the Eastern United States. Government agencies hire mycologists as research scientists and technicians to monitor the health of crops, national parks, and national forests. Mycologists are also employed in the private sector by companies that develop chemical and biological control products or new agricultural products, and by companies that provide disease control services. Because of the key role played by fungi in the fermentation of alcohol and the preparation of many important foods, scientists with a good understanding of fungal physiology routinely work in the food technology industry. Oenology, the science of wine making, relies not only on the knowledge of grape varietals and soil composition, but also on a solid understanding of the characteristics of the wild yeasts that thrive in different wine-making regions. It is possible to purchase yeast strains isolated from specific grape-growing regions. The great French chemist and microbiologist, Louis Pasteur, made many of his essential discoveries working on the humble brewer’s yeast, thus discovering the process of fermentation. Perhaps because mycology is often given short shrift within higher education (many institutions do not even offer mycology courses), many mycologists become teachers. This includes those employed as professors, as well as those who write books, teach workshops, give lectures, or provide other forms of education. As the field of mycology grows, so to do the possibilities for mycologists! Footnote 1 Figure from the 2020 Species Fungorum database. More information can be found in this open-access paper. Attribution Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.01%3A_Introduction_to_Fungi.txt

Learning Objectives • List the characteristics of fungi. • Describe the composition of the mycelium. • Describe the mode of nutrition of fungi. • Explain sexual and asexual reproduction in fungi. The Fungal Body Fungi have well-defined characteristics that set them apart from other organisms. Most multicellular fungal bodies are made up of filaments called hyphae. Hyphae can form a network called a mycelium, which is the thallus (body) of the fungus (Figure \(1\)). Fungi are heterotrophs that excrete enzymes to digest food externally, then absorb the digested food. Because of this feeding strategy, fungi tend to live within whatever their food substrate is. The thin, filamentous hyphal structure allows for maximal surface area and thus, maximal contact with the food substrate. Hyphae that have walls (septa) between the cells are called septate hyphae; hyphae that lack walls and cell membranes between the cells are called nonseptate or coenocytic hyphae (Figure \(\PageIndex{2-3}\)). Early diverging lineages of fungi have coenocytic hyphae, while later lineages (often referred to as "higher fungi") have septate hyphae. In contrast to filamentous fungi, yeasts are unicellular. The budding yeasts reproduce asexually by budding off a smaller daughter cell (Figure \(4\)); the resulting cells may sometimes stick together as a short chain or pseudohypha (Figure \(2\)). Candida albicans (Figure \(5\)) is a common yeast that forms pseudohyphae; it is associated with various infections in humans, including vaginal yeast infections, oral thrush, and candidiasis of the skin. Some fungi are dimorphic, having more than one appearance during their life cycle. These dimorphic fungi may be able to appear as yeasts or filamentous forms, which can be important for infectivity. They are capable of changing their appearance in response to environmental changes such as nutrient availability or fluctuations in temperature, growing as a mold, for example, at 25 °C (77 °F), and as yeast cells at 37 °C (98.6 °F). This ability helps dimorphic fungi to survive in diverse environments. Cell Structure and Function Fungi are eukaryotes, and as such, have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-bound nucleus. The DNA in the nucleus is wrapped around histone proteins, as is observed in other eukaryotic cells. A few types of fungi have structures comparable to bacterial plasmids (loops of DNA); however, the horizontal transfer of genetic information from one mature bacterium to another rarely occurs in fungi. Fungal cells also contain mitochondria and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus. Unlike plant cells, fungal cells do not have chloroplasts or chlorophyll. Many fungi display bright colors arising from other cellular pigments, ranging from red to green to black, though none of these are for photosynthesis. The poisonous Amanita muscaria (fly agaric) is recognizable by its bright red cap with white patches (Figure \(6\)). Pigments in fungi are associated with the cell wall and some play a protective role against ultraviolet radiation. Some fungal pigments are toxic. Like plant cells, fungal cells have a thick cell wall. The rigid layers of fungal cell walls contain complex polysaccharides called chitin and glucans (unlike the cell walls of plants, which contain cellulose). Chitin, also found in the exoskeleton of insects, gives structural strength to the cell walls of fungi. The wall protects the cell from desiccation and predators. Fungi have plasma membranes similar to other eukaryotes, except that the structure is stabilized by ergosterol, a steroid molecule that replaces the cholesterol found in animal cell membranes. Ergosterols are often exploited as targets for antifungal drugs. Most members of the kingdom Fungi are nonmotile. Flagella are produced only in the chytrids. Motile cells have a single, whiplash flagellum, placing these organisms in the Opisthokonts (along with animals). Growth For filamentous fungi, a fungal spore germinates and grows apically. The mycelium is often highly branched and the fungus grows from the apex of each hypha, forming a radial growth pattern (Figure \(8\)). Because fungi grow within their substrate, we often do not see the mycelium, only the fruiting structures. In Figure \(9\), a circle of mushrooms called a fairy ring has formed in a grassy lawn. The original spore would have been deposited in the center of that ring and the mycelium grew outward from there. The mushrooms are produced at the edge of the mycelium. Nutrition Like animals, fungi are heterotrophs; they use complex organic compounds as a source of carbon, rather than fix carbon dioxide from the atmosphere as plants do. In addition, fungi do not fix nitrogen from the atmosphere. Like animals, they must obtain it from their diet. However, unlike most animals, which ingest food and then digest it internally in specialized organs, fungi perform these steps in the reverse order; digestion precedes ingestion. First, exoenzymes are transported out of the hyphae, where they process nutrients in the environment. Then, the smaller molecules produced by this external digestion are absorbed through the large surface area of the mycelium. As with animal cells, the polysaccharide of storage is glycogen, rather than starch, as found in plants. Fungi are mostly saprotrophs, organisms that derive nutrients from decaying organic matter. They obtain their nutrients from dead or decomposing organic matter, mainly plant material. Fungal exoenzymes are able to break down insoluble polysaccharides, such as the cellulose and lignin of dead wood, into readily absorbable glucose molecules. The carbon, nitrogen, and other elements are thus released into the environment. Because of their varied metabolic pathways, fungi fulfill important ecological roles and are being investigated as potential tools in bioremediation. For example, some species of fungi can be used to break down diesel oil and polycyclic aromatic hydrocarbons (PAHs) due to their chemical similarity to the lignin found in wood. Other species take up heavy metals, such as cadmium and lead. Some fungi are parasitic, causing infections in other organisms. Many important plant parasites are rusts, fungi in the Basidiomycota with complex life cycles. In environments poor in nitrogen, some fungi resort to predation of nematodes (small non-segmented roundworms). Species of Arthrobotrys fungi have a number of mechanisms to trap nematodes. One mechanism involves constricting rings within the network of hyphae. The rings swell when they touch the nematode, gripping it in a tight hold. The fungus penetrates the tissue of the worm by extending specialized hyphae called haustoria. Many parasitic fungi possess haustoria, as these structures penetrate the tissues of the host, release digestive enzymes within the host's body, and absorb the digested nutrients. Some fungi live in a mutually beneficial symbiotic relationship with another organism, often a photosynthetic organism such as a plant or alga. The association of fungus and plant root is called mycorrhizae. Over 90% of land plant species benefit from symbiotic mycorrhizal relationships. The plant benefits by more-efficient mineral (e.g. phosphorus) uptake and the fungus benefits by the sugars translocated to the root by the plant. Mycorrhizal fungi may also form conduits for nutrients between plant species, for better or worse. The colorless, and hence heterotrophic ghost pipe (Monotropa uniflora - pictured in Figure \(10\)) is an angiosperm that must secure all its nourishment from mycorrhizal fungi that are attached at the same time to the roots of some autotrophic plant such as a pine tree. Radioactive carbon administered to the pine (as CO2) soon turns up in carbohydrates in nearby ghost pipes. Reproduction Fungi disperse themselves by releasing spores (haploid, in most cases). Fungal spores are present almost everywhere (and are a frequent cause of allergies). Spores of the wheat rust fungus have been found at 4000 m in the air and more than 1450 km (900 miles) from the place they were released. No wonder then that many fungi seem to have a worldwide distribution. Fungi reproduce sexually and/or asexually. Fungi may exhibit asexual reproduction by mitosis with budding (Figure \(13\)), fragmentation of hyphae, and formation of asexual spores by mitosis (Figure \(14\)). Depending on the taxonomic group, sexually produced spores are known as zygospores (in the former Zygomycota), ascospores (in Ascomycota), or basidiospores (in Basidiomycota). In both sexual and asexual reproduction, fungi produce spores that disperse from the parent organism by floating on the wind, hitching a ride on an animal, or some other means. Fungal spores are microscopic and often produced in large numbers. When the giant puffball mushroom bursts open, it releases trillions of spores. The huge number of spores released increases the likelihood of landing in an environment that will support growth (Figure \(12\)). Fungal life cycles are unique and complex, though fungi are typically said to have a haplontic life cycle (Figure \(15\)). In a generalized fungal life cycle, haploid mycelia of different mating types either form hyphae that have gametes at the tips or fuse directly (somatogamy). The cytoplasm fuses in an event called plasmogamy, producing a cell with two distinct nuclei (a dikaryotic, or n+n, cell). At some point later, the nuclei fuse (in an event called karyogamy) to create a diploid zygote. The zygote undergoes meiosis to form haploid spores that germinate and grow into a new haploid mycelium. How these events occur is one of the major ways we classify fungi, and the life cycles of different fungal groups contrast significantly. Review the characteristics of fungi by visiting this interactive site from Wisconsin-online. Summary Fungi are eukaryotic organisms that appeared on land more than 450 million years ago. They are heterotrophs and contain neither photosynthetic pigments such as chlorophyll, nor chloroplasts. Fungi are important decomposers that release essential elements into the environment. However, they have many other important roles in ecosystems as parasites and mutualists. External enzymes digest nutrients that are then absorbed by the mycelium of the fungus, which is composed of filamentous cells called hyphae. A thick cell wall made of chitin surrounds the hyphae. Unicellular fungi are called yeasts and reproduce by budding. Fungi can reproduce asexually (typically referred to as molds) and/or sexually. One of the primary ways fungi were classified into phyla was based on the life cycle and type of sexual structures produced. Characteristics of Fungi: • Eukaryotic • Heterotrophic by absorption • Morphology: Unicellular or a thallus composed of hyphae. If present, motile cells have only a single, whiplash flagellum. • Cell walls: Chitin • Storage carbohydrate: Glycogen • Life cycle: Haplontic (though this one gets a bit weird) • Ecology: Many fungi are decomposers, primarily in terrestrial ecosystems. Other groups of fungi live in symbiosis with other organisms as parasites, mutualists, or commensalists. Attribution Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.02%3A_Characteristics_of_Fungi.txt

Learning Objectives • Describe some of the roles of fungi in ecosystems. • Describe mutualistic relationships of fungi with plant roots and photosynthetic organisms. • Describe the beneficial relationship between some fungi and insects. Fungi play a crucial role in the maintenance of ecosystems. They are found in most habitats on Earth, though they are largely moisture-dependent. Their ability to exist in such a wide variety of habitats is often facilitated by symbiotic relationships with other organisms, whether these are parasitic, mutualistic, or commensal. Fungi are not obvious in the way large animals or tall trees appear, in part because they live within their food, digesting it externally before absorbing it. Like bacteria, they are the major recyclers of organic matter. Habitats Although fungi are primarily associated with humid and cool environments that provide a supply of organic matter, they colonize a surprising diversity of habitats, from seawater to human skin and mucous membranes. Fungi have been found living inside rocks and rocky substrates in marine ecosystems1, high in the Andes mountains on salt crusts2, in the hot springs of the Jurassic period3, and inside just about any organism you can think of. Chytrids are found primarily in aquatic environments. Other fungi, such as Coccidioides immitis, which causes pneumonia when its spores are inhaled, thrive in the dry and sandy soil of the southwestern United States. Fungi that parasitize coral reefs live in the ocean. However, most members of the kingdom Fungi grow on the forest floor, where the damp environment is rich in decaying debris from plants and animals. In these environments, fungi play a major role as decomposers and mutualists, facilitating the transfer of nutrients to members of the other kingdoms. Decomposers and Recyclers The food web would be incomplete without organisms that decompose organic matter (Figure \(1\)). Some elements—such as nitrogen and phosphorus—are required in large quantities by biological systems, and yet are not abundant in the environment. The action of fungi releases these elements from decaying matter, making them available to other living organisms. Trace elements present in low amounts in many habitats are essential for growth, and would remain tied up in rotting organic matter if fungi and bacteria did not return them to the environment via their metabolic activity. The ability of fungi to degrade many large and insoluble molecules is due to their mode of nutrition. As seen earlier, digestion precedes ingestion. Fungi produce a variety of exoenzymes to digest nutrients. The enzymes are either released into the substrate or remain bound to the outside of the fungal cell wall. Large molecules are broken down into small molecules, which are transported into the cell by a system of protein carriers embedded in the cell membrane. Because the movement of small molecules and enzymes is dependent on the presence of water, active growth depends on a relatively high percentage of moisture in the environment. As saprotrophs, fungi help maintain a sustainable ecosystem for the animals and plants that share the same habitat. In addition to replenishing the environment with nutrients, fungi interact directly with other organisms in beneficial, and sometimes damaging, ways (Figure \(2\)). Fungi are essential to the turnover of carbon locked up in woody materials. Lignin is a component of the secondary cell wall in plants, composing much of what we call wood, and is notoriously difficult to break down. Wood decay fungi are generally divided into two major groups: white rotters that break down both lignin and cellulose and brown rotters that have lost their ability to degrade lignin (Figure \(3\)). The lignin-rich material left behind by brown rotters provides moisture retention and a springy, lightness to the soil substrate in forest ecosystems. Mutualistic Relationships Symbiosis (sym - shared, bio - life) is the ecological interaction between two or more organisms of different species that live together in a close physical association. The definition does not describe the quality of the interaction. When both members of the association receive a net benefit, the symbiotic relationship is called mutualistic. When one partner benefits at the expense of the other, it is parasitism. If one partner benefits but the other is unaffected, it is commensalism. Mutualistic relationships, however, are rarely so clear cut. Instead, these relationships often exist somewhere along the parastism-mutualism continuum, displaying elements of each. Fungi form these complex mutualistic associations with many types of organisms, including cyanobacteria, algae, plants, and animals. Mycorrhizal Relationships One of the most remarkable associations between fungi and plants is the establishment of mycorrhizae. Mycorrhiza, which comes from the Greek words myco meaning fungus and rhizo meaning root, refers to the association between vascular plant roots and their symbiotic fungi. Around 90 percent of all plant species form mycorrhizal relationships with fungi. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from the soil into the plant. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the fungus. There are a number of types of mycorrhizae. Ectomycorrhizae (“outside” mycorrhiza) form when fungi envelope the roots in a sheath (called a mantle) and a Hartig net of hyphae that extends into the roots between cells (Figure \(4\) a and Figure \(5\) a). The fungal partner can belong to the Ascomycota, Basidiomycota or occasionally one of the zygospore-forming Endogonales. Ectomycorrhizal relationships tend to be present in temperate and boreal forest trees, though their importance in tropical forests is currently being elucidated. In a second type, fungi in the Glomeromycota form arbuscular mycorrhiza (called endomycorrhizae). The fungi form arbuscules, highly branched hyphal structures that penetrate root cell walls and are the site of the metabolic exchanges between the fungus and the host plant (Figure \(4\) b and Figure \(5\) b). The arbuscules (from the Latin word for little trees) have a shrub-like appearance due to increase surface area for exchange across membranes. Orchids rely on a third type of mycorrhiza. Orchids are a group of plants, often living as epiphytes, that form tiny seeds without much storage to sustain germination and growth--the black specks in vanilla bean ice cream are the seeds of an orchid. Their seeds will not germinate without a mycorrhizal partner (usually a Basidiomycete). The orchid seed attracts a mycorrhizal fungus via chemical signals, then when the relationship is established, begins lysing the fungal cells to gain nutrients from the fungus. It is not until the orchid produces its leaves and can successfully photosynthesize that sugars begin being transferred to the fungus. Plants in the Ericaceae (heath family) represent at least two different types of mycorrhiza: Ericoid and Monotropoid. Evolution Connection Mycorrhizae are the mutually beneficial symbiotic association between roots of vascular plants and fungi. A well-accepted theory proposes that fungi were instrumental in the evolution of the root system in plants and contributed to the success of angiosperms. The bryophytes (mosses and liverworts), which are considered the most primitive plants and the first to survive on dry land, do not have a true root system; some have vesicular–arbuscular mycorrhizae and some do not. They depend on a simple rhizoid (an underground organ) and cannot survive in dry areas. True roots appeared in vascular plants. Vascular plants that developed a system of thin extensions from the rhizoids (found in mosses) are thought to have had a selective advantage because they had a greater surface area of contact with the fungal partners than the mosses and liverworts, thus availing themselves of more nutrients in the ground. Fossil records indicate that fungi preceded plants on dry land. The first association between fungi and photosynthetic organisms on land involved moss-like plants and endophytes. These early associations developed before roots appeared in plants. Slowly, the benefits of the endophyte and rhizoid interactions for both partners led to present-day mycorrhizae; up to about 90 percent of today’s vascular plants have associations with fungi in their rhizosphere. The fungi involved in mycorrhizae display many characteristics of primitive fungi; they produce simple spores, show little diversification, do not have a sexual reproductive cycle, and cannot live outside of a mycorrhizal association. The plants benefited from the association because mycorrhizae allowed them to move into new habitats because of increased uptake of nutrients, and this gave them a selective advantage over plants that did not establish symbiotic relationships. Lichens Lichens are typically defined as a symbiotic relationship between a fungal partner (the mycobiont, typically an ascomycete) and an alga or cyanobacterium (the photobiont). The mycobiont forms the thallus, wrapping a thin layer of photobiont cells in fungal tissue. The fungus therefore houses the photobiont, while the photobiont makes sugars via photosynthesis that the fungus feeds on. The fungus controls the reproduction of the photobiont and when the photobiont gets to eat. The fungus is, in essence, farming the photobiont. Would you consider this a parasitism or mutualism? This association forms a unified thallus that appears to be a single organism, thus lichens have species names. However, the more scientists look, the more interacting organisms they seem to find in lichens. Tripartite lichens contain two photobionts: an alga and a cyanobacteria. Many lichens have been found to contain a second mycobiont (typically a basidiomycete yeast), endohyphal bacteria, and other organisms whose role in the lichen relationship we do not yet understand. See Chapter 3.7 in the Photographic Atlas for a deeper dive into lichens. Other examples of fungus–plant mutualism include the endophytes: fungi that live inside tissue without damaging the host plant. Endophytes release toxins that repel herbivores, or confer resistance to environmental stress factors, such as infection by microorganisms, drought, or heavy metals in soil. Fungal-Animal Mutualism Fungi have evolved mutualisms (and parasitisms!) with numerous insects in phylum Arthropoda: jointed, legged invertebrates. Arthropods depend on the fungus for protection from predators and pathogens, while the fungus obtains nutrients and a way to disseminate spores into new environments. The association between species of Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in underground gardens (Figure \(7\)). A basidiomycete fungus (Leucoagaricus gongylophorus) is cultivated in these disk gardens from bits of mycelium from the queen's original colony, meaning the fungi within these gardens are all genetically quite similar (a monoculture, if you will). The fungus digests the cellulose in the leaves that the ants cannot break down, then produces nutrient-rich structures called gongylidia on which the ants feed. The ants patrol their garden, tending their fungi. There are actinomycetes (filamentous bacteria) that live on the surface of the ant, within its cuticle, that produce antifungal compounds specific to another parasitic fungus (an ascomycete) that often invades these fungal gardens. Both ants and fungi benefit from the association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they cultivate. Watch this process in action in Video \(1\). Video \(1\): Leaf cutter ants and their fungal gardens. Sourced from YouTube. Fungivores Animal dispersal is important for some fungi because an animal may carry spores considerable distances from the source. Fungal spores are rarely completely degraded in the gastrointestinal tract of an animal, and many are able to germinate when they are passed in the feces. Some dung fungi actually require passage through the digestive system of herbivores to complete their lifecycle. The black truffle—a prized gourmet delicacy—is the fruiting body of an underground mushroom. Almost all truffles are ectomycorrhizal, and are usually found in close association with trees. Animals eat truffles and disperse the spores. In Italy and France, truffle hunters use female pigs to sniff out truffles. Female pigs are attracted to truffles because the fungus releases a volatile compound closely related to a pheromone produced by male pigs. Fungal Parasites of Plants Parasitism describes a symbiotic relationship in which one member of the association benefits at the expense of the other. Both parasites and pathogens harm the host; however, the pathogen causes a disease, whereas the parasite usually does not. The production of sufficient good-quality crops is essential to human existence. Plant diseases have ruined crops, bringing widespread famine. Many plant pathogens are fungi that cause tissue decay and eventual death of the host (Figure \(8\)). In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot's alkaloid toxins on humans and animals are of much greater significance. In animals, the disease is referred to as ergotism. The most common signs and symptoms are convulsions, hallucination, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that affect crops. Aflatoxins are toxic, carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of nuts and grains are tainted by aflatoxins, leading to massive recall of produce. This sometimes ruins producers and causes food shortages in developing countries. Summary Fungi occupy nearly all environments on Earth, but are frequently found in cool, moist places with a supply of decaying material. Fungi are saprotrophs that decompose organic matter, mutualists, and parasites. Many successful mutualistic relationships involve a fungus and another organism. Some groups of fungi establish complex mycorrhizal associations with the roots of plants. Approximately 90% of all plant species form some type of mycorrhizal relationship and it is likely that this symbiosis aided early plants in their transition onto land. Lichens are a symbiotic relationship between a fungus and a photosynthetic organism, usually an alga or cyanobacterium. The photosynthetic organism provides energy derived from light and carbohydrates, while the fungus supplies minerals and protection. Some animals that consume fungi help disseminate spores over long distances. Attributions Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.03%3A_Ecology_of_Fungi.txt

Learning Objectives • Use characteristics to distinguish between groups of microfungi. • Describe some of the roles microfungi have in ecosystems. • Explain the relationship between plants and members of Glomeromycota. • Identify structures in the "zygomycete" life cycle and know their ploidy. This small group (~1000 species) is thought to be the most primitive of the fungi. Once all classified as Chytridiomycota, these early, aquatic fungi are now grouped into Blastocladiomycota, Chytridiomycota, and Neocallimastigomycota. Unlike all the other fungi, its members produce flagellated gametes (for sexual reproduction) and flagellated zoospores (for asexual reproduction). They are mostly aquatic. The evolutionary record shows that the first recognizable chytrids appeared during the late pre-Cambrian period, more than 500 million years ago. Like all fungi, chytrids have chitin in their cell walls, but one group of chytrids has both cellulose and chitin in the cell wall. Most chytrids are unicellular; a few form multicellular thalli with filamentous hyphae, which have no septa between cells (coenocytic). They produce gametes and diploid zoospores that swim with the help of a single flagellum. Chytrids usually live in aquatic environments, although some species live on land or as mutualists in the rumens of ungulates. Some species thrive as parasites on plants, insects, or amphibians (Figure \(3\)), while others are saprotrophs. The chytrid genus Allomyces (Figure \(2\)) is well characterized as an experimental organism; fungal sex horomones (specifically sirenin) were first discovered in this group. Its reproductive cycle includes both asexual and sexual phases. Allomyces produces diploid or haploid flagellated zoospores in a sporangium. Parasitic Chytrids Many chytrids are parasites, perhaps due to their need for an aqueous environment. Some chytrid species are parasites of other chytrids (Rozella allomycis is a parasite that lives within Allomyces), some are parasites of algal species (Figure \(3\) and Figure \(4\)), some are parasites of plants (Figure \(5\), while still others are parasites of animals (Figure \(6\). The most infamous chytrid species is a parasite on amphibians, discussed in the following section. Bd (Batrachochytrium dendrobatidis) Batrachochytrium dendrobatidis, commonly called Bd, is a chytrid fungus that infects the skin of amphibians. The infection causes hardening of the permeable skin, making it difficult for the animal to breathe. Swimming spores are produced in lesions on the skin and are easily spread through aquatic environments. Amphibians, who must spend part of their life cycle in water, are highly susceptible to this parasite, particularly as other stressors like climate change and pollution lower their resistance. Bd is contributing to a worldwide decline in many amphibian species (though there are numerous other contributing factors), particularly frogs. Neocallimastix is an anaerobic chytrid that lives in the rumen of some ungulates. Cows and other grazing animals can't actually break down the cellulose in the plants they eat. Instead, this plant material first travels to a pre-stomach called a rumen. A community of anaerobic organisms breaks down the cellulose, producing methane. When the pre-digested plant matter has been transformed into compounds that the cow can break down, it then moves to the stomach of the cow. The methane released by cows is due to this anaerobic activity in the rumen. Characteristics Fungi in the former Zygomycota were recently split into several lineages because they are a paraphyletic group. These fungi produce a large sexual structure called a zygospore and so are called "zygomycetes". They are mainly saprotrophs with coenocytic hyphae and haploid nuclei. They produce haploid sporangiospores by mitosis during asexual reproduction. The group name comes from the zygospores that they use for sexual reproduction (Figure \(8\)), which have hard walls formed from the fusion of reproductive cells from two individuals. Zygomycetes are important for food science and as crop pathogens. One example is Rhizopus stolonifer (Figure \(8\)), an important bread mold that also causes rice seedling blight. Mucor is a genus of fungi that can potentially cause necrotizing infections in humans, although most species are intolerant of temperatures found in mammalian bodies. Figure \(9\): These images show asexually produced spores. (a) This brightfield micrograph shows the release of spores from a sporangium at the end of a hypha called a sporangiophore. The organism is a Mucor sp. fungus, a mold often found indoors. (b) Sporangia grow at the ends of stalks, which appear as the white fuzz seen on this bread mold, Rhizopus stolonifer. The tips of bread mold are the dark, spore-containing sporangia. (credit a: modification of work by Centers for Disease Control and Prevention; credit b right: modification of work by “Andrew”/Flickr) Life Cycle Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are haploid when the organism is in the vegetative stage. Asexual reproduction occurs through mitosporangia that produce sporangiospores by mitosis. These can germinate and develop into a new haploid mycelium that is genetically identical to the parent. The black tips of bread mold are the swollen sporangia packed with black spores (Figure \(8\)). Sexual reproduction starts when conditions become unfavorable. Two different mating strains (type + and type –) must be in close proximity for gametangia from the hyphae to be produced and fuse (plasmogamy), forming a multinucleate zygosporangium. Many sets of haploid nuclei fuse (karyogamy) to form diploid nuclei. The developing diploid zygospores have thick coats that protect them from desiccation and other hazards. They may remain dormant until environmental conditions are favorable. When the zygospore germinates, it undergoes meiosis and produces haploid spores from a sporangium. To differentiate between the sporangia produced in sexual and asexual reproduction, you must trace them back to the base. Did it emerge from a zygospore or from a hypha? Both types of spores are haploid and can germinate to form a new haploid mycelium. Spores that germinate from the sporangium of the zygospore will be genetically distinct from the parent mycelia. Glomeromycota represent the arbuscular endomycorrhizal fungi. These fungi form a mutualistic relationship with plant roots, forming hyphal structures within the plant cell walls (Figure \(12\)), branching to maximize contact with the plasma membrane. Outside of the direct interaction between these fungi and plants, the fungi themselves are not well understood. Molds are fungi that are asexually reproducing or sometimes growing vegetatively. If a mold is coenocytic, it is likely from the zygospore-forming lineages. If the mold is septate, it could be a member of the Ascomycota or Basidiomycota. Spores produced by molds are called conidia (sing. conidium) and the structures they are produced on are called conidiophores (Figure \(13\)). Molds are important decomposers and pathogens. Commercially, molds are important for a variety of uses, such as food production (e.g. cheese making, soy sauce, or the production of citric acid), food spoilage, and the production of antiobiotics. Summary Microfungi is a term used to refer to groups of fungi that form microscopic reproductive structures. The chytrids are early diverging lineages of fungi that have swimming spores with a single flagellum. These lineages are primarily aquatic, but some have evolved to live terrestrially. They have important roles as decomposers, mutualists, and parasites, including one causing worldwide declines in amphibians. The zygospore-forming fungi, formerly classified as zygomycetes, have a haplontic life cycle and some can reproduce asexually by mitosis. When they sexually reproduce, they form a multinucleate zygosporangium that is often thick-walled and highly ornamented. These fungi are commonly found on sugary substrates like fruits or nutrient-dense substrates like dung. Some lineages are pathogens of arthropods. The Glomeromycota are a strange group of fungi that form endomycorrhizal relationships with plants. These fungi penetrate the cells within plant roots and form highly branched structures called arbuscules to increase surface area for nutrient exchange. The plants transfer sugars to the fungus, while the fungus supplies nutrients like phosphorus and nitrogen, as well as water, from the soil substrate. Molds are fungi reproducing asexually and can be from the lineages of microfungi (coenocytic hyphae) or higher fungi (septate hyphae). Attribution Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.04%3A_Microfungi.txt

Learning Objectives • Use life history traits and morphological features to distinguish between Ascomycota and Basidiomycota. • Identify structures in the Ascomycota life cycle and know their ploidy. • Differentiate between different types of ascocarps; locate fertile surfaces within those structures. The majority of described fungal species belong to the Phylum Ascomycota. Fungi in this group have simple septate hyphae and most produce fruiting bodies called ascocarps (Figure \(1\)) for sexual reproduction. Some genera of Ascomycota either only reproduce asexually via conidia or the sexual phases have not been discovered or described. These were referred to as the Fungi Imperfecti or Deuteromycota. When ascomycetes reproduce sexually, they produce haploid ascospores (usually 8) within a sac-like structure called an ascus (Figure \(2\)). The Ascomycota include some ectomycorrhizal fungi (e.g. truffles and morels), fungi that are used as food, others that are common causes of food spoilage (bread molds and plant pathogens), and still others that are human pathogens. Some notable examples of ascomycetes include: • Saccharomyces cerevisiae one of the budding yeasts. It ferments sugar to ethanol and carbon dioxide and thus is used to make alcoholic beverages like beer and wine, to make ethanol for industrial use and in baking (it is often called baker's yeast). Here, it is the carbon dioxide that is wanted (to make bread and cakes "rise" and have a spongy texture). Yeast is also used in the commercial production of some vitamins and in the production - using recombinant DNA technology - of some human therapeutic proteins. • Neurospora crassa, another favorite "model" organism in the laboratory. • The fungal partner in most lichens is an ascomycete. • Powdery mildews that attack ornamental plants. • The chestnut blight, which in a few decades killed almost all of the mature American chestnut trees in the Appalachians of North America. • The Dutch elm disease, which has killed many of the American elms in the United States. • Pneumocystis jirovecii, which is a major cause of illness in immunosuppressed people, e.g., patients with AIDS. • The truffle and the morel, both highly-prized food delicacies. Truffles establish a symbiotic relationship with the roots of such trees as oaks. Ascomycete Life Cycle Asexual reproduction is frequent and involves the production of conidiophores that release haploid conidia. Sexual reproduction starts with the development of special hyphae from either one of two types of mating strains. One strain produces an antheridium and a strain of a complementary mating type develops an ascogonium. At fertilization, the antheridium and the ascogonium combine in plasmogamy without nuclear fusion. Dikaryotic ascogenous hyphae arise, in which pairs of nuclei migrate: one from each parent strain. In each ascus mother cell, two nuclei fuse (karyogamy). During sexual reproduction, thousands of asci may fill a fruiting body called the ascocarp. The diploid nucleus gives rise to four haploid nuclei by meiosis. In most ascomycetes, this is followed by a round of mitosis, producing 8 ascospores. The ascospores are then released, germinate, and form haploid hyphae that are disseminated in the environment and start new mycelia (Figure \(4\)). Types of Ascocarps Apothecium Apothecia are cup-shaped with the asci fully exposed, lining the interior of the cup. Normally, these asci are microscopic. However, in the fungus Ascobolus, the large asci with dark ascospores can be seen with the naked eye or a handlens (Figure \(5\)). The typical cup shape can be inverted and take on strange morphologies (see Figure \(6\)). Perithecium A perithecium is a flask-shaped fruiting structure (Figure \(7\)), often microscopic and embedded within either the substrate it is fruiting in or a fungal structure called a stroma (Figure \(8\)). The asci are almost entirely closed off from the external environment, excepting a small hole in the top of the perithecium called an ostiole. Many plant parasites, such as the causal agents of Dutch elm disease, American chestnut blight, and ergot, are perithecial ascomycetes. Cleistothecium A cleistothecium is a fully-enclosed fruiting structure. These typically have bag-like asci (Figure \(9\)). Some (chasmothecia) split open to release their spores. This type of fruiting body can be found in the powdery mildews, a group of plant pathogenic fungi in the order Erysiphales (Figure \(10\)). Lichenized Fungi Learning Objectives • Explain the lichen symbiosis. • Identify structures in the lichen thallus. Lichens are fungi that live in a symbiotic association with a green alga or cyanobacterium (the "photobiont"), or both. The primary fungal partner (the "mycobiont") in most lichens (98% of them) is an ascomycete. Basidiomycetes make up the remainder. The relationship is often characterized as mutualistic; that is, both partners benefit. However, evidence (see "The British Soldier" below) suggests that while the fungus is dependent on its autotrophic partner, the photobiont is often perfectly content to live alone. Recently many lichens have been found to harbor a second fungal partner, a basidiomycete yeast. Its function remains to be discovered, though the presence of the basidiomycete can change the outward appearance of the lichen (e.g. color). The British Solder The below image is of the colorful lichen called British soldier. The fungus is Cladonia cristatella, an ascomycete. Its name is the name given to the lichen. The photobiont is Trebouxia erici, a green alga. It is found in many other lichens as well, and also can be found growing independently. The algal cells eventually are killed by the fungus, but are continuously replaced by new ones. So, the relationship in this lichen is one of controlled parasitism rather than mutualism. The red cap produces the spores of the fungus, but these alone cannot form new lichens. Other structures (e.g., soredia), containing both partners, are needed to disperse the lichen to new locations. Some lichens release only fungal spores. These mycobionts depend for their continued survival on finding an acceptable photobiont released from other lichens. Phylogenetic trees, based on both ribosomal RNA genes and many protein-coding genes, as well as fossils indicate that lichens have been present on the earth for at least 600 million years. Today about 14,000 species of fungi are known to form lichens. Lichens display a range of colors and textures and can survive in the most unusual and hostile habitats, though they are extremely sensitive to air pollution.. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot penetrate. Lichens can survive extended periods of drought, become completely desiccated, and then rapidly become active once water is available again. In part because of this ability, as well as the pigments in some lichens that protect from UV radiation, lichens are some of the only living things to survive exposure to conditions in space. Explore the world of lichens using this site from Oregon State University. The body of a lichen, referred to as a thallus (Figure \(13\)), is formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides carbon and energy in the form of carbohydrates. If cyanobacteria are involved, they fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate. The thallus of lichens grows very slowly, expanding its diameter a few millimeters per year. Both the fungus and the alga participate in the formation of dispersal units for reproduction. Some lichens produce soredia (Figure \(14\)), clusters of algal cells surrounded by mycelia, for asexual reproduction. Soredia are dispersed by wind and water and form new lichens. To reproduce sexually, the fungus makes spores that must find a new photosynthetic partner shortly after germinating. Learning Objectives • Use life history traits and morphological features to distinguish between Ascomycota and Basidiomycota • Identify the parts of a mushroom • Identify structures in the Basidiomycota life cycle and know their ploidy The Basidiomycota (basidiomycetes) are fungi that produce haploid basidiospores (spores produced through budding) from club-shaped cells called basidia (Figure \(13\)). These are typically formed within fruiting bodies called basidiocarps. They are important as decomposers (particularly of wood), plant pathogens, mutualists, and food sources for many animals. Basidiomycetes include the group of fungi that forms mushrooms, the rusts, and the smuts. Mushrooms are basidiocarps formed from masses of interwoven hyphae growing up from the mycelium. The basidia develop on fertile surfaces of the mushroom and release their spores (typically four from each basidium) into the air. They hyphae of basidiomycetes are septate with clamp connections where the septa form (Figure \(14\)). The septal structure is more complex than in ascomycetes. The septum is swollen around the pore (a dolipore septum) and is flanked by structures called parenthesomes (Figure \(15\)). Fungi with the following structures can be placed in the Basidiomycota*: *It is important to note that these features may look different or not be present at all in some groups of Basidiomycota, such as the rusts (Pucciniomycotina) and smuts (Ustilagomycotina) -- see Chapter 3.6.4: Rusts & Smuts in the Photographic Atlas. However, there are many physiological and genetic similarities that support grouping these organisms together in the Basidiomycota. Basidia and Basidiospores Both karyogamy and meiosis occur within a cell called the basidium (Figure \(15\)). Haploid basidiospores from atop projections on the basidum called sterigmata (sing. sterigma). There are generally four spores, as shown in the image below, though the number of spores produced can vary by species. For example, the mushroom you are likely most familiar with, Agaricus bisporus (though you probably know it as a crimini or button mushroom at its immature stage and portobello at maturity), only produces two spores on each basidium (bi- meaning two). Clamp Connections Basidiomycetes maintain their dikaryotic (n+n) state in each hyphal compartment by making structures called clamp connections (Figure \(16\)). These are not always present, but provide a helpful identification feature when they are! Complex Septations Complex septations are shown in Figure \(17\). General Mushroom Anatomy Though only a subset of basidiocarps look this way, they are the model for how we describe "mushrooms". In mycology, this type of basidiocarp is called "agaricoid" or "agaric" because it is the general form we see in the genus Agaricus. A more complex version of the agaric mushroom is seen in the genus Amanita (Figure \(18\)). The life cycle of basidiomycetes involves an extension of the dikaryotic phase (Figure \(19\)). Mycelia of different mating strains combine (plasmogamy) soon after germination and produce a secondary, dikaryotic mycelium that contains haploid nuclei of two different mating strains (a dikaryon). This is the dikaryotic stage of the basidiomycete life cycle, and it is the dominant stage. Eventually, the secondary mycelium generates a basidiocarp. The basidiocarp can vary greatly in morphology, but in the sense of a standard mushroom (Figure \(15\)), the developing basidia are produced on the surface of gills located under cap.Within the club-shaped basidium, meiosis occurs and a diploid zygote is formed (karyogamy). The zygote divides by meiosis to produce four haploid nuclei. The haploid nuclei migrate into basidiospores, which germinate and generate monokaryotic hyphae. The mycelium that results is called a primary mycelium. Summary Macrofungi are represented by two major groups that can form macroscopic fruiting structures. However, many lineages within these groups might only reproduce asexually, form yeasts, or form microscopic fruiting structures (such as the rusts and smuts). Ascomycetes typically form 8 ascospores within a structure called an ascus. In most lineages, these are produced within an ascocarp, which can be an apothecium (cup), perithecium (flask), or cleistothecium (ball). Ascomycetes have hyphae with simple septations. Their life cycle involves an extended dikaryotic phase that takes place within the ascocarp, forming dikaryotic ascogenous hyphae. These hyphae will eventually form asci, where karyogamy will take place, followed shortly after by meiosis, and usually mitosis. Basidiomycetes typically form 4 basidiospores externally on a basidium. In the Agaricomycotina, these are produced on or in a basidiocarp, what we call mushrooms, specialized for spore dispersal. The basidiomycete life cycle is almost entirely dikaryotic. Haploid spores germinate, form a monokaryon, then must fuse with another monokaryon shortly afterward. These forms a dikaryotic mycelium with dolipore septations and clamp connections. Karyogamy only takes place within the basidia, follow promptly by meisosis to produce basidiospores. Both ascomycetes and basidiomycetes for relationships with photosynthetic partners, such as algae or cyanobacteria, to form lichens. In this mutualism, the photobiont provides sugars from photosynthesis, while the mycobiont forms a protective thallus. In the case of cyanobacteria, these may also provide nitrogen fixation. Attributions Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.05%3A_Macrofungi.txt

Learning Objectives • Describe the importance of fungi to the balance of the environment. • Summarize the role of fungi in food and beverage preparation. • Describe the importance of fungi in the chemical and pharmaceutical industries. • Discuss the role of fungi as model organisms. Although we often think of fungi as organisms that cause disease and rot food, fungi are important to human life on many levels. As we have seen, they influence the well-being of human populations on a large scale because they are part of the nutrient cycles in ecosystems. They have other ecosystem roles as well. As animal pathogens, fungi help to control the population of damaging pests. These fungi are very specific to the insects they attack, and do not infect animals or plants. Fungi are currently under investigation as potential microbial insecticides, with several already on the market. For example, the fungus Beauveria bassiana is a pesticide being tested as a possible biological control agent for the recent spread of emerald ash borer. It has been released in Michigan, Illinois, Indiana, Ohio, West Virginia and Maryland (Figure \(1\)). The mycorrhizal relationship between fungi and plant roots is essential for the productivity of farm land and healthy forests. Without the fungal partner in root systems, most plants would either not survive or have a diminished fitness. The transfer of nutrients and mediation of community structure in forests is increasingly attributed to the regulation of mycorrhizal fungi. Transmission of defense signals and other more nuanced communication between plants via their mycorrhizal partners is currently under investigation. We also eat some types of fungi, whether we are aware of it or not. Mushrooms figure prominently in the human diet of some countries: morels, matsutake, porcini, chanterelles, and truffles are considered delicacies (Figure \(2\)). Molds of the genus Penicillium ripen many cheeses and cure meats. They originate in the natural environment such as the caves of Roquefort, France, where wheels of sheep milk cheese are stacked in order to capture the molds responsible for the blue veins and pungent taste of the cheese. Fermentation of Aspergillus is used to produce soy sauce, miso, and citric acid. Fermentation—of grains to produce beer, and of fruits to produce wine—is an ancient art that humans in most cultures have practiced for millennia. Wild yeasts are acquired from the environment and used to ferment sugars into CO2 and ethyl alcohol under anaerobic conditions. It is now possible to purchase isolated strains of wild yeasts from different wine-making regions. Louis Pasteur was instrumental in developing a reliable strain of brewer’s yeast, Saccharomyces cerevisiae, for the French brewing industry in the late 1850s. This was one of the first examples of biotechnology patenting. Many secondary metabolites of fungi are of great commercial importance. Antibiotics are naturally produced by fungi to kill or inhibit the growth of bacteria, limiting their competition in the natural environment. Important antibiotics, such as penicillin and the cephalosporins, are isolated from fungi. Valuable drugs isolated from fungi include the immunosuppressant drug cyclosporine (which reduces the risk of rejection after organ transplant), the precursors of steroid hormones, and ergot alkaloids used to stop bleeding. Psilocybin is a compound found in fungi such as Psilocybe cyanescens, which have been used for their hallucinogenic properties by various cultures for thousands of years. Psilocybin-producing fungi (though currently illegal to use in most states within America) are currently being investigated as treatment for conditions like depression, anxiety, and even migraines. Fungi are important model research organisms for eukaryotic systems. Many advances in modern genetics were achieved by the use of the mold Neurospora crassa. Additionally, many important genes originally discovered in S. cerevisiae served as a starting point in discovering analogous human genes. As a eukaryotic organism, the yeast cell produces and modifies proteins in a manner similar to human cells, as opposed to the bacterium Escherichia coli, which lacks the internal membrane structures and enzymes to tag proteins for export. This makes yeast a much better organism for use in recombinant DNA technology experiments. Like bacteria, yeasts grow easily in culture, have a short generation time, and are amenable to genetic modification. In addition to the cultural uses you might be more familiar with, fungi are being explored for their use in constructing biodegradable packaging, insulation, and even leather-like material for clothing. Pigments can be extracted from some fungi and lichens, which can then be used to make watercolors or dyes for fabrics (Figure \(3\)). Due to their amazing metabolic diversity, fungi are being used to remediate ecosystems contaminated with organic compounds and heavy metals. Check out Video \(1\) from Science Friday for some of the current innovations using mycelium. Video \(1\): This video explores how innovators are using mycelium fed on waste products to make fungal leather. Summary Fungi are important to everyday human life. Fungi are important decomposers in most ecosystems. Mycorrhizal fungi are essential for the growth of most plants. Fungi, as food, play a role in human nutrition in the form of mushrooms, and also as agents of fermentation in the production of bread, cheeses, alcoholic beverages, and numerous other food preparations. Secondary metabolites of fungi are used as medicines, such as antibiotics and anticoagulants. Fungi are model organisms for the study of eukaryotic genetics and metabolism. Attributions Curated and authored by Maria Morrow using 24.5 Importance of Fungi in Human Life from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org 2.3.07: Chapter Summary Fungi are heterotrophic eukaryotes with cell walls made of chitin and plasma membranes containing ergosterol. They can be unicellular (yeasts) or filamentous, forming a hyphal thallus called a mycelium. The hyphae can be coenocyctic or septate (with cross walls). Many fungi reproduce asexually (molds), producing spores called conidia by mitosis. Sexual reproduction in fungi varies greatly in different evolutionary lineages: several lineages of fungi produce multinucleate zygospores, ascomycetes produce ascospores within asci, and basidiomycetes produce basidiospores externally on basidia. Overall, the general life cycle can be classified as haplontic, though there is a dikaryotic stage that is extended in ascomycetes and extended even further in basidiomycetes. Fungi live within their food substrate, exuding enzymes to digest externally, then absorbing it. They have diverse metabolic strategies and are capable of degrading a wide-range of compounds, making them incredibly important to decomposition and recycling of nutrients. The metabolic diversity of fungi has also lead to their use in the production of foods and medicines. Fungi are not just saprotrophs and have important roles as parasites and mutualists, namely lichens and mycorrhizae. After completing this chapter, you should be able to... • List the characteristics of fungi. • Describe the composition of the mycelium. • Describe the mode of nutrition of fungi. • Explain sexual and asexual reproduction in fungi. • Describe some of the roles of fungi in ecosystems. • Describe mutualistic relationships of fungi with plant roots and photosynthetic organisms. • Describe the beneficial relationship between some fungi and insects. • Use characteristics to distinguish between groups of microfungi. • Describe some of the roles microfungi have in ecosystems. • Explain the relationship between plants and members of Glomeromycota. • Identify structures in the "zygomycete" life cycle and know their ploidy. • Use life history traits and morphological features to distinguish between Ascomycota and Basidiomycota. • Identify structures in the Ascomycota life cycle and know their ploidy. • Differentiate between different types of ascocarps; locate fertile surfaces within those structures. • Explain the lichen symbiosis. • Identify structures in the lichen thallus. • Use life history traits and morphological features to distinguish between Ascomycota and Basidiomycota • Identify the parts of a mushroom • Identify structures in the Basidiomycota life cycle and know their ploidy • Describe the importance of fungi to the balance of the environment. • Summarize the role of fungi in food and beverage preparation. • Describe the importance of fungi in the chemical and pharmaceutical industries. • Discuss the role of fungi as model organisms. Attribution Curated and authored by Maria Morrow using the following sources 24 Fungi and 24.0 Prelude to Fungi from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.03%3A_Fungi/2.3.06%3A_Importance_of_Fungi_in_Human_Life.txt

Protists are an artificial group of eukaryotes that are neither animals, fungi, nor plants. They represent the vast diversity of eukaryotic organisms, and thus span the breadth of possibilities with regard to life history traits. They can be heterotrophs or autotrophs, unicellular to massively multicellular (though rarely with any specialized tissue organization), and can be found across ecosystems worldwide. Photosynthesis within protists is the result of multiple separate endosymbiotic events. • 2.4.1: Introduction to Protists Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation. • 2.4.2: Heterotrophic "Protists" Heterotrophic organisms must consume organic matter to obtain energy. Under the umbrella of protists, there are several heterotrophic groups. This chapter will introduce slime molds and oomycetes, as these are groups commonly discussed in botany courses. However, it is important to note that there is a vast diversity of heterotrophic protist lineages not covered here with important and fascinating ecological roles. • 2.4.3: Photosynthetic "Protists" Photosynthetic protists have derived their chloroplasts from multiple endosymbiotic events. Dinoflagellates, brown algae, and diatoms derived their chloroplasts from the secondary endosymbiosis of a red alga. Red algae, green algae, and plants derived their chloroplasts from the primary endosymbiosis of a cyanobacterium. • 2.4.4: Chapter Summary A brief summary of the chapter concepts. Attribution Maria Morrow (CC BY-NC) Thumbnail image by Melissa Ha, CC BY-NC 2.04: Protists Learning Objectives • Explain how organisms were originally classified under Protista. • Describe the diversity of metabolic strategies and other life history traits within this artificial group. • Identify evolutionary relationships between "protists" using a phylogenetic tree. What are Protists? The term "protist" is a general description for eukaryotic organisms that are not animal, plant, or fungus. These organisms were formerly classified in Kingdom Protista. As we have come to learn about genetics and the evolutionary history of organisms, we have discovered that these organisms come from many distinct evolutionary groups, some of which are closer to fungi and animals than to plants or each other. There are over 100,000 described living species of "protists", and it is unclear how many undescribed species may exist. Since many of these organisms live as commensals or parasites within other organisms, and these relationships are often species-specific, there is a huge potential for diversity that matches the diversity of hosts. As the catchall term for eukaryotic organisms that are not animal, plant, or fungus, it is not surprising that very few characteristics are common to all protists. • They are eukaryotes because they all have a nucleus. • Most have mitochondria although some have later lost theirs. Mitochondria were derived from aerobic alpha-proteobacteria that once lived within their cells. • Many have chloroplasts with which they perform photosynthesis. These chloroplasts were derived from photosynthetic cyanobacteria originally, though have been acquired via secondary endosymbiotic events in several lineages. • Many are unicellular and all groups (with one exception) contain some unicellular members. • The name Protista means "the very first", and some of the 80-odd groups of organisms that we once classified as protists may well have had long, independent evolutionary histories stretching as far back as 2 billion years. Genome analysis added to other criteria show that other lineages are derived from more complex ancestors; that is, some are not "primitive" at all. • Genome analysis also shows that many of the groups placed in the Protista are not at all closely related to one another; that is, the protists do not represent a single clade. • So we consider them here as a group more for our convenience than as a reflection of close kinship, and a better title for this page would be "Eukaryotes that are neither Animals, Fungi, nor Plants". Evolutionary Relationships In the phylogenetic tree above (Figure \(1\)), protists do not share a common ancestry. Slime molds share a more recent evolutionary history with fungi and animals, while red and green algae are more closely related to land plants than they are to the brown algae (located in the Stramenopiles group). The evolutionary history of protists is not a single story of descent, but rather encompasses the evolutionary history of eukaryotes, in its entirety. Because groups of protists do not share a common ancestor with each other that is not also shared with plants, fungi, and animals, "protists" represent a polyphyletic group. Only the characteristic of being eukaryotic unites, but is not exclusive to, this group. In the following sections, you will see some of the diversity of life history traits represented by protists. Cell Structure The cells of protists are among the most elaborate of all cells. Most protists are microscopic and unicellular, but some true multicellular forms exist (such as in the brown algae, Phaeophyta). A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime, or in other cases, like ferns. In fact, many protist cells are multinucleated; in some species, the nuclei are different sizes and have distinct roles in protist cell function. Single protist cells range in size from less than a micrometer to three meters in length to hectares. Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls. Others are encased in glassy silica-based shells or wound with pellicles of interlocking protein strips. The pellicle functions like a flexible coat of armor, preventing the protist from being torn or pierced without compromising its range of motion. Metabolism Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Protists that store energy by photosynthesis belong to a group of photoautotrophs and are characterized by the presence of chloroplasts. Other protists are heterotrophic and consume organic materials (such as other organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called phagocytosis, in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole (Figure \(2\)). The vesicle containing the ingested particle, the phagosome, then fuses with a lysosome containing hydrolytic enzymes to produce a phagolysosome, and the food particle is broken down into small molecules that can diffuse into the cytoplasm and be used in cellular metabolism. Undigested remains ultimately are expelled from the cell via exocytosis. Subtypes of heterotrophs, called saprotrophs, absorb nutrients from dead organisms or their organic wastes. Some protists can function as mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or organic nutrients are available. Motility The majority of protists are motile, but different types of protists have evolved varied modes of movement (Figure \(3\)). Some protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that they coordinately beat to swim. Still others form cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the pseudopodia to a substrate, and pull themselves forward. Some protists can move toward or away from a stimulus, a movement referred to as taxis. Movement toward light, termed phototaxis, is accomplished by coupling their locomotion strategy with a light-sensing organ. Life Cycles Protists reproduce by a variety of mechanisms. Most undergo some form of asexual reproduction, such as binary fission, to produce two daughter cells. In protists, binary fission can be divided into transverse or longitudinal, depending on the axis of orientation; sometimes Paramecium exhibits this method. Some protists such as the true slime molds exhibit multiple fission and simultaneously divide into many daughter cells. Others produce tiny buds that go on to divide and grow to the size of the parental protist. Sexual reproduction, involving meiosis and fertilization, is common among protists, and many protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction is often associated with periods when nutrients are depleted or environmental changes occur. Sexual reproduction may allow the protist to recombine genes and produce new variations of progeny that may be better suited to surviving in the new environment. However, sexual reproduction is often associated with resistant cysts that are a protective, resting stage. Depending on their habitat, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism. Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations that is also used by plants. Life cycles can be generally classified as haplontic, diplontic, and haplodiplontic. In a haplontic life cycle, the multicellular stage is haploid and produces gametes from structures called gametangia. In plants and algae, these haploid organisms are sometimes referred to as gametophytes (meaning gamete plants). This life cycle is also called zygotic meiosis, because the zygote does not grow, but instead divides by meiosis to form haploid spores (see Figure \(4\)). In a diplontic life cycle, the multicellular phase is diploid. The zygote grows by mitosis to form a diploid, multicellular organism. That organism might form sporangia for asexual reproduction. Spores would be diploid and could grow to form a new multicellular diploid organism. Sexual reproduction occurs in gametangia, where cells divide by meiosis to produce gametes. This life cycle is sometimes called gametic meiosis (see Figure \(5\)). The haplodiplontic life cycle, also called alternation of generations, is the most complex. In this life cycle, there are multicelllular haploid and diploid phases. The zygote grows by mitosis to form a diploid sporophyte. The sporophyte, as its name implies, produces haploid spores by meiosis of cells within a sporangium. The spores grow into haploid gametophytes. The gametophytes produce gametes by mitotic division of cells within gametangia. These gametes then fuse to form the diploid zygote. As you saw in Figures \(\PageIndex{d-f}\), there are other distinctions that can be made in life cycles. Isogamous life cycles have gametes that look approximately the same. Oogamous life cycles are heterogamous (meaning the gametes look different, also called anisogamous) in a specific way: the egg is larger and nonmotile, while the sperm are smaller and motile. With all of the complexities in life cycles, it can be helpful to remember this simple rule: spores grow, gametes fuse. Gametes never grow my mitosis, but must fuse together to form a zygote. Spores tend to grow or germinate in some way. Habitats Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay. Summary Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation. Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.01%3A_Introduction_to_Protists.txt

Heterotrophic organisms must consume organic matter to obtain energy. Under the umbrella of protists, there are several heterotrophic groups. Some of these are closely related to photosynthetic lineages of protists that have obtained chloroplasts via endosymbiotic events, such as Oomycota and Phaeophyta. However, due to the relationship between nutritional strategies and ecological roles, it often makes more sense to discuss these lineages in groups of heterotrophs and autotrophs, rather than evolutionary relatedness. This chapter will introduce slime molds and oomycetes, as these are groups commonly discussed in botany courses. However, it is important to note that there is a vast diversity of heterotrophic protist lineages not covered here with important and fascinating ecological roles. Attribution Content by Maria Morrow, CC BY-NC 2.4.02: Heterotrophic Protists Learning Objectives • Differentiate between the three major groups of slime molds. • Differentiate between slime molds, fungi, and plants. • Identify structures and phases in the myxomycete life cycle and know their ploidy. Slime molds are an unusual group of organisms that have previously been classified as animals, fungi, and plants. Like plants, slime molds have cellulose in the cell walls of their spores. Unlike plants, slime molds are heterotrophs! Though they were formally classified as fungi, slime molds do not have chitin in their cell walls and have a diplontic life cycle (Figure \(12\)). These organisms move about as amoebae engulfing bacteria (unlike fungi, who digest food externally). When conditions become unfavorable, whether due to lack of food or lack of moisture, they form spores. They can be found in damp substrates with ample bacteria and are most frequently found on decaying logs and forest duff. There are several different lineages of organisms commonly referred to as slime molds. Cellular slime molds (dictyostelids, Figure \(1\)(a)) are groups of unicellular amoebae that collaborate to form fruiting structures to disperse spores. Protostelids make small fruiting bodies that have cellular stalks. Plasmodial slime molds (classified as Myxogastria or Myxomycetes, Figure \(1\)(b)) form a large, multinucleate amoeba with no cell wall that will eventually wall off individual nuclei to form spores. Dictyostelids The cellular slime molds exist as individual amoeboid cells that periodically aggregate. The individual amoebe can be seen aggregating in Figure \(1\)(a). The aggregate then forms a fruiting body (Figure \(2\)) that produces haploid spores. One cellular slime mold, Dictyostelium discoideum, has been an important study organism for understanding cell differentiation, because it has both single-celled and multicelled life stages, with the cells showing some degree of differentiation in the multicelled form. Watch Video \(1\) to see how these individuals aggregate into a single fruiting body. Video \(1\): Watch the strange behavior of the cellular slime mold Dictostelium discoideum as individual amoebae respond to an aggregation signal (cAMP), form a mobile slug, and eventually produce a stalked fruiting structure and spores. Sourced from YouTube. The organisms in this group have a complex life cycle (Figure \(3\)) during the course of which they go through unicellular, multicellular, spore producing, and amoeboid stages. Thousands of individual amoebae aggregate into a slimy mass - each cell retaining its identity (unlike plasmodial slime molds). The aggregating cells are attracted to each other by the cyclic AMP (cAMP) that they release when conditions become stressful, such as a depletion in food. Individual amoebae respond to the chemical signal by moving to areas of higher cAMP concentration (chemotaxis), eventually aggregating into a single slug. The slug can respond to moisture and light gradients, navigating to a good spot for spore production. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. The spores are disseminated and can germinate if they land in a moist environment. Protostelids Protostelids are a group that has received less attention than either the Dictyostelids or plasmodial slime molds, as each of the latter groups contains a model organism used to study a specific system. Protostelids make simple fruiting bodies, similar to the Dictyostelids, with a stalk and spores at the apex. The slime mold Ceratiomyxa looks more like a plasmodial slime mold, but closer inspection reveals that spores are formed on minute, stalked fruiting bodies covering the external surface of the tentacle-like structures (Figure \(5\)). Ceratiomyxa may not actually be a protostelid, but the small, stalked fruiting bodies formed on the external surface are similar to what would be found in a true protostelid. Plasmodial Slime Molds (Myxogastria) Plasmodial slime molds represent a vast diversity of morphologies. While still a plasmodium (see Figure \(6\)), they can be difficult to distinguish. However, once they have formed into a fruiting structure, they can form distinct, varied, and amazing shapes (see Figures \(\PageIndex{7-10}\))! The Plasmodium In their feeding stage, myxomycetes form one large amoeba called a plasmodium with many nuclei and no cell wall. This plasmodium moves over damp, decaying material looking for bacteria (and sometimes fungi) to engulf and digest. When it dries out or runs out of food, it begins to make fruiting structures called sporangia (sporangium, singular). Inside these sporangia, the diploid nuclei will undergo meiosis and haploid nuclei will be walled off to make spores for aerial dispersal. Dispersal by spores, heterotrophism, and glycogen as a storage carbohydrate originally classified this group within Kingdom Fungi, but this is the end of the similarities. The spores have cell walls made of cellulose, like plants. When these spores land, they will germinate into haploid cells with two flagella (called swarm cells) or amoebae that will fuse together to form a diploid plasmodium. See Figure \(11\) for a diagram of this life cycle. Sporocarp Diversity The diversity of sporulating structures, or sporocarps, has led many to fall in love with this group of organisms. In Hemitrichia serpula, the plasmodium forms into a network of veins that then become fruiting structures (a plasmodiocarp, see Figure \(7\)). In some slime molds, like Fuligo and Lycogala, the entire plasmodium forms a cushion that dries and produces spores (an aethalium, see Figure \(8\)). In other slime molds, individual sporangia are so closely clustered together, they appear to be a single fruiting structure (a pseudoaethalium, see Figure \(9\)). The last type of sporocarp is more familiar, forming many distinct stalked sporangia (see Figure \(10\)). Life Cycle The life cycle of plasmodial slime molds is best classified as diplontic: the "multicellular" (actually just multinucleate) phase is diploid. Haploid cells that germinate from spores (amoebae or biflagellate swarm cells) do not grow until after they have fused with another haploid cell. In some myxomycetes, amoebae or swarm cells produced from the same parent plasmodium can fuse together to form a new plasmodium. This is called homothallism (homo- meaning same, thallus). In other myxomycetes, these gametes must be from different individuals (heterothallism, hetero- meaning other). The discovery of different mating types in myxomycetes, as well as the genes that determine mating type, was made by O'Neil Ray Collins (Figure \(11\)). Summary Slime molds represent several different lineages: the cellular slime molds (Dictyostelids), Protostelids, and plasmodial slime molds (Myxomycetes). These organisms move about as amoebae consuming bacteria until conditions become unfavorable, at which point they form spores. They can be found in damp substrates with ample bacteria and are most frequently found on decaying logs and forest duff. Dictyostelids are model organisms for studying altruism. They are unicellular, but collaborate to form multicellular structures where only some of the individuals involved go on to make spores. Protostelids are less well-understood and form a single sporangium at the tip of a cellular stalk. Plasmodial slime molds (the myxomycetes) form a large, multinucleate amoeba during their feeding stage called a plasmodium. They have diplontic life cycles and there is a lot of morphological diversity of sporocarps represented in this group. Some organisms in this group are studied for their ability to solve mazes and spatial puzzles. Though these organisms seem primitive, they have complex interactions with each other and their environments. Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources: Tags recommended by the template: article:topic

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.02%3A_Heterotrophic_Protists/2.4.2.01%3A_Slime_Molds.txt

Learning Objectives • Compare and contrast oomycetes with plants and fungi. • Explain some of the roles oomycetes have in both terrestrial and aquatic ecosystems. • Identify structures in the Saprolegnia life cycle and know their ploidy. The water molds, phylum Oomycota (“egg fungus”), were so-named based on their filamentous morphology and their use of glycogen as a storage carbohydrate. However, molecular data have shown that the water molds are not closely related to fungi. As diploid spores, many oomycetes have two flagella (one ornamented and one smooth) for locomotion, placing them in the Heterokonts (hetero- different, kont- flagella). The oomycetes are heterotrophic eukaryotes characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. This group of organisms has a diplontic life cycle. Most oomycetes are aquatic and are important decomposers in these ecosystems, but some have evolved to parasitize terrestrial plants (though these still rely on water). One particularly famous plant pathogen is Phytophthora infestans, the causal agent of late blight of potatoes, which caused the nineteenth century Irish potato famine. Some notable water molds: • Some species (e.g., Saprolegnia and Achlya) are parasites of certain fish and can be a serious problem in fish hatcheries. • Downy mildews (Peronosporaceae) damage grapes and other crops. • Phytophthora infestans, the cause of the "late blight" of potatoes. In 1845 and again in 1846, it was responsible for the almost total destruction of the potato crop in Ireland. This led to the great Irish famine of 1845–1860. During this period, approximately 1 million people starved to death and many more emigrated to the New World. By the end of the period, death and emigration had reduced the population of Ireland from 9 million to 4 million. • Phytophthora ramorum, which is currently killing tanoaks and several species of true oaks in California. This pathogen is capable of infecting hundreds of species of plants and was likely introduced to California from ornamental Rhododendron. Saprolegnia Saprolegnia is a genus of primarily saprotrophic water molds. This genus is often studied for the life cycle features of oomycetes. This organism reproduces asexually by producing zoospores (zoospores are spores that swim, zoo- meaning ‘to live’ refers to its motility) inside of an elongated sac called a zoosporangium (-angium meaning vessel, so a zoosporangium is what zoospores are produced inside of). These zoospores grow by mitosis into a diploid thallus, an undifferentiated body. Saprolegnia's sexual reproducing structures include the globose oogonium and smaller, pad-like antheridia (singular, antheridium) that attach to the oogonium. Because these structures produce gametes--much like spores are produced in sporangia--the oogonia and antheridia are also referred to as gametangia (gametangium singular). The oogonium produces haploid eggs via meiosis. These eggs are fertilized by the haploid male nuclei produced by meiosis within the antheridium, creating a diploid, thick-walled zygote called an oospore. The oospore will be released and grow by mitosis to create a new multicellular thallus, completing the diplontic life cycle (Figure \(5\)). Phytophthora Phytophthora is a genus of water molds that parasitize plants. They have specialized zoosporangia that detach, allowing zoospores to be transported terrestrially and await germination until moisture is present. Some notable Phytophthoras are P. ramorum (causal agent of sudden oak death, see Figure \(6\)) and P. infestans (causal agent of late blight of potato and the Irish potato famine, see Figure \(8\)). Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks and stems to decay into black slime (Figure \(8\)). Widespread potato blight caused by P. infestans precipitated the well-known Irish potato famine in the nineteenth century that claimed the lives of approximately 1 million people and led to the emigration of at least 1 million more from Ireland. Late blight continues to plague potato crops in certain parts of the United States and Russia, wiping out as much as 70 percent of crops when no pesticides are applied. At some point in evolutionary history, a heterotrophic heterokont engulfed a red alga. This secondary endosymbiotic event resulted in several lineages of photosynthetic heterokonts, including the brown algae and diatoms. It is possible that the Oomycota also descended from this event, as there are apparent algal and cyanobacterial genes present in the nucleus of oomycetes. However, it is possible that these genes were acquired through horizontal gene transfer or evolved from homologs. As our understanding of genomes improves, so too will our interpretation of these events. Regardless, oomycetes currently live a chloroplast-free lifestyle and lack the vestigial plastids present in many lineages that have acquired and subsequently lost photosynthesis. Summary Oomycota, also called the water molds, is a group of fungus-like organisms with a history of living in aquatic ecosystems. These organisms have swimming spores and at least one stage in their life cycle has heterokont flagella: one whiplash flagellum and one decorated (hairy) flagellum. They have important roles as decomposers and parasites. Some have evolved to live terrestrially and are infamous parasites of plants, namely those in the genus Phytophthora. Among these is Phytophthora infestans the causal agent of late blight of potato and the Irish potato famine that resulted from an infestation during paricularly harsh, synergistic conditions in Ireland. This group is closely related to the diatoms and brown algae. These photosynthetic lineages of heterokonts acquired their 4-membraned chloroplasts through secondary endosymbiosis of a red alga. Members of this group share the following characteristics: • Heterotrophic by absorption • Morphology: Filamentous • Cell wall composition: Cellulose • Storage carbohydrate: Glycogen • Life cycle: Diplontic Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.02%3A_Heterotrophic_Protists/2.4.2.02%3A_Oomycota.txt

Photosynthetic lineages can be found across the phylogenetic tree of protists. Most of the groups are unrelated to each other, as each major lineage acquired its chloroplast (and therefore the ability to photosynthesize) from different endosymbiotic events. For example, red and green algae belong to the same lineage (Archaeplastida). A red algal ancestor engulfed a cyanobacterial ancestor, leading to the first chloroplasts. These were inherited vertically--through reproduction and over evolutionary time--by the lineages of green algae. However, brown algae and diatoms inherited their chloroplasts from a secondary endosymbiotic event where their heterotrophic ancestor (something like an oomycete) engulfed a red alga. This is a horizontal transmission of chloroplasts between lineages, where genes (and here an organelle!) move between organisms through the environment, not through reproduction. Endosymbiosis The horizontal transmission of chloroplasts between lineages via endosymbiosis resulted in several unrelated groups of photosynthetic protists. The lineages covered in this section are: • Dinoflagellates (secondary endosymbiosis) • Brown algae and diatoms (secondary endosymbiosis) • Red and green algae (primary endosymbiosis) Attribution Content by Maria Morrow, CC-BY-NC 2.4.03: Photosynthetic Protists Learning Objectives • Explore some of the ecological roles of dinoflagellates. • Describe the symbiosis between corals and zooxanthellae. • Explain what happens in a red tide. There are currently around 2,000 species of dinoflagellates. They are unicellular, though dinoflagellates exhibit extensive morphological diversity and can be photosynthetic, heterotrophic, or mixotrophic. In photosynthetic dinoflagellates, most use the pigments chlorophylls a and c. Many dinoflagellates are encased in interlocking plates of cellulose. Two perpendicular flagella fit into the grooves between the cellulose plates, with one flagellum extending longitudinally and a second encircling the dinoflagellate (Figure \(1\)). Together, the flagella contribute to the characteristic spinning motion of dinoflagellates. Interestingly, dinoflagellates have a unique nucleus structure, where chromosomes are attached to the nuclear membrane. This is not found in other eukaryotes and so has received its own name: a dinokaryon. These protists exist in freshwater and marine habitats, and are a component of plankton, the typically microscopic organisms that drift through the water and serve as a crucial food source for larger aquatic organisms. Some dinoflagellates generate light, called bioluminescence, when they are jarred or stressed. Large numbers of marine dinoflagellates (billions or trillions of cells per wave) can emit light and cause an entire breaking wave to twinkle or take on a brilliant blue color (Figure \(2\)). For approximately 20 species of marine dinoflagellates, population explosions (also called blooms) during the summer months can tint the ocean with a muddy red color. This phenomenon is called a red tide due to the abundant red pigments present in dinoflagellate plastids. In some cases, such as the 2018/19 event on the Gulf Coast, these dinoflagellate species can secrete an asphyxiating toxin that can kill fish, birds, and marine mammals. Red tides can be massively detrimental to commercial fisheries, and humans who consume these protists may become poisoned. As plankton, dinoflagellates are essential sources of nutrition for many other organisms. In some cases, they are consumed directly. Others serve as producers of nutrition in a more indirect way. For instance, photosynthetic dinoflagellates called zooxanthellae use sunlight to fix inorganic carbon. In this symbiotic relationship, these protists provide nutrients for coral polyps (Figure \(3\)) that house them, giving corals a boost of energy to secrete a calcium carbonate skeleton. In turn, the corals provide the protist with a protected environment and the compounds needed for photosynthesis. This type of symbiotic relationship is important in nutrient-poor environments. Without dinoflagellate symbionts, corals lose algal pigments in a process called coral bleaching, and they eventually die. This explains why reef-building corals do not reside in waters deeper than 20 meters: insufficient light reaches those depths for dinoflagellates to photosynthesize. Summary Dinoflagellates are a group of morphologically and nutritionally diverse acquatic organisms, from the zooxanthellae that live inside coral polyps to the toxin-releasing microbes that cause red-tides. They have essential roles in marine food webs. They are typically unicellular, with cellulose plates and two flagella. Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.03%3A_Photosynthetic_Protists/2.4.3.01%3A_Dinoflagellates.txt

Learning Objectives • Use life history, morphology, and cellular components to identify brown algae. • Identify the components of a kelp thallus. • Identify structures and events in the Fucus life cycle and know their ploidy. • Identify structures and events in the Laminaria life cycle and know their ploidy. • Use life history, morphology, and cellular components to identify diatoms. • Classify diatoms based on symmetry and ecology. • Describe sexual and asexual reproduction in diatoms. Brown algae (class Phaeophyceae) and diatoms (class Bacillariophyceae) belong to the phylum Ochrophyta. They are the result of a secondary endosymbiosis between a heterokont and a photosynthetic eukaryote. Heterokonts, such as the Oomycota, are united by the presence of a textured, or “hairy,” flagellum and an additional flagellum that lacks hair-like projections (Figure \(1\)). Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp. Brown algae, diatoms, and oomycetes belong to a single clade, the stramenopiles (aka heterokonts). The photosynthetic stramenopiles share the following characteristics: • 4-membraned chloroplasts • a yellow-brown pigment (which gives them their color). It is a carotenoid called fucoxanthin. • chlorophylls a and c • most have a diplontic life cycle (as you'll find below, Laminaria has a haplodiplontic life cycle) Phaeophyceae This group is commonly called the brown algae and includes rockweeds and kelps. Kelps are some of the fastest growing organisms on the planet! Brown algae are primarily marine and are often found in the intertidal zone. Members of this phylum are used for food in some coastal areas of the world and harvested in the U. S. for fertilizer and as a source of iodine. Brown algae are brown due to the large amounts of carotenoids they produce, primarily one called fucoxanthin. These organisms are exclusively multicellular and have filamentous, multinucleate cells (much like oomycetes). They can get so large that they require special conductive cells to transport photosynthates from their blades down to the rest of their tissues. These conductive cells are called trumpet hyphae and have sieve plates and resemble sieve tubes found in flowering plants. Brown algae have cellulose cell walls and store carbohydrates in the form of laminarin. The polymer alginate can also be found in the cell walls of brown algae and is used commercially for a variety of purposes, including the high fidelity molds used in dentistry. Kelp Much like Saprolegnia, the body of an alga is termed a thallus because it is not differentiated into specialized tissues. The general morphology of a brown alga includes a holdfast, stipe, gas bladder(s), and blade(s) (Figures \(\PageIndex{2-4}\)). Fucus A model organism for the Phaeophyta life cycle is Fucus (rockweed), which, like its relative Saprolegnia, has a diplontic life cycle. The Fucus thallus has dichotomous branching (forking into two equal branches) and swollen, heart-shaped reproductive tips of the branches. These swollen branch tips are called receptacles (Figure \(5\)). The receptacles are covered in small bumps, each with a pore at the center of the bump called an ostiole. The bumps are conceptacles, chambers that house the gametangia (Figure \(6\)). Phaeophyta produce oognia, globose gametangia that undergo meiosis to produce eggs, and antheridia, branched gametangia that undergo meiosis to produce sperm (Figure \(7\)). Fucus Life Cycle Fucus has a diplontic life cycle (Figure \(8\)) where haploid gametes are produced from a diploid thallus. These haploid gametes do not grow, but fuse together to form a zygote. See Figure \(9\) for an example of alternation of generations in the Phaeophyta. Laminaria Life Cycle A variety of algal life cycles is represented by the stramenopiles, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis (sperm and egg) combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria, haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form (Figure \(9\)). Certain other organisms, such as the red alga Polysiphonia, perform alternation of generations in which both the haploid and diploid forms look the same. • Morphology: Multicellular thallus • Cell wall composition: Cellulose and calcium alginate • Chloroplasts: 4 membranes, pigments are chlorophyll a, chlorophyll c, and fucoxanthin • Storage carbohydrate: Laminarin • Life cycle: Primarily diplontic (alternation of generations in some species) • Ecology: Marine Bacillariophyceae Diatoms are another photosynthetic lineage of photosynthetic heterokonts that was derived from the secondary endosymbiotic event. Diatoms are an incredibly diverse group of unicellular organisms containing anywhere from 20,000 to 2 million species. These organisms are unicellular and surrounded by a frustule, a silica shell made from two distinct valves that enclose the plasma membrane. Frustules are amazingly intricate, covered with small pores in an arrangement specially adapted for capturing sunlight (Figure \(11\)). Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction. Like the brown algae, they have golden chloroplasts with 4-membranes (Figure \(10\)). Diatoms store carbohydrates in the form of chrysolaminarin. The silica frustules of diatoms found in sediments (diatomaceous earth) are used for myriad commercial purposes, including toothpaste additives (as an abrasive), filters, and insulation. Morphology We are still trying to figure out how to determine what a diatom "species" is and, so far, they have been classified based on the morphology of the frustule. Using this classification, historically there were two major groups of diatoms: centric (have radial symmetry, see Figure \(12\)) and pennate (have bilateral symmetry, see Figure \(13\)). These classifications have improved and increased in complexity, so here we will cover just the broad strokes. For a more in-depth look at current diatom morphological classification and fantastic images, check out this website. Ecology In addition to morphology, diatoms can also be classified by where they occur. Free-floating diatoms are planktonic. Diatoms attached to other organisms (like giant kelp) are epiphytic (Figure \(15\)). Epiphytic diatoms can be found in aquatic ecosystems on algae and aquatic angiosperms like eelgrass, as well as terrestrial ecosystems, living in the damp crevices of tree bark. Benthic diatoms tend to dwell toward the bottom of a body of water. In general, these three categorizations refer to aquatic ecosystems. However, diatoms can be found just about anywhere there is water in terrestrial ecosystems. The community composition of diatoms varies depending on location. Because of this, diatoms have been used in forensic investigations to determine where someone drowned (depending on the diatom species present) and how long ago they drown (based on how far the diatoms had migrated into their tissues). Diatoms are major producers in aquatic environments; that is, they are responsible for as much as 40% of the photosynthesis that occurs in fresh water and in the oceans. They serve as the main base of the food chains in these habitats, supplying calories to heterotrophic protists and small animals. These, in turn, feed larger animals. During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprotrophs that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels. Reproduction Diatoms primarily reproduce asexually by binary fission, similar to prokaryotes. During binary fission, the two valves of the frustule are separated and each new cell forms a new valve inside the old one. However, the new valve is always smaller. If diatoms only reproduce in this way, it results in a continual decrease in average size. When some minimal size is reached, this can trigger sexual reproduction. When diatoms sexually reproduce, they have a diplontic life cycle and produce a very large auxospore (Figure \(16\)). Diversity Video \(1\): This video shows some of the incredible diversity of diatom shapes and the amazing art Klaus Kemp makes with them. Sourced from YouTube. Summary of Characteristics for Diatoms • Morphology: Unicellular • Cell wall composition: Silica frustule • Chloroplasts: 4 membranes, pigments are chlorophyll a, chlorophyll c, and fucoxanthin • Storage carbohydrate: Chrysolaminarin • Life cycle: Diplontic • Ecology: Everywhere! Marine, freshwater, and terrestrial. Summary Though brown algae and diatoms seem to have very little in common morphologically, they are descended from a common ancestor. Both of these groups have a diplontic life cycle during some stage of which a cell will have heterokont flagella. They have 4-membraned chloroplasts that contain the pigments chlorophyll a, chlorophyll c, and fucoxanthin. This latter pigment gives the chloroplasts in these groups a golden color. This is about where the similarities end. Brown algae are exclusively multicellular and found in marine habitats, most typically in the intertidal zone. Their cell walls contain cellulose and they store their carbohydrates as laminarin. Diatoms are exclusively unicellular and found in almost every habitat where there is water. Their single cell is surrounded by a silica frustule composed of two distinct valves. They store their carbohydrates as chrysolaminarin. Attribution Curated and authored by Maria Morrow, CC-BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.03%3A_Photosynthetic_Protists/2.4.3.02%3A_Brown_Algae_and_Diatoms.txt

Learning Objectives • Distinguish between different groups of algae using life cycle, morphological features, and cellular composition. • Connect adaptations in the red and green algae to habitat characteristics and ecology. • Identify structures and phases in the Polysiphonia and Spirogyra life cycles; know the ploidy of these structures. Rhodophyta Red algae descended from the same endosymbiotic event as the Glaucophyta. The red algae are almost exclusively marine. Some are unicellular but most are multicellular. Approximately 6,000 species have been identified. They have true chloroplasts with two membranes (no remnant peptidoglycan) containing chlorophyll a. Like the cyanobacteria, they use phycobilins as antenna pigments - phycoerythrin (which makes them red) and phycocyanin. Red pigment allows the red algae to photosynthesize at deeper depths than the green or brown algae, harnessing more of the blue light waves that penetrate deeper into the water column. Unlike green algae and plants, red algae store carbohydrates as Floridean starch in the cytosol. Some are used as food in coastal regions of Asia. Agar, the base for culturing bacteria and other microorganisms, is extracted from a red alga. Selection Pressures and Drivers An important aspect of understanding the life history traits of the Rhodophyta is understanding the challenges of living in a marine environment. 1. Access to sunlight: Most colors of light cannot penetrate into deeper water, as they are scattered by water molecules. The wavelengths of light that reach deepest into the ocean are blue and green. Many fish that live in the deep ocean are red. Because red light does not penetrate to the depths where they live, this makes them virtually undetectable by sight. Remember, we see things because of the light that bounces off of them. Red pigments reflect red light, so no red light, no reflected light. Red algae are using a similar strategy--absorb the wavelengths of light that are not red--with a different goal: to use that absorbed light to make food. The phycoerythrin in their chloroplasts reflects red light, giving them a red appearance, and absorbs the blue light that is able to penetrate to deeper areas in the water column. 2. Fertilization: The ocean is an expansive environment, often with large areas of open space between populations of organisms. In this environment, successful fertilization of an egg by a nonmotile sperm--red algae lack flagella--presents a challenge. Having multicellular haploid and diploid phases provides red algae more opportunities to produce gametes and spores. A diploid stage that clones the zygote, the carposporophyte, provides more opportunities to do meiosis from each fertilization event. 3. Salinity: Marine environments are relatively high in salinity. A possible adaptation for this is to have sulfated polysaccharides in the cell wall, such as the galactans present in Rhodophyta. This is a strategy present in (potentially all) marine algae and is inferred to be an adaptation for salinity-tolerance. See this open-access article for further information. Morphology Red algae have a diverse range of morphologies. Unicellular forms may live solitarily or as colonies but, unlike other members of the Archaeplastida, lack flagella. Flagella are absent from the Rhodophyta, lost at some point in their evolutionary history. Multicellular forms can be filamentous, leafy, sheet-like, coralloid, or even crust-like (some examples in Figure \(4\) and Figure \(5\)). The strange coralline red algae have calcerous deposits in the cell walls that make the thallus hard, like a coral. These can take a variety of forms and are able to live at depths other algae cannot (over 500 feet deep for some!). Polysiphonia Life Cycle Red algae have a haplodiplontic (alternation of generations) life cycle that has an extra diploid stage: the carposporophyte. Polysiphonia is the model organism for the Rhodophyta life cycle. The gametophytes of Polysiphonia are isomorphic (iso- meaning same, morph- meaning form), meaning they have the same basic morphology. Any difference you see in coloration of the images in this section is due to staining. They would all appear a deep red color in an unstained slide. Male Gametophyte The male gametophyte has elongated structures that emerge from the tips of the thallus branches. These are spermatangia, where spermatia are produced by mitosis. Female Gametophyte and Carposporophyte The female gametophyte produces an egg that is contained within a structure called the carpogonium. This structure has a long, thin projection called a trichogyne (trich- meaning hair, -gyne meaning female). During fertilization, a spermatium fuses with the trichogyne and the nucleus of the spermatium travels down the tube to the egg. When the nucleus of the spermatium fuses with the egg, a zygote is produced. This zygote is retained and nourished by the female gametophyte as it grows. The globose structures you see growing from the female gametophyte thallus are called cystocarps. A cystocarp is composed of both female gametophyte tissue (n) and carposporophyte tissue (2n). The outer layer of the cystocarp, the pericarp (peri- meaning around) is derived from the female gametophyte and is haploid. The interior of the cystocarp consists of the carposporophyte, which is diploid, and produces structures called carposporangia, inside of which it produces carpospores by mitosis. All of these--carposporophyte, carposporangia, and carpospores--are diploid. Tetrasporophyte The diploid carpospores are released into the ocean waters, where they will be carried on currents to another location. If a carpospore lands in an appropriate environment, it will grow by mitosis into a tetrasporophyte (2n). The tetrasporophyte produces tetrasporangia (2n) within the branches of the thallus. Each tetrasporangium produces four unique, haploid tetraspores by meiosis. Tetraspores (n) are released and will grow by mitosis into either male or female gametophytes, completing the life cycle. Summary of Characteristics for Red Algae • Morphology: Unicellular to multicellular, no flagellated stages. Cells of multicellular species are connected via incomplete cytokinesis, resulting in pit connections. • Cell wall composition: Cellulose and galactans • Chloroplasts: 2 membranes, pigments are chlorophyll a and phycobilins (primarily phycoerythrin, providing their red color) • Storage carbohydrate: Floridean starch • Life cycle: Alternation of generations with an extra diploid stage, the carposporophyte • Ecology: Primarily marine (97% of species) Green Algae The most abundant group of algae is the green algae. The nature of the evolutionary relationships between the green algae are still up for debate. As of 2019, genetic data supports splitting the green algae into two major lineages: chlorophytes and streptophytes. The streptophytes include several lineages of green algae (such as the charophytes) and all land plants. Streptophytes and chlorophytes represent a monophyletic group called Viridiplantae (literally “green plants”). The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure. They have chlorophyll a and b, have lost phycobilins but gained carotenoids, and store carbohydrates as starch inside plastids. Although some of the multicellular forms are large, they never develop more than a few types of differentiated cells and their fertilized eggs do not develop into an embryo. Green algae are an important source of food for many aquatic animals. When lakes and ponds are "fertilized" with phosphates and nitrates (e.g., from sewage and the runoff from fertilized fields and lawns), green algae often form extensive algal "blooms". Members of this group can be found in freshwater and marine habitats, and many have adapted to life on land, either inside of lichens or free-living (see Figure \(12\)). Selection Pressures and Drivers 1. Sun Damage. Green algae represent a diverse group of organisms with diverse life history traits, many of which are shared with land plants. The development of carotenoids-- yellow, orange, and red pigments that act in both light harvesting and sun protection--offers this group increased access to sunlight while simultaneously protecting against UV damage. UV rays do not penetrate very far into the water column, so organisms moving into shallower waters or terrestrial environments would need to deal with this new challenge. Many terrestrial species of green algae appear orange, rather than green, due to the production of large amounts of carotenoids. Morphology These algae exhibit great diversity of form and function. Similar to red algae, green algae can be unicellular or multicellular. Many unicellular species form colonies and some green algae exist as large, multinucleate, single cells. Green algae primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide it toward light sensed by its eyespot (Figure \(13\)). More complex species exhibit haploid gametes and spores that resemble Chlamydomonas. The alga Volvox is one of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure \(14\)). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism. Volvox can reproduce both asexually and sexually. In asexual reproduction, the gonidia develop into new organisms that break out of the parent (which then dies). In sexual reproduction, the presence of an inducing chemical causes the following: • The gonidia of the males to develop into clusters of sperm. • The gonidia of the females to develop into new spheres each of whose own gonidia develops into a pair of eggs. • The sperm break out of the male parent and swim to the female where they fertilize her eggs. • The zygotes form a resting stage that enables Volvox to survive harsh conditions (Figure \(15\)). Video \(1\): This video shows how sexual reproduction occurs in the colonial green alga Volvox. Sourced from YouTube. The genome of Volvox carteri consists of 14,560 protein-encoding genes - only 4 more genes than in the single-celled Chlamydomonas reinhardtii! Most of its genes are also found in Chlamydomonas. The few that are not encode the proteins needed to form the massive extracellular matrix of Volvox. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure \(16\)). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells. True multicellular organisms, such as the sea lettuce, Ulva, are also represented among the green algae (Figure \(17\) and Figure \(18\)). Spirogyra Life Cycle Though green algae display a diversity of life cycles, many have a haplontic life cycle. A model organism for the green algae is Spirogyra (Figure \(19\)). Spirogyra is a unicellular green algae that grows in long, filamentous colonies, making it appear to be a multicellular organism. Even though it is technically unicellular, its colonial nature allows us to classify its life cycle as haplontic. In the haploid vegetative cells of the colony, the chloroplasts are arranged in spirals, containing darkened regions called pyrenoids where carbon fixation happens. Each haploid cell in the filament is an individual, which makes sexual reproduction between colonies an interesting process. When two colonies of Spirogyra meet that are of a complementary mating type (+/-), sexual reproduction occurs. The two colonies align, each cell across from a complementary cell on the other filament. A conjugation tube extends from each cell in one colony (Figure \(20\)), inducing formation of a tube on the cells in the other colony. The conjugation tubes from each colony fuse together. The contents of one cell will move through the conjugation tube and fuse with the contents of the complementary cell, resulting in a diploid zygote (Figure \(21\)). The zygote appears as a large, egg-like structure contained within the complementary cell. It has a thick wall that provides resistance to desiccation and cold, allowing colonies of Spirogyra to overwinter, when needed. The other colony is now a filament of empty cells that will be broken down by some decomposer. When conditions are right, the zygote undergoes meiosis to produce another vegetative colony of haploid cells. Summary Glaucophytes, red algae, and green algae are part of the Archaeplastida. These organisms are descended from the same primary endosymbiosis event. Glaucophytes are thought to be one of the earliest lineages to diverge due to the presence of remnant peptidoglycan between the membranes of its chloroplast-like cyanelles. Unsurprisingly, glaucophytes and red algae share the same pigments as Cyanobacteria. Red algae (phylum Rhodophyta) are united by several synapomorphies (shared derived characteristics). They lack flagella, have pit connections between cells, and store carbohydrates as Floridean starch. The sulfated galactans in their cell walls allows them increased fitness in marine environments, while the pigment phycoerythrin allows them to photosynthesize deeper in the water column. They have an alternation of generations life cycle with an extra diploid phase, the carposporophyte, that clones the zygote. These characteristics can be connected to the environmental stressors presented by the marine habitats most red algae are found in. Green algae represent several distinct lineages. Like plants, they store carbohydrates as starch within their plastids and have the pigments chlorophyll a and b, as well as carotenoids. Organisms in this group have haplontic (e.g. Spirogyra) or haplodiplontic (e.g. Ulva) life cycles. Many green algae are unicellular, forming complex colonies. Green algae can be found in marine, freshwater, and terrestrial environments (including within lichens!). Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources: 2.4.04: Chapter Summary Protists are an artificial grouping representing all eukaryotic organisms that aren't plants, animals, or fungi. Because of this, the life history traits of protists span the breadth of what is possible. In this book, protists have been divided into heterotrophs and photoautotrophs. The heterotrophic protists use glycogen as a storage carbohydrate, have cellulose in their cell walls (when present), and many have a diplontic life cycle. Despite these latter two traits, they were all formerly classified as fungi. Photoautotrophic protists are the result of endosymbiotic events (Figure \(1\)). One lineage, including the diatoms and brown algae, derived from a secondary endosymbiotic event within the heterokonts. A second lineage, including the glaucophytes, red algae, and green algae, was derived from a primary endosymbiotic event. This latter lineage includes the ancestors of all land plants. After completing this chapter, you should be able to... • Explain how organisms were originally classified under Protista. • Describe the diversity of metabolic strategies and other life history traits within this artificial group. • Identify evolutionary relationships between "protists" using a phylogenetic tree. • Differentiate between the three major groups of slime molds. • Differentiate between slime molds, fungi, and plants. • Identify structures and phases in the myxomycete life cycle and know their ploidy. • Compare and contrast oomycetes with plants and fungi. • Explain some of the roles oomycetes have in both terrestrial and aquatic ecosystems. • Identify structures in the Saprolegnia life cycle and know their ploidy. • Explore some of the ecological roles of dinoflagellates. • Describe the symbiosis between corals and zooxanthellae. • Explain what happens in a red tide. • Use life history, morphology, and cellular components to identify brown algae. • Identify the components of a kelp thallus. • Identify structures and events in the Fucus life cycle and know their ploidy. • Identify structures and events in the Laminaria life cycle and know their ploidy. • Use life history, morphology, and cellular components to identify diatoms. • Classify diatoms based on symmetry and ecology. • Describe sexual and asexual reproduction in diatoms. • Distinguish between different groups of algae using life cycle, morphological features, and cellular composition. • Connect adaptations in the red and green algae to habitat characteristics and ecology. • Identify structures and phases in the Polysiphonia and Spirogyra life cycles; know the ploidy of these structures.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.04%3A_Protists/2.4.03%3A_Photosynthetic_Protists/2.4.3.03%3A_Red_and_Green_Algae.txt

There are four major evolutionary groups of land plants: Bryophytes, Seedless Vascular Plants (SVPs), Gymnosperms, and Angiosperms. These groupings represent major changes in plant structure and life history characteristics over the course of time that coincide with major changes in the evolution of the Earth, as a whole. Early Earth would have looked quite different than the planet you know. When plants first ventured out of the water, there were no soils. The terrestrial landscape would have been rocky, potentially slick with microbial slime. The lack of surrounding water would mean tissues could dry out, as well as increased exposure to oxygen and damaging wavelengths of sunlight. They would also need more structural support, without water to float in, and changes in temperature would be far more extreme and rapid than their former aquatic habitat. However, they would have abundant CO2 and increased access to sunlight for photosynthesis. • 2.5.1: Introduction to Early Land Plants Bryophytes were the first group of plants to evolve on land, followed by the seedless vascular plants. These early plants, accompanied by their fungal mutualists and other microbes, transformed the rocky terrestrial landscape into an ecosystem with stratified soils and complex biotic communities. Synapomorphies of bryophytes derive from the challenges of life on land, while those of seedless vascular plants relate to increases in height and opportunities for meiosis (i.e. competition). • 2.5.2: Bryophytes There are approximately 23,000 species of bryophytes in three distinct lineages: Anthocerotophyta, Marchantiophyta, and Bryophyta. Lacking vascular tissue, these early plants generally have a prostrate form and grow closely appressed to the substrate. They lack true roots but have anchoring cells called rhizoids that extend from the gametophyte. Bryophytes have a gametophyte dominant life cycle and the sporophytes grow from the megagametophyte. • 2.5.3: Seedless Vascular Plants Seedless vascular plants have lignified vascular tissue that allows them to transport water through woody xylem cells up from true roots, through the stems, up to their leaves. Photosynthetic tissues can distribute sugars through living phloem cells throughout the plant. SVPs are sporophyte dominant with reduced, thalloid gametophytes. Sporophytes are branched with many sites for spore production. They can be divided into two lineages: Lycopodiopsida and Polypodiopsida. • 2.5.4: Chapter Summary A brief summary of the chapter concepts. Attribution Maria Morrow (CC-BY-NC) 2.05: Early Land Plants Learning Objectives • List the shared derived characteristics of land plants. • Relate these adaptations to the movement from aquatic to terrestrial habitats. • List the ancestral characteristics that land plants share with green algae. • Describe the basic life cycle shared by plants. Land Plants Land plants are sometimes referred to as “embryophytes” due to the evolution of the embryo, a zygote that is retained and nourished by the female gametophyte as it grows. Embryophytes share many common features, most corresponding to the selective pressures from the initial movement onto land. The embryo is one of these, providing higher likelihood of success for offspring in a new, harsh environment. In addition to the embryo, all plants have the same basic life cycle: alternation of generations (Figure \(1\)). Much like the marine algae, the first plants were living in an environment where they needed to increase their chances of reproductive events. Multicellular stages on both sides of the life cycle increases the number of reproductive propagules. All plants are also multicellular, with tissues and multicellular gametangia. Other adaptations to life on land include the desiccation-resistant compound sporopollenin. This is found in the cell walls of spores of early land plants and in pollen of seed plants, hence the name sporo - pollen - in. It is also found in the cell walls of a few green algae. On the exterior, plants are surrounded by a waxy cuticle that helps protect them from their outer environment. Much like their green algal predecessors, plants store their carbohydrates as starch inside plastids, plastids with two membranes (the result of primary endosymbiosis), cell walls containing cellulose, and have the pigments chlorophyll a, chlorophyll b, and carotenoids. For this reason, along with genetic sequencing, land plants and green algae are grouped together in the Viridiplantae (Figure \(2\)). The First Land Plants Bryophytes and seedless vascular plants were the first groups to evolve on land. While the order of events during this period in plant evolution remains somewhat murky, evidence points to bryophytes evolving first, followed by the SVPs. Bryophytes are the only group of land plants that lacks lignified vascular tissue, though some mosses do contain a form of conducting tissue. They tend to be small of stature and lack true stems, roots, or leaves. Bryophytes are also the only group of land plants to have a gametophyte dominant life cycle. Seedless vascular plants transition to a sporophyte dominant life cycle with a branching sporophyte. They evolve lignified vascular tissue, developing true roots, stems, and leaves. This tough, lignified tissue allows some species within this group to form trees up to 100 feet tall. Attribution Content by Maria Morrow, CC-BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.01%3A_Introduction_to_Early_Land_Plants.txt

Learning Objectives • List the shared derived characteristics of bryophytes. • Connect these characteristics to selection pressures these organisms would have faced. • Name the three phyla included in the bryophytes. Introduction Bryophytes arose in a period of Earth’s history before soils had formed. The terrestrial surface was rocky and consisted primarily of crusts (microbial mats) composed of assemblages of prokaryotes. The exposure to sunlight would have been intense relative to the buffer provided by water. In addition, being surrounded by water would provide regulation of surrounding temperature and structural support. As green algae began to colonize the terrestrial surface, at least one of these lineages accumulated adaptations that were favorable to living on land--a waxy cuticle to prevent water loss, desiccation-resistant dispersal propagules called spores, and retention and feeding of the developing zygote. This lineage of green algae evolved into the ancestor of the bryophytes. These plants do not have true roots to absorb water, nor do they have vascular tissue to transport that water to other regions of the plant. Because of this, bryophytes tend to grow prostrate (close to the surface they are growing on) and stay quite small. They also tend to grow in moist areas where there is access to water and are reliant on water for the dispersal of gametes and fertilization. Characteristics of Bryophytes • Morphology: Generally small, prostrate plants. Complex tissues, including an exterior protective layer. Root-like structures called rhizoids provide anchorage for the gametophyte, which might be thalloid or leafy. Gametophytes possess simple pores (lacking guard cells) for gas exchange • Life cycle: Alternation of generations; gametophyte dominant. Sporophytes grow from and are nourished by the female gametophyte. The gametophyte is nutritionally independent and is generally the larger and longer-lived of the two phases. • Ecology: Terrestrial, gametes are dispersed in water. Selection Pressures and Drivers An important aspect of understanding the life history traits of the bryophytes is understanding the challenges of living in a terrestrial environment. 1. Sun exposure. Sunlight provides the power that drives our biosphere, but some wavelengths of sunlight can be damaging to cellular structure and even DNA. High frequency wavelengths, such as ultraviolet (UV), X-rays, and gamma rays can penetrate outer protective layers like skin, through cell membranes, and causing damage to DNA, proteins, and other biomolecules. Fortunately for organisms on Earth, almost all of these wavelengths are filtered by the atmosphere before they reach us, though some UV rays still make it through. These last UV rays are filtered out for aquatic organisms, but terrestrial organisms need adaptations to protect against UV radiation. Humans have skin with melanin pigments. Terrestrial plants have an epidermis and carotenoid pigments. 2. Desiccation. Transitioning from a completely aquatic environment to a terrestrial one leads to challenges of drying out, also known as desiccation. Temperatures are more extreme outside of the water and evaporation from tissues into the relatively dry air is constant. Terrestrial plants quickly adapted a waxy covering on the epidermis, called a cuticle. This water-tight covering required the evolution of simple pores, and eventually stomata, to allow gas exchange with the outer environment. Because these plants lack vascular tissue, water can only be transported around the organism via osmosis. Thus, these plants must keep all tissues close to water access. 3. Lack of a soil environment. The first organisms to move onto land would have found a relatively barren, rocky landscape. Soils did not yet exist. The rocky substrate experienced physical weathering from rain and wind that would help break it down. Chemical weathering through acidic rain or the interaction of water with compounds in the rock could also assist in breakdown. However, up to this point, contributions from organic matter would be minimal. Bryophytes lack true roots, instead producing structures called rhizoids whose function is anchorage (Figure \(3\)). There are genes present in bryophytes, as well as some fossil evidence, that indicate bryophytes likely had mycorrhizal relationships with fungi that helped them acquire nutrients in this new landscape. Bryophyte Lineages This evolutionary group includes liverworts (phylum Marchantiophyta, Figure \(4\)), mosses (phylum Bryophyta, Figure \(5\)), and hornworts (phylum Anthocerophyta, Figure \(6\)). There are approximately 23,000 known extant species, most of these belonging to the mosses. As of 2019, much is unresolved on the early lineages of plants and who was first on land. Recent genetic analyses interpret bryophytes as being monophyletic, all deriving from a common ancestor that branched from the main line of plants. Read this open-access paper for further information. Content by Maria Morrow, CC-BY-NC 2.5.02: Bryophytes Learning Objectives • Use morphological traits and cellular components to distinguish between hornworts and other bryophytes. • Identify structures and phases in the hornwort life cycle; know their ploidy. • Label a hornwort sporophyte and describe its development. Hornworts, Phylum Anthocerotophyta The name Anthocerotophyta means 'horn flower plant'. These strange plants, called the hornworts, get their name from the horn-like sporophytes they produce. Hornworts have a flattened thalloid gametophyte, out of which grow their long photosynthetic sporophytes (Figure \(1\)), composed of a sporangium with a columella and pseudoelaters. The sporophyte grows from a basal meristem, with the oldest tissues at the apex. When spores have matured, the sporangium dries and dehisces, twisting open to release spores. The long, multicellular pseudoelaters (true elaters are a single cell) within the sporangium assist in dispersing the spores. Hornworts are somewhat rare and quite small, and they prefer shady and wet places. They are often found growing on the muddy sides of waterways, from small ditches to larger creeks. The presence of stomata on sporophytes and the ability of some hornwort sporophytes to branch (and sometimes even live independently from the gametophyte!) lend support for the hypothesis that hornworts are sister to vascular plants (tracheophytes). However, hornworts are discussed first in this chapter due to their strictly thalloid gametophyte morphology. The hornwort life cycle, like all plants, is alternation of generations. The multicellular haploid stage, the gametophyte, is the longer-lived and larger phase of this life cycle. Most hornwort gametophytes are monecious, meaning both types of gametangia (antheridia and archegonia) are produced on the same gametophyte. The life cycle shown in Figure \(6\) features a monoecious gametophyte. If a hornwort is dioecious, the life cycle would have antheridia and archegonia produced on separate gametophytes and the sporophyte would grow from the gametophyte producing archegonia. As will be the case with all plants, archegonia produce one or more eggs and antheridia produce many sperm. These haploid gametes are produced by mitosis. The sperm have two flagella and must swim through water to reach the egg at the base of the archegonium. Fertilization (fusion of the egg and sperm) results in a diploid zygote. This zygote grows within the archegonium, nourished by the gametophyte. All land plants retain and nourish the zygote, called an embryo, and so are sometimes referred to as the embryophytes. Meiosis occurs within the sporangium (also called a capsule), producing haploid spores that are dispersed aerially. Attribution Content by Maria Morrow, CC-BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.02%3A_Bryophytes/2.5.2.01%3A_Anthocerotophyta.txt

Learning Objectives • Use morphological traits and cellular components to distinguish between liverworts and other bryophytes. • Identify structures and phases in the Marchantia life cycle; know their ploidy. The liverworts, formerly the Hepatophyta, got their name from their thalloid gametophytes being compared to the shape of a liver. However, many liverworts produce leafy gametophytes. This group is often presented as a basal lineage of bryophytes due to the lack of stomata present in either stage of the life cycle (among other traits). However, recent genetic evidence does not support this and instead places mosses and liverworts as sister taxa. Liverworts have a global distribution and can be found in many habitats, including a few desert and even arctic species. There are around 5,000 described species of liverworts, though estimates put this at about half of the actual number of species. The type genus for this group, Marchantia, is a common invader of greenhouses and potted plants. Thalloid liverworts have no leaves and their gametophytes look more similar to hornwort gametophytes. Another similarity to hornworts is the presence of simple pores for gas exchange (no guard cells, meaning pores are permanently open). Unlike hornworts, liverwort cells have multiple chloroplasts. Rhizoids in this group are unicellular. Asexual clones, called gemmae (sing. gemma), are sometimes produced in structures called gemmae cups (Figure \(3\)). These are haploid and genetically identical to the parent thallus. The thalloid liverwort Marchantia has complex reproductive structures. Palm tree-like structures called archegoniophores are formed from the haploid gametophyte tissue. Archegonia are produced on the underside of the extending arms. When fertilized, the sporophyte will grow within the archegonium and emerge on the underside of the archegoniophore (see the right side of Figure \(4\)). The antheridia are produced in a separate stalked structure with a flat top called an antheridiophore (see the left side of Figure \(4\)). Water droplets splash onto the flat top, dispersing flagellated spores from the embedded antheridia. Marchantia polymorpha is a thalloid liverwort with a complex life cycle (Figure \(9\)). Asexual reproduction is accomplished through the production of haploid gemmae from the gametophyte thallus. Sexual reproduction occurs from dioecious gametophytes: archegoniophores and antheridiophores are produced on separate gametophytes. Sperm splashed from the antheridial head swim through the water with their dual flagella to reach an egg at the base of an archegonium. These archegonia are situated on the underside of the archegonial head. The diploid zygote grows within the archegonium, surrounded by its remaining tissue (the calyptra). As the sporangium develops, meiosis occurs simultaneously to produce haploid spores. A short seta extends to push the developed sporangium outward, lifting the arms of the archegoniophore. The sporangium dehisces into four valves, exposing the elaters to the external environment where they rapidly twist, flinging the haploid spores into the air. These haploid spores can germinate and grow into male or female gametophytes. Content by Maria Morrow, CC-BY-NC 2.5.2.03: Bryophyta Learning Objectives • Use morphological traits and cellular components to distinguish between mosses and other bryophytes. • Identify structures and phases in the moss life cycle; know their ploidy. • Label a moss sporophyte and describe its development. Mosses, Phylum Bryophyta Most described bryophyte species diversity (around 13,000 species) belongs to the mosses. Unlike other bryophytes, mosses are exclusively leafy. Sporophytes in most species form complex capsules, involving multiple layers of structures. Members of the mosses have defied many of the typical bryophyte descriptors. For example, some mosses have evolved vascular tissue analogs called leptoids (analogous to phloem) and hydroids (analogous to xylem). Other mosses can grow quite tall: Dawsonia superba, the world's tallest moss, can grow up to be nearly 2 feet tall (50-60 cm). Sphagnum is an ancestral genus of mosses that grow in bogs and are commonly referred to as peat moss or peat, in its compressed form. They have large, empty cells (Figure \(2\)) capable of absorbing around 20 times their dry weight in water and can exude compounds to make their environment more acidic. Because of this, and the compounds in their cell walls, the bogs where they grow have slow decomposition, allowing plant matter to accumulate and compress over time. This makes peat, a common source of fuel in higher latitudes. It's use as fuel, flavoring (the smoke), and in horticulture for its water holding capacity have contributed to its commercial importance. Many peat bogs are frozen over for most of the year, halting metabolic activity and slowing the release of methane from anaerobic decomposition. As the climate in northern latitudes warms, so do the peat bogs, increasing the release of methane. Gametophyte Generation Moss gametophytes have spirally arranged leaves that emerge from all sides of the stem (Figure \(3\)). In most mosses, the leaves have a central line of tissue called a costa that looks a bit like a midrib (though it is not, as bryophytes don't have lignified vascular tissue) and are only 1-2 cell layers thick. Rhizoids are produced at the base of the gametophytes. In the common haircap moss, Polytrichum commune, there are three kinds of gametophytes: • Female, which develop archegonia at their tip. A single egg forms in each archegonium. (see Figure \(6\)) • Male, which develop antheridia at their tip. Multiple swimming sperm form in each antheridium. (see Figure \(5\)) • Sterile, which do not form sex organs. Sporophyte Generation When the calyptra falls off, another feature of the sporophyte is visible: the operculum. This is a lid-like structure on the capsule that pops off when the spores are mature. Most mosses have a structure under the operculum that lines the capsule opening, called the peristome. The peristome is a series of cellular flaps (peristome teeth) that line the edge of the capsule opening and aids in spore dispersal via hygroscopic movements. Tetraphis moss (Tetraphis pellucida) produces both asexual propagules (gemmae) and spores, which result from sexual reproduction (Figure \(9\)). In 1991, Robin Wall Kimmerer found that spores were dispersed an average of 20 times farther from the parent plant than gemmae were, but gemmae established more easily. Each reproductive strategy thus served a different purpose: gemmae helped the plant spread locally, and spores were important for colonization of an entirely new location. Mnium Life Cycle Male gametophytes form antheridia at the top of the gametophyte in a structure called the perigonium or antheridial head (Figure \(10\)). These are cup-shaped, and commonly referred to as splash cups. In early spring, raindrops splash sperm from male to female plants. These swim down the canal in the archegonium to the chamber containing the egg. The resulting zygote begins the sporophyte generation. Mitosis of the zygote produces an embryo that grows into the mature sporophyte generation. It consists of: • A foot, which absorbs water, minerals, and food from the parent gametophyte • A stalk (seta), at the tip of which is formed a sporangium (the brownish objects in the photo). The sporangium is • filled with spore mother cells • in most cases, ined by a peristome around the opening • sealed by an operculum • covered with a calyptra. The calyptra develops from the wall of the old archegonium and so is actually a part of the gametophyte generation. It is responsible for the common name ("haircap moss") of this species. During the summer, each spore mother cell undergoes meiosis, producing four haploid spores - the start of the new gametophyte generation. Late in the summer, the calyptra and operculum become detached from the sporangium allowing the spores to be released. These tiny spores are dispersed so effectively by the wind that many mosses are worldwide in their distribution. If a spore reaches a suitable habitat, it germinates to form a filament of cells called a protonema. Soon buds appear and develop into the mature leafy shoots. Thus the gametophyte generation is responsible for sexual reproduction. The sporophyte generation is responsible for dispersal. Attribution Content by Maria Morrow, CC BY-NC, except the following: • Life cycle text from 16.3B Moss Life Cycle from Biology by John. W. Kimball (licensed CC-BY) • Paragraph that goes with Figure \(9\) by Melissa Ha (licensed CC BY-NC)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.02%3A_Bryophytes/2.5.2.02%3A_Marchantiophyta.txt

Learning Objectives • List the shared derived characteristics of seedless vascular plants. • Connect these characteristics to selection pressures these organisms would have faced. • Describe the importance of extinct seedless vascular plants in modern society. Introduction As bryophytes began to colonize the terrestrial surface, they produced organic acids during metabolism that aided in the breakdown of the rocky substrate. When they died, their organic matter mixed with the weathered rock, forming the Earth’s earliest soils. Formerly abundant to the first photosynthesizers to become terrestrial, access to sunlight became competitive as bryophytes expanded. This led to selection for individuals that could lift themselves higher and transport water throughout their tissues. Eventually, this selection resulted in the evolution of vascular tissue -- pipes that could bring water up from the ground so that parts of the plant could be raised upward, and those parts raised upward could transport their photosynthates down to the lower parts of the plant. The cells in the xylem (water-transporting vascular tissue) contained lignin, the tough, decay-resistant compound that wood is made out of. This rigid molecule in the vascular tissue allowed for structural support, allowing plants to grow taller -- some over 100 feet! The vascular system also allowed for the specialization of organs: roots for water absorption, leaves for photosynthesis, and stems for structural support. Seedless vascular plants (SVPs) also began to rely more on the sporophyte stage. The sporophyte became the larger, nutritionally independent stage of the life cycle. Branching sporophytes offered more sites for meiosis to occur, resulting in increased opportunities for variation, which could be interpreted as more options in an increasingly competitive environment. There are approximately 20,000 known extant species, most of which are ferns. SVPs are considered to be a paraphyletic group of organisms, forming two distinct lineages: Ferns and Lycophytes. Attribution Content by Maria Morrow, CC-BY-NC 2.5.03: Seedless Vascular Plants Learning Objectives • Describe the characteristics of lycophytes. • Differentiate between homosporous and heterosporous strobili. Characteristics • Microphylls. Leaves with a single, unbranched vein of vascular tissue. Microphylls may have evolved from enations, scale-like appendages that later gained vascular tissue. Another possibility is that microphylls evolved from sporangia. Note: The term microphyll, confusingly, is not an indication of the size of the leaf. • Rhizomes. Asexual propogation of the sporophyte through underground stems. • Strobili. Cone-like structures where sporangia are produced on leaves called sporophylls (Figure \(1\)). • Homosporous or heterosporous. Haploid spores grow into bisexual gametophytes in Lycopodium. In Selaginella, microspores develop into microgametophytes that produce sperm and megaspores develop into megagametophytes that produce eggs. Lycopodium Members of this genus are homosporous, meaning they produce spores that develop into bisexual gametophytes, producing both antheridia and archegonia on the same thallus. Gametophyte Morphology In seedless vascular plants, the sporophyte is the longer-lived, larger, leafy generation. This trend of sporophyte dominance throughout the evolutionary timeline of plants leads to continually smaller, less complex gametophytes. Gametophytes of this group are seldom seen. They are small and thalloid (Figure \(2\)). In Lycopodium, the gametophyte grows from a homospore and is bisexual, producing both antheridia and archegonia. Sporophyte Morphology Sporophytes branch dichotomously and have true roots, stems, and leaves due to the presence of lignified vascular tissue. This lignified vascular tissue provides rigid structural support, allowing sporophytes to grow tall. The leaves, called microphylls, have a single, unbranched vein of vascular tissue (Figure \(3\)). Asexual propogation of sporophytes can occur via an underground stem that travels horizontally, called a rhizome. To sexually reproduce, these plants produce cone-like structures at the end of their branches, called strobili. A strobilus is composed of leaves called sporophylls that bear sporangia (Figure \(4\)). Meiosis occurs within the sporangia to produce haploid homospores. Unlike the bryophytes, a single sporophyte can produce many sporangia (Figure \(5\)). Selaginella Members of the genus Selaginella are heterosporous, meaning they produce two different types of spores. Larger spores (megaspores) develop within megasporangia and are subtended by megasporophylls. Megaspores develop into gametophytes that produce archegonia. Smaller spores (microspores) develop within microsporangia and are subtended by microsporophylls. Microspores develop into gametophytes that produce antheridia. Megasporangia and microsporangia are found in the same strobilus (Figure \(6\)) Extinct SVPs Extinct lycophytes like Lepidodendron and Sigillaria grew into tall trees, branching dichotomously and producing a moss-like canopy of microphylls over 100 feet (30 m) in the air (Figures \(\PageIndex{7-8}\)). Some of these microphylls were several feet long! Lycophytes first appear in the fossil record over 400 million years ago. By the Carboniferous period (around 300 mya), the landscape was covered with lycophyte forests and shallow swamps. Much of the fossil fuels we use today are derived from these extinct arboreal lycophytes falling into swamps, slowing decomposition and creating layers of carbon-rich material that we now find as coal seams. An ancestor of modern-day Equisetum, Calamites, is thought to look much like the Equisetum species we see today, excepting that it would have been 60 feet (20 m) tall (Figure \(9\)). Most ancient pteridophytes appeared in Silurian period, they were rhyniophytes. Rhyniophyles had well-developed aboveground gametophytes and relatively short, dichotomously branched leafless sporophytes. The next important steps were formation of leaves and further reduction of gametophytes.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.03%3A_Seedless_Vascular_Plants/2.5.3.01%3A_Lycopodiopsida.txt

Learning Objectives • Differentiate between ferns, horsetails, and lycophytes. • Identify features of vegetative and reproductive shoots of Equisetum. • Identify features and phases of the fern life cycle; know their ploidy. • Label a fern gametophyte and sporophyte. The Polypodiopsida includes the horsetails and ferns. These plants produce leaves with branching veins of vascular tissue called megaphylls. Like the lycophytes, asexual reproduction of the sporophyte can be accomplished via rhizomes. Spores produced in this group develop into gametophytes that can produce both antheridia and archegonia. Characteristics • Megaphylls. Leaves have branching veins of vascular tissue. Megaphylls are thought to have evolved from branching stems. Webbing filled in the spaces between the branches, forming the flat blade of the leaf. The arrangement of the leaf veins (vascular bundles) reflects the original branching pattern of the stems. • Rhizomes. Asexual propogation of the sporophyte through underground stems. • Homosporous. Haploid spores grow into bisexual gametophytes that produce both antheridia and archegonia, or are capable of producing one or the other, dependent upon conditions. Equisteum (subclass Equisetidae) Horsetails are a small group with a single extant genus, Equisetum, which has about 30 different herbaceous species that typically live in moist habitats. The common name comes from the characteristic pattern of branching: whorls or rings of branches arising from an above-ground shoot. The leaves of these plants have been reduced to scales, and instead the segmented stems are photosynthetic. If you look closely at the nodes of a green vegetative shoot, you will see that branches and leaves have not only switched roles, they have also switched places, with the photosynthetic branches emerging below the papery, non-photosynthetic leaves. Horsetails often grow in sandy places and incorporate silica in their stem epidermis, which gives it an abrasive surface. Because of this, American pioneers would use this plant to scour pots and pans. This is how it received the nickname “scouring rush.” The stem has multiple canals, an analogous characteristic to stems of grasses. The sporangia are associated with hexangular stalked sporangiophores produced on terminal strobili. Within the sporangia, there are elaters that are not separate cells but parts of the spore walls. Gametophytes are typically minute and dioecious, but the plants themselves are homosporous: smaller suppressed gametophytes develop only antheridia while larger gametophytes develop only archegonia. Gametophyte Morphology Horsetail gametophytes are reduced and thalloid (figure \(1\)). Gametophytes grow from homospores and can produce both antheridia and archegonia. Sporophyte Morphology In some Equisetum species, there are two different types of shoots produced by the sporophyte: vegetative shoots that perform photosynthesis and reproductive shoots that form strobili and undergo meiosis. In other species, the strobilus is formed at the apex of a photosynthetic shoot. Vegetative Shoots On the vegetative shoot, the leaves are dark, papery and non-photosynthetic. Branches are photosynthetic and produced in whorls. Branches and leaves emerge at nodes, separated by regions of the main stem called internodes. Unlike most plants, the branches emerge below the leaves in the node (Figure \(\PageIndex{2-3}\)). The epidermis of the stems contain silica, which has an abrasive texture. Reproductive Shoots Sporangia are produced in a terminal strobilus on the reproductive shoot (figure \(\PageIndex{4-5}\)). In some species, this reproductive shoot lacks chlorophyll and is instead fed through the rhizome of connected vegetative shoots. Spores are photosynthetic and have four hygroscopic arms called elaters. Video \(1\): This video shows how the elaters of Equisetum spores respond to changes in humidity. Retrieved from YouTube. Ferns (subclass Polypodiidae) Some 15,000 species of ferns live on earth today. Many of these are found in the tropics where some — the "tree ferns" — may grow to heights of 40 ft (13 m) or more. The ferns of temperate regions are smaller. They are usually found in damp, shady locations. They produce perennial rhizomes that can overwinter. Their leaves, called fronds due to apical growth, emerge from the rhizome each spring as coiled fiddleheads (Figure \(6\)). These fiddleheads open through a process called circinate vernation, where the growing tissues are protected at the center of the coil and emerge last. True ferns are megaphyllous: their leaves originated from flattened branches and have branching veins of vascular tissue. True ferns have unique sporangia: leptosporangia (Figure \(6\)). Leptosporangia originate from a single cell in a leaf, they have long, thin stalks, and the wall of one cell layer. They also open actively: when sporangium matures (dries), a row of cells with thickened walls on the outside of the sporangium (called an annulus) will shrink slower than surrounding cells and finally would break and release all spores at once. Leptosporangia are grouped in clusters called sori which are often covered with umbrella- or pocket-like indusia. Gametophytes are minute and grow aboveground. While most ferns are homosporous, some genera of true ferns (like the water fern Azolla, water shamrock Marsilea and several others) are heterosporous (Figure \(7\)). True ferns are highly competitive even to angiosperms. In spite of their “primitive” life cycle, they have multiple advantages: abilities to photosynthesize in deep shade (they are not obliged to grow fast), to survive high humidity, and to make billions of reproductive units (spores). Ferns do not need to spend their resources on flowers and fruits, and are also less vulnerable to vertebrate herbivores and insect pests, probably because they do not employ them as pollinators and, therefore, can poison tissues against all animals. Gametophyte Morphology Fern gametophytes are reduced, thalloid, and heart-shaped (Figure \(8\)). They are often referred to as a prothallus or prothallium. Rhizoids are produced from the underside of the thallus, just like in the bryophytes. Similar to the horsetails, whether a gametophyte produces antheridia or archegonia can be regulated by environmental cues (Figure \(9\)). Each antheridium produces many swimming sperm, but archegonia produce only a single egg (Figure \(10\)). Sporophyte Morphology Fern sporophytes are composed of megaphylls, often pinnately compound fronds that emerging as coiled fiddleheads in the spring. Sporangia are produced in clusters called sori (sorus, singular) on the fronds (Figure \(11\)). Circinate vernation is a term used to describe the development of the fern fiddlehead (Figure \(12\)) into a frond. Because plants grow apically, it is important to protect the apical meristems in growing organs (as we have seen in both axillary and terminal buds with the protective bud scales). The fiddlehead is essentially a structure that tucks away the growing tips of the fronds. As the frond develops, it gradually unfurls, releasing the tips last. A sorus (plural, sori) is a cluster of sporangia, often protected by an umbrella-like structure called the indusium as the spores mature (Figure \(13\)). Some sori are protected by an extension of the leaf called a false indusium (Figure \(14\)), while others lack any protective covering. Each sporangium is lined by an inflated strip of cells called an annulus. When the spores have matured, the cells in the annulus begin to dry out, causing the cells to collapse and pull the sporangium open, releasing the spores. Full Life Cycle Diagram Ferns rely on water for dispersal of the sperm, which must swim into an archegonium to fertilize an egg (Figure \(15\)). If moisture is plentiful, the sperm swim to archegonia - usually on another prothallus because the two kinds of sex organs generally do not mature at the same time on a single prothallus. Another method for promoting cross-fertilization: The first spores to germinate develop into prothallia with archegonia. These prothallia secrete a gibberellin into their surroundings. This is absorbed by younger prothallia and causes them to produce antheridia exclusively. Fertilization restores the diploid number and begins a new sporophyte generation. The embryo sporophyte develops a foot that penetrates the tissue of the prothallus and enables the sporophyte to secure nourishment until it becomes self-sufficient. Although it is tiny, the haploid fern prothallus is a fully-independent, autotrophic plant. Soon, the sporophyte is nutritionally independent. It is the larger, longer-lived stage of the life cycle. To reproduce, many sori are formed on the undersides of the fronds. Within each sporangium of the sorus, the spore mother cells undergo meiosis producing four haploid spores each. When the humidity drops, the thin-walled lip cells of each sporangium separate, the annulus slowly straightens out, then the annulus snaps forward expelling the spores. Each of these homospores can then grow into a gametophyte capable of producing antheridia and archegonia.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.03%3A_Seedless_Vascular_Plants/2.5.3.02%3A_Polypodiopsida.txt

The characteristics of early plants can be interpreted best as evolutionary adaptations to life outside of water (a waxy cuticle, stomata, decay- and desiccation-resistant sporopollenin) and a new harsh landscape (multicellular gametangia, matrotrophy, mutualistic symbioses with bacteria and fungi). As these early plants evolved, so too did their environment. Early bryophytes, in association with their fungal partners and perhaps with the help of other lichens, caused chemical weathering of the rocky substrate due to their metabolic activity. Increased moisture retention would result in more physical weathering as water invaded new cracks in the rock, expanding and traveling deeper over cycles of freezing and thawing, respectively. In addition to the mineral substrate being formed, bryophytes would add organic matter as they lived, grew, reproduced, and died. This activity formed Earth's first soils, paving the way for plants to evolve true roots that could excavate into the soil substrate for water and mineral nutrients, increasing both physical and chemical weathering. The non-vascular bryophytes remained relatively restricted to remain close to the substrate and water, but seedless vascular plants were less restricted. Water could be pulled from the soil through lignified xylem tissue and transported through stems and out leaves held over 100 feet in the air, exiting out pores regulated by guard cells. An abundance of photosynthates produced by newly branching sporophytes, able to make large leaves thanks to stomata and vascular tissue, can be transported around the plant through specialized phloem tissue and used to fuel faster growth and more complex structures. Relationships with mutualists continued to develop and forests are formed in tropical swamps, creating the world's first coal deposits. Though they grew tall and adapted to aerial dispersal of spores, early plants continued to be dependent on water for fertilization. After completing this chapter, you should be able to... • List the shared derived characteristics of land plants. • Relate these adaptations to the movement from aquatic to terrestrial habitats. • List the ancestral characteristics that land plants share with green algae. • List the shared derived characteristics of bryophytes. • Connect these characteristics to selection pressures these organisms would have faced. • Name the three phyla included in the bryophytes. • Use morphological traits and cellular components to distinguish between hornworts and other bryophytes. • Identify structures and phases in the hornwort life cycle; know their ploidy. • Label a hornwort sporophyte and describe its development. • Use morphological traits and cellular components to distinguish between liverworts and other bryophytes. • Identify structures and phases in the Marchantia life cycle; know their ploidy. • Use morphological traits and cellular components to distinguish between mosses and other bryophytes. • Identify structures and phases in the moss life cycle; know their ploidy. • Label a moss sporophyte and describe its development. • List the shared derived characteristics of seedless vascular plants. • Connect these characteristics to selection pressures these organisms would have faced. • Describe the importance of extinct seedless vascular plants in modern society. • Describe the characteristics of lycophytes. • Differentiate between homosporous and heterosporous strobili. • Differentiate between ferns, horsetails, and lycophytes. • Identify features of vegetative and reproductive shoots of Equisetum. • Identify features and phases of the fern life cycle; know their ploidy. • Label a fern gametophyte and sporophyte. Attribution Content by Maria Morrow, CC-BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.05%3A_Early_Land_Plants/2.5.04%3A_Chapter_Summary.txt

Fossil from the Devonian period reveal fernlike plants that were heterosporous; that is, produced two kinds of spores: microspores and megaspores. The megaspores were not released from the parent sporophyte. Fertilization took place within the tissue of the parent sporophyte thus freed from dependence on surface water. However, the necessity for the microspores to be carried from one plant to another in order to reach the megagametophyte robbed them of their value as agents of dispersal. This function was taken over by seeds - dormant, protected, embryo sporophytes. • 2.6.1: Introduction to Seed Plants Seeds represent one of the most important innovations in plant evolution: a protected, nutrient-supplied embryo with the ability to await appropriate conditions for germination. Seeds and pollen allowed plants to limit their reliance on water for completion of their life cycle. The first plants to evolve seeds were the gymnosperms, which grew wider and taller with secondary growth. Angiosperms then improved upon seed dispersal and pollination strategies with the evolution of fruits and flowers. • 2.6.2: Gymnosperms In gymnosperms, protective seeds filled with nutritive tissue (including the megagametophtye) replace spores as the dispersal mechanism. Antheridia are lost in the microgametophyte, which is reduced to four cells and is dispersed as a whole (pollen). The evolution of secondary growth allows for the lateral deposition of woody tissues. This latter development, along with xerophytic leaves, allows gymnosperms to tolerate a wide variety of new environmental stressors. • 2.6.3: Angiosperms Angiosperms are plants that produce flowers and fruits. Within the ovule, double fertilization results in the formation of both the zygote and endosperm. New specialized cells are present in the vascular tissue. Meanwhile, the gametophytes are further reduced and archegonia are lost altogether. Nearly 90% of all plants belong to this group. • 2.6.4: Chapter Summary A brief summary of the concepts covered in chapter 7. Attributions Content by Maria Morrow, CC BY-NC Thumbnail image by John Munt, CC BY-NC 2.06: Seed Plants Learning Objectives • Explain how heterospory led to the evolution of seeds. • Connect r- and k-strategies to propagules produced by plants (e.g. spores, gametes, pollen, and seeds). • List a few ways gymnosperms and angiosperms differ in life history traits. Fossil from the Devonian period reveal fernlike plants that were heterosporous; that is, produced two kinds of spores: microspores and megaspores. The megaspores were not released from the parent sporophyte. Fertilization took place within the tissue of the parent sporophyte thus freed from dependence on surface water. However, the necessity for the microspores to be carried from one plant to another in order to reach the megagametophyte robbed them of their value as agents of dispersal. This function was taken over by seeds - dormant, protected, embryo sporophytes. Heterospory: The Next Big Step for Life on Land Vertebrate animals became fully terrestrial only when their fertilization became completely independent from water. Plants started to perform the similar “evolutionary efforts” even earlier, but while reptiles actively approach the sexual partner, plants evolved different solutions. Instead of the active sex, plants use “carpet bombing” with spores; this increased the chance that two spores land nearby and the distance between sperm and egg cell will be minimal. However, increasing the number of spores also results in a waste of resources, so plants minimized spore size; this will also allow for the longer distance of dispersal and fewer resources invested in each spore. On the other hand, some spores must remain large because the embryo (if fertilization occurs) will need the support from the feeding gametophyte. Consequently, plants ended up with division of labor: numerous, minuscule microspores that grow into microgametophytes with antheridia only, and a few large megaspores that make megagametophytes producing only archegonia (Figure \(1\)). Megaspores are larger because they are rich in nutrients, ready to be fertilized and nourish a developing sporophyte. This heterosporic cycle makes fertilization less dependent on water and more dependent on spore distribution and gametophyte features (Figure \(2\)). It also allows for increased variations for selection to act upon. Division of labor allows resources to be used more efficiently and also restricts self-fertilization. In plant evolution, there was a high need for heterospory because it independently arose in several groups of seedless vascular plants (e.g. Selaginella and Azolla) and even among mosses. As the evolutionary trajectory of heterospory progresses, some megaspores do not leave the mother plant and instead germinate there, waiting for the fertilization from a nearby microgametophyte: a step towards the first seeds. Male gametophytes become so small that they can easily be transported as a whole. Entire male gametophytes, rather than just gametes, start to be a mobile stage—this is origin of pollination. Getting Larger: Secondary Growth and the Transition From Seeds to Spores When plants developed secondary growth, a type of growth that allowed for lateral expansion and accumulation of woody tissue, they were able to grow much larger. However, these giants faced a new problem. Big animals like elephants, lions, and whales tend to produce a small number of offspring but increase the child care to ensure survival. Another strategy, usually employed by smaller organisms, is to produce a large number of offspring with low investment in each (such as most fungal spores), though most of them will not survive (Figure \(3\)). Imagine these big, secondary thickening spore plants: they made billions of spores with little nutrients or protection for the developing offspring. Naturally, only few from these billions would survive to become fertilized. Spore reproduction is cheap and efficient but results are unpredictable. Even worse, these spore tree forests were not at all stable: in accidentally good conditions, many spores would survive and make sporophytes, which would all start to grow simultaneously and then suppress each other. But if the environmental conditions are poor, then none of the gametophytes will survive so there would be no new saplings to replace the old trees. Plants evolved a solution to this conundrum: the seed. The idea of a seed is to hide most of the heterosporous life cycle inside the parent plant. In seed plants, everything happens directly on the parent sporophyte: development of gametophytes, syngamy, and growing of offspring sporophyte. Consequently, the megaspore never leaves the sporangium. It germinates inside, waits for fertilization and then the zygote grows into and embryo, still inside the same sporangium. What will finally leave the mother plant is the entire megasporangium with the megagametophyte and embryo inside. This is the seed's chimeric construction: sporophyte, megagametophyte, embryo, and (in angiosperms) endosperm genotypes encased within a single structure. One problem is still left. How will sperm reach the retained megagametophyte and egg cell? The target is now perhaps high above the ground, on a branch of the giant tree. The only possible solution is pollination. Pollination is the distribution of the whole male gametophytes, also called pollen. Plants aren't able to physically go find a mate, so they always need a third party to transport their pollen, usually wind or insects. Once the pollen gets to the intended destination, how would the sperm then swim to the egg cell? Some seed plants excrete a drop of liquid from the top of the ovule (a pollen drop) to create a fluid connection between the pollen grain to the ovule. Another sperm delivery tool, the pollen tube (Figure \(4\)), is made from one of the pollen grain cells in some plants. Fertilization with pollen tube is often called siphonogamy. Consequently, seed plants with the pollen tube do not have flagella on male gametes; these cells are spermatia: non-motile male gametes. A pollen tube allows only two male gametes per gametophyte. Male gametes are usually competing for fertilization—this selects the best genotypes; whereas in higher seed plants, competition is between pollen tubes. The haploid pollen tube grows inside alien tissue of diploid sporophyte, so this growth is extremely slow in many seed plants. However, angiosperms made their pollen tubes grow fast. With all these revolutionary adaptations, seed plants were first to colonize really dry places, and, in turn, allowed all other life to survive in arid climates. Read more about the evolution of seeds in this article from September, 2020. Gymnosperms and Angiosperms Seed plants are composed of two major lineages: gymnosperms (meaning naked seed) and angiosperms (meaning covered seed). These two lineages represent major differences in life history traits connected to the evolutionary conditions during which each evolved. Gymnosperm reproduction differs from that of angiosperms in several ways. In gymnosperms, the megagametophyte is contained within an ovule, present on exposed bracts of the megastrobilus, where seeds develop and are often passively released (though some are dispersed by animals). In angiosperms, the ovule is contained within an enclosed ovary. The ovary then develops into a fruit, specialized for seed protection and dispersal. Double fertilization is a key event in the life cycle of angiosperms, forming a second supply of nutrients for the developing embryo (the endosperm), but is absent in most gymnosperms. The gametophyte structures are produced in separate strobili in gymnosperms, whereas in angiosperms, they are often a part of the same flower. Wind plays an important role in pollination in gymnosperms because pollen is blown by the wind to land on the female cones. Although many angiosperms are also wind-pollinated, animal pollination is more common, resulting in specialized pollination syndromes present in flowers. Attributions Curated and authored by Maria Morrow, CC BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.01%3A_Introduction_to_Seed_Plants.txt

Learning Objectives • Describe the shared derived characteristics of gymnosperms. • Connect these adaptations to the stressors this group of plants would have faced. Toward the end of the Carboniferous period, major changes in the climate occurred. The current day European and North American continents slammed together, forming the Appalachian mountains (which were taller, at that time, than the present-day Himalayas). Fossil and geologic records show a tendency toward a drier climate, with evidence of glaciation and lowered sea levels. Inland seas were increasingly diverted into distinct river channels as woody debris channelled the movement of waterways. In short, the terrestrial surface began to dry out and there was much more of it. The ancestors of birds, reptiles and mammals were adapting eggs that could survive outside of the water -- plants were working toward a similar strategy. Dry conditions would have selected for plants with thicker cuticles, leaves with less surface area to evaporate from, propagules that could survive through dry periods to germinate when water was available, and those that could grow taller than the current canopy. Around this time, a group of animals likely took flight for the first time -- the insects! This would present both new challenges and new opportunities for plants. The plants that would become the gymnosperms evolved xerophytic leaves to prevent desiccation in the dry air (Figure \(1\)). These plants would have the ability to grow wider (and thus taller) via the production of a new layer of secondary xylem, AKA wood, each year. They could also produce exterior layers of dead cells, unlike the living epidermis, called bark. Together, the production of bark and wood are part of a process called secondary growth (Figure \(2\)). These traits allowed some gymnosperms to adapt to extreme environments like the frozen tundra, high alpine, and deserts, to resist herbivory, and live thousands of years. To increase the chances of fertilization in the absence of water, gametes began to be dispersed aerially via pollen. Perhaps most importantly, the zygote and female gametophyte were surrounded in a protective coating and dispersed as seeds. Both seeds and pollen develop within a structure called a cone (or strobilus, see Figure \(3\)). The first fossil records of gymnosperms are from a period called the Permian, just after the Carboniferous. Gymnosperms used to have many more species, but it is likely that the event that wiped out most of the dinosaurs also represented the end for most of those lineages. Extant groups of gymnosperms include the conifers, cycads (similar in appearance to palms), gnetophytes, and single species from the ginkgophytes, Ginkgo biloba. Of the approximately 1000 species of gymnosperms alive today, about 600 of these are conifers, 58 of which are found in California. In fact, some of the oldest (bristlecone pine), tallest (coast redwood), and most massive (giant sequoia) organisms on the planet are conifers and all are native to California. Many lineages of gymnosperms are currently threatened with extinction. Check out this open-access paper (Gymnosperms on the EDGE) for more information about gymnosperm conservation. Selection Pressures and Drivers 1. Competition for sunlight. Seedless vascular plants were able to reach heights up to 100 feet tall. In the lineage leading to the gymnosperms and angiosperms, some plants developed the ability to grow wider as they grew taller. This secondary growth allowed for increased stability and, eventually, to reach heights over 300 feet. 2. Drought. Dry conditions would have selected for plants with thicker cuticles, leaves with less surface area to evaporate from, and propagules that could disperse without water and survive through dry periods to germinate when water was available. 3. Herbivory. In addition to leaves that could resist drought, the presence of insects would have driven selection for plants that could defend against herbivory. The thick cuticle and tough texture of xerophytic leaves made them difficult to eat, while resin canals in both leaves and stems provided another line of defense. Attributions Content by Maria Morrow, CC BY-NC 2.6.02: Gymnosperms Learning Objectives • Use morphological characteristics and life history traits to distinguish between ginkgos and flowering plants. • Explain why Ginkgo biloba is called a living fossil. • Use morphological characteristics and life history traits to distinguish between cycads and ferns. • Define the term dioecious and provide an example. Ginkgophyta As of 2019, the most recent genetic studies have placed ginkgos as the oldest of the extant gymnosperms. This does not mean that it was the first gymnosperm. From the fossil record, it seems that most early gymnosperms went extinct. The sole remaining species in this group, Ginkgo biloba, is a living fossil virtually unchanged from its fossilized ancestors (see Figure \(1\)). This plant is almost extinct in the wild--a few natural populations remain in China--but has a wide distribution as an ornamental tree. It is possible that this species was only kept alive due to cultivation efforts by Buddhist monks for its medicinal properties. Ginkgo biloba is dioecious (as an exception among plants, Ginkgo has sexual chromosomes like birds and mammals) and the pollen is transported by wind to ovulate trees. The microstrobili are reminiscent of the catkins produced on some flowering plants (Figure \(2\)). Pollen grains of ginkgos produce two multi-flagellate spermatozoa. Ovulate have paired ovules at the tips of branches that look much like fruits (Figure \(3\)). The fleshy coating of the seed emits a foul odor as it decays, making staminate trees a more popular choice in ornamental settings. This species is also long-lived, a single tree can live for thousands of years (the oldest is 3,500 years old!), and they are resistant to most pests. This pest resistance, as well as the medicinal properties, can be attributed to a wide variety of secondary metabolites produced in the leaves, including terpenes and flavonoids. A ginkgo tree at the Zenpuku temple in Tokyo, Japan is approximately 750 years old (Figure \(4\)). Ginkgos were the first plants to regenerate after the Hiroshima bombing and were not found to contain any genetic abnormalities. Cycadophyta Although seed ferns are now extinct, some of their living descendants, the cycads, resemble them closely (Figure \(5\)). Cycads are one of the more ancient gymnosperm lineages, appearing in the fossil record around 300 million years ago. Similar to Ginkgo biloba, cycads have sperm with multiple flagella that swim toward the egg. For plants, this is considered an ancestral trait. Cycads and ginkgos emerge as sister taxa that are ancestral to the conifers. Cycads produce leaves that are large and pinnately compound (have leaflets arising from a central axis, like a feather), making them appear frond-like. Unlike ferns, but like other gymnosperms, these leaves are xerophytic (Figure \(6\)): tough, waxy, and more resistant to desiccation. Cycads are dioecious. The microstrobilus is produced on the "male" plant and consists of many microsporophylls bearing microsporangia. It is called a microstrobilus, not because it is small (these can be over a meter in height), but because the it produces smaller and more numerous spores than the megasporangium. Microstrobili are often larger than megastrobili in cycads (see Figure \(7\) and Figure \(8\)). In cycads, pollen is carried to the megastrobilus by insects. The megastrobilus is produced on the "female" plant, and is composed of overlapping megasporophylls. In some cycads, such as Cycas spp., the megasporophylls do not form into a strobilus structure. Ovules are produced on megasporophylls (Figure \(9\)); these ovules will develop into seeds after fertilization. Seeds are then dispersed by animals. Attribution Curated and authored by Maria Morrow, CC-BY-NC, using 7.6 Spermatophyta – Seed Plants from Introduction to Botany by Alexey Shipunov (public domain)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.02%3A_Gymnosperms/2.6.2.01%3A_Cycads_and_Ginkos.txt

Learning Objectives • Use morphological features and life history traits to distinguish conifers from other plants. • Connect the adaptations of conifers to dry and/or cold environments. • Identify structures and phases in the Pinus life cycle; know their ploidy. • Use morphological features and life history traits to distinguish gnetophytes from other plants. • Describe the traits gnetophytes share with angiosperms. Though the gnetophytes have been difficult to place, phylogenetically, recent genetic studies place them as sister to the Pinaceae (pine family, emerging from within the conifers. See this open-access paper for recent genetic work on the evolutionary relationships between gymnosperms. Conifers Conifers are the most species-rich lineage of gymnosperms. From the fossil record, we think there were over 20,000 species of conifers. However, their diversity declined with the dinosaurs. Currently, there are around 600 extant species. These amazing plants represent some of the oldest, tallest, and most massive organisms on the planet. Though currently low in diversity, these amazing plants make up 30% of Earth’s forests. Conifers are the most widely known and economically important among gymnosperms. Conifers include the largest and the oldest of all living organisms. One redwood (Sequoia sempervirens) growing in California is almost 400 feet (122 meters) high. Bristlecone pines (Pinus longaeva, Figure \(1\)) growing in the mountains of eastern California some are more than 5,000 years old. Giant sequioas (Sequiadendron giganteum) Most of them are temperate evergreen trees, but some are deciduous, such as larch (Larix) and the dawn redwood (Metasequoia). The stem has a large amount of xylem, a small cork, and minute pith. Seeds are distributed by wind and animals. Note: The Pinaceae is currently the largest family of conifers, so many of the examples for this group of gymnosperms will be from the type genus Pinus (pines). Xerophytic Leaves in Conifers Xerophytic leaves are adapted to withstand drought conditions. In conifers, we see a wide range of xerophytic leaves with different morphologies that can be shaped by their local environment. Consider the leaves of the coast redwood and the giant sequoia (Figure \(\PageIndex{2-3}\)). Though these two trees belong to different genera--Sequoia and Sequoiadendron, respectively--they are sister taxa. However, the coast redwood has adapted to life on the coast, where the giant sequoia has evolved in inland, higher elevation forests with much more extreme climatic conditions. How can this be seen in the structure of their leaves? There are also resin canals that ring the needle, appearing as holes surrounded by small cells. These secrete resin to protect the plant. Resin is a sticky fluid rich in compounds that protect the plant. It flows through canals in the stems, roots, and leaves and can rush to fill a wound. The resin can gum up the mouth parts of herbivorous insects, offer chemical defense against pathogenic bacteria and fungi, and harden to close the wound (much like a scab). Reproduction in Conifers Unlike other gymnosperms, conifers are monoecious, meaning megastrobili and microstrobili are produced on the same plant. In general, megastrobili tend to be larger and longer-lived, while microstrobili are smaller and ephemeral, disintegrating after pollen is dispersed (see Figure \(\PageIndex{5-6}\)). Some conifers, like junipers (Juniperus) and yews (Taxus), lack woody cones and have fleshy scales. In all, conifer life cycle takes up to two years. Conifers do not have flagellate spermatozoa; their non-motile male gametes (spermatia) move inside long, fast-growing pollen tube. The female cones are larger than the male cones and are positioned towards the top of the tree; the small, male cones are located in the lower region of the tree. Because the pollen is shed and blown by the wind, this arrangement makes it difficult for a gymnosperm to self-pollinate. Seed Cones The megastrobilus, or seed cone, is composed of spirally arranged megasporophylls called ovuliferous scales (Figure \(7\)). Each scale produces two megasporangia, which contain a diploid megasporocyte (also called a megaspore mother cell). Each megasporocyte undergoes meiosis. Only one of the four cells produced will survive to develop into a haploid megagametophyte and the other three will die. The megagametophyte is part of the ovule and contains archegonia, each with an egg cell inside (Figure \(8\)). The megagametophyte is retained within the megasporangium, which becomes the nucellus. Surrounding the nucellus is the integument, which is initially continuous with the ovuliferous scale and has a small opening called a micropyle. Pollen Cones Microstrobili (pollen cones) are formed from overlapping microsporophylls that bear multiple microsporangia. Within the microsporangium, there are microsporocytes (also called microspore mother cells), diploid cells that undergo meiosis to produce haploid microspores. Microspores grow by mitosis into microgametophytes, AKA pollen, within the microsporangium. The microgametophyte in gymnosperms is the four-celled, "winged" pollen grain. Within the pollen grain (Figure \(9\)), there is a generative cell, a tube cell, and two prothallial cells. On either side of the pollen grain, two wing-like structures called air sacs may help orient the pollen grain toward the ovule. A grain of pollen will be transported on the wind and, if lucky, it will land on a seed cone. The seed cone has a drop of sugary liquid (a pollen drop) that it secretes, then retracts, pulling the pollen in toward the ovule. This stimulates the tube cell to germinate a pollen tube, while the generative cell divides by mitosis to produce two spermatia (no flagella). These spermatia travel with the pollen tube, through the micropyle, and into an archegonium where one will fertilize an egg (Figure \(\PageIndex{10-11}\)). It takes approximately one year for the pollen tube to grow and migrate towards the female gametophyte! When fertilization occurs, the micropyle closes and the integument becomes the seed coat. The zygote will grow and develop as an embryo within the seed, nourished by the megagametophyte tissue, as well as the nucellus (Figure \(12\)). The scales of the cones are closed during development of the seed. Seed development takes another one to two years. Once the seed is ready to be dispersed, the bracts of the female cones open to allow the dispersal of seed; no fruit formation takes place because gymnosperm seeds have no covering. The seed will be dispersed by wind or animals and germinate to grow into a diploid pine tree once again. The Full Life Cycle Video \(1\) is an extremely helpful narrated animation of the pine life cycle. You should watch this video or some other walkthrough of the pine life cycle before attempting to interpret the complex diagram (Figure \(13\)). Video \(1\): A narrated video of the pine life cycle, sourced from Youtube. Gnetophytes Gnetophytes are a small group with only three genera that, excepting from their opposite leaves, seem not at all similar: Ephedra, Welwitschia, and Gnetum. Ephedra are horsetail-like desert leafless shrubs, Gnetum are tropical trees, and Welwitschia are strange desert plants that form two large, continuously growing leaves (Figure \(14\)). Gnetophytes represent an anatomically and genetically difficult group to classify. They have several traits in common with angiosperms, such as vessel elements in the xylem, double fertilization, and a covering over their seeds. Even their leaves are angiosperm-like, with netted venation. However, these traits are convergently evolved, meaning that angiosperms and gnetophytes each evolved these traits separately. Genetically, recent studies have placed the gnetophytes as a sister group to the Pinaceae (pine family) within the conifers. This would mean that pines, firs, and spruces are more closely related to strange gnetophytes like Ephedra than they are to other conifers like redwoods, cedars, and Pacific yew. However, the true nature of this evolutionary relationship remains murky and contentious. Ephedra has archegonia, but in Gnetum and Welwitschia they are reduced. On the other hand, Ephedra and Gnetum have double fertilization, a process that you will see in angiosperms where both male nuclei fuse with cells of the one female gametophyte. Double fertilization in gnetophytes results in two competing embryos, and only one of them will survive in the future seed. Both Gnetum and Welwitschia have vessel elements (like angiosperms). Gnetum also has angiosperm-like opposite leaves with netted venation, like the coffee tree (however, this probably is a result of modification of dichotomous venation). Ovules are solitary and covered with an additional outer integument; the male gametes are spermatia moving with the pollen tube instead of swimming (no flagella). Welwitschia is probably most outstanding among gnetophytes. There is only one species and it occurs only in the Namibian desert. The best way to describe this plant is an “overgrown seedling.” It has a small trunk with two wide leaves that have parallel venation. The secondary thickening is anomalous, the wood has vessels. This plant is insect-pollinated and its winged seeds are dispersed by the wind. Fertilization is not double, but, along with pollen tubes, involves some interesting structures: prothallial tubes which grow from female gametophyte and meet with pollen tubes. Characteristics of Gnetophytes • Angiosperm-like features: vessel elements, double fertilization, fruit-like ovule coverings Welwitschia mirabilis This strange plant grows in the desert of Namibia. It has two large leaves that grow from a basal meristem. As the plant gets older the leaves split and start to look like numerous long tentacles (Figure \(15\)). The tips of the leaves are ragged, as these are the oldest parts. The leaves are shiny and the setting is dry, indicating their xerophytic nature. In the center, where the two leaves meet, plants will produce either megastrobili or microstrobili (Figure \(16\)). Ephedra Ephedra spp. have scale-like, opposite leaves produced on tough, photosynthetic stems. They produce swollen megastrobili that look like fruits (Figure \(17\)), and microstrobili have extruded microsporangia, making them look like catkins (a type of inflorescence produced by some angiosperms, (Figure \(18\)). Some Ephedra species produce alkaloids that have been extracted for stimulant use, including ephedrine and pseudoephedrine. Gnetum Gnetum spp. could easily be mistaken for flowering plants. They produce leaves with netted venation and fruit-like megastrobili. These plants are restricted to tropical areas and generally take on a tree-like habit. Attribution Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.02%3A_Gymnosperms/2.6.2.02%3A_Conifers_and_Gnetophytes.txt

Learning Objectives • Describe the shared derived characteristics of angiosperms. • Connect these characteristics to the stressors these plants would have faced. At the end of the Permian period, there was the largest mass extinction this planet has ever experienced. It is estimated that 96% of species that lived at that time went extinct. This event signaled the downturn for some groups and opened up space for others to emerge. The exact timing of the emergence of angiosperms is unknown, so it is difficult to relate their evolution to specific climatic conditions. However, there is relatively new fossil evidence that may place flowering plants as early as the Jurassic period, 174 mya. This was the age of the dinosaurs and coincides with the emergence of the first feathered dinosaurs -- birds! Much like the insects, birds would present interesting opportunities for this new group of plants, working as both pollinators and seed dispersers. Angiosperms can be distinguished from other plants by a set of specialized characteristics that allowed them to compete in an already full world. The (usually) easiest thing to identify about an angiosperm are its flowers. These collections of modified leaves allowed this group of plants to attract pollinators and increase the chances of successful fertilization. Once pollinated, the fertilized seeds are encased in a protective ovary whose structure can be specialized for different methods of dispersal, such as animal ingestion, animal attachment, flotation, or wind dispersal. This protective ovary and the encased seed(s) are more commonly called a fruit. Inside the developing seeds, angiosperms provide an additional food source to the developing zygote, the endosperm. Competing with the gymnosperms for access to sunlight was perhaps hopeless, so the angiosperms adapted ways to work smarter, not harder. In the xylem, they evolved large diameter conducting cells for rapid water uptake called vessel elements, though this made them vulnerable to freezing conditions. In the phloem, sieve cells evolved into sieve tube elements, increasingly specialized for transportation of photosynthates. As you might have guessed from the vast number of species, angiosperms occupy incredibly diverse habitats and span a range of morphologies, from tiny plants floating as a film on the surface of a pond (Figure \(1\)) to towering Eucalyptus trees dominating the forests of Tasmania, rivaling redwoods in height. Selection Pressures and Drivers 1. Competition for space. Present day gymnosperms include the tallest, most massive, and some of the oldest organisms on the planet. With this in mind, you can imagine that they would be difficult to compete with. Angiosperms needed to evolve more efficient methods of transporting water and photosynthates, fertilization, and survival of offspring. 2. Animals. The primary response to animals that we see in gymnosperms is prevention of herbivory, though there is some insect pollination and animal seed dispersal. While herbivory is still a driver of selection for angiosperms, animals also served as a more efficient method of pollen delivery. Insects and birds could be lured in with sugary nectar or scents and colors that mimicked other resources, then dusted with pollen as they investigated. If the lures were specialized enough, they would continue seeking the same resource, leading them to another plant of the same species. These scents, colors, and nectar resources were produced by structures that also produced pollen and ovules -- the flower. Similarly, fruits allowed for the dual purpose of protecting seeds and co-opting animals as dispersal agents, whether by ingestion or attachment. Some fruits evolved production of sugary tissues and bright colors to attract animals, while others evolved hairs or spines to latch onto their bodies. • 2.6.3.1: Flowers Flowers are specialized reproductive structures produced by angiosperms. These structures are composed of highly modified leaves in distinct whorls. The sterile whorls, the calyx and corolla, comprise the perianth. Pollen is produced by the androecium and ovules are produced in the gynoecium. Floral formulas are used to describe the composition and morphology of these whorls. An inflorescence involves the production of multiple florets in place of a flower. • 2.6.3.2: Angiosperm Life Cycle Angiosperms have a complex life cycle. The microgametophyte is reduced to 2 cells, while the megagametophyte is now 7 cells and 8 nuclei. Ovules develop within the ovary or ovaries of the gynoecium. Production of gametophytes and fertilization happens within the flower. The spermatia each fertilize a cell within the ovule (double fertilization), one of which will grow into the embryo. Seeds are protected by the ovary wall, which becomes the fruit, a structure specialized for seed dispersal. Attribution Content by Maria Morrow, CC-BY 2.6.03: Angiosperms Learning Objectives • Identify the components of a flower and to which whorl each belongs. • Write and interpret floral formulas. • Differentiate between flowers and inflorescences. • Explain the difference between raceme-based and cymose inflorescences. Flowers are sets of highly modified leaves that function to attract a pollinator or, if no animal pollinator is used, to optimize spore dispersal in some way. Over the course of evolutionary history and coevolution, this has lead to an incredible diversity of shape, size, color, smell, and just about any other characteristic you can think of. Because most plants are angiosperms and because flowers are often so diverse, learning the terminology to describe flowers is a major step in learning to identify plants. The modified leaves in flowers are called sepals, petals, stamens, and carpels (Figure \(1\)). These components are arranged in whorls and attach to an area called the receptacle, which is at the end of the stem that leads to the flower. This stem is called the peduncle. In the case of an inflorescence, where multiple florets are produced in place of a single flower, the stems leading to the florets are called pedicels (Figure \(2\)). The general characters that a flower has are whorl morphology, sex, merosity, symmetry, and the position of the gynoecium. Merosity is simply the number of parts in each whorl of a plant structure, whether it is the number of sepals, petals in a corolla, or the number of stamens. Each of these characters will be discussed below. Whorls The outermost whorl of a flower is called the calyx and is composed of sepals. Inside the calyx is the corolla, which is composed of petals. The sepals are often smaller and less colorful than the petals, but this general rule can be misleading. For example, lilies and tulips have identical sepals and petals (called tepals, these can be seen in the florets in Figure \(2\)). The only way you can distinguish between them is by location: Which whorl is on the outside? The Perianth: Calyx and Corolla Together, the calyx and corolla are called the perianth (peri- meaning around, anth- meaning flower; Figure \(3\)). The calyx is the outermost whorl of the flower. In most coses, the sepals are not showy--lacking bright colors and typically smaller--and instead serve a protective function in the developing flower. The corolla is the whorl just within the calyx. Petals tend to be the showy part of the flower, specialized for attracting animal pollinators. Reproductive Whorls: Androecium and Gynoecium Inside the perianth is the androecium (house of man), a whorl composed of stamens. Each stamen has a long filament holding up pollen sacs called anthers (Figure \(\PageIndex{4-5}\)). Each lobed anther contains microsporangia, within which meiosis of the diploid microspore mother cells in the anther produces four haploid microspores. Each of these develops into a pollen grain consisting of two cells: a larger vegetative cell (the tube cell), inside of which is a a smaller germ cell (also called the generative cell). At some point, depending on the species, the germ cell divides by mitosis to produce 2 spermatia. Inside the androecium is the gynoecium (house of woman), which is composed of carpels. Each carpel has an ovary at the base where ovules are housed. A style emerges from the ovary and is topped by the stigma (Figure \(6\)), where pollen is deposited. A carpel consists of a single ovary, style and stigma. Often several carpels are fused into a single structure, referred to as a pistil. Within the ovule, a megasporangium produces a megaspore mother cell. Meiosis of the megaspore mother cell in each ovule produces 4 haploid cells, a large megaspore and 3 smaller cells that disintegrate. This megaspore develops into the megagametophyte, all within the ovule. Pollen grains land on the stigma and must grow a tube down the style to reach the ovule and complete fertilization. Incomplete Flowers Most flowers are composed of four whorls. If all whorls are present, a flower is said to be both complete and perfect. If any whorl is missing, the flower is incomplete (Figure \(7\)). If one of those missing whorls is either the androecium (pollen-producing) or gynoecium (seed-producing), the flower is also imperfect (Figure \(8\)). Evolution seems to favor (and be favored by) genetic variability. Genetic variability is promoted by outbreeding - sexual reproduction between genetically dissimilar parents. Just why sexual reproduction is so popular throughout the world of living things is still a hotly-debated question, but the fact remains. Plants, being anchored in position, have a special problem in this regard. Many employ the services of animals (e.g., insects, birds, bats) to transfer pollen from plant to plant. But if the flowers have both sex organs, what is to prevent the pollen from fertilizing its own eggs? Plants have evolved a variety of solutions. One of these is to produce imperfect flowers. There are two types of imperfect flowers: staminate flowers contain only an androecium (Figure \(9\)), and carpellate (or pistillate) flowers have only a gynoecium. Monoecious plants have both types of imperfect flower on the same plant. Dioecious plants have imperfect flowers on separate plants; that is, some plants are male, some female. Examples include willows, poplars, and the date palm. Most dioecious plants use an X-Y system of of sex determination like that in mammals. However, a few species use an X-to-autosome ratio system like that of Drosophila, and a very few use a ZW system like that of birds and lepidopterans. But the vast majority of angiosperms have perfect flowers; that is containing both male and female sex organs. So how do they avoid self-fertilization? Many plants have self-incompatibility genes to prevent successful pollination between two of their own gametes. However, there is also a morphological solution: heteromorphic flowers. The flowers are perfect but come in two structural types; for example • long stamens with a short style • short stamens with a long style A single plant has one type or the other. If the pollinator has a short tongue, pollination is favored from the first type to the second - but not the reverse. Heteromorphic flowers are not common, and even in the angiosperm families that favor them (e.g., primroses, flax), the same biochemical mechanisms of self-incompatibility that we will find in homomorphic flowers are usually present as well. Fusion Within and Between Whorls Determining the merosity of flowers is complicated by floral fusion. In many flowers, parts of a single floral whorl will be partially or completely fused together. When the fusion is between parts of the same whorl, such as the petals fusing together to form a tubular structure (a sympetalous flower), it is called connation. When there is fusion of parts between whorls, such as the stamen fusing the the petals, it is called adnation. A frequent form of connation occurs within the gynoecium. In an apocarpous gynoecium, the carpels are free. In a syncarpous gynoecium, some or all parts of the carpels are fused (see Figure \(10\)) Floral Symmetry Flowers that have multiple lines of symmetry (like a starfish) are radially symmetrical, also called actinomorphic or regular. Flowers with only a single line of symmetry (like you) are bilaterally symmetrical, also called zygomorphic or irregular (Figure \(11\)). Ovary Position We can use the location of the ovary to further distinguish between flowers (Figure \(12\)). If the other whorls of the flower meet below the ovary (the ovary or ovaries look a bit like an egg or eggs in a nest; Figure \(13\)), the ovary is superior (on top of the rest of the flower). This means that the rest of the flower parts are below the gynoecium, so we can also call this flower hypogynous (below the gynoecium). The two terms both describe the same situation, but superior refers only to the ovary while hypogynous refers to the flower, in general. In the opposite situation, the other floral whorls join at a point above the ovary. In this case, the ovary is inferior and the flower is epigynous (on top of the gynoecium). As always, there are less clear situations. In some flowers, as in the rose family, the floral whorls join together and fuse at a point above the ovary, then travel down, around, and below the ovary as a fused unit. This fused unit is called a hypanthium. The ovary is termed semi-inferior, as it is located below the unfused parts of the floral whorls. Because the floral whorls travel around the ovary as the hypanthium, the flower is perigynous (peri- meaning around). Inflorescences An inflorescence is when, in the place of a single flower, multiple florets are formed. Florets can be sessile or attached by a stem called a pedicel. When leaf-like structures are found within the inflorescence, they are called bracts. There are a wide range of possibilities for the structure and development of inflorescences, though most can be split into four models: raceme-based, cymose, panicle, and intercalate (Figure \(14\)). Two models are most widespread. Raceme-based inflorescences are mostly monopodial, having indeterminate growth. This means that the terminal bud continues producing lateral florets, never truly forming a terminal floret. The inflorescence can be simple or compound (Figure \(15\)). Cymose inflorescences are sympodial, having determinate growth. This means there is a terminal floret that forms first, then other florets are produced laterally (Figure \(16\)). The order of lateral floret maturation can be a useful identification feature. Attribution Curated and authored by Maria Morrow, CC BY-NC, using the following sources: Figure \(8\) caption by Melissa Ha.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.03%3A_Angiosperms/2.6.3.01%3A_Flowers.txt

Learning Objectives • Identify structures and phases in the angiosperm life cycle; know their ploidy. • Explain how fertilization occurs within a flower. • Label a developing ovary cross section. Angiosperms have a complex life cycle. The gametophytes have been further reduced: antheridia were lost in the gymnosperms and archegonia were lost in the angiosperms. Both gametophytes are now housed within the flower, a structure composed of highly modified leaves specialized for pollination. From flowers, fruits are produced, a protective structure that (usually) develops from the ovary wall and is specialized for seed dispersal. The Microgametophyte (AKA the Pollen Grain) The microgametophyte develops and reaches maturity within the microsporangia (Figure \(1\)). The microsporangia, which are usually bi-lobed, are also called pollen sacs. These pollen sacs are found in the anther of the stamen, which is at the end of the filament. Within the microsporangium (pollen sac), many microspore mother cells divide by meiosis to each give rise to four haploid microspores, each of which will ultimately form a pollen grain (Figure \(2\)). An inner layer of cells in the microsporangium, known as the tapetum, provides nutrition to the developing microspores and contributes key components to the pollen wall. Upon maturity, the microsporangia burst, releasing the pollen grains from the anther. Each pollen grain has two coverings: the exine (thicker, outer layer) and the intine (Figure \(2\)). The exine contains sporopollenin, a complex waterproofing substance supplied by the tapetal cells. Sporopollenin allows the pollen to survive under unfavorable conditions and to be carried by wind, water, or biological agents without undergoing damage. Mature pollen grains contain two cells: a generative cell and a pollen tube cell. The generative cell is contained within the larger pollen tube cell. When a pollen grain reaches the stigma, it germinates into a pollen tube. The generative cell migrates with the pollen tube to enter the ovary. During its transit inside the pollen tube, the generative cell divides to form two gametes (spermatia). These, along with the tube nucleus (also known as the vegetative nucleus), migrate down the pollen tube as it grows through the style, the micropyle, and into the ovule chamber. In Arabidopsis, the pollen tube follows a gradient of increasing concentration of a small defensin-like protein secreted by the synergids (see The Megagametophyte). The Megagametophyte Within the ovary of the gynoecium, ovules are produced. Ovules consist of a double-layered integument with a small opening called the micropyle. The integument surrounds the megasporangium. Both the micropyle and megasporangium are diploid tissue of the sporophyte and are connected to the ovary wall by a region of tissue called the funiculus. The funiculus connects to a region of the ovary called the placenta, where nutritive support is provided the ovary wall and supplied to the developing ovule. Within the megasporangium a single diploid megaspore mother cell divides by meiosis to produce four haploid megaspores. One of these will survive and three will disintegrate. The nucleus of the surviving megaspore undergoes 3 successive mitotic divisions. The 8 nuclei that result are distributed and partitioned off by cell walls to form the embryo sac (Figure \(3\)). The embryo sac is composed of 7 cells. The egg cell, located near the micropylar end, is flanked by 2 synergid cells. The large central cell contains 2 polar nuclei (a dikaryotic cell). The final three cells are the antipodal cells, located on the opposite side as the egg and synergids (Figure \(4\)). The synergids help guide the pollen tube for successful fertilization, after which they disintegrate. One of the spermatia produced by the pollen's generative cell fuses with the egg to form a diploid zygote. This zygote will grow into the sporophyte. The second spermatium fuses with the polar nuclei to produce a triploid endosperm (Figure \(5\)). This event is called double fertilization. The endosperm will provide additional nutritive tissue for the growing embryo. After fertilization, the integument will close the micropyle and develop into the seed coat, protecting the seed. The ovary wall will develop into the pericarp of the fruit. Fruits An unfertilized ovary, as shown in Figure \(6\), contains one or more developing ovules produced in compartments called locules. Each ovule is attached to a nutritional region of the ovary called the placenta by a strand of tissue called the funiculus. The sporophyte supports the developing ovule through this tissue pathway. Prior to fertilization, there is a small gap in the integument called the micropyle. After fertilization, the ovary wall develops into the fruit, surrounding the seeds. In fleshy fruits that use animals for dispersal, like the pears shown in Figure \(7\), this might include a swelling of the cells, increased sugar production, and a change in pigmentation. These are the type of fruits we are familiar with. However, all flowers turn into fruits. The fruits might be dry, spiky, or in other ways completely unappetizing, and this is become many fruits do not use animal ingestion as their method of dispersal (more on this in Chapter 8.3 Fruits and Dispersal). The Full Life Cycle The angiosperm life cycle is shown in Figure \(12\) and Video \(1\). Watch Video \(1\) to help untangle this complex life cycle. Video \(1\): A digital, narrated rendition of the angiosperm life cycle. Sourced from YouTube. Attribution Curated and authored by Maria Morrow, CC BY-NC, using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.03%3A_Angiosperms/2.6.3.02%3A_Angiosperm_Life_Cycle.txt

Seeds represent one of the most important innovations in plant evolution: a protected, nutrient-supplied embryo with the ability to await appropriate conditions for germination. Seeds and pollen allowed plants to limit their reliance on water for completion of their life cycle. The first plants to evolve seeds were the gymnosperms. Angiosperms then improved upon seed dispersal and pollination strategies with the evolution of fruits and flowers. In gymnosperms, protective seeds filled with nutritive tissue (including the megagametophtye) replace spores as the dispersal mechanism. Antheridia are lost in the microgametophyte, which is reduced to four cells and is dispersed as a whole (pollen). The evolution of secondary growth allows for the lateral deposition of woody tissues. This latter development, along with xerophytic leaves, allows gymnosperms to tolerate a wide variety of new environmental stressors. Cycads and ginkgos are more ancestral lineages of gymnosperms. Ginkgos are represented by a single surviving species: Ginkgo biloba. Cycads are primarily tropical and usually have large pinnately compound leaves. Like the Ginkgos, seeds and pollen are produced in strobili produced on separate plants. Gnetophytes are a group of gymnosperms that have convergently evolved several characteristics with angiosperms: fruit-like cones, vessel elements, and double fertilization. However, it is likely that they are a highly-derived group within the conifers, sister to the pine family! Most extant gymnosperms are conifers; this group includes some of Earth's oldest, largest, and longest lived organisms. The majority of plant species are angiosperms. This is the most recent lineage of plants and, though its origins are murky, its members appear to form a monophyletic clade. Within the angiosperms, there are two major groups: monocots and dicots (the latter of which can be further divided into some early diverging angiosperm lineages and the eudicots). Angiosperms have the most reduced gametophytes of all plant lineages: the mature microgametophyte is composed of just 2 cells, while the megagametophyte has 7 cells (with 8 nuclei!). These gametophytes are housed within flowers, structures composed of highly modified leaves specialized for pollination. Flowers are composed of a series of concentric whorls. The outermost whorl is the calyx, composed of sepals. Inside the calyx is the corolla, which is composed of petals. Together, the calyx and corolla comprise the perianth, which is usually the showy part of the flower in animal-pollinated species. The internal whorls are the fertile whorls. The androecium is composed of stamens, formed from a filament and anther (microsporangia are produced within the anthers). The gynoecium is composed of carpels, formed from an ovary, style, and stigma. The stigma is where pollen is received. The pollen must grow a pollen tube from the stigma to the ovary, traveling down the style to get there. Within the ovary, ovules are housed (megasporangia are produced within the ovules). During pollination, the generative cell of the pollen produces two spermatia. One spermatium fertilizes the zygote, as in most plants, but the second spermatium fertilizes a dikaryotic cell called the central cell, forming a triploid endosperm. This event is called double fertilization. After fertilization, the ovule becomes a seed and the ovary begins to develop into a fruit. Other adaptations within this group include specialized vascular cells: vessel elements in the xylem and sieve tube elements with companion cells in the xylem. After completing this chapter, you should be able to... • Explain how heterospory led to the evolution of seeds. • Connect r- and k-strategies to propagules produced by plants (e.g. spores, gametes, pollen, and seeds). • List a few ways gymnosperms and angiosperms differ in life history traits. • Describe the shared derived characteristics of gymnosperms. • Connect these adaptations to the stressors this group of plants would have faced. • Use morphological characteristics and life history traits to distinguish between ginkgos and flowering plants. • Explain why Ginkgo biloba is called a living fossil. • Use morphological characteristics and life history traits to distinguish between cycads and ferns. • Define the term dioecious and provide an example. • Use morphological features and life history traits to distinguish conifers from other plants. • Connect the adaptations of conifers to dry and/or cold environments. • Identify structures and phases in the Pinus life cycle; know their ploidy. • Use morphological features and life history traits to distinguish gnetophytes from other plants. • Describe the traits gnetophytes share with angiosperms. • Describe the shared derived characteristics of angiosperms. • Connect these characteristics to the stressors these plants would have faced. • Identify the components of a flower and to which whorl each belongs. • Write and interpret floral formulas. • Differentiate between flowers and inflorescences. • Explain the difference between raceme-based and cymose inflorescences. • Identify the components of a flower and to which whorl each belongs. • Write and interpret floral formulas. • Differentiate between flowers and inflorescences. • Explain the difference between raceme-based and cymose inflorescences. Attribution Content by Maria Morrow, CC BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.06%3A_Seed_Plants/2.6.04%3A_Chapter_Summary.txt

It is likely that most plants you see are angiosperms. Of the nearly 400,000 species of land plants described, almost 90% are angiosperms. With the production of flowers specialized for pollination and fruits specialized for dispersal, angiosperms formed complex, interconnected relationships with a wide variety of other organisms. These close coevolutionary relationships may have increased speciation within this group. Regardless, the radiation of angiosperms is unprecedented among plants. • 2.7.1: Monocots and Eudicots It is likely that most plants you see are angiosperms. Of the nearly 400,000 species of land plants described, nearly 90% are angiosperms. Angiosperms can be divided into two major groups: monocots and dicots. Dicots can be further divided into basal angiosperm lineages (magnoliids and ANA grades) and eudicots. Monocots produce one cotyledon, while dicots produce two. However, there are other characteristics that can be used to differentiate between these groups. • 2.7.2: Pollination Syndromes Pollination is the transfer sperm or spermatia from the pollen grain to the egg. This can occur through self-pollination, where an individual's pollen fertilizes its own eggs, or cross-pollination, where pollen is transferred between different individuals. When plants cross-pollinate, they require a pollen vector, which can be biotic (e.g. insects, birds, or bats) or abiotic (e.g. wind or water). Many plants have specialized for their particular vector, resulting in a pollination syndrome. • 2.7.3: Fruits and Dispersal Fruits are structures specialized for seed dispersal, typically adapted for a specific diserpsal mechanism. True fruits are composed from the ovary wall, which becomes the pericarp and can sometimes be separated into three distinct layers: exocarp, mesocarp, and endocarp. The morphology of these layers, whether the fruit is fleshy or dry, and how it opens are all used to determine fruit type. Accessory fruits are sometimes formed from other floral parts, such as the receptacle. • 2.7.4: Angiosperm Families Knowing who is related to whom in the plant world can provide important information. Often, closely related organisms will have similar life history traits, such as defense compounds or other secondary metabolites. While there are over 350,000 species of flowering plants, there are only around 400 families. Being able to quickly narrow an unknown plant to family is an essential skill in plant identification. For many angiosperm families, there will be a characteristic floral formula. • 2.7.5: Chapter Summary A brief summary of the concepts covered in chapter 8. Attribution Content by Maria Morrow, CC BY-NC 2.07: Angiosperm Diversity Learning Objectives • Compare and contrast monocots and eudicots. • Differentiate between monocot and eudicot flowers and leaves. Of over 400 families of angiosperms, some 80 of them fall into a single clade, called monocots because their seeds have only a single cotyledon. The remainder have seeds that produce two cotyledons (Figure \(1\)). This group includes some early diverging angiosperms (ANA grade families and magnoliids), but the large majority of these occupy a single clade called the eudicots. In addition to developmental features, there are a few morphological and anatomical traits you can use to distinguish between these two major groups. Monocots Monocots have a single cotyledon in their seed, parallel venation in their leaves (Figure \(2\)), flower parts in multiples of three (3-merous, see Figure \(3\)), and vascular bundles dispersed throughout the stem in concentric circles. Monocots do not have true secondary growth, though some (such as bamboo) form tough, woody stems. Some major groups of monocots are: • palms (Arecaceae) • orchids (Orchidaceae) • yams, sweet potatoes (Dioscoreaceae) • lilies, onion, asparagus (Liliaceae) • bananas (Musaceae) • all the grasses (Poaceae), which include many of our most important plants such as • corn (maize) • wheat • rice • and all the other cereal grains upon which we depend so heavily for food as well as • sugar cane and bamboo Eudicots Eudicots have two cotyledons in their seeds, netted venation in their leaves (Figure \(4\)), flower parts in multiples of 4 or 5 (4-merous or 5-merous, see Figure \(5\)), and vascular bundles in the stem arranged in a radial pattern like spokes of a wheel. Attribution Content by Maria Morrow, CC-BY

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.07%3A_Angiosperm_Diversity/2.7.01%3A_Monocots_and_Eudicots.txt

Learning Objectives • Explain pollination strategies with regard to genetic diversity. • Explain what is meant by the term pollination syndrome. • Use floral characteristics to predict a plants pollinator(s). In angiosperms, pollination is defined as the placement or transfer of pollen from the anther to the stigma of the same flower or another flower. In gymnosperms, pollination involves pollen transfer from the male cone to the female cone. Upon transfer, the pollen germinates to form the pollen tube and the sperm for fertilizing the egg. Pollination has been well studied since the time of Gregor Mendel. Mendel successfully carried out self- as well as cross-pollination in garden peas while studying how characteristics were passed on from one generation to the next. Today’s crops are a result of plant breeding, which employs artificial selection to produce the present-day cultivars (a term that refers to cultivated varieties). A case in point is today's corn, which is a result of years of breeding that started with its ancestor, a grass called teosinte (see Figure \(1\)). The teosinte that the ancient Mayans originally began cultivating had small seeds—vastly different from today’s relatively giant ears of corn and plump kernels. Interestingly, though these two plants appear to be entirely different, the genetic difference between them is miniscule. Pollination and Genetic Diversity Pollination takes two forms: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Self-pollination occurs in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma. This method of pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators, but results in lower genetic diversity within the population. Self-pollination often exists like a “plan B”, in case cross-pollination is, for some reason, impossible. Sometimes, self-pollinated flowers even do not open; these flowers are called cleistogamous. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individuals of the same species. This method relies on a pollen vector but results in higher genetic diversity. Living species have adapted to ensure survival of their progeny; those that fail become extinct. Genetic diversity is therefore required so that in changing environmental or stress conditions, some of the progeny can survive. Self-pollination leads to the production of plants with less genetic diversity, since genetic material from the same plant is used to form gametes, and eventually, the zygote. In contrast, cross-pollination—or out-crossing—leads to greater genetic diversity because the microgametophyte and megagametophyte are derived from different plants. Because cross-pollination allows for more genetic diversity, plants have developed many ways to avoid self-pollination. In some species, the pollen and the ovary mature at different times. These flowers make self-pollination nearly impossible. By the time pollen matures and has been shed, the stigma of this flower is mature and can only be pollinated by pollen from another flower. Some flowers have developed physical features that prevent self-pollination. The primrose is one such flower. Primroses have evolved two flower types with differences in anther and stigma length: the pin-eyed flower has anthers positioned at the pollen tube’s halfway point, and the thrum-eyed flower’s stigma is likewise located at the halfway point. Insects easily cross-pollinate while seeking the nectar at the bottom of the pollen tube. This phenomenon is also known as heterostyly. Many plants, such as cucumber, have male and female flowers located on different parts of the plant, thus making self-pollination difficult. In yet other species, the male and female flowers are borne on different plants (dioecious). All of these are barriers to self-pollination; therefore, the plants depend on pollinators to transfer pollen. The majority of pollinators are biotic agents such as insects (like bees, flies, and butterflies), bats, birds, and other animals. Other plant species are pollinated by abiotic agents, such as wind and water. In summary, self-incompatibility is a mechanism that prevents self-fertilization in many flowering plant species to increase genetic diversity at the population level. The working of this self-incompatibility mechanism has important consequences for plant breeders because it inhibits the production of inbred and hybrid plants. Incompatibility Genes in Flowers In recent decades, incompatibility genes—which prevent pollen from germinating or growing into the stigma of a flower—have been discovered in many angiosperm species. If plants do not have compatible genes, the pollen tube stops growing. Self-incompatibility is controlled by the S (sterility) locus. Pollen tubes have to grow through the tissue of the stigma and style before they can enter the ovule. The carpel is selective in the type of pollen it allows to grow inside. The interaction is primarily between the pollen and the stigma epidermal cells. In some plants, like cabbage, the pollen is rejected at the surface of the stigma, and the unwanted pollen does not germinate. In other plants, pollen tube germination is arrested after growing one-third the length of the style, leading to pollen tube death. Pollen tube death is due either to apoptosis (programmed cell death) or to degradation of pollen tube RNA. The degradation results from the activity of a ribonuclease encoded by the S locus. The ribonuclease is secreted from the cells of the style in the extracellular matrix, which lies alongside the growing pollen tube. Pollination Syndromes Over time, angiosperms evolved different flower morphologies, smells, and colors that corresponded to their particular pollen vector. These sets of characteristics, called pollination syndromes, allow scientists to predict the pollinators for different plants. For example, cup-shaped flowers are usually pollinated with massive animals like beetles and even bats. Funnel-shaped flowers as well as labiate flowers (with lips), are adapted to flies and bees. Flowers with long spurs attract butterflies and birds (like hummingbirds or sugarbirds). Likewise, many of the organismal vectors evolved features or behaviors to specialize in pollination of particular plants. This tandem evolution toward increasing specificity is called coevolution. Interestingly, flower phenotypes can also correlate to other environmental factors (e.g. Peach et al. 2020). For more images of pollination syndromes, see Chapter 14.1 Pollination Syndromes in the Photographic Atlas. Pollination by Deception Orchids are highly valued flowers, with many rare varieties (Figure \(2\)). They grow in a range of specific habitats, mainly in the tropics of Asia, South America, and Central America. At least 25,000 species of orchids have been identified. Flowers often attract pollinators with food rewards, in the form of nectar. However, some species of orchid are an exception to this standard: they have evolved different ways to attract the desired pollinators. They use a method known as food deception, in which bright colors and perfumes are offered, but no food. Anacamptis morio, commonly known as the green-winged orchid, bears bright purple flowers and emits a strong scent. The bumblebee, its main pollinator, is attracted to the flower because of the strong scent—which usually indicates food for a bee—and in the process, picks up the pollen to be transported to another flower. Other orchids use sexual deception. Chiloglottis trapeziformis emits a compound that smells the same as the pheromone emitted by a female wasp to attract male wasps. The male wasp is attracted to the scent, lands on the orchid flower, and in the process, transfers pollen. Some orchids, like the Australian hammer orchid, use scent as well as visual trickery in yet another sexual deception strategy to attract wasps. The flower of this orchid mimics the appearance of a female wasp and emits a pheromone. The male wasp tries to mate with what appears to be a female wasp, and in the process, picks up pollen, which it then transfers to the next counterfeit mate. Bees Bees are perhaps the most important pollinator of many garden plants and most commercial fruit trees (Figure \(3\)). Most bees that people notice are the social bees, bumblebees and honeybees, though there are thousands of species of solitary bees that have essential pollination roles. Bees have branched hairs covering their bodies, making them excellent pollinators as more pollen grains are likely to be caught upon their external surfaces and transferred onto other plants. Bees collect energy-rich pollen and nectar for their survival and energy needs, so flowers that have coevolved with bees contain both nectar and pollen. Since bees cannot see the color red, bee-pollinated flowers usually have shades of blue, yellow, violet or other colors. They visit flowers that are open during the day, are brightly colored, have a strong aroma or scent, with a landing area of some kind, typically with the presence of a nectar guide. A nectar guide can include regions on the flower with pigments that are visible only to bees, and not to humans (such as UV); it helps to guide bees to the center of the flower, thus making the pollination process more efficient. The pollen sticks to the bees’ fuzzy hair, and when the bee visits another flower, some of the pollen is transferred to the second flower. Recently, populations of honeybees (an introduced European species) have been in decline due to a variety of factors, including pesticides (like neonicotinoids) and parasitic mites. Because solitary bees are not operated by commercial industry, impacts on these populations have been less well-documented. However, declines in bee populations will have extremely important impacts on our food security, as bees are used to pollinate many food crops. Wasps are also important insect pollinators, and pollinate many species of figs. Flies Many fly species are important pollinators. These flies often look and behave much like bees, performing important roles in pollination. However, since these flowers would generally be classified under a bee pollination syndrome, we will instead discuss a second category of fly for the fly pollination syndrome. These insects (flies and sometimes carrion beetles) are typically not looking for a flower, but for a corpse or some dung to feed on or lay eggs in. Some flowers have evolved to trick flies into pollination by emitting a decaying smell or an odor of rotting flesh. These flowers, which produce nectar, usually have dull colors, such as brown or purple. They often feature some kind of trap-like feature so when a fly visits, it has to bounce around inside the flower a bit before leaving (this increases the chance of pollen deposition, both on the flower and on the fly). Examples include the corpse flowers (Amorphophallus and Rafflesia) and dragon arum (Dracunculus). Butterflies and Moths Butterflies, such as the monarch, pollinate many garden flowers and wildflowers, which usually occur in clusters. These flowers are brightly colored, have a strong fragrance, are open during the day, and have nectar guides to make access to nectar easier. The pollen is picked up and carried on the butterfly’s limbs. Moths, on the other hand, pollinate flowers during the late afternoon and night. The flowers pollinated by moths are pale or white and are flat, enabling the moths to land. One well-studied example of a moth-pollinated plant is the yucca plant, which is pollinated by the yucca moth. The shape of the flower and moth have adapted in such a way as to allow successful pollination. The moth deposits pollen on the sticky stigma for fertilization to occur later. The female moth also deposits eggs into the ovary. As the eggs develop into larvae, they obtain food from the flower and developing seeds. Thus, both the insect and flower benefit from each other in this symbiotic relationship. The corn earworm moth and Gaura plant have a similar relationship (Figure \(5\)). Bats In the tropics and deserts, bats are often the pollinators of nocturnal flowers such as agave, guava, and morning glory. The flowers are usually large and white or pale-colored; thus, they can be distinguished from the dark surroundings at night. The flowers have a strong, fruity, or musky fragrance and produce large amounts of nectar. They are naturally large and wide-mouthed to accommodate the head of the bat (Figure \(6\)). As the bats seek the nectar, their faces and heads become covered with pollen, which is then transferred to the next flower. Birds Many species of small birds, such as the hummingbird (Figure \(7\)) and sun birds, are pollinators for plants such as orchids and other wildflowers. Flowers visited by birds are usually sturdy and are oriented in such a way as to allow the birds to stay near the flower without getting their wings entangled in the nearby flowers, such as dangling (pendant). The flower typically has a curved, tubular shape, which allows access for the bird’s beak. Brightly colored, odorless flowers that are open during the day are pollinated by birds. As a bird seeks energy-rich nectar, pollen is deposited on the bird’s head and neck and is then transferred to the next flower it visits. Botanists have been known to determine the range of extinct plants by collecting and identifying pollen from 200-year-old bird specimens from the same site. Wind Most species of conifers, and many angiosperms, such as grasses, maples and oaks, are pollinated by wind. Pine cones are brown and unscented, while the flowers of wind-pollinated angiosperm species are usually green, small, may have small or no petals, and produce large amounts of pollen. Unlike the typical insect-pollinated flowers, flowers adapted to pollination by wind do not produce nectar or scent. In wind-pollinated angiosperm species, the anthers are often large and hang out of the flower, and, as the wind blows, the lightweight pollen is carried with it (Figure \(8\)). The flowers usually emerge early in the spring, before the leaves, so that the leaves do not block the movement of the wind. The pollen is deposited on the exposed feathery stigma of the flower (Figure \(9\)). Water Some plants, such as Australian sea grass and pond weeds, are pollinated by water. The pollen floats on water, and when it comes into contact with the flower, it is deposited inside the flower. Summary Table of Pollination Syndromes Table \(1\) summarizes the pollination syndromes described in the categories above. Table \(1\): Pollination Syndromes (adapted from the US Forest Service). Pollination Syndrome Color Structure Scent Nectar or Pollen Wind Dull, perianth often absent or reduced Large feathery stigmas, large anthers None No nectar, large amounts of pollen Birds Reds and pinks Often tubular or cupped None Lots of hidden nectar, moderate pollen Bees Purples, blues, yellows, white, UV Flat and shallow or tubular, with landing area Sweet, fresh, mild Pollen often sticky and scented, nectar usually present Bats White, dull green, or purple Often bowl-shaped or pendant, anthers protruding Musty or fruity, strong, emitted at night Lots of hidden nectar Moths White, pale pink or purple Often tubular or cupped, no landing pad Strong and sweet, emitted at night Lots of hidden nectar, limited pollen Butterflies Bright colors Tubular, with wide landing pad Faint, fresh Lots of hidden nectar, limited pollen Flies Dark red, purple, brown Shallow, funnel, or trap-like Putrid, rotting No nectar, moderate pollen Attributions Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.07%3A_Angiosperm_Diversity/2.7.02%3A_Pollination_Syndromes.txt

Learning Objectives • Describe the transition from ovary and ovule to fruit and seed. • Use characteristics of fruits, including pericarp morphology, to identify fruit type. • Use characteristics of fruits to predict the dispersal agent for a plant's seeds. All flowers become fruits (Figure \(1\)). This may be surprising at first, as what we culturally refer to as a fruit is a bit different than the botanical definition. Many of the "vegetables" and other plant products (e.g. grains, legumes, and nuts) that you get from the store are actually fruits! The term angiosperm refers to the fruit: angio- means vessel and sperm refers to the seed; fruits are the vessel that houses the seed or seeds. Fruits are a development of the ovary wall and sometimes other flower parts. As seeds mature, they release the hormone auxin, which stimulates the wall of the ovary to develop into the fruit. In fact, commercial fruit growers may stimulate fruit development in unpollinated flowers by applying synthetic auxin to the flower. This chapter section will cover the anatomy of a fruit, including the ovary, different fruit types, and finally, how these fruits are specialized for different dispersal mechanisms. A fruit is defined as ripened ovary, flower, or whole inflorescence. Depending on how these parts interact to form the fruit, we can classify them into different fruit types. The pericarp (Figure \(2\)), which is comprised of the exocarp, mesocarp, and endocarp, is derived from the ovary wall. Ovary Anatomy An unfertilized ovary, as shown in Figure \(3\), contains one or more developing ovules produced in compartments called locules. Within the ovule, the megasporangium is surrounded by tissue within the called the integument. Both of these are diploid tissues of the sporophyte. A diploid megaspore mother cell is produced within the megasporangium, which will divide by meiosis to produce the haploid megagametophyte (see Chapter 7.3.2: Angiosperm Life Cycle for a refresher). Each ovule is attached to a nutritional region of the ovary called the placenta by a strand of tissue called the funiculus. The sporophyte supports the developing ovule through this tissue pathway. Prior to fertilization, there is a small gap in the integument called the micropyle. After fertilization, ovules become seeds. The micropyle closes and the integument becomes the seed coat. The megasporangium, called the nucellus, serves as nutritive tissue for the developing embryo. Angiosperms provide an additional food source to the developing zygote, the endosperm. The ovary wall develops into the pericarp. Fruit Types Fruits may be classified as simple, aggregate, multiple, or accessory, depending on their origin (Figure \(11\)). If the fruit develops from a single carpel or fused carpels of a single ovary, it is known as a simple fruit, as seen in nuts and beans. An aggregate fruit is one that develops from more than one carpel, but all are in the same flower: the mature carpels fuse together to form the entire fruit, as seen in the raspberry. A multiple fruit develops from an inflorescence or a cluster of flowers. An example is the pineapple, where the flowers fuse together to form the fruit. Fruits can be dry or fleshy. An example of dry fruit is a peanut (Arachis), the shell of the peanut is the pericarp, which is dry at maturity. Examples of fleshy fruits include apples (Malus) or oranges (Citrus), where the pericarp or some other part of the floral structure becomes swollen with liquid. Dry fruits can be further classified into dehiscent fruits, which open at maturity, or indehiscent fruits, which do not open independently. Schizocarp fruits are in between: they do not open but break into several parts (usually the distinct locules), and each part contains one seed inside. For example, maple fruit consists of two “wings”, each of them contains part of the full fruit and one seed. In addition, fruits can be monomerous (1-seeded) like a nut or an achene, or bear multiple seeds (like the follicle in a tulip, Tulipa). Accessory Fruits Accessory fruits (sometimes called false fruits) are not derived from the ovary, but from another part of the flower, such as the receptacle (Figure \(4\)) or the hypanthium (Figure \(5\)). Dichotomous Key to Common Fruits Use the following dichotomous key to identify fruit types! Note: If the fleshy part of the fruit is composed of something other than the ovary, it is an accessory fruit. 1. Fruit from one carpel of one flower ........[Simple Fruit].... 2 1. Fruit from more than one carpel or from an inflorescence .... 16 2. Fleshy at maturity ....................................... 3 2. Dry at maturity ............................................ 8 3. Thin exocarp, fleshy mesocarp, stony endocarp surrounding single, large seed ............... Drupe 3. Fruit not as described above............................................................................................... 4 4. Seeds in a linear order, separate from ovary wall, pericarp splits on two seams ...Legume (immature) 4. Fruit not as described above.................................................................................. 5 5. Papery endocarp forms a core. Derived from a perigynous flower..........Pome 5. Endocarp fleshy (not a papery core) ...................................................... 6 6. Thin exocarp, fleshy mesocarp, one to many seeds ........................... Berry 6. Exocarp thickened and leathery (modified berries) ………......... 7 7. Exocarp and mesocarp form leathery rind, locules filled with juice-filled trichomes ……...Hesperidium 7. Exocarp forms tough skin/rind, thick mesocarp, not divided into separate locules ........... Pepo 8. Dehiscent (splits open at maturity), usually many seeds ....... 9 8. Indehiscent (does not split open), usually one seeded .......... 12 9. Derived from a carpel with one locule ............................. 10 9. Derived from a carpel with more than one locule ............ 11 10. Dehiscent along one seam .......................... Follicle 10. Dehiscent along two seams ........................ Legume 11. From two locules with a central partition .............. Silique (elongate) or silicle (round) 11. From more than two locules.................................. Capsule 12. Ovary wall extends to form a wing .................. Samara 12. Fruit not winged ............................................... 13 13. Outer wall not especially thick or hard, seed small ... 14 13. Outer wall hardened, seed relatively large ................ 15 14. Seed not tightly attached to pericarp ............... Achene 14. Seed fused to pericarp, grains ........................ Caryopsis 15. Stony pericarp surrounds one large seed .............................................. Nut 15. Relatively thin exocarp, fibrous mesocarp, single large seed .............. (dry) Drupe 16. Derived from one flower with many free carpels ...... Aggregate Fruit 16. Derived from an inflorescence (many florets) ........... Multiple Fruit Fruit and Seed Dispersal The fruit has a single purpose: seed dispersal. Seeds contained within fruits need to be dispersed far from the mother plant, so they may find favorable and less competitive conditions in which to germinate and grow. Fruits promote the dispersal of their content of seeds in a variety of ways: • Ballistic. Some fruits, as they dry, open explosively expelling their seeds. The pods of many legumes (e.g., wisteria) do this. • Wind. Wind-dispersed fruit are lightweight and may have wing-like appendages that allow them to be carried by the wind. Some have a parachute-like structure to keep them afloat. • Water. Many aquatic angiosperms and shore dwellers (e.g., the coconut palm) have floating fruits that are carried by water currents to new locations. • Animal attachment. The cocklebur and sticktights achieve dispersal of their seeds by sticking to the coat (or clothing) of a passing animal. • Animal ingestion. Nuts and berries entice animals to eat them. Buried and forgotten (nuts) or passing through their g.i. tract unharmed (berries), the seeds may end up some distance away from the parent plant. All of the above mechanisms allow for seeds to be dispersed through space, much like an animal’s offspring can move to a new location. Seed dormancy allows plants to disperse their progeny through time: something animals cannot do. Dormant seeds can wait months, years, or even decades for the proper conditions for germination and propagation of the species. These dormant seeds can accumulate in the soil, forming a seed bank. Areas prone to disturbances, like fire, often rely on the seed bank to regenerate plant communities post-disturbance. Ballistic In ballistic dispersal, seeds are shot from the fruit. This can be accomplished via a build up of turgor pressure within the fruit (as in dwarf mistletoe and wild cucumber), a twisting action, or some other method. Watch Video \(1\) to see ballistic seed dispersal in action! Video \(1\): Watch this fun video of different plants utilizing ballistic seed dispersal. Sourced from YouTube. Wind Fruits dispersed by wind, like samaras or the achenes of a dandelion, are generally winged (Figure \(6\)). In the case of a dandelion, each achene is attached to a modified calyx that forms an umbrella-like structure to catch on the wind. Water Some fruits, such as those of some aquatic plants like lotus or plants adapted to island living, are specialized for water dispersal. This usually involves a buoyant pericarp, as in the fibrous husk of the water-dispersed coconut. Similarly, willow and silver birches produce lightweight fruit that can float on water. Watch Video \(2\) to see the journey of a water-dispersed sea bean. Video \(2\): Watch this clip to see the aquatic journey of the sea bean. Toward the end of the video, be on the lookout for mangrove pneumatophores. Sourced from YouTube. Animal Vectors Many fruits have evolved to use animals for dispersal. Fruits with velcro-like projections or sticky pericarps latch onto mammal fur or bird feet and are transported to a new locale without needing to survive a journey through the digestive tract (Figure \(7\)). Other fruits have specialized for animal ingestion. Among these are the fruits we typically consider fruits, those that are typically sweet, fleshy, often brightly colored and intended for consumption. The seeds must either survive the digestive tract, deposited later in nutrient-rich substrate, or depend on animals who are sloppy eaters, dispersing some of the seeds as they eat others. Some of these are highly specialized, with a single species or group of animals as the intended dispersal vector. For example, hot peppers like habañero chiles are hot because they contain a compound called capsaicin (see Figure \(8\)). They also tend to be red. This is because these peppers have specialized for bird dispersal vectors. Both birds and mammals are attracted to the color red. However, mammals often have a more thorough digestive tract, meaning seeds need more investment in protection to survive the journey. However, mammals like you and I interpret capsaicin as spicy, perhaps painful, and are often deterred by it (though many exceptions apply among humans), while birds are immune to these effects. Because of this interesting difference in physiology, some people add cayenne pepper to their suet bird feeders to keep the squirrels away. Some animals, like squirrels, bury seed-containing fruits for later use; if the squirrel does not find its stash of fruit, and if conditions are favorable, the seeds germinate. Some birds are also known to cache nuts for later. Plants that produce nuts generally rely on this storage behavior in their animal dispersers. Attributions Curated and authored by Maria Morrow using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.07%3A_Angiosperm_Diversity/2.7.03%3A_Fruits_and_Dispersal.txt

Learning Objectives • Interpret a floral formula. • Describe the characteristics used to identify each of the four largest angiosperm families. Knowing who is related to whom in the plant world can provide important information. Often, closely related organisms will have similar life history traits, such as defense compounds or other secondary metabolites. Identifying which family an unknown plant belongs to might provide insight into potential interactions with other organisms (see Orchidaceae below), its capability to resist particular environmental conditions or stressors, its edibility or toxicity, or whether it produces compounds that might be used medicinally. For example, plants like poison oak (Toxicodendron diversilobum) and poison ivy (Toxicodendron radicans) are in the family Anacardiaceae and produce an oil called urushiol. This oil causes a (sometimes severe) allergic reaction in many people, resulting in an itchy, blistering rash. Mango (Mangifera indica) and cashew (Anacardium occidentale). also belong to this family, but these are not known for giving itchy rashes. However, as someone who is quite allergic to poison oak, I unknowingly ate a mango with the skin on and broke out in a rash all around my mouth and lower face, just like how I react to touching poison oak. Indeed, cashews are just the seed of the cashew fruit. The rest of the fruit and seed coat are removed due to the urushiol content. Additionally, while there are over 350,000 species of flowering plants, there are only around 400 families. Being able to quickly narrow an unknown plant to family is an essential skill in plant identification. So how can we tell who belongs to the same family among plants? For flowering plants, we can use floral formulas. Floral Formulas Since there are so many terms about flowers, and at the same time, flower structure and diversity always were of immense importance in botany, two specific ways were developed to make flower description more compact. First is a flower formula. This is an approach where every part of flower is designated with a specific letter, numbers of parts with digits, and some other features (whorls, fusion, position) with other signs. • Symmetry: * means radial symmetry, while X means bilateral symmetry. • Whorls: K is the calyx, C is the corolla, A is the androecium, and G is the gynoecium. The number that follows each letter represents the number of parts in that whorl. For the gynoecium, a line under the number indicates an inferior ovary, while a line above the number indicates a superior ovary. • Fusion: In most representations, connation is indicated by circling the number, while adnation is indicated by drawing a line connecting the numbers of the fused whorls. Here are a few examples of floral formulas, followed by their interpretation: $\ast K_{4}C_{4}A_{2+4}G_{\underline{(2)}}$: flower actinomorphic, with four sepals, four petals and six stamens in two whorls, ovary superior, with two fused carpels $\uparrow K_{(5)}[C_{(1,2,2)}A_{2,2}]G_{\underline{(2\times2)}}$: flower zygomorphic, with five fused sepals, five unequal fused petals, two-paired stamens attached to petals, superior ovary with two subdivided carpels $\ast K_{(5)}C_{(5)}[A_{5}G_{\underline{(3)}}]$: actinomorphic flower with five fused sepals and five fused petals, five stamens attached to pistil, ovary inferior, with three fused carpels The following signs are used to enrich formulas: PLUS “+” is used to show different whorls; minus “$-$” shows variation; “$\vee$” = “or BRACKETS “[]” and “()” show fusion. In most representations, connation is indicated by circling the fused whorl, while adnation is indicated by drawing a line underneath the formula connecting those whorls. COMMA “,” shows inequality of flower parts in one whorl MULTIPLICATION “$\times$” shows splitting INFINITY “$\infty$” shows indefinite number of more than 12 parts Flower diagram is a graphical way of flower description. This diagram is a kind of cross-section of the flower. Frequently, the structure of pistil is not shown on the diagram. Also, diagrams sometimes contain signs for the description of main stem (axis) and flower-related leaf (bract). The best way to show how to draw diagram is also graphical (Figure $1$); formula of the flower shown there is $\ast K_{5}C_{5}A_{5}G_{\underline{(5)}}$. Review of Terms and Formula Designations FLOWER PARTS occur in whorls in the following order—sepals, petals, stamens, pistils. (The only exceptions are flowers of Eupomatia with stamens then perianth, Lacandonia with pistils then stamens, and some monocots like Triglochin, where stamens in several whorls connect with tepals.) PEDICEL flower stem RECEPTACLE base of flower where other parts attach HYPANTHIUM cup-shaped receptacle (Figure $2$) PERIANTH = CALYX + COROLLA SEPALS small and green, collectively called the CALYX, formula: K PETALS often large and showy, collectively called the COROLLA, formula: C TEPALS used when sepals and petals are not distinguishable, they form SIMPLE PERIANTH, formula: P ANDROECIUM collective term for stamens: formula: A STAMEN = FILAMENT + ANTHER ANTHER structure containing pollen grains FILAMENT structure connecting anther to receptacle GYNOECIUM collective term for pistils/carpels, formula: G. Gynoecium can be composed of: 1. A single CARPEL = simple PISTIL, this is MONOMERY 2. Two or more fused CARPELS = compound PISTIL, this is SYNCARPY 3. Two or more unfused CARPELS = two or more simple PISTILS, this is APOCARPY (Note that variant #4, several compound pistils, does not exist in nature.) To determine the number of CARPELS in a compound PISTIL, count LOCULES, points of placentation, number of STYLES, STIGMA and OVARY lobes.PISTIL Collective term for carpel(s). The terms CARPEL and PISTIL are equivalent when there is no fusion, if fusion occurs then you have 2 or more CARPELS united into one PISTIL. CARPEL structure enclosing ovules, may correspond with locules or placentas OVARY basal position of pistil where OVULES are located. The ovary develops into the fruit; OVULES develop into seeds after fertilization. LOCULE chamber containg OVULES PLACENTA place of attachment of OVULE(S) within ovary STIGMA receptive surface for pollen STYLE structure connecting ovary and stigma FLOWER Floral unit with sterile, male and female zones ACTINOMORPHIC FLOWER A flower having multiple planes of symmetry, also called radially symmetrical, formula: $\ast$ ZYGOMORPHIC FLOWER A flower having only one plane of symmetry, also called bilaterally symmetrical, formula: $\uparrow$ PERFECT FLOWER A flower having both sexes MALE / FEMALE FLOWER A flower having one sex, formula: ♂ / ♀ MONOECIOUS PLANTS A plant with unisexual flowers with both sexes on the same plant DIOECIOUS PLANTS A plant with unisexual flowers with one sex on each plant, in effect, male and female plants SUPERIOR OVARY most of the flower is attached below the ovary, formula: $G_{\underline{\dots}}$ INFERIOR OVARY most of the flower is attached on the top of ovary, formula: $G_{\overline{\dots}}$ (Inferior ovary only corresponds with monomeric or syncarpous flowers.) WHORL flower parts attached to one node Major Families This section will cover some of the largest families of angiosperms, including their floral formula and general characteristics. Orchidaceae, the Orchid Family Orchids are one of the most species-rich group of plants, containing over 28,000 species (Figure $1$). These plants tend to be tropical and epiphytic (growing on other plants). However, as can be assumed from their vast diversity, orchids can be found in many ecosystems and growing on a variety of substrates, including rocks! Their flowers are often highly modified, including long nectar spurs, hairy petals, and strange morphologies. Many orchids are fly pollinated. Follow this link to see observations of orchids from across the globe and in your region! Orchids make a large number of tiny seeds, i.e. the tiny black specks in vanilla bean ice cream are the seeds of the orchid Vanilla plantifolia. An interesting, r-selected strategy with a twist: the seeds parasitize mycorrhizal fungi. Orchid seeds will not germinate if they do not have a fungal partner. As the fungal hyphae penetrate into the orchid cells, they formed coiled structures. The orchid feeds on the fungal hyphae until it has produced its first leaves and can photosynthesize on its own. At this point, the relationship can be shifted toward mutualism, with sugars transfered from plant to fungus. However, some orchids have lost the ability to make chlorophyll and instead, continue to feed from their fungal partner. These plants are referred to as mycoheterotrophs. The mycoheterotrophic orchid Rhizanthella gardneri undergoes its entire life cycle underground! Asteraceae, the Aster Family or Composite Family There are more than 32,000 accepted species in Asteraceae—a recent and dramatic increase in described species has sent them soaring past the orchids (for the time being). They have a cosmopolitan distribution, but are better represented in temperate and subtropical regions. This family is primarily herbaceous but does contain some woody species. Members of this family produce head inflorescences with one or two different types of florets that all attach to a common receptacle (Figure $4$). Disc florets have radial symmetry, while ligulate florets have bilateral symmetry (Figure $5$). Some inflorescences contain only disc florets (e.g. thistle), some only ligulate florets (e.g. dandelions), and others contain a combination of the two (e.g. daisy). The inflorescence is subtended by layers of bracts called phyllaries, forming an involucre. The calyx is reduced to hairs or bristles (pappus, see Figure $\PageIndex{6-7}$), petals are fused into a tube or ligula (with 5 or 3 teeth). The pollen is lifted up and distributed by the outer sides of the stigmas, called secondary pollen presentation (Figure $6$). Florets have inferior ovaries. The fruit is an achene and the mature seed has almost no endosperm. Many plants withing the Asteraceae are used for oils, vegetables, ornamentals and medicinal plants are distributed in multiple subfamilies. The most commercially important of these are: • Carduoideae: mostly tubular flowers -Centaurea—knapweed -Cynara—artichoke -Carthamus–safflower • Cichorioideae: mostly 5-toothed ligulate (pseudo-ligulate) flowers + lacticifers with latex -Taraxacum—dandelion -Lactuca—lettuce • Asteroideae: tubular + 3-toothed ligulate flowers -Helianthus—sunflower (BTW, “canola”, or Brassica napus from Cruciferae is the second main source of vegetable oil) -Artemisia—sagebrush -Tagetes—marigold and lots of other ornamentals Fabaceae, the Legume Family With around 19,000 species, Fabaceae (Figure $8$) is the third largest angiosperm family after orchids and asters. This family is widely distributed throughout the world, but does particularly well in the tropics. These plants form root nodules with nitrogen-fixing bacteria. Leaves are alternate, pinnately compound (once or twice), with stipules. Plants in this family have legumes as fruits (one locule dehiscent along a single suture). There are three subfamilies (Caesalpinioideae, Mimosoideae, Papilionoideae) with distinct characteristics. In Papilionoideae the petals are mostly free, unequal and have special names: banner, keel and wing (Figure $9$). In Mimosoideae, they fuse and form a tube with radial symmetry. There are usually 10 stamens with 9 fused and one free; in Mimosoideae, stamens are numerous. There is a single carpel in the gynoecium, meaning the ovary will have a single locule. Some representatives of Fabaceae include: • Mimosoideae: stamens numerous, petals connected -Acacia—dominant tree of African and Australian savannas, often with phyllodes -Mimosa—sensitive plant • Papilionoideae: stamens 9+1, petals mostly free; this subfamily contains many extremely important food plants with high protein value -Glycine—soybean -Arachis—peanut with self-buried fruits -Phaseolus—bean -Pisum—pea Poaceae, the Grass Family Grasses are monocots. There are approximately 12,000 species of grasses widely distributed throughout the world, but most genera concentrate in the tropics. Grasses tend to be wind dispersed and prefer dry, sunny places. They often form turf (tussocks)—compact structures where old grass stems, rhizomes, roots, and soil parts are intermixed. Grasses form grasslands—specific ecological communities widely represented on Earth (for example, North American prairies are grasslands). Grasses are also important components of other ecosystems (e.g. wetlands). Stems of grasses are usually hollow and round. The leaves have sheathing bases. Grass florets are reduced, wind-pollinated, usually bisexual (Figure $10$), and form complicated spikelets. Each spikelet bears two glumes; each flower has lemma and palea scales (Figure $11$). The perianth is reduced to lodicules. Stamens from 6 to 1 (most often 3), with large anthers. The fruit of grasses is a caryopsis, what we commonly refer to as a grain. Grasses are incredibly important commercially as food sources, construction, biofuels, and components of many products: rice, corn, wheat, sugarcane, barley, rye, sorghum, and bamboo are all grasses. The study of grasses is called agrostology--it can be both aggravating and glumey. Attribution Curated and authored by Maria Morrow using the following sources: 2.7.05: Chapter Summary Angiosperms are an incredibly diverse group of plants. They have many avenues in which to specialize and speciate. Lineages of flowering plants have evolved in tandem with their pollinators by forming increasingly specialized flowers. These sets of specialized floral characteristics--including morphology, color, smell, and the presence of nectar or pollen--are considered together as the plant's pollination syndrome. Wind pollinated flowers are reduced and lack strong odors or nectar, though they contain large amounts of pollen. Bird pollinated flowers contain lots of nectar that they hide in tubular structures, often pigmented red or pink (colors that birds see well, but bees can't distinguish from greens), and lacking strong scents. Bee pollinated flowers can be a variety of colors, but tend toward blues, purples, and yellows. They tend to have sweet, fresh scents and a place for the bee to land. Moth and bat pollinated flowers are white and open at night. Some flowers have even evolved to trick flies into accidental pollination by mimicking a corpse. They have also evolved fruits specialized for their particular seed dispersal agent. Some fruits release seeds on their own through a variety of explosive mechanisms. Others rely on wind (using wing-like structures) or water (using floats) for dispersal. Still others have coevolved with animals. Some have evolved velcro-like spines or sticky substances to attach to passing animals. Others have evolved to be eaten, some only by specific animals, and hope to survive the digestive tract or have at least some seeds escape the process. These opportunities for specialization, as well as perhaps the influence of self-incompatibility genes and other factors, has resulted in over 350,000 species of angiosperms classified into over 400 families. However, much of angiosperm diversity can be found in a few major families. Among these are the asters (32,000), orchids (28,000), legumes (19,000), and grasses (12,000). After completing this chapter, you should be able to... • Compare and contrast monocots and eudicots. • Differentiate between monocot and eudicot flowers and leaves. • Explain pollination strategies with regard to genetic diversity. • Explain what is meant by the term pollination syndrome. • Use floral characteristics to predict a plants pollinator(s). • Describe the transition from ovary and ovule to fruit and seed. • Use characteristics of fruits, including pericarp morphology, to identify fruit type. • Use characteristics of fruits to predict the dispersal agent for a plant's seeds. • Interpret a floral formula. • Describe the characteristics used to identify each of the four largest angiosperm families. Attribution Content by Maria Morrow, CC BY-NC

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/02%3A_Biodiversity_(Organismal_Groups)/2.07%3A_Angiosperm_Diversity/2.7.04%3A_Angiosperm_Families.txt

Plants cells are complex structures with several organelles lacking in animal cells. Among these are the cell wall, central vacuole, and plastids (the most familiar of which are chloroplasts). There are three main tissue types, called epidermal, ground, and vascular tissue. Each tissue type consists of specialized cells adapted for unique functions. Plants have two organ systems: the root system and the shoot system (figure \(\PageIndex{a}\)). The root system is typically belowground and consists of roots, which specialized in water and nutrient absorption. The shoot system consists of stems and leaves and is typically aboveground. Stems function in supporting the plant and transporting materials (conduction), and leaves function in photosynthesis. This unit will explore these structure at the macroscopic and microscopic level. • 3.1: Cells and Tissues A cell is the smallest unit of a living thing. Organisms can be unicellular or multicellular. Thus, cells are the basic building blocks of all organisms. Several plant cells of one kind that interconnect with each other and perform a shared function form tissues. • 3.2: Roots Roots are an important plant organ. They anchor the plant, transport water, minerals, and sugars, and store excess nutrients. • 3.3: Stems The stem is an organ of the shoot system that functions in support, conduction, photosynthesis, and storage. • 3.4: Leaves Leaves are the organs of the shoot system adapted for photosynthesis. They often consist of a petiole and a blade. Leaves differ with respect to their arrangement on the venation, and shape. Internally, leaves consist of three main tissues: epidermis, mesophyll, and vascular bundles. Some leaves are modified for other functions such as defense, storage, or attachment. Thumbnail Image: Cross section of a beach grass leaf from Berkshire Community College Bioscience Image Library (public domain). 03: Plant Structure Plants are multicellular organisms composed of eukaryotic cells. Cells are the basic building blocks of the organism. Plants are autotrophic and thus many of their cells contain large amounts of chloroplast, the organelle for photosynthesis (Figure \(1\)). The green color of leaves are due to the large amounts of chloroplast within the cells. Plant cells obtain many other organelles, which we will study in this chapter (Figure \(2\)). Cells with similar functions are arranged in tissues, which are arranged into plant organs such as roots, stems, and leaves. Together, these organs and their associated organ systems form the plant organism. • 3.1.1: Introduction to Cells The cell theory states that 1) all plants and animals are composed of cells and that (2) cell is the most basic unit of life, and (3) all cells arise by reproduction from previous cells. Eukaryotic cells are generally around 10 - 100 μm in size. As a cell increases in size, its surface area-to-volume ratio decreases, decreasing the efficiency of transport. • 3.1.2: Plant Cell Structure All cells have a plasma membrane, cytoplasm, and ribosomes. Eukaryotic cells are typically larger, have a true nucleus , and have other membrane-bound organelles that allow for compartmentalization of functions. • 3.1.3: Plant Tissues Tissue is a union of cells which have common origin, function and similar morphology. Tissues belong to organs: organ is a union of different tissues which have common function(s) and origin. Plants have simple and complex tissues. The simple tissues (tissues with uniform cells) are composed of the same type of cells; complex tissues (tissues with more than one type of cells) are composed of more than one type of cell, these are unique to plants. • 3.1.4: Chapter Summary Attribution Kammy Algiers (CC-BY-NC) 3.01: Cells and Tissues Learning Objectives • Describe the role of cells in organisms. • Summarize cell theory. • Address the significance of cell size. A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a plant, Figure \(1\)), we call it an organism. Thus, cells are the basic building blocks of all organisms. Several plant cells of one kind that interconnect with each other and perform a shared function form tissues. An example of a plant tissue would be the epithelial tissue found on the surface of a leaf. These tissues combine to form an organ, such as a leaf. and several organs comprise an organ system (in this case, the shoot system). Two two plant organ systems, the shoot and root system, make up the plant. Here, we will examine the structure and function of cells. Cell Theory In 1665, Robert Hooke looked at cork under a microscope and saw multiple chambers which he called “cells”. In 1838, Schleidern and Schwann stated that (1) all plants and animals are composed of cells and that (2) cell is the most basic unit (“atom”) of life. In 1858, Virchow stated that (3) all cells arise by reproduction from previous cells (“Omnis cellula e cellula” in Latin). These three statements became the base of the cell theory. Cell Size At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm (Figure \(2\). The prokaryotes' small size allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport. Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had a cube shape (Figure \(3\)). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide. Other ways are to increase surface area by foldings of the cell membrane, become flat or thin and elongated, or develop organelles that perform specific tasks. These adaptations lead to developing more sophisticated cells, which we call eukaryotic cells. Attributions Curate and authored by Kammy Algiers using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.01%3A_Cells_and_Tissues/3.1.01%3A_Introduction_to_Cells.txt

Learning Objectives • Describe the structures that all cells share in common. • State the role of the plasma membrane. • Describe the structures of eukaryotic cells. • Summarize the functions of the major cell organelles. Components of All Cells All cells contain these same four components: 1. plasma (cell) membrane, a phospholipid bilayer with a mosaic of proteins, which functions as a barrier between the cell and its environment. 2. cytoplasm, the region between the region of DNA and plasma membrane, and the cytosol, a fluid, jelly-like region inside the cell where chemical reactions take place. 3. DNA, the heredity information of cells, which can be found in a nucleus of eukaryotic cells and the a nucleoid region of prokaryotic cell. 4. ribosomes, or protein-synthesizing structures composed of ribosomes and proteins. These structures can be found on the image of the plant cell (Figure \(1\)). The Plasma Membrane Both prokaryotic and eukaryotic cells have a plasma membrane (Figure \(2\)), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane. The plasma membrane are semi-permeable and allow small and/or non-polar molecules to pass through. Water, being small, can pass through the membrane and will move from an area of low solute concentration to an area of high solute concentration by the process of osmosis. The Cytoplasm The cytoplasm is the cell's entire region between the plasma membrane and the nuclear envelope (a structure we will discuss shortly). It is comprised of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure \(1\)). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are also there. Ions of sodium, potassium, calcium, and many other elements also dissolve in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm. DNA In eukaryotic cells, the DNA is typically housed in a nucleus (plural = nuclei), the most prominent organelle in a cell (Figure \(1\). This organelle directs the synthesis of ribosomes and proteins. Let’s look at it in more detail (Figure \(3\)). The Nuclear Envelope The nuclear envelope is a double-membrane structure that constitutes the nucleus' outermost portion (Figure \(3\). Both the nuclear envelope's inner and outer membranes are phospholipid bilayers. The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus. Chromatin and Chromosomes To understand chromatin, it is helpful to first explore chromosomes, structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nucleus of each cell. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins attach to chromosomes, and they resemble an unwound, jumbled bunch of threads. We call these unwound protein-chromosome complexes chromatin (Figure \(4\). Chromatin describes the material that makes up the chromosomes both when condensed and decondensed. The Nucleolus We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out through the pores in the nuclear envelope to the cytoplasm. Ribosomes Ribosomes are the cellular structures responsible for protein synthesis. They are not organelles. They can be small dot-like structures that float freely in the cytoplasm (known as free ribosomes) or they may be attached to the plasma membrane's cytoplasmic side or the endoplasmic reticulum's cytoplasmic side and the nuclear envelope's outer membrane, and called attached ribosomes (Figure \(1\)). Ribosomes are large protein and RNA complexes consisting of two subunits, a large and a small (Figure \(5\). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA transcribes into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins. Because protein synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), there are ribosomes in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function. Components Unique to Eukaryotic Cells All cells contain DNA, as described above. However, plant cells, which are eukaryotic, contain organelles and a nucleus while prokaryotic cells do not possess organelles or a membrane bound nucleus. We will start by going over the structures that are unique to all eukaryotic. Next, we will go over structures unique to plant cells. Endomembrane System The endomembrane system (endo = “within”) is a group of membranes and organelles (Figure \(6\)) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the tonoplast (see below), and the endoplasmic reticulum and Golgi apparatus. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include either mitochondria or chloroplast membranes. The Endoplasmic Reticulum The endoplasmic reticulum (ER) (Figure \(6\)) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. They are formed as an extension of the nuclear membrane and fold out towards the cytoplasm. The two functions of the ER take place in separate areas: the rough ER and the smooth ER, respectively. The rough endoplasmic reticulum (RER) can be found has ribosomes along its surface, and the proteins they create are either secreted or incorporated into membranes in the cell. The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (Figure \(6\)). SER functions include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storing calcium ions. Vesicles Transport vesicles, composed of endomembrane system material, bud off the from the RER, carrying material into the Golgi Apparatus, the next component of the endomembrane system. Golgi Apparatus The lipids or proteins within the transport vesicles still need sorting, packaging, and tagging so that they end up in the right place. Sorting, tagging, packaging, and distributing lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes (Figure \(6\)). We call the side of the Golgi apparatus that is closer to the ER the cis face. The opposite side. closer to the plasma membrane, is the trans face. The transport vesicles that formed from the ER travel to the cis face of the Golgi, fuse with it, and empty their contents into the Golgi apparatus' lumen. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is adding short sugar molecule chains. These newly modified proteins and lipids then tag with phosphate groups or other small molecules in order to travel to their proper destinations. Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the Golgi's trans face. While some of these vesicles deposit their contents into other cell parts where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell. In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which other cell parts use. Cytoskeleton The cellular skeleton is a collection of protein filaments within the cytoplasm. Microtubules are key organelles in cell division, they form the basis for cilia and flagella. Plant cells do not have cilia, which are short projections from the cell that function in movement, but the sperm cells of early diverging plants, like bryophytes and seedless vascular plants, have flagella. These are long projections that function in movement. Microtubules are also are guides for the construction of the cell wall, and cellulose fibers are parallel due to the microtubules. The movement in microtubules is based on tubulin-kinesin interactions. In contrast, the movement of microfilaments is based on actin-myosin interactions. Microfilaments guide the movement of organelles within the cell. Mitochondria Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making a nucleic acid called adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct. In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need a lot of energy to keep your body moving. When your cells don’t get enough oxygen, they do not make a lot of ATP. Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid. Mitochondria are oval-shaped, double membrane organelles (Figure \(7\)) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration. Peroxisomes Eukaryotic cells frequently have smaller vesicles including peroxisomes which, among other functions, help in photosynthesis in plant cells. In addition, many plant cells accumulate lipids as oil drops located directly in cytoplasm. Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water.) For example, alcohol is detoxified by peroxisomes in liver cells. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Components Unique to Plant Cells The following structures are found exclusively in plant cells and are absent in animal cells. Cell wall Though a cell wall is commonly found in prokaryotes and fungi as well as plants, their diversity is due to convergent evolution, not common ancestry, when it comes to these three groups of organisms. Plant cell walls are composed of cellulose are an excretion found outside the plasma membrane. They serve as a covering that provides structural support and gives shape to the cell. Central Vacuole The central vacuole is a large, membrane-bound structure that fills much of the plant cell. The membrane surrounding the central vacuole is called the tonoplast. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That’s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm (Figure \(8\)). As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the plant's cell walls results in the wilted appearance. The central vacuole also supports the cell's expansion. When the central vacuole holds more water, the cell becomes larger without having to invest considerable energy in synthesizing new cytoplasm. Lastly, central vacuoles store nutrients, accumulate ions, or become a place to store wastes. Plastids Plastids are a group of storage organelle found in plants and algae. Chloroplasts are a type of plastid that store chlorophyll and other pigments for photosynthesis. Chromoplasts are plastids that store orange or yellow pigments, found in plants and fruit such as bell peppers. They are rich in carotenes and xanthophyls. Amyloplasts store starch and can be found in plants such as potato tubers, carrot roots, sweet potato roots, and grass seeds. Chloroplasts store their pigments in interconnected sacs called thylakoids (Figure \(9\)). These sacs are often found in stacks called grana (singular granum). The fluid portion of the double membraned chloroplast is called the stroma. Because the thylakoid stores chlorophyll a, b, and accessory pigments, it is the main region for the first reaction of photosynthesis, where sunlight is used to create molecular energy. In the stroma, the products of the first reaction are used to produce organic molecules such as glucose. The combination of these reactions allow these autotrophic organisms to produce their own organic food. The chloroplast, like the mitochondria, contains its own DNA, ribosomes, and is double membraned. Evolution Connection- Endosymbiosis We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why an organelle would have its own DNA and ribomosome? The Endosymbiosis Theory explains: Symbiosis is a relationship in which organisms from two separate species depend on each other for their survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. For example, there are microbes that produce vitamin K living inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and from drying out, and they receive abundant food from the environment of the large intestine. Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just as mitochondria and chloroplasts do. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts. Attributions Curated and authored by Kammy Algiers using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.01%3A_Cells_and_Tissues/3.1.02%3A_Plant_Cell_Structure.txt

Learning Objectives • Describe the difference between meristematic and non-meristematic tissues. • Compare and contrast dermal, ground, and vascular tissue. Plants are multicellular eukaryotes with tissue systems made of various cell types that carry out specific functions. Plant tissues are composed of cells that are similar and perform a specific function. Together, tissue types combine to form organs. Each organ itself is also specific for a particular function. Plant tissue systems fall into one of two general types: meristematic tissue, and permanent (or non-meristematic) tissue. Cells of the meristematic tissue are found in meristems, which are plant regions of continuous cell division and growth. Meristematic tissue cells are either undifferentiated or incompletely differentiated, and they continue to divide and contribute to the growth of the plant. In contrast, permanent tissue consists of plant cells that are no longer actively dividing. Meristematic tissues consist of three types, based on their location in the plant. Apical meristems contain meristematic tissue located at the tips of stems and roots, which enable a plant to extend in length. Lateral meristems facilitate growth in thickness or girth in a maturing plant. Intercalary meristems occur only in monocots, at the bases of leaf blades and at nodes (the areas where leaves attach to a stem). This tissue enables the monocot leaf blade to increase in length from the leaf base; for example, it allows lawn grass leaves to elongate even after repeated mowing. Meristems produce cells that quickly differentiate, or specialize, and become permanent tissue. Such cells take on specific roles and lose their ability to divide further. They differentiate into three main types: dermal, vascular, and ground tissue. Dermal tissue covers and protects the plant. The ground tissue serves as a site for photosynthesis, provides a supporting matrix for the vascular tissue, and helps to store water and sugars. The vascular tissue transports water, minerals, and sugars to different parts of the plant. Ground tissue is a simple tissue, meaning that each ground tissue consists of only one cell type. Dermal and vascular tissues are complex tissues because they consist of multiple cell types. Dermal Tissue Dermal tissue covers the plant and can be found on the outer layer of roots, stems and leaves. Its main functions are transpiration, gas exchange and defense. The epidermis is an example of dermal tissue (Figure \(1\)). It is composed of a single layer of epidermis cells. It may contains stomata and guard cells that allow gas exchange. It may contain root hairs that increase surface area or or trichomes used in transpiration or defense. It may contain a waxy cuticle if found on the upper surface of leaves, to aid with lowering transpiration. In woody plants, the epidermis breaks apart into a thick periderm as secondary growth allows the plant to grow in girth. The cork cambium, which makes cork cells, the cork cells (which are dead at maturity), and the phelloderm (parenchyma cells on the inside of the cork cambium) together make up the periderm (Figure \(2\)). The periderm functions as the first line of defense for the plant, protecting it from fire or heat injury, dehydration, freezing conditions, and/or disease. Ground Tissue Often times, tissues that are not considered dermal or vascular tissue are noted as ground tissue. These cells store molecules (such as starch), photosynthesize (such as mesophyll cells), or support the plant. There are three types of ground tissue: collenchyma, sclerenchyma, and parenchyma. Collenchyma (Figures \(\PageIndex{3-4}\)) is living supportive tissue that has elongated cells and an unevenly thickened primary cell wall. Its main function is the mechanical support of young stems and leaves via turgor. Sclerenchyma is a dead supportive tissue that consists of long sclerenchyma fibers (Figure \(4\)) or short, crystal-like cells (sclereids; Figure \(5\)). Sclerenchyma fibers occur in groups (bundles). Sclereids may be branched or not and occur individually or in small clusters. Each cell has a uniformly thick secondary wall that is rich in lignin. Its main function is a support of older plant organs, and also hardening different parts of plants (for example, make fruit inedible before ripeness so no one will take the fruit before seeds are ready to be distributed). Without sclerenchyma, if a plant isn’t watered, the leaves will droop because the vacuoles will decrease in size which lowers the turgor. Fibers inside phloem (see below) are sometimes regarded as a separate sclerenchyma. Parenchyma (Figure \(4\)) are spherical, elongated cells with a thin primary cell wall. It is a main component of young plant organs. The basic functions of parenchyma are photosynthesis and storage. They are also important in regeneration because they are totipotent (capable of differentiating into any cell type). Parenchyma cells are widespread in plant body. They fill the leaf, frequent in stem cortex and pith and is a component of complex vascular tissues (see below). Vascular Tissue Vascular tissue is the plumbing system of the plant. It allows water, minerals, and dissolved sugars from photosynthesis to pass through roots, stems, leaves, and other parts of the plant. It is primary composed of two types of conducting tissue: xylem and phloem. The veins on leaves are an example of vascular tissue, moving material through the plant in the same manner that our blood vessels carry nutrients through our body. The xylem and phloem always lie adjacent to each other (Figure \(6\)). In stems, the xylem and the phloem form a structure called a vascular bundle; in roots, this is termed the vascular stele or vascular cylinder. Xylem tissue transports water and minerals from the roots to different parts of the plant. The conducting cells of the xylem are called tracheary elements. Parenchyma cells are also found in the xylem, and sclerenchyma fibers and sclereids are sometimes present. There are two type of tracheary elements: vessel elements and tracheids (Figure \(7\)). Both cell types that are dead at maturity and have thickened secondary cell walls. These cells connect to one another and allow water to be transported through them. Structurally, the vessel elements are wider than tracheids and contain perforation plates between adjacent vessel elements (Figure \(\PageIndex{7-8}\)). Wide openings (slits or pores) in perforation plates allow water to flow vertically between vessel elements, forming a continuous tube. Both types of tracheary elements contain pits, gaps in their secondary cell walls. Adjacent cells have pits in the same locations, forming pit pairs, which allow water and minerals to flow between adjacent cells through the pit membrane (the remaining, thin primary cell walls in these regions; Figure \(\PageIndex{9-10}\)). Therefore, water flows through both perforation plates and pit pairs in vessel elements but only through pit pairs in tracheids. While water can move more quickly through vessel elements, they are more susceptible to air bubbles. An air bubble disrupts cohesion in the column of water moving up the tube of vessel elements preventing use of that particular pathway. In tracheids, an air bubble would only decommission a single tracheid rather than an entire column of vessel elements. Vessel elements are found only in angiosperms, but tracheids are found in both angiosperms and gymnosperms. Phloem tissue transports organic compounds such as sugars from the site of photosynthesis to rest of the plant (Figure \(\PageIndex{11-12}\)). The conducting cells of the phloem are called sieve elements. In comparison to tracheary elements, sieve elements have only primary cell walls (and thus thinner cell walls overall) and are alive at maturity; however, they lack certain organelles, including a nucleus. Sieve-tube elements are the sieve elements found only in angiosperms while sieve cells are found only in gymnosperms while. Both types of sieve elements have pores in their cell walls (sieve areas) that allow transfer of materials between adjacent cells, but these are concentrated at sieve plates in sieve-tube elements and evenly distributed in sieve cells. Because they lack essential organelles, sieve elements rely on specialized parenchyma cells to support them. Companion cells support sieve-tube elements in angiosperms, and albuminous cells support sieve cells in gymnosperms. Additionally parenchyma cells and sclerenchyma cells (phloem fibers) are also found in the phloem. The table below summarizes differences between xylem and phloem: Xylem Phloem Contains mostly Dead cells Living cells Transports Water & Minerals Sugar Direction Up Up and Down Biomass Big Small Meristematic Tissue Meristems produce cells that quickly differentiate, or specialize, and become permanent tissue. Such cells take on specific roles and lose their ability to divide further. They differentiate into three main types: dermal, vascular, and ground tissue. Dermal tissue covers and protects the plant, and vascular tissue transports water, minerals, and sugars to different parts of the plant. Ground tissue serves as a site for photosynthesis, provides a supporting matrix for the vascular tissue, and helps to store water and sugars. Attributions Curated and authored by Kammy Algiers and Melissa Ha using the following sources: 3.1.04: Chapter Summary A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a plant), we call it an organism. Thus, cells are the basic building blocks of all organisms. Eukaryotic cells are generally around 10 to 100 μm in size. As a cell increases in size, its surface area-to-volume ratio decreases, decreasing the efficiency of transport. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. All cells contain these same four components: 1. plasma (cell) membrane, 2. cytoplasm and the fluid region, cytosol, 3. DNA, and 4. ribosomes. Eukaryotic cells contain organelles and a membrane-bound nucleus that is attached to an endomembrane system. The main structures that comprise the endomembrane system are the endoplasmic reticulum, vesicles, and the Golgi body. Furthermore, eukaryotic cells contain cytoskeleton and a mitochondria. Plant cells contain some structures animal cells don't possess: a cell wall, central vacuole, peroxisomes, and plastids, most notably chloroplasts. The mitochondria and chloroplast have evolved via the Endosymbiosis Theory. Several plant cells of one kind that interconnect with each other and perform a shared function form tissues. Plant tissue systems fall into one of two general types: meristematic tissue, and permanent (or non-meristematic) tissue. Dermal tissue covers the plant and can be found on the outer layer of roots, stems and leaves. Vascular tissue is the plumbing system of the plant. It allows water, minerals, and dissolved sugars from photosynthesis to pass through roots, stems, leaves, and other parts of the plant. It is primary composed of two types of conducting tissue: xylem and phloem. Tissues that are not considered dermal or vascular tissue are noted as ground tissue. These cells store molecules (such as starch), photosynthesize (such as mesophyll cells), or support the plant. Ground tissue is often divided into three cell types: collenchyma, sclerenchyma, and parenchyma. After completing this chapter, you should be able to... • Describe the role of cells in organisms. • Summarize cell theory. • Address the significance of cell size. • Describe the structures that all cells share in common. • State the role of the plasma membrane. • Describe the structures of eukaryotic cells. • Summarize the functions of the major cell organelles. • Describe the difference between meristematic and non-meristematic tissues. • Compare and contrast dermal, ground, and vascular tissue. Attribution Curated and authored by Kammy Algiers using 4.1 Studying Cells and 4.3 Eukaryotic cells from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.01%3A_Cells_and_Tissues/3.1.03%3A_Plant_Tissues.txt

Roots are plant organs that are usually found underground. They not only anchor the plant, but also transport water, minerals, and sugars. In many plants, carbohydrates are stored in the roots so they can be used when needed. Roots can be very deep, and spread out very far. Some roots are as deep as the tree is high. Roots can also spread far beyond the canopy of the tree. However, being underground, they are often gone unnoticed. Attribution Kammy Algiers (CC BY-NC) 3.02: Roots Learning Objectives • Describe the types of organs and organ systems in plants. • Describe the function of roots. Plant tissues form organs (such as leaves, stems, or roots), each of which perform a specific set of functions. Together, organs often work to form organ systems. Vascular plants have two distinct organ systems: a shoot system, and a root system. The shoot system consists of two portions: the vegetative (non-reproductive) parts of the plant, such as the leaves and the stems, and the reproductive parts of the plant, which include flowers and fruits. The shoot system generally grows above ground, where it absorbs the light needed for photosynthesis. The root system, which anchors the plant into the ground, absorbs water and minerals, and serves as a storage site for food is usually underground. (Figure \(1\)) shows the organ systems of a typical plant. Attribution Curated and authored by Kammy Algiers using 30.3 Roots from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org. 3.2.02: External Root Structure Learning Objective Identify the types of root systems found in plants. There are two types of root systems. The first is a fibrous root system which has multiple big roots that branch and form a dense mass which does not have a visible primary root (“grass-like”). The other is the tap root system which has one main root that has branching into lateral roots (“carrot-like”). Root systems are mainly of two types (Figure \(1\)). Eudicots have a tap root system, while monocots have a fibrous root system. A tap root system has a main root that grows down vertically, and from which many smaller lateral roots arise. Dandelions are a good example; their tap roots usually break off when trying to pull these weeds, and they can regrow another shoot from the remaining root). A tap root system penetrates deep into the soil. In contrast, a fibrous root system is located closer to the soil surface, and forms a dense network of roots that also helps prevent soil erosion (lawn grasses are a good example, as are wheat, rice, and corn). Some plants have a combination of tap roots and fibrous roots. Plants that grow in dry areas often have deep root systems, whereas plants growing in areas with abundant water are likely to have shallower root systems. Along with having different systems, there are primary root that originated from the root of the seedling (Figure \(\PageIndex{2a}\)) and secondary (lateral) roots originate from the primary roots, and adventitious roots originate on stems or leaves, rather than from the base of the embryo. Adventitious roots can grow if plant cuttings are placed in water (Figure \(\PageIndex{2b}\)). Attribution​ Curated and authored by Kammy Algiers using 5.5 The Root from Introduction to Botany by Alexey Shipunov (public domain)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.02%3A_Roots/3.2.01%3A_Organs_and_Organ_Systems.txt

Learning Objectives • Describe the different structures and zones of a root. • Compare and contrast a monocot root to a eudicot root. • Describe secondary root growth and the function of vascular and cork cambium. Root Anatomy Root growth begins with seed germination. When the plant embryo emerges from the seed, the radicle of the embryo begins to grow downward and forms the root system. As the root system grows, various structures begin to appear. Longitudinal Section If you were to cut a root down longitudinally, you would see the various layers inside. The tip of the root is protected by the root cap, a structure exclusive to roots and unlike any other plant structure. The root cap is continuously replaced because it gets damaged easily as the root pushes through soil. The root tip can be divided into three zones: a zone of cell division, a zone of elongation, and a zone of maturation and differentiation (Figure \(1\)). The zone of cell division is a continuation of the root cap; it is made up of the actively dividing cells of the root meristem. The zone of elongation is where the newly formed cells begin to increase in length, thereby lengthening the root. They are older than cells at the zone of cell division. Beginning at the first root hair is the zone of cell maturation where the root cells begin to differentiate into special cell types. The root has an outer layer of cells called the epidermis, which surrounds areas of ground tissue and vascular tissue. The epidermis provides protection and helps in absorption. Root hairs, which are extensions of root epidermal cells, increase the surface area of the root, greatly contributing to the absorption of water and minerals. All three zones are in the first centimeter or so of the root tip. Cross Section If you were to cut a cross section of the leaf, you could see other features that are not as obvious in the longitudinal section. Inside the root, the ground tissue may form two regions: the cortex and the pith (Figure \(2\)). When comparing roots to stems, roots have much more cortex and very little pith. Whereas eudicot roots have no central pith, monocots have a small pith. Both cortex and pith include cells that store photosynthetic products. The cortex is between the epidermis and the vascular tissue, whereas the pith lies between the vascular tissue and the center of the root. The inner portion of the root contains the vascular tissue (xylem and phloem). This area is called the stele. A layer of cells known as the endodermis borders the stele (Figure \(2\)) and is considered the innermost layer of the cortex. The endodermis is exclusive to roots, and serves as a checkpoint for materials entering the root’s vascular system. A waxy substance called suberin is present on the walls of the endodermal cells. This waxy region, known as the Casparian strip, forces water and solutes to cross the plasma membranes of endodermal cells instead of slipping between the cells. This ensures that only materials required by the root pass through the endodermis, while toxic substances and pathogens are generally excluded. The outermost cell layer of the root’s vascular tissue is the pericycle, an area that can give rise to lateral roots. Monocots Note that the size of the stele in the monocot cross section is large (everything inside the green ring (Figure \(3\)). The vascular tissue is arranged in a ring around the pith. This arrangement is called a siphonostele. The cortex surrounds the stele. The endodermis is the innermost layer of the cortex, and the exodermis is the outermost layer of the cortex. The exodermis controls the flow of water, ions, and nutrients. The outermost layer of the root (external to the cortex) is the epidermis, which covers the root and aids in absorption. In eudicot roots, the vascular tissue fills the center of the root, and there is no pith. This arrangment is called a protostele. The xylem and phloem of the stele are arranged alternately in an X shape (Figure \(4\)). Most of the root is composed of cortex tissue, and the endodermis, the innermost layer of the cortex, borders the stele. The outer layer of the root (external to the cortex) is the epidermis. Secondary Root Growth Many roots have secondary growth as well as primary growth (figures \(\PageIndex{5-6}\)). This occurs by the production of two types of meristemic tissue, the vascular cambium and the cork cambium. The cork cambium is responsible for the girth or growth in the diameter of the root. This occurs by the cork cambium adding vascular tissue to the root. Cells of the pericycle and procambium (the meristematic tissue between the primary phloem and xylem) begin division, and form a vascular cambium around the primary xylem. The vascular cambium then divides to form secondary xylem on the inside and secondary phloem on the outside. Some roots with secondary growth may form a periderm (a protective layer, replacing the epidermis). This occurs by the formation of a cork cambium which originate from the pericycle. The cork cambium produces parenchyma tissues called phelloderm to the inside of the root and the cork on the outside of the root. Cork cells (phellem) are dead at maturity. They are hollow and the addition of air space in the tissue functions as a protective layer. They also produce a waxy substance called suberin. This wax functions to aid in water loss. It also makes the root more resistant to bacterial and fungal infections. The three layers 1. phelloderm 2. cork cambium and 3. cork cells are collectively known as the periderm. Attributions Curated and authored by Kammy Algiers and Melissa Ha from the following sources

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.02%3A_Roots/3.2.03%3A_Internal_Root_Structure.txt

Learning Objective Describe the types of modified roots and their functions. Root structures may be modified for specific purposes. For example, some roots are bulbous and store starch. Tap roots in plants such as carrots, turnips, and beets, are examples of roots that are modified for food storage (Figure $1$). Aerial roots are forms of aboveground roots that provide additional support to anchor the plant. Epiphytic roots are a type of aerial root that enable a plant to grow on another plant. For example, the epiphytic roots of orchids develop a spongy tissue to absorb moisture. The banyan tree (Ficus sp.) begins as an epiphyte, germinating in the branches of a host tree. The plant's aerial roots develop from the branches and eventually reach the ground, providing additional support (Figure $2$). In screwpine (Pandanus sp.), a palm-like tree that grows in sandy tropical soils. Plants which grow on sand have another problem: their substrate constantly disappears. To avoid this, plants developed contractile roots which may shorten and pull plant body deeper into the sand. Plants growing in ocean coastal swamps need additional specializations. Roots of mangroves are frequently modified into supportive aerial roots called stilt roots. Stilt roots are adventitious and grow from lateral branches. Swamp plants are often flooded and need additional adaptations for respiration. Pneumatophores are specialized roots that grow upward and allow oxygen and carbon dioxide exchange from the plant's root system. They passively catch the air via multiple pores (Figure $3$). Some aerial roots will function as photosynthetic organs as well. Though rare, you can see green photosynthetic roots in some plants such as epiphytic orchids (Figure $4$). In some cases, the plant is leaf-less so all the photosynthesis is done by the aerial roots. In other plants, the aerial roots aid in photosynthesis. Root nodules present on the roots of nitrogen-fixing plants, they contain bacteria capable to deoxidize atmospheric nitrogen into ammonia: N$_2$ $\rightarrow$ NH$_3$. Root nodules contain also hemoglobin-like proteins which facilitate nitrogen fixation by keeping oxygen concentration low. Nitrogen-fixing plants are especially frequent among faboid rosids: legumes (Leguminosae family) and many other genera (like alder, Alnus, or Shepherdia, buffaloberry) have root nodules with bacteria. Some other plants (mosquito fern, Azolla and dinosaur plant, Gunnera) employ cyanobacteria for the same purpose. Mycorrhiza is a root modification started when fungus penetrates root and makes it more efficient in mineral and water absorption: it will exchange these for organic compounds. In addition to mycorrhizal fungi, endophytic fungi inhabit other plant organs and tissues. Attributions Curated and authored by Kammy Algiers using 30.3 Roots from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org. 3.2.05: Chapter Summary Roots help to anchor a plant, absorb water and minerals, and serve as storage sites for food. Taproots and fibrous roots are the two main types of root systems. In a taproot system, a main root grows vertically downward with a few lateral roots. Fibrous root systems arise at the base of the stem, where a cluster of roots forms a dense network that is shallower than a taproot. The growing root tip is protected by a root cap. The root tip has three main zones: a zone of cell division (cells are actively dividing), a zone of elongation (cells increase in length), and a zone of maturation (cells differentiate to form different kinds of cells). The root's ground tissue contains cortex and pith while its vascular tissue contains xylem and phloem. Monocots and eudicots have different organization of their vascular tissues, with the monocot vascular tissue organized into a characteristic ring around the central pith while the eudicot vascular tissue forms an "X" shape in the center of the root and lacks a pith. Many roots have secondary growth as well as primary growth. Secondary growth occurs by the production of two types of meristemic tissue, the vascular cambium and the cork cambium. In some habitats, the roots of certain plants may be modified and adapted for various environments. Some examples of these modifications result in storage roots, aerial roots, epiphytic roots, contractile roots, stilt roots, penumatophores, and photosynthetic roots. Root nodules and mycorrhizae are root adaptations that increase the efficiency of nutrient uptake. After completing this chapter, you should be able to ... • Describe the types of organs and organ systems in plants. • Describe the function of roots. • Identify the types of root systems found in plants. • Describe the different strictures and zones of a root. • Compare and contrast a monocot root to a eudicot root. • Describe secondary root growth and the function of vascular and cork cambium. • Describe the types of modified roots and their functions. Glossary adventitious root Casparian strip endodermis fibrous root system pericycle root cap root hair stele tap root system

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.02%3A_Roots/3.2.04%3A_Root_Modifications.txt

The shoot system of a plant consists of stems and leaves (Figure \(1\)). Stems may range in length from a few millimeters to hundreds of meters, and also vary in diameter, depending on the plant type. Stems are usually aboveground, although the modified stems of some plants, such as the potato, also grow underground. Stems may be herbaceous (soft) or woody in nature. A stem may be unbranched, like that of a palm tree, or it may be highly branched, like that of a magnolia tree. The stem of the plant functions in support, conduction, photosynthesis, and storage. Stems support leaves, flowers, and buds. They connect the roots to the leaves, helping to transport absorbed water and minerals to different parts of the plant. It also helps to transport the products of photosynthesis, namely sugars, from the leaves to the rest of the plant. Stems also store food for the plant, mainly in the form of starch. Attributions Curated and authored by Melissa Ha using the following sources: Thumbnail image: Cross section of the woody stem of Aristolochia. Image by Berkshire Community College Bioscience Image Library (public domain). 3.03: Stems Learning Objective Identify the main external structures of the shoot system, including the nodes, internodes, leaves, axillary buds, and axillary shoots. Plant stems, whether above or below ground, are characterized by the presence of nodes and internodes (Figure \(1\)). Nodes are points of attachment for leaves. Leaves often consist of a thin region that attaches to the stem (the petiole) and a broader blade (see Leaves). The stem region between two nodes is called an internode. An axillary bud is usually found in the axil—the area between the base of a leaf and the stem—where it can give rise to a branch called an axillary shoot (Figure \(2\)). The shoot apex at the tip shoot contains the shoot apical meristem surrounded by developing leaves called leaf primordia (see Meristems). Attributions Curated and authored by Melissa Ha from 30.2 Stems from Biology 2e by OpenStax (licensed CC-BY) 3.3.02: Internal Anatomy of the Primary Stem Learning Objectives • Identify the structures representing each of the three tissue systems in stems. • Compare the structure of solenosteles, eusteles, and atactosteles. • Explain the arrangement of leaf traces, leaf trace gaps, branch traces, and branch trace gaps. The primary stem refers to the herbaceous (non-woody) stem, which has not undergone secondary growth (the growth that produces bark and wood). Some species (all monocots and some eudicots) remain herbaceous for their entire lives, maintaining the primary stem. Other species of eudicots initially form a primary stem but later become woody, replacing the primary stem with the secondary stem. The anatomy of the stem (internal structure) can be examined through longitudinal sections (cutting the stem lengthwise) or in cross sections (cutting a slice of the stem perpendicular to the length). All three tissue types are represented in the primary stem. The epidermis is the dermal tissue that surrounds and protects the stem. The epidermis typically consists of one layer of cells. A waxy cuticle on the outside of these cells limits water loss. Epidermal cells are the most numerous and least differentiated of the cells in the epidermis. Pores in the epidermis called stomata (singular: stoma) allow for gas exchange. Each stoma is bordered by a pair of guard cells, which regulate stomatal opening. While stomata are present in stems, they occur at higher densities in leaves. Trichomes are hair-like structures on the epidermal surface. They help to reduce transpiration (the loss of water by aboveground plant parts), increase solar reflectance, and store compounds that defend the leaves against predation by herbivores (Figure \(1\)). Ground tissue fills much of the stem, forming the cortex directly within the epidermis and the pith (if present) in the center. The outermost portion of the cortex is usually a few layers of collenchyma cells. The remainder of the cortex and pith consist of parenchyma cells. The arrangement of vascular tissue in the stem depends on the species (see below). Cross sections reveal three possible arrangements of vascular tissue (steles) in the stem. The first arrangement (solenostele) is present in a few eudicots, such as basswood (Tilia). In the solenostele, the vascular tissue appears as a continuous ring (vascular cylinder; Figure \(2\)). The interfascicular regions (pith rays) of parenchyma cells that separate vascular tissue are thus extremely narrow. The second arrangement (eustele) is present in most eudicots such as sunflower (Helianthus) and buttercup (Ranunculus). In the eustele, vascular tissue is clustered into distinct vascular bundles arranged in a ring, allowing for thicker interfascicular regions in between them (Figure \(\PageIndex{3-4}\)). In these solenosteles and eusteles, the vascular tissue separates ground tissue into an outer cortex and central pith. The third arrangement (atactostele) is present in most monocots, such as corn (Zea mays) and a few eudicots. In the atactostele, vascular bundles are scattered throughout the stem (Figure \(\PageIndex{3, 5}\)). While vascular bundles near the outside of the stem are packed more densely in this third arrangement, their distribution is somewhat disorderly. There is no distinction between the cortex and pith in the third arrangement. The cells of embryonic tissue called the procambium (see Meristems) divides to produce primary xylem internally and primary phloem externally. In some vascular bundles, some procambial cells remain and form the fascicular cambium in the center of the vascular bundle. Once the stem has finished lengthening, sclerenchyma fibers called primary phloem fibers are produced just outside of the primary phloem. The primary phloem fibers of each vascular bundle are sometimes called phloem caps (bundle caps). If primary phloem fibers surrounded the entire vascular bundle, they form a bundle sheath (Figure \(6\)). Vascular bundles connect leaves and stems. The strands of vascular tissue that connect the leaves to the stem are called leaf traces. Just above leaf traces are portions of stem without vascular tissue called leaf trace gaps. Similarly, branch traces connect axillary shoots to the main stem, leaving branch trace gaps just above them (Figure \(\PageIndex{7-8}\)). Attributions Curated and authored by Melissa Ha from the following sources: • From 5.4: The Stem from Introduction to Botany by Alexey Shipunov (public domain) • From 30.2 Stems from Biology 2e by OpenStax (licensed CC-BY)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.03%3A_Stems/3.3.01%3A_Stem_Morphology_%28External_Structure%29.txt

Learning Objectives • Compare the origin and function of the vascular cambium and cork cambium. • Define bark and distinguish between inner and outer bark. • Explain the production of wood and relate this to annual rings. • Distinguish between heartwood and sapwood. • Distinguish between softwood and hardwood. • Identify the external features of winter twigs. Primary growth occurs as a stem increases in length as a result of cell division in the shoot apical meristem. Secondary growth is characterized by an increase in thickness or girth of the plant, and is caused by cell division secondary meristems. Herbaceous plants mostly undergo primary growth, with hardly any secondary growth or increase in thickness. Secondary growth or “wood” is noticeable in woody plants; it occurs in some eudicots, but occurs very rarely in monocots. Secondary Meristems (Lateral Meristems) Two secondary meristems (lateral meristems) are responsible for secondary growth: the vascular cambium and cork cambium (Figure \(1\)). The vascular cambium produces secondary vascular tissue. The fusiform initials are the cells of the vascular cambium that divide to produce secondary xylem internally and secondary phloem externally. The ray initials are the cells of the vascular cambium that produce vascular rays (xylem rays and phloem rays). These are bands of parenchyma that are perpendicular to the concentric layers of xylem and phloem (Figure \(2\)). They function in storage, producing secondary compounds (molecules used by the plant that are not essential parts of metabolism), and transporting materials between the xylem and phloem. As the secondary stem thickens, the phloem rays thicken externally (becoming wedge-shaped) to accommodate the increasing diameter. While the vascular cambium is technically only a single layer cell layer, it looks similar to the layers of cells that surround it (that it recently divided to produce), and this entire region is sometimes called the vascular cambium as a result. The vascular cambium arises from stem cells within and between the vascular bundles in some silenosteles and eusteles. Within vascular bundles, such stem cells (specifically, procambial cells) form the fascicular cambium. In the interfascicular regions between vascular bundles is interfascicular cambium (Figure \(3\)). The fascicular cambium and interfascicular cambium ultimately form the vascular cambium. In contrast, the vascular cambium in roots arises from the procambium and pericycle. The cork cambium divides to produce phelloderm internally and cork externally. Together, the phelloderm, cork cambium, and cork form the periderm, the dermal tissue of the secondary plant body (figure \(4\)). The first cork cambium produced by a stem arises from the cortex, but subsequent cork cambia are produced by the parenchyma cells of the secondary phloem. (In contrast, the cork cambium arises from the pericycle in roots.) Palm trees, which are monocots, do not have secondary meristems and true wood. Some thickening does occur in a palm but this happens at the base of the tree, as a result of adventitious roots growing. Palms may also have diffuse secondary growth which is division and enlargement of some parenchyma cells. These processes do not compensate the overall growth of plant, and palms frequently are thicker on the top than on the bottom. Another monocot, dragon blood tree (Dracaena), has anomalous secondary growth, which employs cambium but this cambium does not form the stable ring. Periderm and Bark At the end of the secondary stem's first year of growth, the periderm replaces the epidermis, but the cortex and pith are retained. In contrast, roots that undergo secondary growth do not have piths to begin with, and the cortex is lost during secondary growth. Like the epidermis, most of the periderm is not permeable to water vapor, carbon dioxide, and gaseous oxygen. This is due to the waxy suberin that fills the cork cells, which are dead at maturity. However, gas exchange with the environment is possible at lenticels, elevated regions of the periderm with many intercellular air spaces (Figure \(\PageIndex{5-6}\)). To produce lenticels, some cork cambium cells divide and grow much faster, which will finally break the periderm open. Woody stems do not do regular gas exchange as primary stems do by opening and closing stomata, but woody plants still have leaves with high densities of stomata to regulate gas exchange. Bark consists of all of the tissue layers external to the vascular cambium. It protects the plant against physical damage and helps reduce water loss. In a one-year stem from inside to outside, this would be the secondary phloem, primary phloem fibers, cortex, phelloderm, cork cambium, and cork. The cork cambium divides the inner and outer bark. The inner bark is everything within the cork cambium. The outer bark is the cork cambium and everything external to it (Figure \(7\)). A secondary stem ultimately produces multiple layers of periderm. The inner bark in an older stem thus consists of the newest secondary phloem and the newest phelloderm. Only the conducting phloem of the inner bark contains live cells and transports materials while the nonconducting phloem of the inner bark contains dead cells that are used for storage. As the secondary stem ages, the old layers of the secondary phloem are pushed externally and crushed, with the exception of the phloem fibers, which have thickened cell walls. The outer bark in an older stem would be the newest cork cambium, newest cork, and concentric layers of old phloem and old periderm. If the multiple periderms form perfect circles, the bark is smooth. More often, multiple periderm do not overlap evenly, resulting in rough bark with scales. Wood (Secondary Xylem) Wood consists of the secondary xylem produce by the vascular cambium (Figure \(8\)). In contrast to the phloem, old layers of secondary xylem are retained and are not easily crushed. However, the oldest secondary xylem (close to the center of the secondary stem) no longer conducts water. This is the heartwood, which stores various compounds and appears darker than the surrounding wood. To block the flow of water in the heartwood, plants use tylosesvessel element “stoppers”, which also help control winter functioning of vessels. A tylose forms when a cell wall of parenchyma grows into the tracheary element; they look like bubbles. The sapwood surrounds the heartwood, is lighter in color, and consists of the conducting xylem, which was more recently produced (Figure \(7\)). In the spring of temperate regions, the vascular cambium produces wide tracheary elements (the conducting cells of the xylem, either vessel elements or tracheids). These transport large volumes of water, which is abundant due to spring rains. During the summer, the vascular cambium produces narrow tracheary elements as a result of lower water availability. In the winter, the vascular cambium's activity is low. It resumes the next spring by again producing the wide tracheary elements of early wood (spring wood), which distinctly contrast with the adjacent late wood (summer wood) from the previous year. Early wood appears lighter and is less dense than late wood. Each year of wood production is thus visible in a cross section of a woody stem because it consists of a light layer and a dark layer. These are called annual rings (tree rings; Figure \(\PageIndex{9-10}\)) and can be used to determine the age of a tree or branch through the study of dendrochronology. Furthermore, thick annual rings indicate wet years, and thin annual rings indicate dry years. Some trees (like oaks, Quercus) have large vessel elements are found primarily in early wood; this pattern is known as ring porous (Figure \(10\)). Large vessel elements of other trees (like elm, Ulmus) occur more evenly in both early and late wood. This pattern is known as diffuse porous wood: with large vessel elements in both early and late wood. (Diffuse porous species still produce annual rings due to differences in tracheid size.) Trees growing in climates without well-expressed seasons, such as the tropical rainforest, will not make annual rings at all. Hardwoods are produced by angiosperms and contain both vessel elements and tracheids (figure \(10\)). Softwoods are produced by conifer trees (in the gymnosperm phylum Coniferophyta) and contain only tracheids (Figure \(11\)). These terms are misnomers to an extent, however, because hardwoods are not always denser than softwoods. Xylem rays tend to occupy a greater volume in hardwoods relative to softwoods. Additionally, the arrangement of cells appears more disorderly in hardwoods due to the large size of vessel elements. Finally, softwoods contain resin ducts (Figure \(11\)), which contain a thick substance (resin) important in defense and response to injury. Winter Twigs Winter deciduous trees and shrubs in temperate regions become dormant in winter. The twigs of these species have the basic external features of a stem (axillary buds, nodes, etc.), but they are modified to facilitate dormancy in the winter and resumption of growth in the spring. At the end of a winter twig is the terminal bud, which contains a shoot apex surrounded by protective structures called bud scales. When the terminal bud resumes growth, the bud scales fall off and leave marks called terminal bud-scale scars. These form a ring around the twig, marking the winter of each year. Lateral buds are similar in structure to terminal buds, but they are found at each node. Just below the lateral buds are leaf scars, where the leaves were formerly attached. Within the leaf scars are bundle scars, marking leaf traces (consisting of vascular bundles) that moved from the stem to the leaf (Figure \(12\)). Attributions Curated and authored by Melissa Ha from the following sources: • From 5.4: The Stem from Introduction to Botany by Alexey Shipunov (public domain)​ • From 30.2 Stems from Biology 2e by OpenStax (licensed CC-BY)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.03%3A_Stems/3.3.03%3A_Secondary_Stem.txt

Learning Objective Define and provide examples of the major stem and shoot modifications. Stems (or entire shoots) of some species deviate in structure and function from a typical stem. These are called stem modifications (shoot modifications). While leaves are part of the shoot, modifications involving just the leaf are discussed separately (see Leaf Modifications). Rhizomes and stolons are horizontal stems that function in propagation (Figure \(1\)). Rhizomes are belowground stems that burrow into the ground just below the soil surface. They have short internodes and usually have small, scale-like leaves that are not photosynthetic. Buds from the axils of the leaves make new branches that will grow to become aboveground shoots. Ginger (Zingiber) and Johnson grass (Sorghum halepense) form rhizomes. Stolons (runners) are aboveground horizontal shoots, which sprout and produce a new plants. Compared to rhizomes, stolons have long internodes. Examples include strawberry (Fragaria), spider plants (Chlorophytum), and Bermuda grass (Cynodon dactylon). Tubers, corms, and bulbs are modified for starch storage. Tubers, such as potatoes, are thick, belowground stems found at the tips of rhizomes or stolons (figure \(2\)). The “eyes” of potato are actually lateral buds, and the tuber body is comprised of many parenchyma cells that contain amyloplasts with starch. Corms and bulbs are modified shoots. A corm is a short, thick underground storage stem with thin scaly leaves (for example, Gladiolus and Crocus; Figure \(3\); Video \(1\)). A bulb, such as an onion, differs from a corm in the fact that it stores its nutrients in its fleshy leaves (Figure \(3\)). Lilies and tulips also form bulbs. Some plants have sharp, generally narrow projections that function in defense against herbivores. Such structures are called thorns when they arise from an entire stem. Hawthorn (Crataegus) and Bougainvillea produce thorns. In contrast, prickles form from the surface tissues (epidermis and cortex) of the stem rather than the whole organ (figure \(4\)). Rose (Rosa) and blackberry (Rubus) produce prickles. Spines are similar structures derived from leaves (see Leaf Modifications). Tendrils are thin, string-like structures that allow the shoot to attach to other surfaces to access light. Tendrils can be derived from stems, leaves, or leaflets, and they are common in vines. Morning glory and sweet potato (Ipomoea), grapes (Vitis), and many members of the cucumber family (Cucurbitaceae) such as cucumbers, pumpkin, and squash have tendrils that arise from stems (Figure \(5\)). Cladophylls (cladodes) are stems that resemble leaves in function and appearance, arise from the axils of a shoot, and have determinate growth (stop growth after reaching a certain size). They may be cylindrical (Asparagus; Figure \(6\)) or flattened (butcher's broom, Ruscus; figure \(7\)). Phylloclades are flattened stems that resemble leaves that can continue growing indeterminately (Figure \(8\)). They are subtended by reduced, scale-like leaves. Examples include prickly pear cactus (Opuntia), Christmas cactus (Schlumbergera), and ribbon plant, Homalocladium. Phyllodes are similar are similar to cladophylls and phylloclades, but they are modified petioles (see Leaf Modifications). Some shoots are modified as insect traps are used by some carnivorous plants, such as bladderwort (Utricularia; Video \(1\)). Video \(1\): This video shows a waterflea caught in a bladderwort insect trap. This video has no sound. Here is a description of what occurs during the video: Bladderwort and water fleas. Taken through a Leica microscope 60X objective- standard microscope lighting. The water fleas are tiny crustaceans, and they are swimming around in slow motion. At 3:50, one water flea is about to get caught. It swims into the cup-shaped leaf and escapes. A slow-motion replay of that moment shows the leaf close around the water flea temporarily before it escapes. Attributions Curated and authored by Melissa Ha using 7.4: Modified Shoot from Introduction to Botany by Alexey Shipunov (public domain) 3.3.05: Chapter Summary The stem of a plant bears leaves, flowers, and fruits. Stems are characterized by the presence of nodes (the points of attachment for leaves or branches) and internodes (regions between nodes). All three tissue systems can be found in stems. In the primary stem, dermal tissue is represented by the epidermis, the outer covering of the plant. The cortex and pith (if present) represent ground tissue, and vascular tissue is found in the vascular cylinder or vascular bundles. Vascular tissue may be arranged in a continuous ring (silenostele), in vascular bundles forming a ring (eustele), or in scattered vascular bundles (ataktostele). Primary growth occurs at the tips of roots and shoots, causing an increase in length. Woody plants may also exhibit secondary growth, or increase in thickness. Secondary meristems (lateral meristems) are responsible for secondary growth. The vascular cambium produces secondary phloem externally and secondary xylem internally, and the cork cambium produces cork externally and phelloderm internally. The cork, cork cambium, and phelloderm form the periderm, the secondary dermal tissue. Bark consists of all the tissue layers external to the vascular cambium, and wood consists of secondary xylem. Annual rings in wood reflect differences in growth due to changing water availability throughout the year. Some plant species have modified stems or modified shoots that help to propagate new plants, store food, or deter herbivores. Examples of such modifications are rhizomes, stolons, tubers, corms, bulbs, tendrils, and thorns. After completing this chapter, you should be able to... • Identify the main external structures of the shoot system, including the nodes, internodes, leaves, axillary buds, and axillary shoots. • Identify the structures representing each of the three tissue systems in stems. • Compare the structure of silenosteles, eusteles, and ataktosteles. • Explain the arrangement of leaf traces, leaf trace gaps, branch traces, and branch trace gaps. • Compare the origin and function of the vascular cambium and cork cambium. • Define bark and distinguish between inner and outer bark. • Explain the production of wood and relate this to annual rings. • Distinguish between heartwood and sapwood. • Distinguish between softwood and hardwood. • Identify the external features of winter twigs. • Define and provide examples of the major stem and shoot modifications. Attribution Curated and authored by Melissa Ha using 30.2 Stems from Biology 2e by OpenStax (licensed CC-BY)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.03%3A_Stems/3.3.04%3A_Stem_Modifications.txt

Leaves are specialized organs of the shoot for performing photosynthesis. A leaf is often a relatively large, flat surface used to optimize sunlight capture. Most leaves have determinate growth, meaning that growth stops once the leaf reaches a certain size. This is in contrast to the overall plant body, which grows indeterminately. Leaves arise from the shoot apical meristem through leaf primordia. Usually, true leaves are easily distinguishable, but in some species, modified stems (cladophylls and phyloclades) or leaflets (parts of leaves) superficially appear like whole leaves. True leaves subtend an axillary bud in the axil and are lateral (rather than at the tip, or apex of the shoot; Figure \(1\)). New shoots and leaves do not arise from true leaves. Most leaves are usually green, due to the presence of chlorophyll in the chloroplasts of their cells. However, some leaves may have different colors, caused by other plant pigments that mask the green chlorophyll. The thickness, shape, and size of leaves are adapted to the environment. Each variation helps a plant species maximize its chances of survival in a particular habitat. Attributions Curated and authored by Melissa Ha using the following sources: Thumbnail image: The red petal-like structures of the poinsettia plant are actually modified leaves called bracts, which are adapted to attract pollinators. The true flowers tiny structures where the bracts meet. Image by Scott Bauer (public domain). 3.04: Leaves Learning Objectives • Identify the main parts of a leaf. • Compare petiolate and sessile leaves. • Distinguish among alternate, opposite, and whorled phyllotaxes. • Compare simple, pinnately compound, and palmately compound leaves. • Compare parallel, pinnate, and palmate venation in leaves. • Recognize common leaf margins and shapes. Each leaf typically has a flat, wide portion called the blade (lamina), which is also the widest part of the leaf (Figure \(1\)). Some leaves are attached to the plant stem by a stalklike petiole and are called petiolate leaves (Figure \(2\)). Although petioles are narrow and often resemble stems, they are considered part of the leaf. A petiolate leaf thus consists of the blade and the petiole. Petioles usually attach at to the margin (edge) of the blade along the base, but in peltate leaves, the petiole is attached underneath the blade (Figure \(3\)). Leaves that do not have a petiole and are directly attached to the plant stem are called sessile (apetiolate) leaves (Figure \(4\)). In a special type of sessile leaves called perfoliate leaves, the stem passes through the center of the blade (Figure \(4\)). Many leaves have a midrib, which travels the length along the center of the leaf. The midrib contains the main vein (primary vein) of the leaf as well as supportive ground tissue (collenchyma or sclerenchyma). Small, green appendages usually found at the base of the petiole are known as stipules (Figure \(5\)). Other structures located near leaf base sheath (typical for grasses, lilies, and related species) and ocrea (typical for buckwheat family, Polygonaceae). Phyllotaxy The arrangement of leaves on a stem is known as phyllotaxy. The number and placement of a plant’s leaves will vary depending on the species, with each species exhibiting a characteristic leaf arrangement. Leaves arrangements are classified as either alternate, opposite, or whorled (Figure \(6\)). Plants that have only one leaf per node have leaves that are said to be alternate, and alternate leaves often spiral up the stem. In an opposite leaf arrangement, two leaves arise at the node (with the leaves usually connecting opposite each other along the branch). Pairs of opposite leaves may face all in the same direction, or each pair can rotate at 90\(^\circ\) (decussate). If there are three or more leaves connected at a node, the leaf arrangement is classified as whorled, and each whorl can also rotate. Each type of spiral phyllotaxis has its own angle of divergence. Simple and Compound Leaves Leaves may be simple or compound (Figure \(7\)). In a simple leaf, the blade is either completely undivided (Figures \(\PageIndex{8, 12, 13}\))—or it has lobes, but the separation does not reach the midrib, as in the maple leaf. In a compound leaf, the leaf blade is completely divided, forming leaflets, as in the locust tree. Each leaflet may have its own stalk but is attached to the rachis. A palmately compound leaf resembles the palm of a hand, with leaflets radiating outwards from one point (Figure \(8\)). Examples include the leaves of poison ivy, the buckeye tree, or the familiar houseplant Schefflera sp. (common name “umbrella plant”). Pinnately compound leaves take their name from their feather-like appearance; the leaflets are arranged along the midrib, as in rose leaves (Rosa sp.), or the leaves of hickory, pecan, ash, or walnut trees (Figure \(8\)). Trifoliate leaves, such as in clover or strawberry, have only three leaflets (Figure \(9\)) Simple leaves have just one level of hierarchy whereas compound leaves have two or more levels of hierarchy (Figure \(10\)). Pinnately compound leaves with two levels of hierarchy are unipinnate. Those with three levels of hierarchy are called bipinnate (twice pinnate; doubly compound), and those with four levels of hierarchy are tripinnate. For compound leaves, a botanist could describe characteristics of the leaf overall as well as the shape, margin, and venation (see below) of the leaflets. Venation Leaf veins are vascular bundles coming to the leaf from stem. The arrangement of veins in a leaf is called the venation pattern. Frequently, there is one or more main vein (primary vein) and secondary veins that branch from it. Tertiary veins branch from secondary veins (Figure \(11\)). There are three main arrangements of the most prominent (major) of the leaf. They may all run longitudinally (parallel venation, Figure \(12\)), they may branch from a single midvein (pinnate venation, Figure \(\PageIndex{8a, 12}\)), or they may arise from a single point at the base of the leaf (palmate venation; Figure \(13\)). Parallel venation is found in monocots, and pinnate and palmate venation is common in eudicots. The maidenhair tree, ginkgo (Ginkgo biloba), has a unique venation pattern in which each vein divides into two similar parts. This is known as dichotomous venation (Figure \(12\)). The less prominent (minor) veins of a leaf may form a branching, netlike pattern, which is called reticulate venation (Figure \(14\)). In contrast, the minor veins are arranged neatly, forming a ladderlike structure in percurrent venation. Margins The margin describes the outline of a simple leaf or leaflet (Figure \(15\)). Leaves with smooth margins are called entire. Those with irregularly wavy margins are undulate. Lobate (lobed) leaves may be palmately lobate (with lobes outlining the palmate venation pattern of veins arising from a single point at the base of the leaf) or pinnately lobate (with lobes outlining the pinnate venation pattern of secondary veins branching from a midvein; Figure \(16\)). Toothed leaves have small projections (teeth) and indentations that do not align with the venation. For serrate leaves, the sharp teeth point forward, like a serrated knife. For dentate leaves, sharp teeth are symmetrical, like equilateral triangles. For crennate leaves, the teeth are rounded rather than sharp. Shape There are several general leaf shapes (Figure \(17\)). The widest part of ovate leaves is near the based whereas the widest portion of obovate leaves is near the apex (tip). If the widest portion of the leaves is equidistant form the apex and base, the leaf may be elliptic or oblong. In elliptic leaves, a single wide middle portion tapers as it approaches the apex or base. Oblong leaves are similarly, but there is a longer section in the middle of these leaves that is uniformly wide. Linear leaves are long and thin. Lanceolate leaves are lance-shaped and somewhat intermediate between ovate and linear. The leaf shape can be described in further detail using specific terminology that applies to the leaf apex (Figure \(18\)) and leaf base (Figure \(19\)). The leaf apex could be rounded, acute (forming an angle less than 90º), obtuse (forming an angle greater than 90º), attenuate (tapering to a point), or acuminate (dramatically curving inward to a narrow point). The base of the leaf blade could be rounded, acute, obtuse, truncate (straight), cuneate (wedge-shaped or triangular), or cordate (indented in the center, like an upside-down heart). Hetrophylly Heterophylly refers to a plant having more than one kind of leaf. A plant can have both juvenile leaves and adult leaves, water leaves and air leaves, or sun leaves and shade leaves. In California live oak, leaves growing closely to the ground have sharp teeth, presumably to deter herbivores such as deer. Leaves at the top of the plant are too high for herbivores to reach and have entire margins. California sycamore has both palmately lobed leaves and small, perfoliate leaves (Figure \(20\)). Attributions Curated and authored by Melissa Ha using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.04%3A_Leaves/3.4.01%3A_External_Structure_of_Leaves.txt

Learning Objectives • Describe the microscope internal structure of leaves, including the epidermis, mesophyll, and vascular bundles. • Compare the adaptations of mesophytic, hydrophytic, and xerophytic leaves. • Identify the unique features of pine and corn leaves. • Compare the structures of sun and shade leaves. Tissue Organization in Leaves All three tissue types are represented in leaves. The epidermis represents the dermal tissue, the mesophyll that fills the leaf is ground tissue, and the vascular bundles that form the leaf veins represent vascular tissue (Figure \(1\)). These three tissues will be discussed using a eudicot leaf that is adapted to a moderate amount of water (mesophytic leaf). Variations in leaf structure are discussed later on this page. Epidermis The outermost layer of the leaf is the epidermis; it is present on both sides of the leaf and is called the upper and lower epidermis, respectively. Botanists call the upper side the adaxial surface (or adaxis) and the lower side the abaxial surface (or abaxis). The epidermis helps in the regulation of gas exchange. It contains stomata (singular = stoma; Figure \(2\)), openings through which the exchange of gases takes place. Two guard cells surround each stoma, regulating its opening and closing, and the guard cells are sometimes flanked by subsidiary cells. Guard cells are the only epidermal cells to contain chloroplasts. In most cases, the lower epidermis contains more stomata than the upper epidermis because the bottom of the leaf is cooler and less prone to water loss. The epidermis is usually one cell layer thick; however, in plants that grow in very hot or very cold conditions, the epidermis may be several layers thick to protect against excessive water loss from transpiration. A protective layer called the cuticle covers surface of the epidermal cells (Figure \(3\)). The cuticle is rich in lignin (which lends some rigidity) and waxes (which function in waterproofing). The cuticle reduces the rate of water loss from the leaf surface. Other leaves may have small hairs (trichomes) on the leaf surface. Trichomes help to deter herbivory by restricting insect movements, or by storing toxic or bad-tasting compounds; they can also reduce water loss by blocking air flow across the leaf surface (Figure \(4\)). For this reason, trichomes (like stomata) are frequently denser on the lower side of the leaf. Mesophyll Below the epidermis are layers of cells known as the mesophyll, or “middle leaf.” Mesophyll cells contain many chloroplasts and specialize in photosynthesis. The mesophyll of most leaves typically contains two arrangements of parenchyma cells: the palisade parenchyma and spongy parenchyma (Figure \(5\)). The palisade parenchyma (also called the palisade mesophyll) has column-shaped and may be present in one, two, or three layers. The palisade cells specialize in capturing incoming sunlight (including slanted sun rays), rotating chloroplasts to the top of the leaf and then allowing them to regenerate by cycling them toward the leaf's center. They also decrease the intensity of sunlight for the spongy mesophyll. Although palisade cells may appear tightly packed in a cross section because there are many rows of cells behind those in the foreground, there is actually ample space (intercellular air spaces) between them. Below the palisade parenchyma are seemingly loosely arranged cells of an irregular shape. These are the cells of the spongy parenchyma (or spongy mesophyll). The intercellular air spaces found between mesophyll cells facilitate gaseous exchange. Vascular Bundles (Veins) Like the stem, the leaf contains vascular bundles composed of xylem and phloem (Figure \(\PageIndex{6-7}\)). When a typical stem vascular bundle (which has xylem internal to the phloem) enters the leaf, xylem usually faces upwards, whereas phloem faces downwards. The conducting cells of the xylem (tracheids and vessel elements) transport water and minerals to the leaves. The sieve-tube elements of the phloem transports the photosynthetic products from the leaf to the other parts of the plant. The phloem is typically supported by a cluster of fibers (sclerenchyma) that increase structural support for the veins. A single vascular bundle, no matter how large or small, always contains both xylem and phloem tissues. Leaf Adaptations The broad, flat shape of most leaves increases surface area relative to volume, which helps it capture sunlight; however this also provides more opportunity for water loss. The anatomy of a leaf has everything to do with achieving the balance between photosynthesis and water loss in the environment in which the plant grows. Plants that grow in moist areas can grow large, flat leaves to absorb sunlight like solar panels because sunlight is likely more limiting than water. Plants in dry areas must prevent water loss and adapt a variety of leaf shapes and orientations to accomplish the duel tasks of water retention and sunlight absorption. In general, leaves adapted to dry environments are small and thick with a much lower surface area-to-volume ratio. In regards to water, there are three main types of plants: mesophytes, hydrophytes, and xerophytes. Mesophytes are typical plants which adapt to moderate amounts of water ("meso" means middle, and "phyte" means plant). Many familiar plants are mesophytes, such as lilac, Ranunculus (buttercup), roses, etc. Hydrophytes grow in water ("hydro" refers to water). Their leaf blades are frequently highly dissected (deeply lobed) to access gases dissolved in water, and their petioles and stems have air canals to supply underwater organs with gases. Hygrophytes (not discussed further) live in constantly wet environment, their leaves adapted to rapidly release water through the stomata. They sometimes even excrete of water drops through the leaf margins (guttation). Xerophytes are adapted to the scarce water ("xero" refers to dryness). Xerophytes are found in deserts and Mediterranean climates (such as in much of California), where summers are hot and dry. The leaves of mesophytes are called mesophytic, hydrophyte leaves are called hydrophytic, and so on. The structure of mesophytic leaves was already described (Figure \(1\)). Adaptaions in hydrophytic and xerophytic leaves and discussed below in more detail. Hydrophytic Leaves The structure of a hydrophytic leaf differs from a mesophytic leaf due to selective pressures in the environment -- water is plentiful, so the plant is more concerned with staying afloat and preventing herbivory. Hydrophytic leaves have a thin epidermal layer and the absence of stomata in the lower epidermis (Figure \(8\)). In the spongy mesophyll, there are large pockets where air can be trapped, helping the leaf float. This type of parenchyma tissue, specialized for trapping gases, is called aerenchyma. Sharp, branched sclereids (astrosclereids) traverse the mesophyll of a hydrophytic leaf. These provide the leaf structural support, as well as prevention of herbivory. Vascular tissue is somewhat reduced in hydrophytic leaves. Xerophytic Leaves Xerophytic leaves (Figure \(9\)) have thick cuticles to limit water loss, especially on the upper epidermis (Figure \(10\)). Both the upper and lower epidermis consists of several layers (multiple epidermis). Sometimes the additional layers are called the hypodermis ("hypo" meaning under; "dermis" meaning skin). Depressions in the lower epidermis creates a pockets that are lined with trichomes, and the stomata are located at the base of these pockets (called stomatal crypts; figure \(10\)). The trichomes help capture evaporating moisture and maintain a relatively humid environment around the stomata. These stomatal crypts are located only on the underside of the leaves, where they experience less sun exposure and therefore less water loss. The upper epidermis is free from stomata. Pine Leaves Pines evolved during a period in Earth’s history when conditions were becoming increasingly dry, and pine needles have many adaptations to deal with these conditions. Many of these adaptations are similar the xerophytic leaves of some angiosperms (described above) because pines themselves are xerophytes. The epidermis of the leaf seems to be more than one cell layer thick (figure \(11\)). These subsequent layers of epidermis-like tissue under the single, outer layer of true epidermis are called the hypodermis , which offers a thicker barrier and helps prevent water loss. The epidermis itself is coated on the outside by a thick layer of wax called the cuticle. Because waxes are hydrophobic, this also helps prevent water loss through the epidermis. The stomata are typically sunken, occurring within the hypodermis instead of the epidermis. Sunken stomata create a pocket of air that is protected from the airflow across the leaf and can aid in maintaining a higher moisture content (figure \(12\)). Within the mesophyll, there are several canals that appear as large, open circles in the cross section of the leaf. These are resin canals. The cells lining them secrete resin (the sticky stuff that coniferous trees exude, often called pitch), which contains compounds that are toxic to insects and bacteria. When pines evolved, not only was the Earth becoming drier, but insects were evolving and proliferating. These resin canals are not features that help the plant survive dry conditions, but they do help prevent herbivory. In addition to prevention of herbivory, resin can aid in closing wounds and preventing infection at wound sites. There are two bundles of vascular tissue embedded within a region of cells called transfusion tissue, which functions in transporting materials to and from the mesophyll cells. The transfusion tissue and vascular bundles are surrounded by a distinct layer of cells called the endodermis. This is similar to the tissue of the same name in the root, but the cells are not impregnated with the water-repelling compound suberin. Finally, the overall shape of the leaf allows for as little water loss as possible by decreasing the relative surface area, taking a rounder shape as opposed to a flatter one. This low surface area-to-volume ratio is characteristic of xerophytes. Corn Leaves The model organism for monocots in botany is usually corn (Zea mays). In corn, there are approximately the same number of stomata on both the upper and lower epidermis. The mesophyll is not divided into two distinct types. The vascular bundles all face the same directly (appearing circular in cross section) because they run parallel to each other. Corn is not necessarily a xerophyte, but it is adapted to deal with high temperatures. One of these adaptations, C4 type photosynthesis is discussed in Photorespiration and Photosynthetic Pathways and results in a cell arrangement called Kranz anatomy. The vascular bundles are surrounded by obviously inflated parenchyma cells that form a structure called a bundle sheath, and these are packed with chloroplasts (Figure \(13\)). (Bundle sheaths surround vascular bundles of other types of leaves as well, but the bundle sheath cells are much smaller). Mesophyll cells encircle the bundle sheath cells. In C4 photosynthesis, carbon dioxide is first gathered by the mesophyll cells and temporarily stored as a four-carbon sugar. This four-carbon sugar is transferred to the bundle sheath cells, where it is broken down to release carbon dioxide. It is in the bundle sheath cells where a process called the Calvin cycle, and glucose is ultimately produced. C4 photosynthesis concentrates carbon dioxide inside the bundle sheath cells, reducing the need to frequently open stomata for gas exchange. This helps conserve water. When moisture is plentiful, the corn leaves are fully expanded and able to maximize photosynthesis. When moisture is limited, the leaves roll inward, limiting both moisture loss and photosynthetic capacity. This is accomplished by the presence of bulliform cells in the upper epidermis (Figure \(14\)). These clusters of enlarged cells are swollen with water when there is abundant water available. As the water content in the plant decreases, these cells shrivel, causing the upper epidermis to curl or fold inward at these points. This adaptation to sun exposure can be found in many other grasses, as well (corn is a member of the Poaceae, the grass family). Sun and Shade Leaves The light intensity experienced by a developing leaf influences its structure. Leaves that develop when consistently exposed to direct sunlight (sun leaves) thus differ from leaves exposed to low light intensities (shade leaves) in several ways (Figure \(15\)). Relative to shade leaves, sun leaves are smaller and thicker. This reduces surface area relative to volume, conserving water, which would otherwise be easily lost under bright sunlight and resultantly warmer temperatures. In contrast, the broad, thin shape of shade leaves helps capture sufficient light when light intensity is low. The thicker cuticle of sun leaves also limits water loss. They have more palisade parenchyma and more vascular tissue. Sun leaves can maintain a high photosynthetic rate at high light intensities, but shade leaves cannot. ​Attributions Curated and authored by Melissa Ha using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.04%3A_Leaves/3.4.02%3A_Internal_Leaf_Structure.txt

Learning Objective Identify common leaf modifications and their functions, including storage leaves, succulent leaves, spines, tendrils, phyllodes, showy bracts, plantlets, and insect traps. The structure and function of a leaf can be modified over the course of evolution as a plant adapts to a particular environment (Figure \(1\)). When function of the leaf blade is no longer primarily photosynthesis, some other plant part is usually modified to take its place. Storage leaves are thick leaves underground that store starch (as with a bulb; see Stem Modifications). Succulent leaves are also thickened leaves, but they are found above ground, still conduct photosynthesis, and function primarily in water storage (Figure \(2\)). Spines are sharp projections derived from leaves that function in plant defense. Almost all cacti (in the plant family Cactaceae) have spines (Figure \(3\)). Other examples include barberry and some Acacia species, in which large spines house mutualist ants. Spines can also be formed from stipules (stipular spines) or bud scales. Recall from Stem Modifications that thorns and prickles have the same function, but they are derived from whole stems or the outer tissue layers of stems, respectively. Tendrils are another structure that can originate from multiple structures, including stems, leaves, or leaflets. These are narrow, coiling structures that climbing plants attach to nearby structures for support (Figure \(4\)). A phyllode resembles cladodes and phylloclades but refers to a flattened petiole that resembles a leaf blade (rather than a narrow stalk). The Australian acacias (Acacia) have phyllodes (Figure \(5\)). Showy bracts are brightly colored leaves function in attracting pollinators. From a distance, showy bracts often appear like the petals of a flower. However, the actual flowers are typically small and in a cluster surrounded by the bracts (Figure \(6\)). Plantlets are mini plants that grow on the main plant and then fall off and grow into new plants. In Kalanchoë , mitosis at meristems along the leaf margins produce tiny plantlets that fall off and grow independently into mature plants. This is a form of asexual reproduction (Figure \(7\)). Carnivorous plants grow in bogs where the soil is low in nitrogen, and their leaves are adapted to help them to survive this nutrient-poor environment. In these plants, leaves are modified as traps to capture insects. While they still conduct photosynthesis to capture energy and synthesize sugars (and are thus autotrophs), they rely on insect-capturing leaves as a supplementary source of much-needed nitrogen, similar to fertilizer. Several examples of carnivorous plants are the cobra lily (Darlingtonia), various pitcher plants (Nepenthes [Figure \(8\)], Cephalotus, Sarracenia), the butterwort (Utricularia), the sundew (Drosera; Figure \(9\)), and the best known, the Venus flytrap (Dionaea; Figure \(\PageIndex{h}\)). Attributions Modified by Melissa Ha from the following sources: 3.4.04: Chapter Summary Leaves are the main site of photosynthesis. A typical leaf consists of a blade (the broad part of the leaf, also called the lamina) and a petiole (the stalk that attaches the leaf to a stem). The arrangement of leaves on a stem, known as phyllotaxy, enables maximum exposure to sunlight. Each plant species has a characteristic leaf arrangement and form. The pattern of leaf arrangement may be alternate, opposite, or whorled, while leaf form may be simple or compound (consisting of multiple leaflets). Leaves also differ in the venation patterns, margins (edges), and shape. Leaf tissue consists of the epidermis, which forms the outermost cell layer, and mesophyll and vascular bundles (veins), which make up the inner portion of the leaf. Leaves may be mesophytic (adapted to moderate water availability), hydrophytic (adapted to on water), or xerophytic (adapted for dry conditions). Pine leaves share some characteristics with other xerophytic leaves. The leaves of corn, a monocot, are characterized by Kranz anatomy, parallel vascular bundles, and bulliform cells. Leaves that develop in the sun tend to be thicker, have a thicker cuticle, and have more palisade mesphyll than those that develop in the shade. In some plant species, leaf form is modified for functions other than photosynthesis, form structures such as tendrils, spines, or bracts. After completing this chapter, you should be able to... • Identify the main parts of a leaf. • Compare petiolate and sessile leaves. • Distinguish among alternate, opposite, and whorled phyllotaxes. • Compare simple, pinnately compound, and palmately compound leaves. • Compare parallel, pinnate, and palmate venation in leaves. • Recognize common leaf margins and shapes. • Describe the microscope internal structure of leaves, including the epidermis, mesophyll, and vascular bundles. • Compare the adaptations of mesophytic, hydrophytic, and xerophytic leaves. • Identify the unique features of pine and corn leaves. • Compare the structures of sun and shade leaves. • Identify common leaf modifications and their functions, including storage leaves, succulent leaves, spines, tendrils, phyllodes, showy bracts, plantlets, and insect traps. Attribution Curated and authored by Melissa Ha using 30.4 Leaves from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/03%3A_Plant_Structure/3.04%3A_Leaves/3.4.03%3A_Leaf_Modifications.txt

Plant physiology focuses on the chemistry and physics of how plants function. Plants capture light energy and produce sugars through photosynthesis and break down these sugars through aerobic cellular respiration. They respond to a variety of environmental conditions through growth changes, life events like germination or flowering, and even, in special cases, through movement. Plants rely on soils for mineral nutrients and water, and biogeochemical cycles replenish soils with these nutrients. Once water and minerals are absorbed, they must be transported through the xylem, and this movement is driven by the loss of water vapor from leaves (transpiration) and the cohesive and adhesive properties of water. Likewise, sugar-rich assimilate must be moved, or translocated, through the phloem. Five main types of hormones in plants are responsible for relaying messages throughout the plant body. Throughout this unit are examples of how plants regulate their internal conditions whether it the concentration of carbon dioxide in the leaves; the positioning of stems, roots, and leaves; or the movement and retention of water (Figure \(1\)). Attribution Melissa Ha (CC-BY-SA) • 4.1: Photosynthesis and Respiration Photosynthesis is the process by which plants, algae, and photosynthetic bacteria capture carbon dioxide and synthesize sugars using light energy. Oxygen is released as a byproduct in this process. There are two steps of photosynthesis: the light-dependent reactions and the light-independent reactions. Sugars are commonly broken down to release usable energy through the process of aerobic cellular respiration. • 4.2: Environmental Responses Animals can respond to environmental factors by moving to a new location. Plants, however, are rooted in place and must respond to the surrounding environmental factors. Plants have sophisticated systems to detect and respond to light, gravity, temperature, and physical touch. Receptors sense environmental factors and relay the information to effector systems—often through intermediate chemical messengers—to bring about plant responses. • 4.3: Nutrition and Soils Essential elements are those that are required for plant growth. Plants acquire many essential elements from the soil, a matrix of organic matter, inorganic matter, air, and water. These elements move through nutrient cycles, which influences their availability. • 4.4: Hormones Hormones are long-distance chemical signals in plants. They coordinate many responses including growth, reproduction, dormancy, and stress responses. The five major categories of plant hormones are auxins, cytokinins, gibberellins, abscisic acid, and ethylene. • 4.5: Transport The structure of plant roots, stems, and leaves facilitates the transport of water, nutrients, and photosynthates throughout the plant. The phloem and xylem are the main tissues responsible for this movement. Water potential, evapotranspiration, and stomatal regulation influence how water and nutrients are transported in plants. To understand how these processes work, we must first understand the energetics of water potential. • 4.6: Development Development refers to the process by which a plant changes over its life. Growth occurs at apical, primary, and lateral meristems. Embryogenesis is the development of the embryo inside the seed. A mature seed consists of the seed coat surrounding the embryo, which typically contains a epicotyl, hypocotyl, radicle, and cotelydon(s), but the precise structure differs between eudicots and monocots. Upon germination, the plant resumes growth. A mature plant flowers according to the ABCDE model. Thumbnail image: A normal Arabidopsis plant (left) and a mutant that does not respond properly to the hormone auxin. Image by William M. Gray (CC-BY). 04: Plant Physiology and Regulation Photosynthesis and aerobic cellular respiration are key metabolic pathways. Photosynthesis is essential to all life on earth; both plants and animals depend on it (Figure \(1\))​​. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that most organisms use to power their metabolism through aerobic cellular respiration or other pathways. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago. Attribution Curated and authored by Melissa Ha using the following sources: • 4.1.1: Energy and ATP • 4.1.2: Aerobic Cellular Respiration Through aerobic cellular respiration, organisms break down sugars to produce usable energy in the form of ATP. This process consumes gaseous oxygen and releases carbon dioxide and water. There are four steps: glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation. • 4.1.3: Photosynthesis Overview and Equation Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. • 4.1.4: Discovery of Photosynthesis The history of the studies done on photosynthesis dates back into the 17th century with Jan Baptist van Helmont. He rejected the ancient idea that plants take most of their biomass from the soil. • 4.1.5: The Light-dependent Reactions Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules. However, autotrophs only use a few specific components of sunlight. • 4.1.6: Light-independent Reactions The enzymatic stage has many participants. These include carbon dioxide, hydrogen carrier with hydrogen (NADPH), ATP, ribulose biphosphate (RuBP), and RuBisCO along with some other enzymes. Everything occurs in the matrix (stroma) of the chloroplast. • 4.1.7: Photorespiration and Photosynthetic Pathways Photorespiration occurs when RuBisCO binds to gaseous oxygen rather than carbon dioxide. It undoes the good anabolic work of photosynthesis, reducing the net productivity of the plant. Plants in different environments have adaptations to reduce photorespiration while minimizing water loss. • 4.1.8: Chapter Summary Thumbnail: Plant cells with visible chloroplasts (from a moss, Plagiomnium affine). (CC BY SA 3.0 Unported; Kristian Peters). 4.01: Photosynthesis and Respiration Learning Objectives • Describe the different types of energy. • Describe the structure and function of ATP. Understanding photosynthesis and aerobic cellular respiration relies on the fundamentals of energy. Energy is defined as the ability to do work, and there are several types of energy (Figure \(1\)). Kinetic energy is the energy of motion. Examples include a ball rolling down a hill, heat energy, and light energy. Heat energy is technically energy that is transferred between systems without doing work. The higher the temperature, the faster molecules in matter move. Potential energy is the energy that matter possesses but is not currently being used. For example, a ball sitting a the top of the hill that has not yet rolled down the hill possesses potential energy. Chemical energy is an example of potential energy that is stored in molecules. When molecules that are higher energy and less stable react to form products that are lower energy and more stable, this stored energy is released. Adenosine triphosphate (ATP) is considered the energy currency of the cell because it provides usable energy. Structurally, ATP resembles a modified nucleotide (the building blocks of DNA and RNA). Specifically, it consists of adenine, ribose, and three phosphate groups (Figure \(2\)). The bonds between the phosphate groups are unstable. When these bonds are broken, more stable bonds are formed in their place, releasing energy. Phosphorylation refers to adding a phosphate group (PO43-) to a molecule. However, it often refers specifically to synthesizing ATP by adding a phosphate group to adenosine diphosphate (ADP).

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.01%3A_Energy_and_ATP.txt

Learning Objectives • Identify the reactants and products of aerobic cellular respiration. • Explain each step of aerobic cellular respiration and where in the cell it occurs. Not only do plants produce sugars through photosynthesis, but they also break down these sugars to generate usable energy in the form of ATP through aerobic cellular respiration. Glucose begins its breakdown outside of the mitochondria in a metabolic pathway called glycolysis. However, the majority of the reactions that produce ATP happen within the mitochondria (in eukaryotic cells; Figure $1$). During these reactions, electron carriers are created and oxygen pulls the electrons through an electron transport chain to create ATP, which powers cellular activity. The oxygen you breathe in combines with electrons to form water, which you breathe out. The carbon dioxide you breathe out comes from the carbon in glucose, which your body metabolized. Here is a net reaction for cellular respiration: $\ce{C_6H_{12}O_6 + 6O_2\rightarrow6CO_2 + 6H_2O + ATP} \nonumber$ glucose + oxygen $\ce{\rightarrow}$ carbon dioxide + water + energy Step 1: Glycolysis When glucose is transported into the cytoplasm of cells, it is broken down into two molecules of pyruvate (Figure $2$). This process is called glycolysis (glyco- for glucose and -lysis, meaning to break apart). Glycolysis involves the coordinated action of many different enzymes. As these enzymes start to break the glucose molecule apart, an initial input of energy is required. This initial energy is donated by molecules of ATP. Though two molecules of ATP are used to get glycolysis going, four more molecules of ATP are produced during the reaction, resulting in the net production of two ATP per molecule of glucose. In addition to ATP, two molecules of nicotinamide adenine dinucleotide (NAD+) are reduced to form NADH (Figure $3$). When NAD+ is reduced to NADH, two high energy electrons derived from breaking the bonds of glucose are added to it. One of those negatively charged electrons is balanced by the positive charge (+) on NAD+. The other is balanced by adding a proton (H+) to the molecule. Step 2: Pyruvate oxidation If oxygen is present, aerobic cellular respiration can continue. The two molecules of pyruvate are transported into the matrix of the mitochondrion. During transport, each pyruvate is converted into a 2-carbon molecule called acetyl-$\ce{CoA}$. The other carbon atom from each pyruvate molecule exits the cell as $\ce{CO2}$. The electrons from this broken bond are captured by another molecule of NAD+, reducing it to NADH. Because two molecules of pyruvate are produced from each glucose molecule during glycolysis, two acetyl CoA molecules are produced (one from each pyruvate) during pyruvate oxidation (Figure $4$). Step 3: The Citric Acid (Krebs) Cycle The two acetyl-$\ce{CoA}$ molecules enter a cycle which, much like glycolysis, involves the action of many different enzymes to release energy and transport it in energy-carrying molecules, including 2 ATP, 6 NADH, and 2 $\ce{FADH2}$, another electron carrier (Figure $4$). This cycle takes place within the matrix of the mitochondrion. Step 4: Oxidative Phosphorylation This stage of cellular respiration has two steps. During the electron transport chain, our electron carriers power a series of proton pumps that move $\ce{H+}$ ions from the mitochondrial matrix to the space between the inner and outer mitochondrial membranes. During chemiosmosis, an enzyme called ATP synthase allows the protons to flow back into the mitochondrial matrix, using the physical flow of the protons to turn ADP into ATP. The Electron Transport Chain NADH and $\ce{FADH2}$ drop off their electrons at a protein complex within the inner mitochondrial membrane. This effectively “turns on” this protein complex, which pumps a $\ce{H+}$ from the mitochondrial matrix to the intermembrane space. The electrons are then passed down a line of protein complexes, much like a current of electricity, powering these complexes to each pump a $\ce{H+}$ from the matrix into the intermembrane space. This is appropriately named the electron transport chain (Figure $5$). At the end of the electron transport chain, the low energy electrons need to be picked up to make space for more electrons. An oxygen atom picks up two electrons and, to balance the charge, two $\ce{H+}$ from the matrix, forming a water molecule ($\ce{H2O}$). In cellular respiration, oxygen is the terminal electron acceptor, because it picks up the electrons at the end (the terminus) of the electron transport chain. This job is so important that, as you saw above, if oxygen is not present, this part of cellular respiration will not occur. Chemiosmosis Why are the protein complexes pumping $\ce{H+}$ into the intermembrane space? The intermembrane space is relatively small. As more $\ce{H+}$ are added to this area, the intermembrane space becomes increasingly positively charged, while the matrix becomes increasingly negatively charged. This is similar to how a battery stores energy--by creating an electrochemical gradient. The positive charges repel each other and would “prefer” to be balanced across both sides of the membrane. However, they cannot directly pass through the membrane. Even though they are small, $\ce{H+}$ ions carry a full charge, making them too polar to pass through the nonpolar tails of the phospholipid bilayer that composes the mitochondrial membranes. An enzyme called ATP synthase allows the $\ce{H+}$ to move back into the matrix. This enzyme is structured much like a waterwheel or turbine -- the flow of protons through the enzyme physically rotates it, converting the potential energy stored in the electrochemical gradient into kinetic energy (movement)! This kinetic energy is used to force another phosphate group onto ADP, converting the kinetic energy back into chemical energy, which is stored in the bonds of ATP Attributions Curated and authored by Melissa Ha using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.02%3A_Aerobic_Cellular_Respiration.txt

Learning Objectives • Explain the relevance of photosynthesis to other living things. • Identify the substrates and products of photosynthesis. • Describe the main structures involved in photosynthesis. • Relate the light-dependent and light-independent reactions. Plants, algae, and certain bacteria (cyanobacteria and green and purple sulfur bacteria) are among the organisms capable of performing photosynthesis (Figure \(1\)). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs. The importance of photosynthesis is not just that it can capture sunlight’s energy. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via celluar respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. Photosynthesis Equation Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure \(2\)). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive. The following is the chemical equation for photosynthesis (Figure \(3\)). Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Structures of Photosynthesis Before learning the details of how photoautotrophs turn sunlight into food, it is important to review the structures involved. Recall from the Leaves chapter that leaves consist of several layers of cells, and the process of photosynthesis occurs in the mesophyll (middle layer). Note that other parts of the plant, such as the stems, are photosynthetic as well. The gas exchange of carbon dioxide and oxygen occurs through the stomata (singular: stoma), which also participate in water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate their opening and closing. In all autotrophic eukaryotes, photosynthesis takes place inside the chloroplast. For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. As shown in Figure \(4\), a stack of thylakoids is called a granum (plural: grana), and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis). Steps of Photosynthesis Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions (Calvin cycle). In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. Light-dependent reactions require water and produce oxygen and energy in the form of ATP. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize ATP and nicotinamide adenine dinucleotide phosphate (NADPH) to temporarily store the energy. Because NADPH carries two high-energy electrons, it is often referred to as an electron carrier. It can be thought of as “full” because it is rich in energy in its reduced state. When a molecule is reduced, electrons have been added to it. Electrons have a negative charge, so this is termed “reduction”. NAPDH move energy from light-dependent reactions to light-independent reactions. After the energy is released, the “empty” (oxidized) version, NADP+, returns to the light-dependent reactions to obtain more high-energy electrons. Likewise, the ATP produced during the light-dependent reactions fuels the light-independent reactions. It then returns in a lower-energy form (ADP) to the light-dependent reactions to become phosphorylated again. Figure \(5\) illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place. Attribution Curated and authored by Melissa Ha using the following sources: 4.1.04: Discovery of Photosynthesis Learning Objective Summarize the experimental results that revealed details about the process of photosynthesis. The history of the studies done on photosynthesis dates back into the 17th century with Jan Baptist van Helmont. He rejected the ancient idea that plants take most of their biomass from the soil. For the proof, he performed an experiment using a willow tree. He started with a willow tree with a mass of 2.27 kg. Over 5 years, it grew to 67.7 kg. However, the mass of the soil only decreased by 57 grams. Van Helmont came to the conclusion that plants must obtain most of their mass from water. He did not know about gases. Joseph Priestley ran a series of experiments in 1772 (Figure \(1\)). He tested a mouse, a candle, and a sprig of mint under hermetically sealed (no air can go in or out) jar. He first observed that a mouse and a candle behave very similarly when covered, in that they both “spend” the air. However, when a plant is placed with either the candle or mouse, the plant “revives” the air for both. Further ideas were brought about in the late 1700’s. Jan Ingenhousz and Jean Senebier found that the air is only reviving in the day time and that CO\(_2\) is assembled by plants. Antoin-Laurent Lavoiser found that “revived air” is a separate gas, oxygen. But what is the oxygen “maker”? There are many pigments in plants, and all accept and reflect some parts of rainbow. To identify the culprit, Thomas Engelmann ran an experiment (Figure \(2\)) using a crystal prism that shine different wavelengths (colors) of visible light on the algae Spirogyra algae. He then measured oxygen production with aerotactic bacteria, which move towards areas of high oxygen concentration. A high density of bacteria cells accumulated in the blue and red parts of the spectrum, indicating this was where the most oxygen was produced and the most photosynthesis was conducted. This was a huge find. It tells that the key photosynthetic pigment should accept blue and red rays, and thus reflect green rays. The photosynthetic pigment chlorophyll a best fits this description. Another important fact was discovered by Frederick Blackman in 1905. He found that if light intensity is low, the increase of temperature actually has very little effect on the rate of photosynthesis. However, the reverse is not exactly true, and light is able to intensify photosynthesis even when it is cold. This could not happen if light and temperature are absolutely independent factors. If temperature and light are components of the chain, light was first (“ignition”) and temperature was second. This ultimately shows that photosynthesis has two stages (now called the light-dependent and light-independent stages). The light-dependent stage relates the to intensity of the light. The light-independent stage relates more with the temperature as it involves many enzymes. Attribution Curated and authored by Melissa Ha using 8.1 Overview of Photosynthesis from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.03%3A_Photosynthesis_Overview_and_Equation.txt

Learning Objectives • Relate wavelength, energy, and the type of electromagnetic radiation (and the color of visible light). • Explain how plants absorb energy from sunlight. • Detail the steps of the light-dependent interactions. How can light be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules (Figure \(1\)). However, photoautotrophs only use a few specific components of sunlight. What Is Light Energy? The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which portion is therefore referred to as “visible light”. The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between consecutive points of a wave. A single wave is measured from two consecutive points, such as from crest to crest or from trough to trough (Figure \(2\)). The difference between wavelengths relates to the amount of energy carried by them. Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation (Figure \(3\)). Several types of electromagnetic radiation originate from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, explaining why both X-rays and UV rays can be harmful to living organisms. Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy. Absorption of Light Light energy initiates the process of photosynthesis when pigments absorb the light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to excite electrons in the retinal pigments. Energy levels higher than those in blue light will physically tear these molecules apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm to 400 nm light, which is therefore called visible light. For the same reasons, plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy (Figure \(4\)). Understanding Pigments Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color. Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in plant chloroplasts and will be the focus of the following discussion. With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum. The graph in Figure \(5\) shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths. Many photosynthetic organisms have a mixture of pigments; using them, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth (Figure \(6\)). Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation (Figure \(7\)). When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases. How Light-Dependent Reactions Work The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. In the light-dependent reactions protein complexes and pigment molecules work together to produce NADPH and ATP (Figure \(8\) and Video \(1\)). Video \(1\): Here is an animation of the light-dependent reactions. Photosystems Absorb Light Energy The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem, two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and photosystem I (PSI) (Figure \(9\)). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons). Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center, where the photochemistry takes place. Each photosystem is serviced antenna complex, which passes energy from sunlight to the reaction center. The antenna complex consists of multiple antenna proteins that contain a mixture of 300–400 chlorophyll a and b molecules as well as other pigments like carotenoids. (Technically, photosystems consist of the reaction center and the antennae complex, and a photosytem plus light-harvesting complexes comprises a photosystem complex, but in Figure \(9\), the light-harvesting complex is labeled as the antennae complex.) The absorption of a single photon, or distinct quantity or “packet” of light, by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons. The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron. It is at this step in the reaction center, this step in photosynthesis, that light energy is converted into an excited electron. Electrons Move Down the Electron Transport Chain, Providing Energy to Pump Protons into the Thylakoid Lumen The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time, to the primary electron acceptor, and through the electron transport chain (Pq to cytochrome b6f complex to plastocyanine) to PSI (Figure \(10\)). The cytochrome b6f complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), ultimately facilitating the transfer of electrons from PSII to PSI. During this process, cytochrome b6f pumps protons from the stroma into the thylakoid lumen using the energy from electrons moving down the electron transport chain. Photophosphorylation The synthesis of ATP in the light-dependent reactions is called photophosphorylation. The buildup of protons inside the thylakoid lumen creates a concentration gradient. The passive movement (facilitated diffusion) of protons from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP. The protons build up energy at high concentrations because they all have the same electrical charge, repelling each other. To release this energy, protons will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the proton stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP (Figures \(\PageIndex{10-11}\)). The flow of protons through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure. Water Photolysis P680’s missing electron is replaced by extracting a low-energy electron from water; thus, water is split (water photolysis) and PSII is re-reduced. Splitting one H2O molecule releases two electrons, two protons, and one atom of oxygen (Figures \(\PageIndex{10-11}\)). Those protons, in addition to the ones transported by cytrochrome b6f, accumulate in the thylakoid lumen and fuel photophosphorylation. Splitting two molecules is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support aerobic cellular respiration, the process of breaking down glucose to generate ATP. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration. Reduction of NADP+ Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700). P700 is oxidized and sends high-energy electrons to the electron carrier NADP+ to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP+ into NADPH. The two photosystems work in concert, in part, to guarantee that the correct proportions of NADPH and ATP needed for the light-independent reactions are generated. Other mechanisms exist to fine tune that ratio to exactly match the chloroplast’s constantly changing energy needs. Attribution Curated and authored by Melissa Ha using 8.2 The Light-Dependent Reactions of Photosynthesis from Biology 2e by OpenStax (licensed CC-BY). Access for free at openstax.org.

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.05%3A_The_Light-dependent_Reactions.txt

Learning Objectives • Detail the three steps of the light-independent reactions. • Define carbon fixation. After the energy from the sun is converted into chemical energy temporarily stored in the bonds of ATP and NADPH molecules, the cell has the fuel needed to build carbohydrate molecules for long-term energy storage. The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light-independent reactions (carbohydrates and other forms of reduced carbon) can survive for hundreds of millions of years. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? It comes from carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals. In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis (Figure \(1\)). The light-independent reactions (also known as the Calvin cycle) can be organized into three basic stages: fixation, reduction, and regeneration (Video \(1\)). Video \(1\): Here is an animation of the light-independent reactions (Calvin cycle): Stage 1: Fixation In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose-1,5-bisphosphate (RuBP), as shown in Figure \(2\). RuBP has five atoms of carbon, flanked by two phosphates. RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound, 3-phosphoglycerate (3-PGA), form. 3-PGA has three carbon atoms and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3 CO2 + 15 atoms from 3 RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation, because CO2 is “fixed” from an inorganic form into organic molecules. Stage 2: Reduction ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and re-energized. Stage 3: Regeneration Interestingly, at this point, only one of the G3P molecules leaves the light-independent reactions and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the cycle to fix enough net carbon to export one G3P. But each turn makes two G3P, thus three turns make six G3P. One of these six is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions. Evolution Connection: Photosynthesis During the evolution of photosynthesis, a major shift occurred from the bacterial type of photosynthesis that involves only one photosystem and is typically anoxygenic (does not generate oxygen) into modern oxygenic (does generate oxygen) photosynthesis, employing two photosystems. This modern oxygenic photosynthesis is used by many organisms—from giant tropical leaves in the rainforest to tiny cyanobacterial cells—and the process and components of this photosynthesis remain largely the same (Figure \(3\)). Photosystems absorb light and use electron transport chains to convert energy into the chemical energy of ATP and NADPH. The subsequent light-independent reactions then assemble carbohydrate molecules with this energy. Attribution Curated and authored by Melissa Ha using the following sources:

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.06%3A_Light-independent_Reactions.txt

Learning Objectives • Define photorespiration. • Explain how C3, C4, and CAM plants reduce photorespiration. • Outline the C4 pathway and compare its use by C4 plants and CAM plants. Different plant species have adaptations that allow them to do different variations of the light-independent reactions. These are called photosynthetic pathways. Plants are classified as C3, C4, or CAM depending on their use of these pathways, but note that some plants can switch photosynthetic pathways depending on environmental conditions. The process for light-independent reactions described in the previous section was the C3 pathway: the compound formed during fixation (3-PGA) has three carbon atoms. Before discussing the details of the C4 pathway, it is important to understand the circumstances that led to these adaptations. Photorespiration As its name suggests, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes two different reactions. The first is adding CO2 to ribulose-1,5- bisphosphate (RuBP) — the carboxylase activity. The second is adding O2 to RuBP — the oxygenase activity. The oxygenase activity of RuBisCO forms the three-carbon molecule 3-phosphoglycerate (3-PGA), just as in the light-independent reactions, and the two-carbon molecule glycolate. The glycolate enters peroxisomes, where it uses O2 to form intermediates that enter mitochondria where they are broken down to CO2. So this process uses O2 and liberates CO2 as aerobic cellular respiration does, which is why it is called photorespiration. It undoes the work of photosynthesis, which is to build sugars. Which action of RuBisCO predominates depends on the relative concentrations of O2 and CO2 with high CO2, low O2 favoring the carboxylase action and high O2, low CO2 favoring the oxygenase action. The light reactions of photosynthesis liberate oxygen, and more oxygen dissolves in the cytosol of the cell at higher temperatures. Therefore, high light intensities and high temperatures (above ~ 30°C) favor the second reaction and result in photorespiration. C3 Plants One solution to photorespiration is for plants to open their stomata to release O2 and obtain CO2. However, if conditions are hot or dry, this will result in too much water loss (transpiration). For this reason, C3 plants, which only do the C3 pathway and do not use the C4 pathway to prevent photorespiration (see below), do best in cool, moist areas. Rice and potatoes are examples of C3 plants. C4 Plants Many angiosperms have developed adaptations which minimize the losses to photorespiration. They all use a supplementary method of CO2 uptake which initially forms a four-carbon molecule compared to the two three-carbon molecules that are initially formed in the C3 pathway. Hence, these plants are called C4 plants. Note that C4 plants will eventually conduct the light-independent reactions (C3 pathway), but they form a four-carbon molecule first. C4 plants have structural changes in their leaf anatomy so that synthesizing the four-carbon sugar (the C4 pathway) and resuming the light-independent reactions (C3 pathways) are separated in different parts of the leaf with RuBisCO sequestered where the CO2 level is high and the O2 level low. After entering through stomata, CO2 diffuses into a mesophyll cell (Figure \(1\)). Being close to the leaf surface, these cells are exposed to high levels of O2, but they have no RuBisCO so cannot start photorespiration (nor the light-independent reactions). Instead, the CO2 is inserted into a three-carbon compound called phosphoenolpyruvic acid (PEP) forming the four-carbon compound oxaloacetic acid. Oxaloacetic acid is converted into malic acid or aspartic acid (both have 4 carbons), which is transported through plasmodesmata into a bundle sheath cell. Bundle sheath cells are deep in the leaf, so atmospheric oxygen cannot diffuse easily to them (Figure \(2\)). Additionally, they often have thylakoids with reduced photosystem II complexes (the one that produces O2). Both of these features keep oxygen levels low in bundle sheath cells, which is where the four-carbon compound is broken down into carbon dioxide, which enters the light-independent reactions (C3 pathway) to form sugars and pyruvic acid, which is transported back to a mesophyll cell where it is converted back into PEP. These C4 plants are well adapted to (and likely to be found in) habitats with high daytime temperatures and intense sunlight. Because they use the C4 pathway to prevent photorespiration, they do not have to open their stomata to the same extent as C3 plants and can thus conserve water. Some examples crabgrass, corn (maize), sugarcane, and sorghum. Although comprising only ~3% of the angiosperms by species, C4 plants are responsible for ~25% of all the photosynthesis on land. CAM Plants CAM stands for crassulacean acid metabolism because it was first studied in members of the plant family Crassulaceae. CAM plants also do the C4 pathway. However, instead of segregating the C4 and C3 pathways in different parts of the leaf, CAM plants separate them in time instead (Table \(1\)). As a result, CAM plants do not need to open their stomata in the daytime to reduce photorespiration because they have already formed a four-carbon molecule at night that can be broken down to release carbon dioxide during the day. Table \(1\): Activities of CAM plants at night and in the morning. Night Morning • CAM plants take in CO2 through their open stomata (they tend to have reduced numbers of them). • The CO2 joins with PEP to form the four-carbon oxaloacetic acid. • This is converted to four-carbon malic acid that accumulates during the night in the central vacuole of the cells. • The stomata close (thus conserving moisture as well as reducing the inward diffusion of oxygen). • The accumulated malic acid leaves the vacuole and is broken down to release CO2. • The CO2 is taken up into the light-independent reactions (C3 pathway). CAM plants thus thrive in conditions of high daytime temperatures, intense sunlight, and low soil moisture. Some examples of CAM plants include cacti (Figure \(3\)), pineapples, all epiphytic bromeliads, sedums, and the "ice plant" that invade the California coast line. Attribution Curated and authored by Melissa Ha using 16.2E Photorespiration and C4 Plants from Biology by John W. Kimball (licensed CC-BY)

textbooks/bio/Botany/Botany_(Ha_Morrow_and_Algiers)/04%3A_Plant_Physiology_and_Regulation/4.01%3A_Photosynthesis_and_Respiration/4.1.07%3A_Photorespiration_and_Photosynthetic_Pathways.txt