Chapter 27: Bacteria and Archaea – Structure, Function, and Diversity

Bacteria and Archaea: Structure, Function, and Diversity

Ubiquity of Prokaryotes

Prokaryotes are found in nearly every environment on Earth due to several key characteristics that enable their survival and rapid adaptation.

• Small Size & Rapid Reproduction: Their small cell size allows for efficient nutrient uptake and waste removal. Rapid binary fission enables quick population growth.

• Mutations & Rapid Evolution: High reproduction rates increase the chance of mutations, fueling rapid evolution and adaptation.

• Endospores: Some prokaryotes form endospores, dormant structures that withstand extreme conditions (e.g., heat, desiccation, chemicals).

• Ubiquitous: The term means the ability to live anywhere, from deep oceans to hot springs.

Structural Adaptations of Prokaryotes

Prokaryotes exhibit several structural features that contribute to their adaptability and survival.

• Unicellular: Most prokaryotes consist of a single cell.

• Very Small: Typically 0.5–5 μm in diameter.

• Variety of Shapes: Common shapes include cocci (spherical), bacilli (rod-shaped), and spirilla (spiral).

Cell-Surface Structures

The cell surface of prokaryotes is specialized for protection, interaction, and environmental adaptation.

• Bacterial Cell Wall: Composed of peptidoglycan, a polymer of sugars and amino acids.

• Archaeal Cell Wall: Made of polysaccharides and proteins, often containing pseudomurein (not peptidoglycan).

Gram Staining: Classification by Cell Wall

Bacteria are classified based on cell wall structure using the Gram stain technique.

• Gram-Positive: Thick peptidoglycan layer; stains purple.

• Gram-Negative: Thin peptidoglycan layer plus an outer membrane; stains pink/red.

Key Differences: Gram-negative bacteria have an additional outer membrane containing lipopolysaccharides, making them more resistant to antibiotics.

Protective Structures

• Capsule: A sticky layer of polysaccharide or protein outside the cell wall; protects against desiccation and immune attack, and aids in adherence to surfaces.

Endospores

• Metabolic Activity: Endospores are metabolically inactive, serving as dormant survival forms until conditions improve.

Surface Appendages

• Fimbriae: Hair-like projections for attachment to surfaces or other cells.

• Pili: Longer than fimbriae; involved in DNA transfer during conjugation (sex pili).

• Flagella: Tail-like structures for motility; rotate to propel the cell.

Specialized Membrane Structures

• Some prokaryotes have infolded plasma membranes or internal membranes that carry out metabolic processes (e.g., photosynthesis, cellular respiration).

Genetic Material

• Circular Chromosome: Main DNA molecule, located in the nucleoid region.

• Plasmids: Small, circular DNA molecules carrying accessory genes (e.g., antibiotic resistance).

• Ribosomes: Sites of protein synthesis; structurally different from eukaryotic ribosomes and can be targeted by antibiotics.

Reproduction and Mutation

• Binary Fission: Most prokaryotes reproduce asexually by binary fission, producing genetically identical offspring.

• Mutation Rates: Although mutation rates per division are low, rapid reproduction leads to significant genetic variation.

Genetic Recombination in Prokaryotes

Prokaryotes increase genetic diversity through three main mechanisms:

• Transformation: Uptake of naked DNA from the environment.

• Transduction: Transfer of DNA via bacteriophages (viruses that infect bacteria).

• Conjugation: Direct transfer of DNA between cells via a pilus (sex pilus). Involves F+ (donor, with F plasmid) and F- (recipient, without F plasmid) cells.

Nutritional Modes

Prokaryotes display diverse nutritional strategies, classified by energy and carbon sources:

• Photo-: Energy from light (e.g., cyanobacteria).

• Chemo-: Energy from chemicals (organic or inorganic).

• Auto-: Carbon from CO2 or inorganic sources.

• Hetero-: Carbon from organic compounds.

Examples: Photoautotrophs (light & CO2), Chemoheterotrophs (chemicals & organic carbon).

Oxygen Requirements

• Obligate Aerobes: Require oxygen for cellular respiration.

• Facultative Anaerobes: Can use oxygen but also grow without it (fermentation or anaerobic respiration).

• Obligate Anaerobes: Poisoned by oxygen; survive only in its absence.

Nitrogen Fixation

• Definition: Conversion of atmospheric nitrogen (N2) into ammonia (NH3), a form usable by living organisms.

Equation:

$\mathrm{N_2 + 8H^+ + 8e^- \rightarrow 2NH_3 + H_2}$

Genetic Diversity Transmission

• Horizontal Gene Transfer (HGT): Movement of genes between organisms other than by descent (not parent to offspring).

• Vertical Gene Transfer: Transmission from parent to offspring (common in eukaryotes).

• HGT complicates evolutionary relationships; traits like shape or metabolism do not always reflect ancestry.

Phylogenetic Relationships

• Archaea and Eukaryotes: Archaea are more closely related to eukaryotes than to bacteria.

Major Bacterial Groups

• Proteobacteria: Mostly gram-negative; diverse nutritional modes; mitochondria likely evolved from an ancestral proteobacterium.

• Chlamydia: Intracellular parasites; gram-negative.

• Spirochetes: Spiral-shaped, gram-negative; some are parasites (e.g., Treponema pallidum, syphilis).

• Cyanobacteria: Gram-negative, photosynthetic; ancestors of chloroplasts.

• Gram-Positive Bacteria: Thick peptidoglycan; includes Streptomyces (antibiotic production).

Archaeal Diversity and Extremophiles

• Extremophiles: Thrive in extreme environments.

• Halophiles: Live in highly saline environments.

• Thermophiles: Thrive at high temperatures.

• Acidophiles: Prefer acidic conditions.

• Alkalinophiles: Prefer alkaline (basic) environments.

Comparison of the Three Domains of Life

The following table summarizes key differences among Bacteria, Archaea, and Eukarya.

Feature	Bacteria	Archaea	Eukarya
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Cell Wall Composition	Peptidoglycan	Polysaccharides, proteins, pseudomurein	Cellulose (plants), chitin (fungi), or none
Membrane Lipids	Ester-linked, unbranched	Ether-linked, branched	Ester-linked, unbranched
Genetic Material	Circular DNA, plasmids	Circular DNA, plasmids	Linear chromosomes
Introns in Genes	Rare	Some genes	Common
Membrane-bound Organelles	No	No	Yes
Ribosome Size	70S	70S	80S
Examples	Escherichia coli, Streptococcus	Halobacterium, Thermoproteus	Plants, animals, fungi, protists

Additional info: Table entries inferred and expanded for completeness based on standard biology textbooks.