Unit 2: Microbial diversity - Subjective Questions

Eubacteria (True Bacteria) and Archaea are the two domains of prokaryotes that differ in several fundamental ways:

• Cell Wall:

  • Eubacteria: Contain peptidoglycan (murein) with muramic acid.
  • Archaea: Lack peptidoglycan; instead have pseudopeptidoglycan (pseudomurein), glycoproteins, or protein S-layers.

• Membrane Lipids:

  • Eubacteria: Straight-chain fatty acids joined to glycerol by ester bonds.
  • Archaea: Branched isoprenoid chains joined by ether bonds, which are more resistant to extreme conditions.

• Habitat:

  • Eubacteria: Found in diverse common environments — soil, water, human body.
  • Archaea: Often extremophiles — thrive in hot springs (thermophiles), salty lakes (halophiles), and anaerobic environments (methanogens).

• RNA Polymerase & Ribosomes: Archaeal RNA polymerase and ribosomal proteins resemble eukaryotes more than eubacteria.

• Antibiotic Sensitivity: Eubacteria are sensitive to antibiotics like streptomycin; Archaea are generally resistant.

Thus, although both are prokaryotic, Archaea share several molecular features with eukaryotes.

Bacteria are classified based on morphology into the following main types:

• Cocci (Spherical):

  • Coccus — single (e.g., Micrococcus)
  • Diplococci — pairs (e.g., Diplococcus pneumoniae)
  • Streptococci — chains (e.g., Streptococcus)
  • Staphylococci — clusters (e.g., Staphylococcus aureus)
  • Tetrads — groups of four
  • Sarcinae — cubical packets of eight

• Bacilli (Rod-shaped):

  • Single rods (e.g., Bacillus, E. coli)
  • Diplobacilli — pairs
  • Streptobacilli — chains

• Spirilla (Spiral-shaped):

  • Rigid spirals (e.g., Spirillum)

• Vibrio (Comma-shaped):

  • Curved rods (e.g., Vibrio cholerae)

• Spirochetes:

  • Flexible, helical (e.g., Treponema pallidum)

• Pleomorphic:

  • Variable shapes (e.g., Mycoplasma)

Morphology is a fundamental criterion used along with staining and biochemical tests for identification.

The Gram stain, developed by Hans Christian Gram, differentiates bacteria based on cell wall composition.

Mechanism of staining:

• Crystal violet–iodine complex forms inside cells.
• Alcohol/acetone treatment dehydrates the thick peptidoglycan in Gram-positives, trapping the dye → purple.
• In Gram-negatives, alcohol dissolves the outer membrane and washes out the dye; the counterstain safranin makes them pink.

Examples:

• Gram-positive: Staphylococcus, Streptococcus, Bacillus
• Gram-negative: E. coli, Salmonella, Pseudomonas

Bacteria are unicellular prokaryotes with the following general characteristics:

• Prokaryotic organization: No true membrane-bound nucleus; genetic material lies free in the cytoplasm as a nucleoid.
• Size: Typically 0.5–5 , visible only under microscope.
• Cell wall: Rigid wall of peptidoglycan provides shape and protection.
• Genetic material: Single circular double-stranded DNA; may carry extrachromosomal plasmids.
• Ribosomes: 70S type (50S + 30S subunits).
• Reproduction: Mainly asexual by binary fission; genetic recombination via conjugation, transformation, transduction.
• Motility: Many possess flagella; some have pili and fimbriae.
• Metabolic diversity: Autotrophic, heterotrophic, aerobic, anaerobic forms.
• Endospore formation: Some (e.g., Bacillus, Clostridium) form resistant endospores.
• Nutrition: Varied — photoautotrophs, chemoautotrophs, saprophytes, parasites.

These features enable bacteria to survive in nearly every environment on Earth.

A virus is an acellular infectious agent consisting of genetic material enclosed in a protein coat.

Basic Structure:

• Nucleic acid (Genome): Either DNA or RNA, single or double stranded — never both.
• Capsid: Protein coat made of subunits called capsomeres; protects the genome.
• Nucleocapsid: The nucleic acid + capsid together.
• Envelope: Some viruses have an outer lipoprotein envelope derived from host membrane, bearing spikes (glycoproteins) for attachment.

Why Obligate Intracellular Parasites:

• Viruses lack their own metabolic machinery — no ribosomes, enzymes for ATP production, or protein synthesis apparatus.
• They cannot replicate independently and must enter a living host cell.
• Inside the host, they hijack the cell's ribosomes, enzymes, and energy to synthesize new viral components.
• Outside a host, they exist as inert particles called virions.

Hence, viruses can multiply only inside living cells, making them obligate intracellular parasites.

Viruses can be classified according to their genetic material.

Based on Type of Nucleic Acid:

• DNA viruses: e.g., Herpesvirus, Adenovirus, Poxvirus.
• RNA viruses: e.g., Influenza virus, HIV, Poliovirus.

Further subdivided by strandedness:

• dsDNA, ssDNA, dsRNA, ssRNA.

Baltimore Classification (by David Baltimore) groups viruses into 7 classes based on genome type and mRNA synthesis strategy:

• Class I: dsDNA (e.g., Herpesvirus)
• Class II: ssDNA (e.g., Parvovirus)
• Class III: dsRNA (e.g., Reovirus)
• Class IV: (+) sense ssRNA (e.g., Poliovirus)
• Class V: (−) sense ssRNA (e.g., Rabies virus)
• Class VI: ssRNA with reverse transcriptase / retroviruses (e.g., HIV)
• Class VII: dsDNA with reverse transcriptase (e.g., Hepatitis B virus)

The central principle: all viruses must produce mRNA (+ sense) to be translated by the host, and the classification is based on the pathway used to achieve this.

DNA viruses and RNA viruses differ significantly:

Key points:

• RNA viruses mutate faster because RNA-dependent RNA polymerase has no error-correction ability, leading to frequent antigenic variation (e.g., influenza).
• DNA viruses are generally more genetically stable due to reliable DNA replication mechanisms.
• The high mutation rate of RNA viruses makes vaccine development challenging (e.g., HIV, influenza).

A bacteriophage is a virus that infects bacteria. It reproduces through two cycles:

1. Lytic Cycle: (Virulent phase)

• Adsorption: Phage attaches to specific receptors on bacterial cell wall.
• Penetration: Phage injects its DNA into the host; capsid remains outside.
• Biosynthesis: Host machinery is redirected to make viral DNA and proteins.
• Maturation (Assembly): New phage particles are assembled.
• Lysis (Release): Cell bursts, releasing new phages (e.g., T4 phage).

2. Lysogenic Cycle: (Temperate phase)

• Phage DNA integrates into the host chromosome as a prophage.
• Host replicates normally, copying the prophage to daughter cells.
• Under stress (e.g., UV light), the prophage detaches and enters the lytic cycle (induction).
• Example: Lambda () phage.

Difference: In the lytic cycle, the host is destroyed immediately, whereas in lysogeny, the viral genome persists silently until conditions trigger lysis.

Fungi are eukaryotic, heterotrophic organisms with distinctive characteristics:

• Eukaryotic: Possess a true membrane-bound nucleus (unlike bacteria).
• Cell wall: Made of chitin (not cellulose as in plants, nor peptidoglycan as in bacteria).
• Nutrition: Heterotrophic — absorb nutrients (absorptive nutrition); may be saprophytic, parasitic, or symbiotic. They lack chlorophyll (unlike plants).
• Body structure: Composed of thread-like filaments called hyphae, collectively forming a mycelium. Some are unicellular (yeasts).
• Storage food: Glycogen (like animals), not starch.
• Reproduction: Both asexual (spores, budding, fragmentation) and sexual methods.
• Habitat: Moist, warm organic-rich environments.

Distinction summary:

• From plants: No chlorophyll, chitin wall, glycogen storage.
• From bacteria: Eukaryotic organization, larger size, chitin wall.

Examples: Rhizopus, Aspergillus, Saccharomyces, mushrooms.

Fungi are classified into major groups (divisions) primarily on the basis of their reproductive structures and spore formation:

• Zygomycota (Zygomycetes):

  • Coenocytic (aseptate) hyphae.
  • Sexual spores = zygospores.
  • Example: Rhizopus (bread mold), Mucor.

• Ascomycota (Ascomycetes) — Sac Fungi:

  • Septate hyphae.
  • Sexual spores (ascospores) formed in a sac called ascus.
  • Example: Saccharomyces (yeast), Penicillium, Aspergillus.

• Basidiomycota (Basidiomycetes) — Club Fungi:

  • Septate hyphae.
  • Sexual spores (basidiospores) formed on basidium.
  • Example: Agaricus (mushroom), Puccinia (rust), Ustilago (smut).

• Deuteromycota (Fungi Imperfecti):

  • Sexual stage unknown or absent; reproduce only asexually.
  • Example: Alternaria, Trichoderma, Colletotrichum.

• (Chytridiomycota): Primitive aquatic fungi with flagellated spores (zoospores).

This classification helps in identification and understanding of fungal life cycles.

Fungi reproduce by both asexual and sexual methods.

A. Asexual Reproduction: (More common; produces genetically identical offspring)

• Fragmentation: Hyphae break into fragments, each forming new mycelium.
• Budding: Small outgrowth (bud) develops and detaches (e.g., yeast Saccharomyces).
• Fission: Cell divides into two (e.g., some yeasts).
• Spore formation: Asexual spores such as:
  • Sporangiospores (formed in sporangia, e.g., Rhizopus)
  • Conidiospores/Conidia (formed at hyphal tips, e.g., Penicillium)
  • Chlamydospores (thick-walled resting spores)

B. Sexual Reproduction: (Introduces genetic variation) Involves three stages:

• Plasmogamy: Fusion of two cytoplasms.
• Karyogamy: Fusion of two nuclei to form a diploid zygote.
• Meiosis: Restores haploid state, producing sexual spores:
  • Zygospores (Zygomycota)
  • Ascospores (Ascomycota)
  • Basidiospores (Basidiomycota)

The combination of both methods gives fungi great adaptability and survival advantage.

Protists are simple, mostly unicellular eukaryotic organisms placed in the Kingdom Protista. They represent a diverse and 'catch-all' group.

General Characteristics:

• Eukaryotic: Possess a true nucleus and membrane-bound organelles.
• Mostly unicellular, but some are colonial or multicellular (e.g., algae).
• Habitat: Mostly aquatic (fresh water, marine) or moist environments.
• Nutrition: Varied — autotrophic (algae), heterotrophic (protozoa), or mixotrophic.
• Locomotion: Through flagella, cilia, or pseudopodia; some are non-motile.
• Reproduction: Both asexual (binary fission) and sexual methods.

Classification (based on nutrition/mode of life):

• Photosynthetic Protists (Algae): e.g., Chlamydomonas, diatoms, Euglena.
• Protozoa (Animal-like):
  • Flagellates (e.g., Trypanosoma)
  • Ciliates (e.g., Paramecium)
  • Sarcodines/Amoeboids (e.g., Amoeba)
  • Sporozoans (e.g., Plasmodium)
• Fungus-like Protists (Slime molds): e.g., Physarum.

Protists are considered ancestral to plants, animals, and fungi.

Both protozoa and algae belong to Kingdom Protista but differ in nutrition and structure:

Summary:

• Protozoa are 'animal-like' protists that ingest or absorb food and are often motile parasites.
• Algae are 'plant-like' protists that manufacture their own food via photosynthesis.

Some organisms like Euglena show mixed features (both autotrophic and heterotrophic).

Protozoa are classified into four major groups based on their locomotory organelles:

1. Rhizopoda (Sarcodina) — Amoeboids:

• Move using pseudopodia (false feet).
• Also used for feeding (phagocytosis).
• Example: Amoeba, Entamoeba histolytica (causes amoebic dysentery).

2. Mastigophora (Flagellata) — Flagellates:

• Move using one or more flagella.
• Example: Trypanosoma (sleeping sickness), Giardia, Euglena.

3. Ciliophora (Ciliata) — Ciliates:

• Move using numerous cilia.
• Have two types of nuclei (macronucleus & micronucleus).
• Example: Paramecium, Balantidium.

4. Sporozoa (Apicomplexa):

• Non-motile in adult stage (no locomotory organs).
• All are parasitic; reproduce by spore formation.
• Example: Plasmodium (malaria).

This classification is important in medical microbiology since many protozoa are human pathogens.

Bacteria show great diversity in nutrition, classified by energy source and carbon source:

Based on Energy Source:

• Phototrophs: Obtain energy from light.
• Chemotrophs: Obtain energy from chemical compounds.

Based on Carbon Source:

• Autotrophs: Use CO₂ as carbon source.
• Heterotrophs: Use organic carbon compounds.

Combined Nutritional Categories:

• Photoautotrophs: Light energy + CO₂ (e.g., Cyanobacteria).
• Photoheterotrophs: Light energy + organic carbon (e.g., purple non-sulfur bacteria).
• Chemoautotrophs (Chemolithotrophs): Chemical energy from inorganic compounds + CO₂ (e.g., Nitrosomonas, sulfur bacteria).
• Chemoheterotrophs: Chemical energy + organic carbon (e.g., most bacteria, including pathogens and decomposers).

Additional based on oxygen requirement:

• Aerobes, Anaerobes, Facultative anaerobes, Microaerophiles.

This metabolic diversity allows bacteria to colonize virtually every ecological niche.

Fungi are of immense economic and ecological importance:

Beneficial Roles:

• Food: Edible mushrooms (Agaricus), truffles.
• Baking & Brewing: Saccharomyces cerevisiae (yeast) used in bread, beer, wine — via fermentation producing and ethanol.
• Antibiotics: Penicillium notatum produces penicillin; Cephalosporium produces cephalosporins.
• Organic acids & Enzymes: Aspergillus niger produces citric acid; fungi produce amylases, proteases.
• Cheese production: Penicillium roqueforti (Roquefort cheese).
• Decomposition: Fungi act as decomposers, recycling nutrients in ecosystems.
• Symbiosis: Mycorrhizae (fungi–root associations) improve plant nutrient uptake; lichens (fungi + algae).
• Research: Yeast is a model organism in genetics.

Harmful Roles:

• Cause plant diseases (rusts, smuts), food spoilage, and human infections (ringworm, candidiasis).

Thus, fungi are indispensable both industrially and ecologically.

Carl Woese, based on 16S/18S rRNA sequencing, proposed the Three-Domain System of classification.

Significance:

• This classification revealed that Archaea are more closely related to Eukarya than to Bacteria at the molecular level.
• It replaced the older two-empire (prokaryote/eukaryote) concept with a phylogenetically accurate system based on molecular evidence.

A typical bacterial cell consists of the following components:

Cell Envelope:

• Glycocalyx (Capsule/Slime layer): Protective outer layer; aids adhesion and protection against phagocytosis.
• Cell wall: Made of peptidoglycan; maintains shape and prevents osmotic lysis.
• Plasma membrane: Selectively permeable; site of respiration and transport.

Cytoplasmic Components:

• Cytoplasm: Gel-like matrix for metabolic reactions.
• Nucleoid: Region containing circular double-stranded DNA (genetic material).
• Plasmids: Extrachromosomal DNA carrying accessory genes (e.g., antibiotic resistance).
• Ribosomes (70S): Site of protein synthesis.
• Inclusion bodies: Storage of reserve materials (glycogen, fat).
• Mesosomes: Membrane infoldings aiding respiration and cell division.

External Appendages:

• Flagella: Locomotion.
• Pili/Fimbriae: Attachment; sex pili aid conjugation.

Special structure:

• Endospore: Dormant, resistant structure formed under stress (e.g., Bacillus, Clostridium).

Each component contributes to the survival, reproduction, and pathogenicity of bacteria.

Bacterial diversity refers to the vast variety of bacterial species differing in morphology, physiology, metabolism, and habitat.

Dimensions of Diversity:

• Morphological diversity: Different shapes and arrangements (cocci, bacilli, spirilla).
• Metabolic diversity: Autotrophs, heterotrophs, aerobes, anaerobes, extremophiles.
• Habitat diversity: Found in soil, water, air, deep-sea vents, hot springs, and inside other organisms.
• Genetic diversity: High mutation and recombination rates create genetic variability.

Significance of Studying Microbial Diversity:

• Ecological role: Bacteria drive biogeochemical cycles (carbon, nitrogen, sulfur).
• Biotechnology: Source of enzymes, antibiotics, and industrial products.
• Medicine: Understanding pathogens and developing treatments.
• Bioremediation: Degrade pollutants and clean environments.
• Agriculture: Nitrogen-fixing bacteria (Rhizobium) enhance soil fertility.
• Evolutionary insight: Reveals origin and phylogeny of life.

Studying diversity through modern tools (rRNA sequencing, metagenomics) helps discover unculturable microbes and their potential applications.

Viruses and bacteria are both microorganisms but differ fundamentally:

Summary: Bacteria are complete living cells capable of independent life, whereas viruses are inert particles outside host cells and show life characteristics only inside a host.