Chapter 27: Bacteria and Archaea

Introduction

This chapter explores the biology of prokaryotes, focusing on their structural and functional adaptations, genetic diversity, nutritional and metabolic strategies, phylogenetic classification, ecological roles, and their impact on humans. Prokaryotes, which include Bacteria and Archaea, are among the most ancient and diverse forms of life on Earth.

Structural and Functional Adaptations of Prokaryotes

Cell Structure and Morphology

Prokaryotes were the first organisms to inhabit Earth and are found in nearly every environment. Their small size and simple structure contribute to their success.

• Size: Most prokaryotic cells are 0.5–5 μm, much smaller than eukaryotic cells.

• Shapes: The three most common shapes are:

  • Cocci: Spherical (ball-shaped)

  • Bacilli: Rod-shaped

  • Spirilla: Spiral-shaped

Surface Structures

• Cell Wall: Maintains cell shape, protects the cell, and prevents it from bursting in hypotonic environments.

• Bacterial Cell Walls: Contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides.

• Archaeal Cell Walls: Contain polysaccharides and proteins but lack peptidoglycan.

• Gram Stain: Used to classify bacteria:

  • Gram-positive: Simpler walls with a thick layer of peptidoglycan.

  • Gram-negative: Less peptidoglycan and an outer membrane containing lipopolysaccharides.

• Capsule: Sticky outer layer of polysaccharide or protein that allows adherence to surfaces and protects against the immune system.

• Endospores: Metabolically inactive structures that can survive harsh conditions for long periods.

• Pili and Fimbriae: Hair-like appendages for attachment and DNA transfer (sex pili).

• Flagella: Structures for movement; prokaryotic flagella differ from eukaryotic flagella in structure and mechanism.

Genetic Organization and Diversity

Genomic Structure

• Nucleoid: Region where the circular chromosome is located; not membrane-bound.

• Plasmids: Small, circular DNA molecules that replicate independently and often carry beneficial genes (e.g., antibiotic resistance).

Reproduction and Mutation

• Binary Fission: Prokaryotes reproduce asexually by dividing into two identical cells.

• Rapid Reproduction: Enables quick population growth and adaptation.

• Mutation: Although mutation rates are low, rapid reproduction leads to accumulation of genetic changes.

Genetic Recombination

• Transformation: Uptake of foreign DNA from the environment.

• Transduction: Movement of genes between bacteria by bacteriophages (viruses).

• Conjugation: Transfer of DNA between bacteria via a pilus; involves F factor plasmid.

• Antibiotic Resistance: R plasmids carry resistance genes and can be transferred between bacteria, leading to the spread of antibiotic resistance.

Nutritional and Metabolic Diversity

Modes of Nutrition

Prokaryotes are classified by how they obtain energy and carbon:

• Photoautotrophs: Use light as energy source and CO2 as carbon source. Example: Cyanobacteria

• Chemolithoautotrophs (Chemoautotrophs): Use inorganic compounds (e.g., H2S, NH3, Fe2+) for energy and CO2 for carbon. Example: Sulfolobus

• Photoheterotrophs: Use light for energy and organic compounds for carbon. Example: Rhodobacter

• Chemoheterotrophs: Use organic compounds for both energy and carbon. Example: Most bacteria, including E. coli

Role of Oxygen and Nitrogen

• Obligate Aerobes: Require oxygen for cellular respiration.

• Obligate Anaerobes: Poisoned by oxygen; use fermentation or anaerobic respiration.

• Facultative Anaerobes: Can use oxygen if present or switch to anaerobic metabolism.

• Nitrogen Fixation: Some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3), making nitrogen available to other organisms.

Metabolic Cooperation

• Prokaryotes may cooperate to exploit resources, such as in biofilms or specialized cells (e.g., heterocysts in Anabaena for nitrogen fixation).

Phylogenetic Diversity of Prokaryotes

Major Groups of Bacteria

• Proteobacteria: Large, diverse group of gram-negative bacteria with five subgroups:

  • Alpha: Includes Rhizobium (nitrogen-fixing), hypothesized ancestor of mitochondria.

  • Beta: Includes Nitrosomonas (ammonia oxidizer).

  • Gamma: Includes Thiomargarita namibiensis (sulfur bacteria), Salmonella, Vibrio cholerae, E. coli.

  • Delta: Includes myxobacteria (fruiting bodies), bdellovibrios (predators).

  • Epsilon: Includes Helicobacter pylori (causes ulcers), Campylobacter.

• Chlamydias: Intracellular parasites; Chlamydia trachomatis causes blindness and STDs.

• Spirochetes: Spiral-shaped; includes Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease).

• Cyanobacteria: Photosynthetic, oxygen-producing bacteria; ancestors of chloroplasts.

• Gram-Positive Bacteria: Includes Bacillus anthracis (anthrax), Clostridium botulinum (botulism), Staphylococcus, Streptococcus, and Mycoplasmas (lack cell walls).

Major Groups of Archaea

• Extreme Halophiles: Live in highly saline environments.

• Extreme Thermophiles: Thrive in very hot environments.

• Methanogens: Produce methane as a metabolic byproduct; live in swamps and marshes; strict anaerobes.

Ecological Roles of Prokaryotes

Role in Ecosystems

• Decomposers: Chemoheterotrophic prokaryotes break down dead organisms and recycle nutrients.

• Biogeochemical Cycles: Prokaryotes play a major role in cycling elements such as carbon, nitrogen, and sulfur.

• Symbiosis: Prokaryotes form close ecological relationships with other organisms:

  • Mutualism: Both partners benefit.

  • Commensalism: One benefits, the other is unaffected.

  • Parasitism: One benefits at the expense of the other.

Prokaryotes and Human Health

Beneficial and Harmful Effects

• Pathogens: Some prokaryotes cause diseases in humans (e.g., Streptococcus, Salmonella, Helicobacter pylori).

• Mutualists: Many prokaryotes in the human gut aid digestion and synthesize vitamins.

• Exotoxins: Secreted proteins that cause disease even if the bacteria are not present.

• Endotoxins: Released only when bacteria die and their cell walls break down.

Prokaryotes in Research and Technology

• Model Organisms: E. coli is widely used in genetic research.

• CRISPR-Cas System: Prokaryotic immune system used for gene editing.

• Bioremediation: Use of prokaryotes to remove pollutants from the environment.

• Industrial Applications: Production of ethanol, antibiotics, and other chemicals.

Key Equations

• Binary Fission: Where is the number of cells at time , is the initial number of cells, and is the number of generations.

• General Formula for Nitrogen Fixation:

Example

• Antibiotic Resistance: Overuse of antibiotics selects for bacteria with R plasmids, leading to the spread of resistant strains.

• Symbiosis: Rhizobium bacteria form nodules on legume roots, fixing nitrogen for the plant.

Additional info: Some context and terminology were expanded for clarity and completeness, including definitions, examples, and tables summarizing key differences between domains and bacterial groups.