Section 4.1: The Bacteria

Overview of Bacterial Structure and Diversity

Bacteria are single-celled prokaryotic organisms with diverse structures and arrangements. Understanding their cellular components and morphology is essential for microbiology.

• Common Structures in All Bacteria:

  • Cell membrane: Phospholipid bilayer controlling transport.

  • Cytoplasm: Gel-like matrix for metabolic activities.

  • Chromosome (nucleoid): Single, circular DNA molecule.

• Structures Found in Some Bacteria:

  • Flagella: Motility appendages.

  • Pili: DNA transfer and attachment.

  • Fimbriae: Surface attachment.

  • Capsules and slime layers: Protective coatings.

  • Plasmids: Extra-chromosomal DNA.

  • Endospores: Dormant, resistant structures.

• Bacterial Shapes:

  • Coccus: Spherical, oval, bean-shaped, or pointed.

  • Bacillus: Rod-shaped, can be blocky, spindle-shaped, filamentous, club-shaped, or drumstick-shaped.

  • Curved: Includes vibrio (comma-shaped), spirillum (rigid spiral), spirochete (flexible spiral).

• Pleomorphism: Variation in size and shape within a single species due to genetic or nutritional factors.

• Bacterial Arrangements:

  • Diplococci: Pairs of cocci.

  • Tetrads: Groups of four cocci.

  • Staphylococci/micrococci: Irregular clusters.

  • Streptococci: Chains of cocci.

  • Sarcina: Cubical packets (8, 16, or more).

  • Diplobacilli: Pairs of bacilli.

  • Streptobacilli: Chains of bacilli.

  • Palisades: Side-by-side rows of bacilli.

• Mycoplasmas: Bacteria lacking cell walls, showing extreme shape variation.

• Bacterial Size:

  • Average: 1 μm

  • Thiomargarita namibiensis: 100–750 μm

  • Ultrasmall bacteria: 200–500 nm

• Biofilms: Cooperative communities of microbes living in a shared matrix, often on moist surfaces.

Table: Bacterial Shapes and Arrangements

Example:

Streptococcus pyogenes forms chains of cocci, characteristic of streptococcal arrangement.

Section 4.2: External Structures

Bacterial Appendages and Surface Coatings

Bacterial external structures play key roles in motility, attachment, and protection. These include flagella, pili, fimbriae, nanowires, and surface layers.

• Flagella: Long, whip-like appendages for motility. Composed of basal body, hook, and filament.

• Flagellar Arrangements:

  • Monotrichous: Single flagellum.

  • Lophotrichous: Tufts of flagella.

  • Amphitrichous: Flagella at both poles.

  • Peritrichous: Flagella all over the cell surface.

• Axial Filaments (Periplasmic Flagella): Internal flagella in spirochetes, imparting twisting motion.

• Chemotaxis and Phototaxis:

  • Chemotaxis: Movement toward (positive) or away from (negative) chemical stimuli.

  • Phototaxis: Movement toward light, seen in some photosynthetic bacteria.

• Run vs. Tumble:

  • Run: Counterclockwise flagellar rotation, smooth movement.

  • Tumble: Clockwise rotation, abrupt change in direction.

• Pili: Tubular structures for DNA transfer (conjugation) and attachment; found in gram-negative bacteria.

• Fimbriae: Short, bristle-like fibers for adhesion; important in biofilm formation and pathogenicity.

• Nanowires: Tubular extensions for transfer of amino acids and electrons between cells.

• Surface Coatings:

  • S layer: Protein layer for protection, produced in hostile environments.

  • Glycocalyx: Polysaccharide coating, includes slime layer (loose) and capsule (dense).

• Specialized Functions:

  • Capsules: Protect against phagocytosis, increase pathogenicity.

  • Biofilms: Enable long-term survival and resistance, e.g., dental plaque.

Table: Comparison of Capsule and Slime Layer

Example:

Escherichia coli uses fimbriae to adhere to epithelial cells in the urinary tract, contributing to infection.

Section 4.3: The Cell Envelope

Structure and Function of the Bacterial Cell Envelope

The cell envelope is a multi-layered boundary providing protection and structural integrity. It varies between gram-positive and gram-negative bacteria.

• Layers of the Cell Envelope:

  • Cell wall: Peptidoglycan-based, determines shape and resists osmotic pressure.

  • Cytoplasmic membrane: Phospholipid bilayer with proteins, controls transport.

  • Outer membrane: Present in gram-negative bacteria, contains lipopolysaccharides.

• Gram Stain: Differentiates bacteria based on cell envelope structure.

  • Gram-positive: Thick peptidoglycan, teichoic acids, no outer membrane.

  • Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS).

• Peptidoglycan: Polymer of glycan chains cross-linked by peptides, provides rigidity and flexibility.

• Teichoic and Lipoteichoic Acids: Found in gram-positive cell walls, involved in cell wall maintenance and cell division.

• Lipopolysaccharide (LPS): Found in gram-negative outer membrane, acts as endotoxin causing fever and shock.

Table: Gram-Positive vs. Gram-Negative Cell Envelope

Example:

Staphylococcus aureus is gram-positive, while Escherichia coli is gram-negative.

Section 4.4: Bacterial Internal Structure

Internal Components and Their Functions

Bacterial cells contain several internal structures essential for survival, metabolism, and genetic exchange.

• Cytoplasm: Site of biochemical reactions, contains water, nutrients, and cell machinery.

• Chromosome (Nucleoid): Single, circular DNA molecule, genetic blueprint.

• Plasmids: Small, circular DNA molecules, confer traits like antibiotic resistance.

• Ribosomes: Sites of protein synthesis; bacterial ribosomes are 70S, eukaryotic are 80S.

• Inclusion Bodies: Storage granules for nutrients.

• Cytoskeleton: Protein filaments (actin-like) for cell shape and division.

• Endospores: Highly resistant, dormant structures formed under stress.

Endospore Formation and Germination

• Sporulation: Triggered by nutrient depletion; cell forms a tough, protective spore.

• Germination: Spore returns to vegetative state when conditions improve.

• Resistance: Endospores withstand heat, radiation, chemicals.

Table: Diseases Caused by Endospore-Forming Bacteria

Example:

Bacillus anthracis spores can persist in soil for decades, causing outbreaks of anthrax.

Section 4.5: The Archaea

Unique Features and Ecological Roles of Archaea

Archaea are prokaryotes distinct from bacteria, often inhabiting extreme environments. They share some features with eukaryotes and possess unique adaptations.

• Genetic and Structural Differences:

  • Unique rRNA sequences.

  • Distinct membrane lipids and cell wall composition (no peptidoglycan).

  • Special DNA compaction methods.

• Ecological Types:

  • Methanogens: Produce methane from CO2 and H2.

  • Extreme halophiles: Require high salt concentrations.

  • Psychrophiles: Thrive at low temperatures.

  • Hyperthermophiles: Thrive at high temperatures (80–113°C).

Table: Types of Archaea

Example:

Halobacterium species use red pigments to synthesize ATP in salty environments.

Section 4.6: Classification Systems for Bacteria and Archaea

Taxonomy and Identification

Bacteria and archaea are classified based on phenotypic and genetic traits. Bergey's Manuals are key resources for identification and taxonomy.

• Bergey's Manual of Systematic Bacteriology: Comprehensive, combines phenotype and rRNA sequencing.

• Bergey's Manual of Determinative Bacteriology: Focuses on phenotypic traits for practical identification.

• Major Divisions:

  • Gracilicutes: Gram-negative, thin cell walls.

  • Firmicutes: Gram-positive, thick cell walls.

  • Tenericutes: Lack cell walls.

  • Mendosicutes: Archaea.

• Species Definition: Collection of cells sharing similar traits; subspecies/strains differ in minor characteristics.

• Serotype: Subgroup distinguished by unique surface molecules, elicits specific antibody responses.

Table: Major Taxonomic Divisions

Example:

Clinical labs use Bergey's Manual of Determinative Bacteriology for rapid identification of pathogens.

Additional info:

• Equations and chemical formulas relevant to peptidoglycan structure: