Bacteria and Archaea Microbiology

General Characteristics of Bacteria and Archaea

  • DNA Packaging:
    • Bacteria and Archaea: No nucleus.
    • Eukaryotes: Have a nucleus.
  • Internal Structures:
    • Bacteria and Archaea: No complex, membrane-bound organelles.
    • Eukaryotes: Have complex, membrane-bound organelles.

Bacterial Cell Structure

  • Structures in All Bacteria:
    • Cytoplasmic (cell) membrane: Controls material flow, surrounds cytoplasm.
    • Bacterial chromosome or nucleoid: Condensed DNA, directs genetics and protein coding.
    • Ribosomes: Sites of protein synthesis, composed of protein and RNA, 70S70S.
    • Cytoplasm: Water-based solution filling the cell.
    • Cell wall: Provides structural support and shape.
    • Inclusions/Granules: Stored nutrients.
  • Structures in Some Bacteria:
    • S layer: Single protein layer for protection/attachment.
    • Fimbriae: Fine, hairlike bristles for adhesion.
    • Outer membrane: Extra membrane in Gram-negative bacteria, contains lipopolysaccharide (LPS).
    • Actin cytoskeleton: Long protein fibers for cell shape.
    • Pilus: Appendage for DNA transfer (conjugation).
    • Capsule/Glycocalyx: External coating for protection, adhesion, and receptors.
    • Bacterial microcompartments: Protein-coated packets for enzyme localization.
    • Endospore: Dormant body for survival in adverse conditions.
    • Plasmid: Double-stranded DNA circle with extra genes.
    • Nanowires/Nanotubes: Thin tubular membrane extensions for electron/nutrient transfer.
    • Flagellum: Specialized appendage for motility.

Bacterial Morphology

  • Shapes:
    • Coccus: Spheres, oval, bean-shaped.
    • Bacillus: Rod-shaped (blocky, spindle, round-ended, filamentous, club-shaped).
    • Curved: Vibrio, spirillum, corkscrew, spirochete.
    • Pleomorphism: Variations in size/shape within a species.
  • Arrangements of Cocci:
    • Diplococci: Pairs.
    • Tetrads: Groups of four.
    • Staphylococci: Irregular clusters.
    • Streptococci: Chains.
    • Sarcina: Cubical packets of 88 , 16+16+ cells.
  • Arrangements of Bacilli:
    • Diplobacilli: Pairs with attached ends.
    • Streptobacilli: Chains.
    • Palisades: Cells remain attached, fold back forming side-by-side rows.

Biofilms

  • Microbial habitats where bacteria live in cooperative associations.
  • Form on moist inert surfaces, colonizing organisms secrete substances and extracellular matrix.

External Structures: Appendages

  • Motility Appendages:
    • Flagella:
      • Structure: Filament, hook, basal body.
      • Arrangement: Monotrichous (single), Lophotrichous (bunches), Amphitrichous (both poles), Peritrichous (dispersed).
      • Movement: Chemotaxis (chemical signals), Phototaxis (light). Run (smooth, linear) vs. Tumble (flagellum reverses, change course).
    • Periplasmic Flagella (Axial Filament): Internal flagella in spirochetes, impart twisting motion.
  • Attachment/Channel Formation Appendages:
    • Fimbriae: Bristle-like fibers for adhesion to surfaces/cells, contribute to biofilms.
    • Pili: Long, rigid, tubular structures (Gram-negative), used in conjugation (DNA transfer).
    • Nanowires/Nanotubes: Very thin extensions for transferring amino acids/electrons.

Surface Coatings

  • S Layer: Single protein layer for protection, produced in hostile environments.
  • Glycocalyx: Polysaccharide (with/without protein) coating.
    • Slime layer: Loosely forms, protects against water/nutrient loss.
    • Capsule: Tightly bound, denser, thicker. Protects against phagocytosis. Functions in biofilms.

The Cell Envelope

  • Layers: Cell wall, Cytoplasmic membrane, Outer membrane (in some).
  • Gram Stain: Differentiates bacteria based on cell envelope structure.
    • Gram-positive: Thick peptidoglycan cell wall, inner cytoplasmic membrane.
    • Gram-negative: Outer membrane, thin peptidoglycan cell wall, inner cytoplasmic membrane.
  • Cell Wall Structure:
    • Determines shape, provides structural support.
    • Peptidoglycan: Unique macromolecule of glycan chains cross-linked with peptides.
    • Gram-Positive Cell Wall: Thick (20−8020-80 nm) peptidoglycan; contains teichoic and lipoteichoic acids for maintenance and acidic charge.
    • Gram-Negative Cell Wall: Thin (1−31-3 nm) peptidoglycan; greater flexibility, sensitivity to lysis.
  • Nontypical Cell Walls:
    • Mycobacterium and Nocardia: Cell wall bulk composed of mycolic acid (long-chain fatty acid), contributes to pathogenicity, resistance to chemicals/dyes. Diagnosed with acid-fast stain.
    • Mycoplasmas: Lack a cell wall, membrane stabilized by sterols, pleomorphic.

Cytoplasmic Membrane

  • Structure: Lipid bilayer with phospholipids (30%−40%30\%-40\%
    ) and proteins (60%−70%60\%-70\%
    ).
  • Functions: Energy reactions, nutrient processing, synthesis, transport regulation (selective permeability), secretion.

Gram-Negative Outer Membrane

  • Lipopolysaccharide (LPS): Polysaccharide chains (cell markers/receptors) and endotoxin (stimulates fever/shock).
  • Porin proteins: Span outer membrane, allow small molecules, can block harmful chemicals.

Bacterial Internal Structure

  • Cytoplasm: Gelatinous solution with water (70%−80%70\%-80\%
    ), sugars, amino acids, salts, chromatin body, ribosomes, granules, cytoskeleton.
  • Bacterial Chromosome: Single, circular DNA, aggregated in nucleoid.
  • Plasmids: Nonessential, double-stranded DNA circles, duplicated, confer protective traits, important in genetic engineering.
  • Ribosomes: RNA and protein, 70S70S, dispersed in cytoplasm, sites of protein synthesis.
  • Inclusion Bodies: Storage sites for nutrients.
  • Cytoskeleton: Long protein polymers (actin-like), helical ribbons under membrane, contribute to cell shape.

Bacterial Endospores

  • Function: Withstand hostile conditions, facilitate survival.
  • Life Cycle: Vegetative cell (metabolically active) ↔ Endospore (inert, resting).
  • Sporulation: Spore formation induced by nutrient depletion.
  • Resistance: Can resist heating, drying, freezing, radiation, chemicals.
  • Germination: Stimulated by water and germination agent, breaks down cortex, core rehydrates, bacterium grows out.
  • Medical Significance: Causative agents of diseases (e.g., Anthrax, Tetanus, Botulism), resistant to cleaning, often contaminate medical settings/food.

The Archaea

  • Relatedness: More closely related to Eukarya than Bacteria (shared rRNA, similar protein synthesis/ribosomal structure).
  • Differences from Bacteria: Unique rRNA sequences, DNA compaction, membrane lipids (branched hydrocarbons with ether linkages), cell wall composition (lacks peptidoglycan), pilin proteins.
  • Habitats: Live in extreme environments (heat, salt, acid, pH, pressure).
  • Types:
    • Methanogens: Convert CO<em>2CO<em>2 and H</em>2H</em>2 to methane (CH4CH_4).
    • Extreme Halophiles: Require high salt (36%36\% NaCl).
    • Psychrophiles: Grow at very low temperatures.
    • Hyperthermophiles: Grow at very high temperatures (80∘C80 \circ C to 113∘C113 \circ C).

Classification Systems for Bacteria and Archaea

  • Evolutionary Relationships: Determined by rRNA nitrogen base comparison (stable nucleic acid content).
  • Bergey’s Manual: Definitive source for classification.
    • Bergey’s Manual of Systematic Bacteriology: Comprehensive, combines phenotypic and rRNA sequencing.
    • Bergey’s Manual of Determinative Bacteriology: Based on phenotypic characteristics, used for quick identification in labs.
  • Taxonomic Scheme (Major Divisions):
    • Gracilicutes: Gram-negative, thin-skinned.
    • Firmicutes: Gram-positive, thick and strong.
    • Tenericutes: Lack cell wall, soft (Mycoplasmas).
    • Mendosicutes: Archaea.
  • Bacterial Species: Collection of cells sharing similar traits.
    • Subspecies/Strain/Type: Bacteria of same species with differing characteristics.
    • Serotype: Species representatives stimulating distinct antibody responses due to surface molecules.