Unit 2: Microbial diversity

The microbial world spans cellular and acellular forms whose classification rests on the three-domain system proposed by Carl Woese (1977) from small-subunit ribosomal RNA sequence comparisons. Diversity here is organised by cell architecture (prokaryotic vs. eukaryotic), the presence or absence of a nucleus, and molecular signatures. This section fixes the framework the later sections keep referring to.

• Three domains: Bacteria (Eubacteria), Archaea, and Eukarya — separated chiefly by 16S/18S rRNA sequences.
• Prokaryote vs. eukaryote: prokaryotes (Bacteria, Archaea) lack a membrane-bound nucleus and organelles; eukaryotes (fungi, protists) possess both.
• Acellular agents: viruses lie outside the three domains — no cells, no independent metabolism, obligate intracellular parasites.
• Ribosome as classifier: 70S ribosome in prokaryotes, 80S in eukaryotic cytoplasm — the primary molecular yardstick.
• Taxonomic hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species, written as binomial Genus species.

II. Overview of Bacterial Diversity

Eubacteria and Archaea contrasted

The two prokaryotic domains share cellular organisation but differ fundamentally in membrane chemistry, cell-wall composition, and habitat range.

A. Domain Eubacteria (true bacteria)

Definition: prokaryotes with peptidoglycan cell walls and ester-linked membrane lipids, occupying nearly every habitat.

• Cell wall: peptidoglycan (murein) — chains of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by peptides.
• Membrane lipids: straight-chain fatty acids joined to glycerol by ester bonds.
• RNA polymerase: single type, sensitive to the antibiotic rifampicin.
• Examples: Escherichia coli (gut commensal), Bacillus subtilis, Streptococcus pneumoniae.

B. Domain Archaea

Definition: prokaryotes lacking peptidoglycan, distinguished by unique membrane lipids, often thriving in extreme environments.

• Cell wall: no peptidoglycan — instead pseudopeptidoglycan (pseudomurein) or S-layers of protein/glycoprotein.
• Membrane lipids: branched isoprenoid chains joined by ether bonds; some form monolayers, giving heat stability.
• Extremophile groups: methanogens (produce CH₄), halophiles (high salt, e.g. Halobacterium), thermoacidophiles (Sulfolobus, hot acid springs).
• Molecular parity with eukaryotes: several RNA-polymerase subunits and histone-like proteins resemble those of Eukarya more than Bacteria.

C. Significance of the divide

• Evolutionary insight: the Archaea–Eukarya molecular link supports the view that eukaryotes arose from an archaeal lineage.
• Antibiotic relevance: peptidoglycan-targeting drugs (penicillin) act on Eubacteria but not Archaea, which lack the target.

III. Bacteria: Basic Classification and Characteristics

The workhorses of the prokaryotic world

Bacteria are unicellular prokaryotes 0.5–5 µm across, classified by shape, staining, oxygen need, and nutrition.

A. Basic classification

• By shape (morphology):
  • Cocci: spheres — arranged as diplococci, streptococci (chains), staphylococci (clusters).
  • Bacilli: rods — e.g. Bacillus anthracis.
  • Spiral forms: vibrio (comma, Vibrio cholerae), spirillum (rigid coil), spirochaete (flexible, Treponema).
• By Gram stain (cell-wall type):
  • Gram-positive: thick peptidoglycan retains crystal violet — appear purple.
  • Gram-negative: thin peptidoglycan plus outer membrane with lipopolysaccharide (LPS) — take counterstain safranin, appear pink.
• By oxygen requirement: obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles.
• By nutrition: photoautotrophs, chemoautotrophs, photoheterotrophs, chemoheterotrophs.

B. Basic characteristics

• Genetic material: single circular chromosome in a nucleoid; accessory plasmids carry resistance or virulence genes.
• Reproduction: asexual binary fission; genetic exchange by transformation, transduction, conjugation.
• Surface structures: flagella (motility), pili/fimbriae (attachment, conjugation), capsule (protection, virulence).
• Endospores: dormant, heat-resistant survival forms in Bacillus and Clostridium.
• Growth curve phases: lag → log (exponential) → stationary → death.

IV. Virus: Basic Classification and Characteristics

Acellular obligate intracellular parasites

Viruses are non-cellular infectious particles consisting of a nucleic-acid genome enclosed in a protein coat, replicating only inside host cells.

A. Basic classification

• By nucleic acid (Baltimore basis):
  • DNA viruses: double-stranded (herpesvirus) or single-stranded (parvovirus).
  • RNA viruses: double-stranded (reovirus), single-stranded positive-sense (poliovirus), single-stranded negative-sense (influenza).
  • Reverse-transcribing: retroviruses (HIV) copy RNA → DNA via reverse transcriptase.
• By capsid symmetry:
  • Helical: protein subunits spiral around the genome (tobacco mosaic virus).
  • Icosahedral: 20 triangular faces (adenovirus).
  • Complex: combined forms (bacteriophage T4 — icosahedral head, helical tail).
• By envelope: enveloped (lipid membrane from host, e.g. influenza) vs. naked (protein capsid only).
• By host: bacteriophages, plant viruses, animal viruses.

B. Basic characteristics

• Structure: genome (DNA or RNA) + capsid of capsomere subunits; sometimes an envelope with glycoprotein spikes.
• Metabolic status: no ribosomes, no ATP generation — inert outside the host (obligate parasitism).
• Replication cycle: attachment → penetration → uncoating → biosynthesis → assembly → release.
  • Lytic cycle: host cell lyses, releasing progeny virions.
  • Lysogenic cycle: viral genome integrates as a prophage, replicating passively until induced.
• Size: 20–300 nm — visible only by electron microscopy.

V. Fungi: Basic Classification and Characteristics

Eukaryotic, heterotrophic decomposers and pathogens

Fungi are eukaryotic, chitin-walled heterotrophs that feed by absorption, ranging from unicellular yeasts to filamentous moulds.

A. Basic classification

• By phylum (spore type):
  • Zygomycota: coenocytic hyphae, sexual zygospores — e.g. Rhizopus (bread mould).
  • Ascomycota: sexual spores in a sac (ascus) — e.g. Saccharomyces, Penicillium.
  • Basidiomycota: spores on a club (basidium) — mushrooms, Agaricus.
  • Deuteromycota (Fungi Imperfecti): no known sexual stage — e.g. Candida.
• By body form:
  • Yeasts: unicellular, reproduce by budding.
  • Moulds: filamentous mycelium of hyphae.
  • Dimorphic: switch between yeast and mould with temperature (Histoplasma).

B. Basic characteristics

• Cell wall: chitin (a polymer of N-acetylglucosamine), not cellulose or peptidoglycan.
• Nutrition: heterotrophic by absorption — saprophytes (on dead matter), parasites, or mutualists (mycorrhizae, lichens).
• Body structure: hyphae (threads) forming a mycelium; hyphae may be septate (with cross-walls) or coenocytic (aseptate, multinucleate).
• Storage product: glycogen, as in animals — not starch.
• Reproduction: asexual by spores (conidia, sporangiospores) and budding; sexual by fusion producing zygospores, ascospores, or basidiospores.

VI. Protists: Basic Classification and Characteristics

The eukaryotic catch-all kingdom

Protists are mostly unicellular eukaryotes that do not fit fungi, plants, or animals, grouped traditionally by mode of nutrition and locomotion.

A. Basic classification

• Protozoa (animal-like, heterotrophic), grouped by locomotion:
  • Amoeboid (Rhizopoda): move by pseudopodia — Amoeba, Entamoeba histolytica.
  • Flagellates (Mastigophora): move by flagella — Trypanosoma, Giardia.
  • Ciliates (Ciliophora): move by cilia, have two nuclei — Paramecium.
  • Sporozoa (Apicomplexa): non-motile adults, obligate parasites — Plasmodium (malaria).
• Algae (plant-like, photosynthetic):
  • Euglenoids: flexible, mixotrophic — Euglena.
  • Dinoflagellates: two flagella, cause red tides.
  • Diatoms: silica cell walls (frustules).
• Slime moulds (fungus-like): feed as amoeboid masses, reproduce by spores.

B. Basic characteristics

• Cell type: eukaryotic — true nucleus, mitochondria, and (in algae) chloroplasts.
• Nutrition modes: photoautotrophic (algae), heterotrophic by ingestion/absorption (protozoa), or mixotrophic (Euglena switches with light).
• Locomotory organelles: pseudopodia, flagella, or cilia — the primary sorting trait among protozoa.
• Reproduction: asexual by binary or multiple fission; sexual by conjugation (Paramecium) or gamete fusion.
• Habitat: predominantly aquatic — freshwater, marine, and moist soil.

C. Medical and ecological significance

• Disease agents: Plasmodium (malaria via Anopheles), Entamoeba histolytica (amoebic dysentery), Trypanosoma (sleeping sickness).
• Ecological role: phytoplankton (diatoms, dinoflagellates) form the base of aquatic food chains and generate a large share of atmospheric oxygen.