Viruses, Bacteria, and Fungi: A Comprehensive Study Guide

Microorganisms are microscopic organisms vital for the environment, human health, agriculture, and industry. They are broadly categorized into three major groups, each with distinct structural, functional, and ecological characteristics.

I. Introduction to Microorganisms

• Viruses: Acellular, obligate intracellular parasites.
• Bacteria: Prokaryotic, independent life forms.
• Fungi: Eukaryotic, heterotrophic decomposers and pathogens.

II. Viruses

A. Basic Characteristics

• Nature: Acellular; not considered living organisms.
• Size: 20-300 nm.
• Structure: Nucleic acid core (DNA/RNA), protein capsid; some have an envelope.
• Replication: Must hijack host cell machinery to replicate.
• Metabolism: No metabolism, no ribosomes.
• Host Range: Specific to certain hosts (bacteria, plants, animals).
• Examples: Influenza virus, HIV, SARS-CoV-2, Poliovirus.

B. Structure of a Virus

• Key Components:
  • Nucleic Acid Core: Viral genome (DNA or RNA).
  • Capsid: Protein shell made of capsomeres, protecting the genome.
  • Envelope (optional): Lipid bilayer derived from host cell membrane, with embedded viral proteins (e.g., spike proteins like hemagglutinin).
  • Tegument (some viruses): Layer between capsid and envelope.
• Spike proteins: Essential for attachment to host cells (e.g., hemagglutinin).
• Symmetry types:
  • Icosahedral
  • Helical
  • Complex (e.g., Bacteriophage)
• Nucleic Acid:
  • May be single-stranded (ss) or double-stranded (ds).
  • Linear or circular.

C. Classification of Viruses

1. Baltimore Classification (Based on genome type and replication strategy)

Group	Genome Type	Examples
I	dsDNA	Adenovirus
II	ssDNA	Parvovirus
III	dsRNA	Reovirus
IV	(+)ssRNA	Poliovirus, Coronavirus
V	(-)ssRNA	Influenza, Rabies
VI	(+)ssRNA with RT	HIV, Retroviruses
VII	dsDNA with RT	Hepatitis B virus

2. ICTV Classification System

International Committee on Taxonomy of Viruses classifies viruses into: Order, Family, Genus, Species.

• Example:
  • Family: Herpesviridae
  • Genus: Simplexvirus
  • Species: Human herpesvirus 1

D. Methods of Identification

• Electron Microscopy: Visualize morphology.
• Serology: ELISA, neutralization assays (detect antibodies or antigens).
• PCR & RT-PCR: Detect viral nucleic acids.
• Cell Culture: Grow in live host cells.
• Sequencing: Whole-genome sequencing.
• Hemagglutination Assay: Detects RBC-agglutinating viruses.
• Western Blot: Confirmatory test for antibodies.

E. Life Cycle of a Virus

1. Attachment: Virus binds to specific host cell receptors.
2. Penetration: Virus enters the host cell.
3. Uncoating: Viral capsid breaks down, releasing the genome.
4. Replication: Viral genome is replicated and transcribed.
5. Assembly: New viral particles are constructed.
6. Release: New virions exit the host cell.

Lytic vs. Lysogenic Cycles (for bacteriophages):

• Lytic: Immediate replication and destruction of host cell.
• Lysogenic: Integration of viral DNA into host genome (prophage), can later enter lytic cycle.

F. Medical Significance

Disease	Causative Virus
AIDS	HIV
Common Cold	Rhinovirus
Chickenpox / Shingles	Varicella zoster virus
Hepatitis	HBV, HCV
Measles	Paramyxovirus
COVID-19	SARS-CoV-2

G. Treatment

• Antiviral Drugs: Acyclovir, Oseltamivir, Remdesivir, Antiretrovirals.
• Vaccines: Live attenuated, Inactivated, Subunit, mRNA.

III. Bacteria

A. Basic Characteristics

• Cell Type: Prokaryotic.
• Size: 0.5-5 µm.
• Shape: Coccus (round), Bacillus (rod), Spiral.
• Cell Wall: Peptidoglycan present.
• Motility: Flagella, pili, gliding.
• Metabolism: Autotrophic/heterotrophic; aerobic/anaerobic.
• Reproduction: Binary fission.
• Genetic Material: Single circular chromosome + plasmids.
• Examples: E. coli, Staphylococcus aureus, Mycobacterium tuberculosis.

B. Structure of a Typical Bacterial Cell

Key components:

• Capsule: Protection, virulence factor.
• Cell Wall: Peptidoglycan layer.
• Plasma Membrane: Selective permeability.
• Cytoplasm: Contains enzymes, ribosomes.
• Nucleoid: Region containing chromosomal DNA.
• Plasmid: Extrachromosomal DNA.
• Flagellum: Locomotion.
• Pilus/Fimbria: Attachment/adhesion.
• Ribosome: Protein synthesis.
• Mesosome: Invagination of the plasma membrane (function debated).
• Endospore (dormant structure): E.g., Clostridium.

C. Classification of Bacteria

1. Based on Gram Stain

Type	Stain Color	Cell Wall Structure
Gram-positive	Purple	Thick peptidoglycan layer
Gram-negative	Pink/Red	Thin peptidoglycan + outer membrane

2. Based on Oxygen Requirement

Requirement	Description	Examples
Obligate aerobe	Requires O2	Mycobacterium tuberculosis
Obligate anaerobe	Killed by O2	Clostridium
Facultative anaerobe	Grows with or without O2	E. coli

3. Based on Morphology

Shape	Description	Examples
Coccus	Round	Staphylococcus
Bacillus	Rod-shaped	E. coli
Spiral	Curved or spiral	Campylobacter, Treponema

4. Molecular Classification

• 16S rRNA sequencing: Gold standard.
• Major phyla include:
  • Proteobacteria (e.g., E. coli)
  • Firmicutes (e.g., Staphylococcus, Clostridium)
  • Actinobacteria (e.g., Mycobacterium)

D. Methods of Identification

• Gram Staining: Differentiates Gram+ and Gram-.
• Acid-fast Staining: For Mycobacterium.
• Culture: On agar plates (e.g., blood agar, MacConkey agar).
• Biochemical Tests: Catalase, coagulase, indole, oxidase, sugar fermentation.
• MALDI-TOF MS: Rapid identification based on protein profile.
• PCR & Sequencing: Detect and identify species-specific genes.
• Microscopy: Phase contrast, dark field, electron microscopy.

E. Reproduction

1. Binary Fission

1. DNA replication.
2. Elongation of cell.
3. Septum formation.
4. Division into two daughter cells.

2. Horizontal Gene Transfer

• Transformation: Uptake of naked DNA from the environment.
• Transduction: Gene transfer by bacteriophages.
• Conjugation: Direct transfer of DNA via a pilus.

F. Medical Significance

Disease	Causative Bacteria
Tuberculosis	Mycobacterium tuberculosis
Food poisoning	Salmonella, Staphylococcus
Pneumonia	Streptococcus pneumoniae, Klebsiella pneumoniae
UTI	E. coli
Syphilis	Treponema pallidum
Tetanus	Clostridium tetani

G. Treatment

• Antibiotics:
  • Beta-lactams
  • Aminoglycosides
  • Fluoroquinolones
  • Macrolides

H. Challenges

• Antibiotic resistance (MRSA, CRE).
• Biofilm formation.
• Endotoxin/exotoxin effects.

IV. Fungi

A. Basic Characteristics

• Cell Type: Eukaryotic.
• Size: Yeast: 5-10 µm; Mold: up to several cm.
• Cell Wall: Chitin and glucans.
• Nutrition: Heterotrophic (absorptive).
• Reproduction: Spores (sexual/asexual).
• Growth Forms: Yeast, Mold, Mushrooms.
• Examples: Saccharomyces cerevisiae, Aspergillus, Candida albicans.

B. Structure of Fungal Cells

1. Yeast Cell

• Components: Cell wall (chitin, glucan), Plasma membrane, Nucleus, Mitochondria, Ribosomes, Vacuole, Golgi apparatus.
• Budding scar: Site of reproduction.

2. Filamentous Fungi (Molds)

• Hyphae: Long filaments.
• Septa: Cross walls within hyphae (may be absent in some).
• Nucleus: Eukaryotic nucleus.
• Spores: Reproductive units.
• Fruiting body: Structure producing spores (e.g., mushroom).
• Conidiophore: Spore-producing stalk.
• Mycelium: Network of hyphae.

C. Classification of Fungi (Traditional Subdivisions/Phyla)

Subdivision	Phylum/Class	Spores/Conidia	Septa Present	Motile Spores	Examples
Zygomycotina	Mucoromycota	Sporangiospores / Zygospores	No	No	Rhizopus, Mucor
Ascomycotina	Ascomycota	Ascospores / Conidia	No	Yes	Candida, Aspergillus
Basidiomycotina	Basidiomycota	Basidiospores	No	Yes	Cryptococcus
Deuteromycotina	Fungi Imperfecti	Conidia	No	Yes	Candida, Aspergillus
Mastigomycotina	Chytridiomycota	Zoospores	Yes	No	Batrachochytrium

D. Methods of Identification

• KOH Mount: Reveals fungal elements.
• India Ink: Detects capsule in Cryptococcus.
• Culture: Sabouraud Dextrose Agar (SDA), CHROMagar.
• Staining: PAS, Grocott's methenamine silver (GMS), Calcofluor white.
• Biochemical Tests: Germ tube test, urease test.
• Molecular Techniques: ITS sequencing, PCR.
• Antigen Detection: Galactomannan, β-glucan assay.

E. Reproduction

1. Asexual

• Spores (conidia, sporangiospores).
• Budding (yeasts like Candida).

2. Sexual

• Formation of ascospores (Ascomycota) or basidiospores (Basidiomycota).
• Mating types involved.

F. Medical Significance

Disease	Causative Fungi
Athlete's foot	Trichophyton rubrum
Thrush	Candida albicans
Ringworm	Dermatophytes
Aspergillosis	Aspergillus fumigatus
Cryptococcal meningitis	Cryptococcus neoformans
Histoplasmosis	Histoplasma capsulatum

G. Treatment

• Antifungal Agents:
  • Azoles
  • Polyenes
  • Echinocandins
  • Allylamines

H. Challenges

• Selective toxicity due to eukaryotic nature (shared with host).
• Resistance (e.g., azole-resistant Candida auris).
• Biofilms in chronic infections.

V. Comparative Summary Table

Feature	Viruses (Acellular)	Bacteria (Prokaryotic)	Fungi (Eukaryotic)
Cellularity	Acellular	Prokaryotic	Eukaryotic
Cell Wall	No	Yes (peptidoglycan)	Yes (chitin/glucan)
Reproduction	Inside host	Binary fission	Spores
Genome	DNA/RNA	DNA (circular)	DNA
Metabolism	None	Yes	Yes
Pathogenesis	Cytopathic effect	Toxins, invasion	Invasion, hypersensitivity
Identification	EM, PCR, serology	Staining, culture, MALDI-TOF	KOH, culture, molecular
Treatment	Antivirals, vaccines	Antibiotics	Antifungals