General Microbiology Lecture Notes

Hagellum Lounitine CAFRI SAG Carnitine

• Referencing various molecules, enzymes, and complexes possibly involved in cellular respiration or metabolism.
• Mentions of ACENT-COA, 2MT, LEADH, MADH K, Lyt.c, IV, TIL, Fumarate, ZHT, ADT, and MATAUX, which seem to be components or abbreviations in a biochemical pathway.
• Mentions of KREBS CYCLE, SUCCINATE, FADH, and NADH, indicating the citric acid cycle and electron transport chain.
• References to MATRIX, INTERMEMBRANE SPACE, and COMPLEXES I, III, and IV, suggesting mitochondrial components and the electron transport chain.
• Mentions of FMN, FMNH, Fe-S, Q, Cytochrome C, and Cu, which are electron carriers in the electron transport chain.
• Reference to ATP synthase and its role in ATP production.
• Mentions of ADP and Pi, the building blocks of ATP.
• Mentions of Meryl CoA and citric acid cycle, linking to metabolic processes.

General Microbiology Topics 2025

• Importance of microorganisms and characterization of organisms within microbiology.
• Environmental factors relevant to microbes.
• Major discoveries in microbiology.
• Structure and morphology of virions; molecular characterization and classification.
• Replication (multiplication) of viruses; procession of viral infection.
• General characterization of the prokaryotic cell; presentation of bacterial cell structure. Comparison of G+ and G- bacterial cell wall. External cell surface structures.
• The structure and functions of the cell membrane. Structures and functions of the bacterial genetic materials. The process of spore formation. Special prokaryotic organelles.
• General presentation of fungi. The division of the real fungi: Chytridiomycota and Zygomycota phylum.
• The general presentation of the Ascomycota and Basidiomycota fungi phylum and its significance. The process of sexual reproduction of Ascomycota.
• Grouping and characterization of antimicrobial drugs (antibiotics); properties of an ideal antibiotic; treatment methods and usage of antibiotics.
• Antibacterial and antifungal drugs and their targets; Grouping of antibacterial and antifungal drugs based on targets and mechanism of action.
• Molecular mechanisms of antibiotic resistance. Methods for antibiotic susceptibility measurement. Sensitivity, tolerance, resistance. Types and mechanisms of antibiotic resistance. Determination of antibiotic susceptibility and minimal inhibitory concentration.

Importance of Microorganisms

• Microorganisms are fundamental to life on Earth and were the first living systems.
• Microbial metabolic and ecological activity created the biosphere, enabling multicellular life.
• Multicellular organisms evolved from unicellular microorganisms.
• Microbes constitute over 50% of terrestrial biomass.
• Microbiology focuses on organisms too small to be seen clearly by the naked eye.
• Most microorganisms, except viruses, are organized into cells, unicellular or multicellular without tissues, and separated from their environment by a cell membrane.
• Microorganisms are vitally important in many fields:
  • Healthcare: pathogens, antibiotics, and vaccines.
  • Agriculture: nitrogen fixation and plant symbiosis.
  • Food industry: fermentation (cheese, yogurt, beer).
  • Environmental protection: biodegradation and waste treatment.
  • Biotechnology: molecular tools from microbes.

Studying Microorganisms and Their Classification

• Studying microorganisms has led to major scientific breakthroughs; research on yeast Schizosaccharomyces pombe led to the discovery of the cdc2 gene, homologous to human Cdk1 gene, essential for cell cycle regulation.
• Microbiology encompasses several major groups:
  • Bacteria and Archaea: prokaryotes.
  • Viruses, virions, satellites, prions: acellular and non-living.
  • Fungi (yeast, mold), Protists (Algae, and Protozoa): eukaryotic.
• Also includes:
  • Water molds and Slime molds.
  • Chromista (Yellow-green algae, Brown algae, and Diatoms).
  • Red algae (Rhodophyta) and Green algae (Chlorophyta).
• Microbial cellular structure and reproductive strategies align with microbiological study, especially in evolutionary and environmental microbiology.
• Microorganisms are essential in understanding evolution; life is grouped into three domains based on rRNA sequence comparisons:
  • Bacteria
  • Archaea
  • Eukarya

LUCA (Last Universal Common Ancestor)

• Classification traces back to LUCA, which likely lived around 3.9 to 4 billion years ago.
• LUCA likely had:
  • A cell wall, cytoplasm, and DNA.
  • A universal genetic code, with transcription and translation systems.
  • Key metabolic features like glutamine synthetase (GS), nitrogenase (Nif), and antiporters (Mrp).
  • Enzymes involved in carbon and nitrogen fixation, such as the Wood–Ljungdahl pathway enzymes.
  • Adaptations to extreme conditions, like H_2-dependence and anaerobic thermophily.
• Modern cells retain these basic systems, highlighting the central role of microbes in the history of life.
• Microorganisms are ecologically dominant, biochemically diverse, and scientifically indispensable.
• Their study has advanced medicine, industry, molecular biology, and evolutionary theory.
• The diversity includes organisms like Giardia, plant viroids, chromists, and extremophilic archaea.
• Microbiology remains one of the most important fields in biology today.

Environmental Factors Relevant to Microbes

• Environmental factors determine microbial growth, survival, and distribution.
• Microorganisms are highly sensitive to external conditions and unlike multicellular organisms they cannot regulate their internal environment effectively.
• Most critical environmental factors:

Oxygen Concentration:

• Aerobes require oxygen for growth.
• Anaerobes cannot tolerate oxygen and may find it toxic.
• Facultative anaerobes can grow with or without oxygen.
• Microaerophiles require low levels of oxygen.
• Clostridium species are obligate anaerobes.
• Pseudomonas species are aerobes and found on moist surfaces like skin and medical equipment.

Osmotic Concentration and Salinity:

• Nonhalophiles can’t tolerate salt.
• Halotolerant microbes can survive in moderate salt conditions.
• Halophiles require salt (e.g., marine organisms).
• Extreme halophiles, like Halobacterium, thrive in very high salinities.
• Salt concentration affects microbial water balance and enzyme activity.

Temperature:

• Psychrophiles grow at ~0–15°C (B. psychrophilus).
• Psychrotolerant grow at low temperatures but prefer 20–30°C (Pseudomonas fluorescens).
• Mesophiles grow best at 20–45°C (Escherichia coli).
• Thermophiles prefer 55–65°C (Thermus aquaticus).
• Hyperthermophiles thrive at 85–113°C (Sulfolobus acidocaldarius).
• Adaptations include heat-stable enzymes, high proline content in proteins, DNA-stabilizing proteins like reverse DNA gyrase, and saturated branched lipids in membranes.

Water Activity (a_w)

• Availability of free water in a substance.
• Most Gram-negative bacteria need a_w > 0.95.
• Yeasts grow at a_w between 0.91–0.88.
• Halophilic bacteria and Staphylococcus aureus can grow at a_w as low as 0.75.
• Xerophilic molds and osmophilic yeasts like Saccharomyces rouxii thrive at even lower water activities (~0.65).
• Water activity is crucial for enzymatic activity and cell structure stability.

pH:

• Acidophiles: pH 0–5.5
• Neutrophiles: pH 5.5–8.0
• Alkaliphiles: pH 8–11.5
• Most bacteria and protists are neutrophiles, fungi prefer slightly acidic conditions, and many archaea are acidophiles.
• Sulfolobus acidocaldarius thrives in hot, acidic springs.

UV Radiation:

• UV-C light at 265 nm is a powerful disinfectant that damages microbial DNA and membranes.
• Used to sterilize water and surfaces without toxic byproducts, effective even against chlorine-resistant organisms.
• Environmental factors such as oxygen, salinity, temperature, water activity, pH, and UV radiation are central to microbial ecology and physiology.
• Microorganisms have developed diverse strategies to adapt to extreme conditions, making them useful in biotechnology and environmental applications.

Major Discoveries in Microbiology

• The history of microbiology is marked by groundbreaking discoveries that fundamentally changed medicine, science, and public health.

Antony van Leeuwenhoek (1632–1723)

• Dutch cloth merchant, was the first to observe and describe microorganisms using a handcrafted microscope.
• His discovery laid the foundation for microbiology, even though he had no formal scientific training.

Edward Jenner (1749–1823)

• Developed the first successful vaccine against smallpox (Poxvirus variolae) in 1798; Used material from cowpox lesions, giving rise to the term “vaccine” (vacca = cow in Latin).
• This was the first step toward immunology.

Ignác Semmelweis (1818–1865)

• Known as “The savior of mothers,” Dramatically reduced maternal deaths by introducing hand washing with chlorinated lime in obstetrics, long before the germ theory of disease was accepted.

Joseph Lister (1827–1912)

• Pioneered antiseptic surgery using carbolic acid (phenol), reducing surgical mortality; Introduced the concept of asepsis, preventing microbial contamination.

Louis Pasteur (1822–1895)

• One of the most influential figures in microbiology:
  • Developed vaccines for rabies, anthrax, and chicken cholera.
  • Invented pasteurization, a method to kill pathogens in liquids.
  • Refuted the spontaneous generation theory, proving that life arises only from pre-existing life through the famous swan-neck flask experiment.
  • Showed that specific microbes are linked to specific diseases.

Robert Koch (1843–1910)

• Established Koch’s postulates, a set of criteria to link specific pathogens to specific diseases.
  • Discovered the causative agents of tuberculosis (Mycobacterium tuberculosis) and cholera (Vibrio cholerae).
  • Developed pure culture techniques using solid media (gelatin, then agar).
  • Won the Nobel Prize in 1905 for his work on tuberculosis.

Elie Metchnikoff (1845–1916)

• Discovered phagocytosis, a fundamental immune defense mechanism, earning the Nobel Prize in 1908 alongside Paul Ehrlich.

Paul Ehrlich (1854–1915)

• Studied antibodies and developed the first effective antimicrobial drug, Salvarsan, against syphilis; He’s considered the father of chemotherapy.

Alexander Fleming (1881–1955)

• In 1929, Fleming discovered penicillin from Penicillium notatum, which had a profound impact on medicine. Later, Florey and Chain purified and mass-produced penicillin by 1940, revolutionizing antibiotic therapy.

Griffith’s Transformation (1928)

• Frederick Griffith showed that a ‘transforming principle’ could turn non-pathogenic bacteria into pathogenic forms. This hinted at DNA as the genetic material.

Oswald Avery (1944)

• Confirmed that the transforming principle was DNA, providing direct evidence that DNA carries genetic information.

Luria and Delbrück (1943)

• Demonstrated that bacterial mutations occur spontaneously, not as a result of selective pressure.

Lederberg and Tatum (1946)

• Discovered bacterial conjugation, the transfer of genetic material between bacteria—a major mechanism of genetic diversity.
• These discoveries established microbiology as a science and continue to influence medicine, biotechnology, and genetics today.

Structure and Morphology of Virions. Molecular Characterization and Classification of Virions

• Virions are the extracellular, morphologically complete forms of viruses, capable of surviving outside a host and initiating infection. Structurally, they are infectious nucleoproteins, composed of genetic material (either RNA or DNA) surrounded by protein — and sometimes lipids and carbohydrates.

Basic Structure of Virions

• A virion consists of:
  • Nucleic acid genome:
    • DNA or RNA
    • Single- or double-stranded
    • Linear or circular
    • Segmented or non-segmented
    • e.g., SARS-CoV-2 has a single-stranded (+) RNA genome.
  • Capsid:
    • A protein coat made of capsomeres that protects the genome and ensures delivery into the host cell.
    • Together, the genome and capsid form the nucleocapsid.
  • Envelope (in some viruses):
    • Derived from the host cell membrane and contains virus-encoded glycoproteins (peplomers) for attachment.
    • Makes enveloped viruses sensitive to heat, desiccation, and solvents (e.g., influenza virus, HIV).
  • Additional Components:
    • Enzymes (like reverse transcriptase in retroviruses or lysozyme in bacteriophages),
    • Lipid and carbohydrate components embedded in the envelope for immune recognition and host specificity.

Morphological Types (based on symmetry and structure)

• Viruses are classified into four major morphological groups:
  1. Helical symmetry:
     • The capsid proteins wrap around the nucleic acid in a spiral.
     • E.g., Tobacco mosaic virus, rabies virus, influenza virus.
  2. Icosahedral (cubical) symmetry:
     • Capsid proteins form a 20-sided polygon with symmetrical facets.
     • E.g., Adenoviruses, Parvoviruses, Picornaviruses.
  3. Complex viruses:
     • No clear symmetrical structure, often large and layered.
     • E.g., Poxviruses – oval-shaped with multiple envelope layers and surface spikes.
  4. Binary (bacteriophages):
     • Combine icosahedral heads and helical tails with tail fibers.
     • E.g., T4 phage, Mu phage, λ phage.
• Virions may also appear spherical, ovoid, bacillus-like, or amorphous, often due to envelope structure. Example: SARS-CoV-2 has an envelope giving it a spherical shape with spike proteins.

Molecular Characterization

• Nucleic Acids:
  • Classified by genome type:
    • dsDNA (e.g., Adenoviruses)
    • ssDNA (e.g., Parvoviruses)
    • dsRNA (e.g., Reoviruses)
    • (+)ssRNA (e.g., Coronaviruses)
    • (−)ssRNA (e.g., Influenza)
    • RNA with DNA intermediate (e.g., Retroviruses – HIV)
• Structural Proteins:
  • External capsid proteins and internal core proteins.
  • Functions:
    • Protect nucleic acid,
    • Attach to host cells,
    • Act as antigens (trigger immune response),
    • Determine host specificity and virus shape.
• Viral Enzymes:
  • Include polymerases, proteases, integrases, neuraminidase, and lysozyme (in phages).
  • Essential for genome replication, protein processing, and cell entry.
• Envelope Glycoproteins:
  • Viral-coded, inserted into host-derived membrane.
  • Involved in receptor binding, membrane fusion, and immune neutralization.

Classification Criteria for Viruses

1.  Morphology: shape, envelope, size
2.  Genome Type: DNA/RNA, strandedness, sense/ polarity
3.  Replication Mechanism: Baltimore classification (Groups I–VII)
4.  Host Range: vertebrate, invertebrate, plant, bacteria
5.  Antigenic Properties: immune recognition and vaccine development
6.  Physicochemical Stability: sensitivity to pH, heat, solvents

• Virions are diverse in structure but share core features: a nucleic acid genome, protective protein capsid, and in some, a lipid envelope. Their classification is based on morphology, genome, and replication strategy. Understanding virion structure is essential for diagnosing, treating, and preventing viral diseases.

Replication (Multiplication) of Viruses. Procession of Viral Infection

• Viruses are obligate intracellular parasites, meaning they cannot replicate independently. Instead, they hijack a host cell’s machinery to synthesize viral components, assemble them, and release new virions. This process is called the viral replication cycle and consists of seven key stages:
  1. Attachment (Adsorption)
  • The virus binds to specific receptor molecules on the host cell surface.
  • This interaction determines host specificity and tissue tropism.
  • For example, HIV binds to CD4 receptors on T-cells.
  • Bacteriophages use lysozyme and tail fibers to bind and penetrate bacterial cell walls.
  1. Entry (Penetration)
  • Viruses enter cells in several ways, depending on their structure:
    • Endocytosis (e.g., herpesvirus, SARS-CoV-2): Virus is engulfed by the host membrane.
    • Membrane fusion (e.g., measles virus): Viral envelope fuses with the host cell membrane.
    • Injection of nucleic acid (e.g., T4 bacteriophage): Tail contracts to inject DNA into bacteria.
    • Through pili or direct penetration: Non-enveloped viruses may directly inject or enter.
    • Plant viruses enter passively via wounds or insect vectors.
  1. Uncoating (Decapsidation)
  • The capsid is broken down, releasing the viral genome into the host cell.
  • This is often mediated by lysosomal enzymes in endosomes.
  • Some viruses (e.g., poxviruses) begin transcription even before full uncoating.
  1. Eclipse Phase (Synthetic Events)
  • During this phase:
    • No infectious virus is detectable.
    • The viral genome undergoes replication and transcription, often using host or viral enzymes.
    • Viral mRNA is translated to produce early, structural, and late proteins.
    • Depending on the virus:
      • (+ssRNA viruses) (e.g., SARS-CoV-2) directly serve as mRNA.
      • (–ssRNA viruses) and retroviruses require RNA-dependent RNA or DNA polymerases.
      • DNA viruses replicate in the nucleus (e.g., herpesvirus), while most RNA viruses replicate in the cytoplasm.
  1. Assembly
  • Newly synthesized viral genomes and proteins assemble into new virions.
  • This is an autocatalytic process that may occur in the cytoplasm (RNA viruses) or nucleus (DNA viruses).
  • For viruses with segmented genomes, all segments must assemble correctly — or the virion is non-infectious.
  1. Maturation
  • Structural rearrangements occur to make the virus infectious.
  • Capsid proteins fold correctly, and the nucleocapsid condenses around the genome.
  • Some viruses incorporate host ribosomes or enzymes during this step (e.g., Arenaviruses).
  1. Release
  • Non-enveloped viruses typically cause cell lysis, releasing progeny virions.
  • Enveloped viruses bud from the cell membrane or organelles, acquiring their envelope in the process.
  • Some viruses can spread directly from cell to cell via membrane fusion, avoiding the immune system.
  • A single infected cell can produce 100,000–200,000 virions.

Additional Concepts:

• The Baltimore classification system groups viruses (I– VII) based on genome type and replication strategy:
  • e.g., Group IV: (+)ssRNA, Group VI: Retroviruses (RNA → DNA → RNA).
• Replication efficiency varies: For RNA viruses, <1% of virions may be infectious; DNA viruses and bacteriophages have much higher efficiency.
• Viral replication is a precise, multi-stage process that relies entirely on host cells. It includes attachment, entry, uncoating, synthesis, assembly, maturation, and release. Each step involves specific host-virus interactions, making these stages crucial targets for antiviral therapies and vaccine development.

General Characterization of the Prokaryotic Cell. Presentation of Bacterial Cell Structure. Comparison of Gram-Positive and Gram-Negative Cell Walls. External Cell Surface Structures

• A prokaryotic cell is a simple, unicellular organism lacking a membrane-bound nucleus and organelles. Prokaryotes include Bacteria and Archaea, which were among the first life forms on Earth — appearing about 3.9–4 billion years ago.
• Prokaryotic cells are typically small (0.2–10 µm), enabling fast reproduction and efficient nutrient absorption due to a high surface-area-to-volume ratio. They reproduce rapidly through binary fission and grow in exponential fashion: 1-2-4-8-16…

Structure of a Typical Bacterial Cell:

• Key internal and external components include:
  • Cell membrane: a phospholipid bilayer (no sterols, except in Mycoplasma) with hopanoids for membrane stability.
  • Cytoplasm: contains nucleoid (circular dsDNA), ribosomes (70S), plasmids, and inclusions (e.g. glycogen, PHB, sulfur).
  • Ribosomes: consist of 50S + 30S subunits, critical for protein synthesis.
  • Mesosome: folded region of the membrane involved in DNA attachment and respiration.
  • Plasmids: small circular DNA with genes for antibiotic resistance, toxin production, etc.

External Structures:

1.  Cell Wall:
*   Composed of peptidoglycan (murein): repeating units of NAG and NAM linked by peptides.
*   Gives shape and protects against osmotic stress.
2.  Gram-positive (G+) Cell Wall:
*   Thick peptidoglycan layer (10–80 nm) with teichoic and lipoteichoic acids, which act as antigens.
*   No outer membrane or periplasmic space.
*   Example: Staphylococcus aureus.
3.  Gram-negative (G−) Cell Wall:
*   Thin peptidoglycan layer in a periplasmic space, between:
    *   Inner membrane and
    *   Outer membrane (contains lipopolysaccharides – LPS).
*   LPS (endotoxin): composed of lipid A, core polysaccharide, and O-antigen; triggers strong immune responses.
*   Example: Escherichia coli.
4.  Glycocalyx:
*   Outer layer of polysaccharides or glycoproteins.
*   Capsule: organized and tightly bound – increases virulence (e.g., Streptococcus pneumoniae).
*   Slime layer: loose and unstructured.
5.  Fimbriae and Pili:
*   Fimbriae: numerous, short projections for adhesion (e.g., to tissues).
*   Pili: longer, fewer – especially sex pilus for conjugation and gene transfer (e.g., R-plasmid transfer).
*   Made of pilin protein.
6.  Flagella:
*   Long, whip-like structures for motility, made of flagellin.
*   Powered by a rotary motor, not ATP.
*   Arrangements:
    *   Monotrichous (e.g., Vibrio cholerae),
    *   Lophotrichous,
    *   Amphitrichous,
    *   Peritrichous (e.g., E. coli).

Importance of Gram-staining:

• Gram-positive bacteria retain crystal violet due to thick peptidoglycan.
• Gram-negative lose crystal violet after alcohol wash and stain pink with safranin.
• The structural differences are crucial for antibiotic selection, as many drugs (e.g., β-lactams) target peptidoglycan synthesis.
• Prokaryotic cells are simple but extremely efficient. They have no nucleus, use polycistronic mRNA, and perform transcription and translation simultaneously. Their external features — capsule, pili, fimbriae, flagella — play vital roles in pathogenicity, survival, and genetic exchange, while the Gram stain remains a cornerstone of bacterial classification and clinical microbiology.

General Characterization of the Prokaryotic Cell. The Structure and Functions of the Cell Membrane. Structures and Functions of the Bacterial Genetic Materials. The Process of Spore Formation. Special Prokaryotic Organelles

• A prokaryotic cell is a unicellular, nucleus-lacking organism, typically classified into Bacteria and Archaea. Despite their simplicity, prokaryotes are metabolically versatile, adaptable, and genetically efficient. They thrive in environments from soil and water to extreme pH, temperature, and salinity.

The Cell Membrane

• The bacterial cell membrane is a 7–8 nm thick phospholipid bilayer without sterols (except Mycoplasma). Instead, hopanoids stabilize the membrane. It serves multiple critical functions:
  • Selective permeability and transport (nutrients, ions).
  • Respiratory enzymes and electron transport chains are embedded here.
  • Site for lipid, cell wall polymer, and DNA replication-related synthesis.
  • In photosynthetic bacteria, such as cyanobacteria, thylakoid membranes carry photosynthetic enzymes.
• In Gram-positive bacteria, the membrane forms mesosomes — infoldings that serve as DNA attachment sites and possibly division centers.

Bacterial Genetic Material

• The bacterial genome typically consists of:
  • One circular, double-stranded DNA molecule, located in the nucleoid.
  • No histones, but histone-like proteins compact the DNA.
  • Haploid (one genome copy per cell).
  • Polycistronic mRNA allows multiple genes to be transcribed together.
  • No separation between transcription and translation.
• Plasmids are small, extra-chromosomal DNA circles. They carry genes for:
  • Antibiotic resistance (R-plasmids),
  • Virulence factors (e.g., toxins like colicin),
  • Metabolic enzymes, and
  • Conjugation (e.g., F-plasmid/sex pilus formation).
• In some species like Streptomyces or Borrelia burgdorferi, the chromosome may be linear.

Spore Formation

• Some Gram-positive bacteria (especially Bacillus and Clostridium) form endospores:
  • Extremely resistant to heat, radiation, desiccation, and chemicals.
  • Contain calcium dipicolinate, which helps dehydration and heat resistance.
  • In unfavorable conditions, the spore forms internally, survives dormant for centuries, and germinates when conditions improve.
• Endospores should not be confused with:
  • Exospores, produced externally by Actinomycetes (e.g., Streptomyces), through septation in the aerial mycelium — less resistant but asexual.

Special Prokaryotic Organelles and Inclusions

• Prokaryotes lack membrane-bound organelles, but they have several specialized structures:
  • Gas vacuoles: Provide buoyancy in aquatic photosynthetic bacteria (adjust depth for optimal light and oxygen).
  • Carboxysomes: Found in cyanobacteria; contain RubisCO enzyme for {CO_2} fixation — crucial for autotrophic metabolism.
  • Magnetosomes: Membrane-bound magnetite (Fe3 O4) crystals help bacteria navigate using the Earth’s magnetic field (e.g., in nutrient-rich sediments).
  • Chlorosomes: Present in green sulfur bacteria (Chlorobaculum tepidum); contain light-harvesting pigments like bacteriochlorophyll for photosynthesis.
  • Storage inclusions: For energy and nutrients. Common types include:
    • PHB granules (polyhydroxybutyrate – for biodegradable plastic synthesis),
    • Glycogen,
    • Sulfur globules, and
    • Polyphosphate granules.
• These inclusions reflect a highly organized cell capable of environmental adaptation, energy storage, and efficient nutrient use.
• The prokaryotic cell is deceptively simple yet highly efficient. Its membrane is multifunctional, its genome compact and versatile, and its ability to form spores and special organelles allows it to survive and adapt in nearly every environment. Understanding these features is crucial in medicine, biotechnology, and evolutionary biology.

General Presentation of Fungi. The Division of the Real Fungi: Chytridiomycota and Zygomycota Phylum

• Fungi form a distinct kingdom of eukaryotic, heterotrophic, and chemoorganotrophic organisms. They lack chlorophyll, so they don’t perform photosynthesis. Instead, they absorb dissolved nutrients across their entire surface — a process called absorptive nutrition.
• Fungi are single-celled or multicellular, and their bodies often consist of branching filaments called hyphae, which form a mycelium. Their cell walls contain chitin and glucan — but not cellulose, which distinguishes them from plants. Some species also have mannan and chitosan in their walls.
• They reproduce both sexually and asexually, often producing spores. The asexual spores include conidia, sporangiospores, and chlamydospores. In yeasts like Saccharomyces cerevisiae, reproduction occurs through budding or fission, and some pathogenic yeasts like Candida albicans form pseudomycelium.
• In terms of lifestyle, fungi may be:
  • Saprotrophs – decomposing dead organic material,
  • Parasites – living off living hosts,
  • Symbionts – forming mutualistic relationships (like mycorrhizae).

Chytridiomycota

• Chytridiomycetes are considered the earliest-diverging lineage of fungi.
• They are aquatic, often unicellular or coenocytic (i.e., without septa in their hyphae).
• Their hallmark is motile cells: they produce zoospores with a single posteriorly inserted flagellum (opisthokont flagella), which is unique among true fungi.
• Most are saprotrophs, but some are parasites that secrete chitinase to degrade host walls. An example is Olpidium brassicae, which parasitizes plant roots like cabbage. Reproduction in chytrids involves gametogamy (fusion of gametes with flagella) or somatic copulation.

Zygomycota

• Zygomycetes are coenocytic, meaning they have aseptate hyphae — septa form only during reproduction.
• They are mostly terrestrial saprotrophs, but some are facultative pathogens, affecting the lungs or CNS (e.g., Mucor, Rhizopus).
• Their name comes from the formation of zygosporangia during sexual reproduction. Zygomycetes can also reproduce asexually via sporangiospores housed in sporangia.
• Rhizopus stolonifer, the black bread mold, is a classic example. It grows on moist bread or fruit and reproduces both sexually and asexually. Industrially, zygomycetes are important for producing organic acids (citric, lactic, acetic), cortisone, and enzymes for starch hydrolysis. However, they cannot digest cellulose or lignin.
• Chytridiomycota are mostly aquatic fungi with flagellated spores, while Zygomycota are terrestrial fungi with coenocytic hyphae and are important both medically and industrially. Both groups are basal lineages in fungal evolution and play diverse ecological and biotechnological roles.

The General Presentation of the Ascomycota and Basidiomycota Fungi Phylum and Its Significance. The Process of Sexual Reproduction of Ascomycota

• The phyla Ascomycota and Basidiomycota represent the two most advanced and diverse groups of the true fungi (Eumycota). Together, they include many ecologically, medically, and industrially important species.

Ascomycota – ‘Sac Fungi’

• The most abundant fungal group: approximately 45% of all described fungi. Named after their defining sexual structure: the ascus, a sac-like structure where meiosis and sometimes mitosis produce ascospores. The asci are often found in fruiting bodies called ascocarps (e.g., cleistothecium, perithecium, apothecium).
• Ascomycota exhibit great morphological diversity: they include unicellular yeasts, filamentous molds, and macrofungi like morels (Morchella esculenta). Hyphae are septate, meaning they are divided by cross walls (septa), and in some species, dikaryotic stages (cells with two nuclei) appear.
• Sexual Reproduction Process in Ascomycota:
  1. Plasmogamy: Fusion of compatible hyphae tips from two mating types.
  2. Dikaryotic phase: Two haploid nuclei coexist in the same cell.
  3. Karyogamy: The two nuclei fuse to form a diploid zygote nucleus within the ascus.
  4. Meiosis: Diploid nucleus divides into four haploid nuclei.
  5. Mitosis: Often occurs once more to produce eight ascospores, which are eventually released from the ascus.
  • Example species and importance:
    • Neurospora crassa: model organism for studying meiosis and gene regulation.
    • Saccharomyces cerevisiae: used in baking, brewing, biotechnology.
    • Claviceps purpurea: parasitic on rye; produces ergot alkaloids (important in pharmaceuticals but also toxic).
    • Aspergillus and Penicillium: used in industrial enzyme and antibiotic production, but also cause food spoilage.
    • Pathogens like Histoplasma capsulatum, Trichophyton, and Microsporum cause systemic and skin fungal infections.

Basidiomycota – ‘Club Fungi’

• Known for producing basidiospores on a specialized cell called a basidium.
• Includes many familiar mushrooms, bracket fungi, puffballs, rusts, and smuts.
• Hyphae are septate, often with clamp connections, and the dikaryotic phase dominates the life cycle.
• Basidiomycota are among the most complex fungi morphologically and ecologically.
  • Key Features:
    • Sexual reproduction typically leads to four basidiospores per basidium.
    • Fruiting bodies called basidiocarps include the mushroom cap, where gills house basidia.
    • Many species decompose lignin and cellulose, contributing to wood decay:
      • White rot fungi degrade lignin and cellulose.
      • Brown rot fungi degrade only cellulose.
  • Example species and significance:
    • Agaricus bisporus – the common edible mushroom.
    • Ustilago maydis – causes corn smut, but also a model organism and edible delicacy (huitlacoche).
    • Cryptococcus neoformans – causes cryptococcosis, especially in immunocompromised patients (e.g., HIV/ AIDS).
    • Mycorrhizal fungi (e.g., Boletus spp.)