BIO 102: General Biology II PDF

BIO 102: GENERAL BIOLOGY II MCB Basic Characteristics, Identification, and Classification of Viruses Viruses are a unique group of biological entities that can infect eukaryotic or prokaryotic organisms. Although some viruses do contain a few enzymes, they are obligate parasites that have no metabol...

BIO 102: GENERAL BIOLOGY II MCB Basic Characteristics, Identification, and Classification of Viruses Viruses are a unique group of biological entities that can infect eukaryotic or prokaryotic organisms. Although some viruses do contain a few enzymes, they are obligate parasites that have no metabolic capacity and rely on host metabolism to produce viral parts that self-assemble. Viruses consist of nucleic acid encapsulated within a protein coat known as the capsid of variable size and morphology. Viral nucleic acids can consist of single- or double-stranded DNA or RNA. The replication of a virus can be described in five steps: (1) adsorption; (2) penetration; (3) replication; (4) maturation; and (5) release. All viruses share a common mechanism of replication at the molecular level, but different viruses replicate at varying rates. For example, prokaryotic viruses known as bacteriophage or phage infect bacteria and often replicate rapidly, in minutes, whereas a typical animal virus replicates in hours to days. Coliphages are viruses that infect coliform bacteria such as Escherichia coli. All viruses begin infection by adsorption to the host via specific receptors and injection of the nucleic acid or uptake of the total virus particle into the cell. The cycle then goes into what is known as the eclipse phase, a period during which no virus particles can be detected because of release and incorporation of the nucleic acid in the host cell machinery. Finally, new viral components are produced, assembled, and released from the host by disruption of the cell or budding at the cell membrane surface. The latter release mechanism is less destructive to the host cell and may support a symbiotic condition between the virus and the host. Infective Nature of Viruses Outside their hosts, viruses are inert objects, incapable of movement. Thus, these tiny infectious agents require a vehicle, such as air or water, for transport. Once in contact with a potential host, viruses find their way into target cells using specific receptor sites on their capsid or envelope surfaces. This is why viruses of bacteria or plants do not normally infect humans and vice versa. Once viruses invade host cells and replicate, they can invade neighboring cells to continue the infection process. Infection of a cell by a virus is often but not always draining to the cell’s regular functions. Thus, viral infection may be asymptomatic or may cause acute, chronic, latent, or slow infections, or may cause cell death. In bacteria, some viral infections appear to cause no immediate harm to the host cell. A phage can infect a host cell and remain dormant, carrying its genetic material within the host's chromosome. This is called lysogeny, where the phage becomes a temperate or lysogenic phage, persisting in a stable and non-infectious form called a prophage, passed on to daughter cells. The phage may remain latent for many generations and then suddenly be mobilized and initiate replication and eventually cause host lysis. Typically, only a portion of temperate phage becomes lysogenic, while other members of the population remain virulent, multiplying, and lysing host cells. Similar to lysogenic bacteriophage, animal retroviruses integrate their nucleic acid into the cell chromosome, producing persistent infections. Such a cycle is typical of herpesvirus infections in humans. In fact, the herpes virus may be passed from grandparent to grandchild, remaining dormant through two generations. 1 Half of the human population is estimated to be infected by the age of 1 year, and up to 85% of the population is seropositive by puberty. Most latent animal viruses, such as mumps and measles viruses, lack the ability to lyse the host cell or prevent host cell division. Infection is therefore ensured by the production of infected daughter host cells. In latent infections, an equilibrium is reached between host and parasite until a nonspecific stimulus, such as compromised host immunity, evokes active infection. Structure and Function Viruses exist as inert particles outside the host cell and only become active upon entering a host cell. The virion consists of: Nucleic acid: This can be either RNA or DNA, which carries the genetic information necessary for replication. Protein coat (capsid): Made up of protein subunits called capsomeres, the capsid protects the viral genome and facilitates attachment to host cell receptors. Capsid: Provides structural support and protection for the viral genome. Capsid proteins are encoded by the viral genome. Nucleocapsid: This is the combination of nucleic acid and nucleoprotein. Enveloped viruses have an additional outer lipid bilayer with embedded glycoproteins. Fig. 1. Structure of a Virion Classification of Viruses Viruses are classified based on several criteria, including their size, shape, chemical composition, and genome structure. These characteristics help in understanding the diversity and functionality of viruses, as well as their evolutionary relationships. The two main morphological classifications are helical and icosahedral. Morphology Helical Morphology Helical viruses are characterized by their filamentous shape, where the capsid proteins 2 are arranged in a helical structure around the viral genome. The capsid, composed of identical protein subunits called protomers, forms a spiral or helix around the nucleic acid. This arrangement allows for a rod-shaped or filamentous appearance. Examples is the Tobacco Mosaic Virus (TMV) which is one of the most studied helical viruses, it infects plants and has a rigid, rod-shaped structure. Influenza Virus although enveloped, the internal structure of the nucleocapsid of the influenza virus is helical. The helical arrangement is often flexible, which can aid in the virus's ability to package its genome efficiently and interact with host cell structures. Icosahedral Morphology Icosahedral viruses are characterized by a spherical shape, where the capsid proteins are arranged in a symmetric pattern forming a polyhedron with 20 triangular faces. The icosahedral structure provides a highly efficient way to enclose the viral genome, maximizing internal volume while minimizing surface area. The capsid is composed of repeating units of capsomeres arranged in a geometric pattern. Examples is the Adenovirus, which is known for causing respiratory illnesses, adenoviruses have a distinct icosahedral structure with protruding fiber proteins at each vertex. Herpes Simplex Virus (HSV): An enveloped virus with an icosahedral nucleocapsid that causes oral and genital herpes. The icosahedral shape allows for strong structural integrity and efficient packaging of the viral genome. The geometric arrangement of capsomeres provides stability and aids in the virus's ability to withstand environmental conditions. Fig. 2. Helical and Icosahedral Morphology Chemical Composition and Replication Viruses exhibit a diverse range of genetic compositions and replication strategies, which are crucial for their classification and understanding of their life cycles. Viral Genome Composition The viral genome can be composed of either DNA or RNA, and it can be single-stranded (ss) or double-stranded (ds), linear or circular. These variations in the genome determine the mechanisms of replication and the strategies used by the virus to hijack 3 the host's cellular machinery. DNA Viruses Single-stranded DNA (ssDNA): Viruses with a single-stranded DNA genome, such as Parvoviruses, must convert their genome into double-stranded DNA once inside the host cell for replication and transcription. Double-stranded DNA (dsDNA): Viruses with a double-stranded DNA genome, such as Herpesviruses and Poxviruses, often utilize the host cell's nuclear machinery for replication and transcription. RNA Viruses Single-stranded RNA (ssRNA): Positive-sense RNA (+ssRNA): These viruses have genomes that can directly serve as messenger RNA (mRNA) for protein synthesis. Examples include Poliovirus and Coronaviruses. Their replication typically occurs in the cytoplasm. Negative-sense RNA (-ssRNA): These viruses have genomes that are complementary to the mRNA. They require an RNA-dependent RNA polymerase to synthesize a complementary RNA strand that can function as mRNA. Examples include Influenza virus and Ebola virus. Double-stranded RNA (dsRNA): These viruses have genomes consisting of two complementary RNA strands. Examples include Rotaviruses. Their replication also typically occurs in the cytoplasm. Retroviruses: These viruses, such as Human Immunodeficiency Virus (HIV), have an RNA genome but replicate through a DNA intermediate. They use the enzyme reverse transcriptase to convert their RNA into DNA, which is then integrated into the host cell genome. Replication Strategies The replication strategies of viruses depend on their genome type and the cellular machinery they exploit: DNA Viruses: Typically replicate in the nucleus of the host cell using the host's DNA polymerase enzymes. Some, like Poxviruses, replicate in the cytoplasm using their own replication machinery. RNA Viruses: Generally, replicate in the cytoplasm. Positive-sense RNA viruses can be directly translated into viral proteins, while negative-sense RNA viruses must first produce a complementary RNA strand. Retroviruses: Use reverse transcription to integrate their genome into the host's DNA, ensuring long-term persistence in the host cell. 4 Fig. 3. Virus Replication Pathways Nomenclature and Classification The classification of viruses considers several factors, including genome structure, replication mode, and physical characteristics. Genome Structure and Replication Mode Single-stranded RNA viruses: Positive-sense RNA viruses: Their RNA genome can directly serve as mRNA for protein synthesis. Examples include Poliovirus, Coronaviruses. Negative-sense RNA viruses: Require a complementary RNA strand to be synthesized by an RNA-dependent RNA polymerase before it can serve as mRNA. Examples include Influenza virus, Rabies virus. Additional Classification Criteria Site of Capsid Assembly: The location within the host cell where the capsid assembles is a classification criterion. For instance, some viruses assemble in the nucleus (e.g., Adenoviruses), while others assemble in the cytoplasm (e.g., Poxviruses). Site of Envelopment (for Enveloped Viruses): Enveloped viruses acquire their lipid bilayer from the host cell membrane. This can occur at different cellular sites: Plasma Membrane: Many enveloped viruses, such as Influenza virus, acquire their envelope by budding from the plasma membrane. Endoplasmic Reticulum/Golgi Apparatus: Some viruses, like Coronaviruses, assemble and bud into the endoplasmic reticulum or Golgi apparatus before being transported to the cell surface for release. Helical Symmetry: The protein subunits (capsomeres) and the nucleic acid form a continuous helical structure. This structure is usually flexible, allowing the virus to adopt a variety of shapes. Icosahedral Symmetry: Characterized by 20 triangular faces and 12 vertices, providing a highly efficient way to enclose a space. It allows for maximum internal volume relative 5 to the surface area, which is advantageous for accommodating the viral genome. Example: The adenovirus, which features 252 capsomeres arranged in a T=25 symmetry pattern. Virus Envelope Many viruses have an envelope derived from modified host cell membranes. This envelope is a lipid bilayer that encases the nucleocapsid. The envelope is often embedded with glycoproteins that play key roles in virus attachment and entry into host cells. Enveloped viruses acquire their envelope by budding through the host cell membrane, which can be the plasma membrane or an internal membrane (such as the Golgi apparatus or endoplasmic reticulum). Virus Families Viruses that infect humans are grouped into 21 families based on their morphology, chemical composition, and mode of replication. Examples include: Helical viruses: Such as the tobacco mosaic virus, which has a helical structure. Enveloped helical viruses: Such as the Sendai virus, which has both a helical nucleocapsid and an outer lipid envelope. Identification of Viruses Several techniques are employed for the identification of viruses, each with specific applications and advantages: Electron Microscopy: Enables the visualization of virus morphology, including the size, shape, and structural details such as capsomeres and nucleocapsids. This method is crucial for identifying virus particles and observing their structural integrity. X-ray Diffraction: Provides detailed information about the three-dimensional structure of viruses, particularly useful for understanding the arrangement of viral proteins and nucleic acids. Negative Staining Electron Microscopy: Enhances contrast in electron microscopy images, making it easier to observe structural features of viruses, particularly icosahedral viruses, facilitating classification by capsomere number and pattern. Molecular Techniques: Techniques such as Polymerase Chain Reaction (PCR) and sequencing are used to identify viral genomes based on nucleic acid sequences. These methods are highly sensitive and specific, allowing for the detection and identification of viruses even at low concentrations. Serology: Detects specific viral antigens or antibodies in a host's blood. This is useful 6 for diagnosing viral infections, determining past exposure, and epidemiological studies. Culture Techniques: Involve growing viruses in cell cultures to observe cytopathic effects (CPE). This confirms the presence of infectious virus particles and helps in studying virus behavior and replication. Basic Characteristics of Bacteria Bacteria are among the most diverse and widespread organisms on Earth. As single- celled prokaryotes, they lack a true nucleus and membrane-bound organelles, differentiating them from eukaryotic cells. Fundamental characteristics of bacteria include 1. Cell Structure Cell Wall: Most bacteria have a cell wall that provides structural support and protection. The composition of the cell wall is a key factor in bacterial classification: Gram-positive Bacteria: These bacteria have a thick peptidoglycan layer in their cell wall, which retains the crystal violet stain used in Gram staining, resulting in a purple color. They often contain teichoic acids. Gram-negative Bacteria: These bacteria have a thinner peptidoglycan layer and an additional outer membrane containing lipopolysaccharides. They do not retain the crystal violet stain but take up the counterstain (safranin) and appear pink. Cell Membrane: A phospholipid bilayer that encloses the cytoplasm and controls the movement of substances in and out of the cell. Cytoplasm: A jelly-like substance where metabolic activities occur, containing enzymes, nutrients, and the cell’s genetic material. Nucleoid: The region within the cytoplasm where the bacterial chromosome is located. Unlike eukaryotic cells, the nucleoid is not enclosed by a membrane. Plasmids: Small, circular DNA molecules that replicate independently of the chromosomal DNA. Plasmids often carry genes for antibiotic resistance and can be transferred between bacteria through processes like conjugation. Ribosomes: Structures composed of RNA and proteins that are responsible for protein synthesis. Bacterial ribosomes are smaller than eukaryotic ribosomes (70S vs. 80S). 2. Morphology Shapes: Bacteria exhibit a variety of shapes, including: Cocci: Spherical-shaped bacteria (e.g., Staphylococcus aureus, Streptococcus pneumoniae). Bacilli: Rod-shaped bacteria (e.g., Escherichia coli, Bacillus anthracis). Spirilla: Spiral-shaped bacteria with rigid bodies (e.g., Spirillum minus). Spirochetes: Flexible, spiral-shaped bacteria (e.g., Treponema pallidum, Borrelia 7 burgdorferi). Vibrios: Comma-shaped bacteria (e.g., Vibrio cholerae). Arrangement: Bacterial cells can group together in characteristic arrangements: Diplococci: Pairs of cocci (e.g., Neisseria gonorrhoeae). Streptococci: Chains of cocci (e.g., Streptococcus pyogenes). Staphylococci: Clusters of cocci resembling grapes (e.g., Staphylococcus aureus). Palisades: Bacilli arranged side by side like a fence (e.g., Corynebacterium). 3. Reproduction Binary Fission: The primary mode of bacterial reproduction. A single bacterial cell divides into two identical daughter cells. This process involves DNA replication, elongation of the cell, and division by the formation of a septum. Genetic Exchange Mechanisms: Bacteria can exchange genetic material through several mechanisms, enhancing genetic diversity: Conjugation: Transfer of genetic material between bacteria through direct contact, typically involving plasmids. Transformation: Uptake of free DNA from the environment by a bacterial cell. Transduction: Transfer of bacterial DNA by a bacteriophage (virus that infects bacteria). Bacterial Metabolism The four major types of metabolism based on the source of energy and carbon used for growth are chemoheterotroph, chemoautotroph, photoautotroph and photoheterotroph. Energy can be obtained from light through photosynthesis (phototroph), or from the oxidation of organic or inorganic chemicals (chemotroph). Carbon is obtained either from carbon dioxide (autotroph) or from organic compounds such as glucose (heterotroph or organotroph). Thus, chemoheterotrophs (chemoorganotrophs) use organic compounds both for energy and for carbon, chemoautotrophs (chemolithotrophs) obtain their energy from the oxidation of inorganic compounds and their carbon from carbon dioxide, photoautotrophs obtain energy from light and fix carbon from carbon dioxide and, finally, photoheterotrophs obtain energy from light and carbon from organic compounds. There are two ways in which bacteria can harvest energy to use for building new cell material, respiration, and fermentation. Cells generate energy through: 1. Aerobic respiration (with oxygen): most efficient, producing 38 ATP/glucose. 2. Anaerobic respiration (without oxygen): less efficient, using alternative electron acceptors. 3. Fermentation (anaerobic, no electron transport chain): least efficient, producing 2 ATP/glucose and organic acids/alcohols. 8 Oxygen availability determines the type of respiration that occurs. Identification of Bacteria Identifying bacteria is crucial for understanding their roles in various environments, diagnosing infections, and developing treatments. Common methods for bacterial identification include: 1. Microscopy Gram Staining: A differential staining technique that classifies bacteria into Gram- positive and Gram-negative based on the characteristics of their cell walls. The process involves four steps: crystal violet staining, iodine treatment, alcohol decolorization, and counterstaining with safranin. Morphological Observation: Examining the shape, size, and arrangement of bacterial cells under a microscope. 2. Culture Techniques Agar Plates: Solid media where bacteria can be grown to form colonies. Colony morphology, including size, shape, color, and texture, can aid in identification. Specialized media can indicate specific metabolic properties (e.g., MacConkey agar for lactose fermentation). Broth Cultures: Liquid media used to grow bacteria. Observing growth patterns, such as turbidity, pellicle formation, or sedimentation, can provide clues about bacterial identity. 3. Biochemical Tests Catalase Test: Detects the presence of the enzyme catalase by adding hydrogen peroxide to a bacterial culture. Bubbles indicate a positive result. Oxidase Test: Identifies bacteria that produce cytochrome c oxidase. A color change on a special reagent-soaked swab or filter paper indicates a positive result. Fermentation Tests: Assess the ability of bacteria to ferment specific sugars, producing acid and/or gas. This can be observed using pH indicators and Durham tubes. 4. Molecular Techniques Polymerase Chain Reaction (PCR): Amplifies specific DNA sequences to detect and identify bacteria. Highly sensitive and specific. 16S rRNA Sequencing: Analyzes the genetic sequence of the 16S ribosomal RNA gene, which is highly conserved among bacteria but contains variable regions that can distinguish different species. Classification of Bacteria Bacterial classification involves categorizing bacteria based on various criteria, including morphology, genetic makeup, metabolic properties, and ecological roles. 1. Gram Stain Reaction 9 Gram-Positive Bacteria: Bacteria with a thick peptidoglycan layer that retains the crystal violet stain and appears purple under a microscope. Examples: Staphylococcus, Streptococcus, Bacillus, Clostridium. Gram-Negative Bacteria: Bacteria with a thin peptidoglycan layer and an outer membrane that do not retain the crystal violet stain but take up the counterstain and appear pink. Examples: Escherichia coli, Salmonella, Pseudomonas, Neisseria. 2. Shape and Arrangement Cocci (Spherical): Streptococci: Chains of cocci (e.g., Streptococcus pyogenes). Staphylococci: Clusters of cocci (e.g., Staphylococcus aureus). Diplococci: Pairs of cocci (e.g., Neisseria gonorrhoeae). Bacilli (Rod-shaped): Single Rods: Individual rod-shaped cells (e.g., Escherichia coli). Chains of Rods: Chains of bacilli (e.g., Bacillus anthracis). Spirilla (Spiral-shaped): Rigid Spirals: Rigid, spiral-shaped cells (e.g., Spirillum minus). Spirochetes: Flexible, spiral-shaped cells (e.g., Treponema pallidum). Vibrios (Comma-shaped): Comma-shaped bacteria (e.g., Vibrio cholerae). 3. Oxygen Requirement Aerobes: Bacteria that require oxygen for growth (e.g., Mycobacterium tuberculosis). Anaerobes: Bacteria that grow in the absence of oxygen. Obligate Anaerobes: Cannot tolerate oxygen and are often harmed by its presence (e.g., Clostridium botulinum). Facultative Anaerobes: Can grow with or without oxygen, but generally prefer oxygen (e.g., Escherichia coli). Microaerophiles: Require low levels of oxygen for growth (e.g., Helicobacter pylori). 4. Metabolic Characteristics Autotrophic Bacteria: Synthesize their own food using inorganic sources. Photoautotrophs: Use light energy to convert carbon dioxide into organic compounds (e.g., Cyanobacteria). 10 Chemoautotrophs: Obtain energy from the oxidation of inorganic substances (e.g., Nitrosomonas). Heterotrophic Bacteria: Obtain nutrients from organic matter. Saprophytic Bacteria: Decompose dead organic matter and recycle nutrients (e.g., Bacillus subtilis). Parasitic Bacteria: Obtain nutrients from living hosts, often causing diseases (e.g., Mycobacterium tuberculosis). Fig. 4. Bacterial Classification Basic Characteristics of Fungi Fungi are a diverse group of eukaryotic organisms that include yeasts, molds, and mushrooms. They play critical roles in decomposition, nutrient cycling, and as symbionts or pathogens of plants, animals, and humans. While bacteria may represent the most abundant microorganisms in terms of numbers of individuals, the fungi, which are a physically larger group of eukaryotic microorganisms, have the greatest biomass. In a landmark paper, 1.5 million fungal species were estimated to exist (Hawksworth, 2001) with only 7% of them identified so far (Crous et al., 2006). Traditionally, the identification of fungi has been based on morphology, spore structure and membrane fatty acid composition. However, more recent estimates using high throughput sequencing methods suggest that as many as 5.1 million fungal species exist (Blackwell, 2011). Fungi are ubiquitous and primarily found in the soil environment where they can adapt to a variety of conditions and have a primary role as decomposers. As with bacteria, some fungi are pathogenic to both humans and plants (in fact, economically, fungi are the most important plant pathogens). Other fungi are important in industrial processes involving fermentation, and in biotechnology to produce 11 antimicrobial compounds. Metabolically, fungi are chemoheterotrophs. Most fungi are obligately aerobic, but yeasts are facultative anaerobes and the zoosporic fungi found in ruminants are obligately anaerobic. These anaerobic fungi generally ferment sugars and in doing so produce a variety of useful by-products, such as ethanol, acetic acid and lactic acid, making them important commercially for production of many staple foods (e.g., yogurt, cheese, bread, pickles) and alcoholic products such as beer and wine. In addition to their primary metabolism which supports biosynthesis and energy production, fungi are known for producing secondary metabolites (compounds produced during the stationary phase of growth). These secondary metabolites have revolutionized medicine, biotechnology and agriculture. For example, fungi are responsible for such antimicrobials as penicillin produced by Penicillium notatum, cephalosporin produced by Cephalosporium acremonium and griseofulvin produced by Penicillium griseofulvum. While the fungal production of antimicrobials under in situ conditions is not well understood, it is hypothesized that they help reduce competition from other microorganisms for nutrient. Major characteristics of fungi include: Cell Structure Fungal membranes and cell walls are complex structures that act as selectively permeable barriers and protective outer barriers, respectively. The composition of these two structures varies somewhat among genera, in part due to the large variation in behaviors and life cycles, habitats and physiologies seen in the fungi. As eukaryotes, fungi have membrane-bound organelles in addition to a cytoplasmic membrane composed of a phospholipid bilayer with interspersed proteins for transport and degradation. Fungal membranes can be quite complex with structural and compositional differences observed in organelle membranes and in the life cycle stages. In addition to phospholipids, fungal membranes can include sterols, glycolipids, and sphingolipids, which can be used for fungal identification as the ratio, type and amount of lipids can be species specific. Fungal cell walls are multilayered structures composed of chitin, the glucose derivative N-acetylglucosamine. Fungal cell walls may also contain cellulose, galactosans, chitosans and mannans. Other cell wall components include proteins and lipids. Similarly to bacteria, the fungal cell wall lies outside of the cytoplasmic membrane, protecting the membrane from damage. The cell wall additionally provides the scaffolding for the fairly complex three-dimensional structures characteristic of some fungi, e.g., mushrooms. 12 Fig. 5. Basic Structure of Fungal Cells Fungal Diversity Fungi can be divided into three general groups based on morphological descriptions: molds, mushrooms and yeasts. Molds, such as Aspergillus, Penicillium, Rhizopus and Pilobolus, are filamentous fungi which are found in many fungal phyla. Each filamentous fungal cell is called a hypha (pl. hyphae), which grows in mass to form tufts of hyphae or mycelia. Some hyphae extend out from the mycelium to form aerial hyphae responsible for the formation of asexual spores or conidia ranging from 1 to 50 μm in diameter. The fuzzy appearance of mold colonies is due to the aerial hyphae and the color of fungal colonies is the result of the coloration of the spores. Some molds produce sexual spores as the result of sexual reproduction. While not as resistant as bacterial spores, both asexual and sexual spores can be resistant to extreme temperatures, desiccation, and chemicals, and are in large part responsible for the widespread occurrence of molds. The mushrooms are part of the Basidiomycota, which are filamentous fungi that form the large fruiting bodies referred to as mushrooms. Aerial mycelia come together to form the macroscopic mushroom, whose main purpose is dispersal of the sexual basidiospores found underneath the cap. The rest of the mushroom fungus is below ground as a mycelium that extends outward for nutrient absorption. Both molds and mushrooms are important decomposers of natural products, such as wood, paper, and cloth. However, both groups of fungi can additionally produce sticky extracellular substances that bind soil particles to each other to form stable soil aggregates that reduce soil erosion. In some cases, fungi are thought to play a more important role in controlling erosion than plants. The yeasts are unicellular fungi that can ferment under anaerobic conditions. Most important are Saccharomyces and Candida, which are members of the Ascomycota. While the yeasts do not produce spores, they are prolific in sugary environments, and are particularly associated with fruits, flowers, and sap from trees. With a few exceptions where sexual reproduction occurs, yeasts reproduce by budding where the daughter cell forms as an outgrowth from the mother cell, eventually pinching off as a single cell. The number of 13 bud scars left behind with each budding event can be used to estimate the number of replications cycles a particular yeast cell has undergone. While commonly found in the environment, yeasts, especially Saccharomyces, play a significant role in commercial applications, including the production of food, alcoholic, and medicinal products. Some yeasts, e.g., Candida, can cause vaginal, oral, and respiratory infections, and can experience a filamentous stage during pathogenesis. Some fungi, usually members of the Ascomycota, establish symbiotic relationships with algae and cyanobacteria to form lichens. These are extremely important because lichens encourage mineral weathering through the secretion of organic acids that degrade rocks and other inorganic surfaces. The fungus: phototroph relationship occurs when fungal haustoria (hyphal projections) penetrate the algal cell wall. Both organisms must be nutritionally deprived to establish their relationship. In exchange for the oxygen and organic carbon provided by the alga, the fungus provides water and minerals in addition to protection from harsh environmental conditions. Fungal Environmental Aspects Fungi are chemoheterotrophic microorganisms that rely on simple sugars for carbon and energy. However, simple sugars are limiting in many environments due to intense competition. Consequently, many fungi secrete extracellular enzymes (exoenzymes) to break down complex polymers to simple carbon compounds for cell utilization. Often referred to as saprophytic, fungi are extremely important in the degradation and recycling of dead plant, insect and animal biomass, especially the complex polymers associated with these organisms, e.g., cellulose and lignin found in plants, and chitin found in insects. The filamentous fungi and mushrooms are especially adapted to a saprophytic lifestyle due to the large surface area provided by their hyphae. Because of their unique ability to degrade complex polymers, fungi have been found to have the ability to degrade a variety of environmental contaminants making them important in waste degradation and recycling. For example, the yeast-like fungus Aureobasidium pullulans has been found to degrade polyvinyl chloride (PVC) containing plastics (Webb et al., 2000), and filamentous fungi such as Penicillium, Stachybotrys, Allescheriella and Phlebia can degrade the aromatic hydrocarbons associated with petroleum products and agricultural pesticides (Boonchan et al., 2000; D’Annibale et al., 2006). A second important environmental group of fungi are the mycorrhizae. Mycorrhizae form symbiotic relationships with many plants. Through their increased surface area, mycorrhizae can increase the absorptive area of a plant’s roots by hundreds of thousands of times, help to prevent desiccation of the roots and increase uptake of nutrients, especially phosphates. In return, the plant provides the fungus with sugars made during photosynthesis. Mycorrhizal fungi are present in 92% of all plant families studied and include ectomycorrhizal fungi (Wang and Qiu, 2006) and endomycorrhizal fungi (Rinaldi et al., 2008). Endophytes are defined as microbes that live within plants and include fungal species; they are frequently a source of natural products. For example, recently a novel endophytic fungus was isolated from wild pineapples in the Bolivian Amazon basin. This endophyte produces volatile organic compounds with antibiotic properties capable of killing plant pathogens such as Pythium ultimum and human pathogens such as Mycobacterium tuberculosis and Staphylococcus aureus (Mitchell et al., 2010). Phenotypically like both fungi and protozoa, slime molds produce 14 spores but move with amoeba-like gliding motility. Phylogenetically, slime molds are more related to the amoeboid protozoa than the fungi. There are two types of slime molds. The cellular slime molds are composed of single amoeboid cells during their vegetative stage, while the vegetative acellular slime molds are comprised of plasmodia, amorphic masses of protoplasm. Both forms can be found in moist environments on decaying organic matter where they consume bacteria and other microorganisms via phagocytosis. Environmental factors, such as nutrients or stress, can trigger cell accumulation and differentiation into fruiting bodies for the production and dispersal of spores. The spores can later germinate into vegetative amoeboid cells. The consensus of individual vegetative cells coming together and forming fruiting bodies, implying cell- to-cell communication involving chemical signals, is of much interest to scientists. Fungal identification involves a combination of morphological, biochemical, and molecular techniques. Key methods include: Microscopy Morphological Observation: Examining fungal structures such as hyphae, spores, and fruiting bodies under a microscope. Stains like lactophenol cotton blue can highlight fungal features. Spore Characteristics: Observing spore shape, size, color, and arrangement helps identify specific fungal species. Culture Techniques Growth on Media: Fungi are cultured on specialized media such as Sabouraud dextrose agar, potato dextrose agar, or malt extract agar. Colony morphology, color, and growth rate provide important identification clues. Temperature Tolerance: Some fungi can be identified based on their ability to grow at specific temperatures (e.g., thermotolerant fungi). Biochemical Tests Enzyme Activity: Tests to produce specific enzymes such as catalase, urease, and various proteases and lipases can help differentiate fungal species. Metabolic Profiling: Assessing the ability of fungi to utilize different carbon and nitrogen sources. Molecular Techniques Polymerase Chain Reaction (PCR): Amplifies specific DNA sequences for identification and classification. DNA Sequencing: Analyzing genes such as the ribosomal RNA genes (18S rRNA, ITS regions) for precise identification and phylogenetic studies. Restriction Fragment Length Polymorphism (RFLP): Detects genetic variation by analyzing the patterns of DNA fragments produced by restriction enzyme digestion. Classification of Fungi 15 Fungal classification is based on a combination of morphological, genetic, and reproductive characteristics. Major fungal groups include: Chytridiomycota (Chytrids): They are Primarily aquatic fungi with flagellated spores (zoospores). They are often saprophytic or parasitic. Examples include Batrachochytrium dendrobatidis (causes chytridiomycosis in amphibians). Zygomycota (Zygomycetes): Characterized by the formation of zygospores during sexual reproduction. Hyphae are typically coenocytic. Examples are Rhizopus stolonifer (common bread mold), Mucor. Ascomycota (Ascomycetes): They are known as sac fungi; they produce sexual spores (ascospores) within specialized cells called asci. They also form asexual spores (conidia). Examples are Saccharomyces cerevisiae (baker's yeast), Aspergillus, Penicillium, Candida. Basidiomycota (Basidiomycetes): Known as club fungi, they produce sexual spores (basidiospores) on club-shaped structures called basidia. This group includes many familiar mushrooms. Examples include Agaricus bisporus (common mushroom), Cryptococcus neoformans, Puccinia (rust fungi). Deuteromycota (Fungi Imperfecti): A diverse group of fungi that primarily reproduce asexually (anamorphs). Sexual stages (teleomorphs) are often unknown. Many former members have been reclassified into Ascomycota and Basidiomycota based on molecular data. Glomeromycota: Form arbuscular mycorrhizae with plant roots, aiding in nutrient exchange. Examples Glomus species. Ecological and Economic Importance of Fungi Fungi play crucial roles in various ecological processes and have significant economic importance: Decomposition and Nutrient Cycling Fungi decompose organic matter, breaking down complex molecules into simpler substances that can be utilized by plants and other organisms. This process is essential for nutrient cycling in ecosystems. Symbiotic Relationships Mycorrhizae: Mutualistic associations between fungi and plant roots, enhancing nutrient and water uptake for the plant and providing carbohydrates for the fungus. Lichens: Symbiotic partnerships between fungi and photosynthetic organisms (algae or cyanobacteria), contributing to soil formation and nutrient cycling in harsh environments. 16 Pathogenic Fungi: Fungi can cause diseases in plants, animals, and humans. For example: Plant Pathogens; Puccinia (rust fungi) and Fusarium (wilt fungi) cause significant crop losses. Animal Pathogens; Batrachochytrium dendrobatidis affects amphibians. Human Pathogens: Candida albicans causes candidiasis, and Cryptococcus neoformans can lead to severe infections in immunocompromised individuals. Industrial and Biotechnological Applications Fermentation: Yeasts like Saccharomyces cerevisiae is used in baking, brewing, and winemaking. Antibiotics: Fungi such as Penicillium produce antibiotics like penicillin. Enzymes: Fungi produce enzymes used in various industries, including food processing, textiles, and biofuel production. Biocontrol: Certain fungi are used to control agricultural pests and diseases. 17