Bacteria and Archaea: Structure, Diversity, and Roles in Biology

Chapter 27: Bacteria and Archaea

Introduction

This chapter explores the biology of Bacteria and Archaea, two of the three domains of life. These prokaryotic organisms are fundamental to understanding the diversity, evolution, and ecological roles of life on Earth.

Three Domains of Life

Woese's Three-Domain System (1977)

• Domains of Life:

  • Bacteria (Prokaryotes)

  • Archaea (Prokaryotes)

  • Eukarya (Eukaryotes)

• Prokaryotes include Bacteria and Archaea, which lack a nucleus and membrane-bound organelles.

• Eukaryotes (Eukarya) possess a true nucleus and organelles.

• Phylogenetic Observations:

  • Some groups are paraphyletic (contain an ancestor and some, but not all, descendants).

  • Multicellularity has evolved multiple times independently (polyphyletic).

Example: Animals, plants, and fungi are all eukaryotes, but multicellularity arose separately in each lineage.

Prokaryotes: Two Clades and Ancestral Characteristics

Bacteria and Archaea

• Prokaryotes are divided into two main clades: Bacteria and Archaea.

• Modern prokaryotes provide insight into early forms of life and the transition to eukaryotes.

• For much of Earth's history, prokaryotes were the only life forms.

Prokaryotic Cell Structure

Cell Shape and Arrangement

• Common shapes:

  • Cocci: Spherical

  • Bacilli: Rod-shaped

  • Spirilla: Spiral-shaped

• Size typically ranges from 0.5 to 5 micrometers.

Cell Wall Composition

• Most prokaryotes have a cell wall for protection and shape maintenance.

• Bacteria cell walls contain peptidoglycan, a polymer of sugars and amino acids.

• Archaea cell walls lack peptidoglycan and have unique structural molecules.

Gram Staining

• Gram-positive bacteria: Thick peptidoglycan layer; stain purple.

• Gram-negative bacteria: Thin peptidoglycan layer and outer membrane; stain pink/red.

Other Structures

• Capsule: Polysaccharide or protein layer outside the cell wall for protection and adhesion.

• Fimbriae: Hair-like appendages for attachment.

• Flagella: Used for locomotion; can push or pull the cell.

• Nucleoid region: Area in the cytoplasm where the chromosome is located (no membrane-bound nucleus).

• Plasmids: Small, circular DNA molecules independent of the chromosome.

Prokaryotic Metabolism

Energy and Carbon Sources

• Photoautotrophs: Use light as energy and CO2 as carbon source (e.g., cyanobacteria, plants).

• Chemolithoautotrophs: Obtain energy from inorganic chemicals and use CO2 as carbon source.

• Photoheterotrophs: Use light for energy but require organic compounds for carbon.

• Chemoheterotrophs: Obtain both energy and carbon from organic compounds (e.g., most bacteria, animals, fungi).

Oxygen Requirements

• Obligate aerobes: Require oxygen for respiration.

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

• Facultative anaerobes: Can use oxygen if present or switch to anaerobic methods if not.

Reproduction and Genetic Variation

Asexual Reproduction: Binary Fission

• Prokaryotes reproduce by binary fission: rapid genome duplication and cell division.

• Generation times can be as short as 20 minutes under optimal conditions.

• Large populations and rapid reproduction increase the chance of mutations.

Genetic Recombination

• Transformation: Uptake of foreign DNA from the environment.

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

• Conjugation: Direct transfer of DNA between cells via a pilus.

• These processes create new genotypes and increase genetic diversity.

Diversity of Bacteria and Archaea

Major Bacterial Clades

Clade	Key Features	Examples
Proteobacteria	Highly diverse; includes nitrogen fixers, pathogens	Salmonella, Neisseria
Chlamydias	Obligate intracellular parasites	Chlamydia trachomatis
Spirochetes	Spiral-shaped; move by rotating internal flagella	Treponema pallidum (syphilis), Borrelia burgdorferi (Lyme disease)
Cyanobacteria	Photosynthetic; ancestors of chloroplasts	Anabaena, Nostoc
Gram-positive bacteria	Thick peptidoglycan wall; some produce antibiotics	Bacillus anthracis, Streptomyces

Major Archaeal Clades

• Extremophiles:

  • Halophiles: Thrive in high-salt environments (e.g., 10x seawater concentration).

  • Thermophiles: Thrive in high-temperature environments (e.g., hot springs, boiling water).

  • Methanogens: Produce methane as a metabolic byproduct; obligate anaerobes.

• Some archaea are mutualists in animal guts (e.g., ruminants).

Ecological and Biological Roles

Nutrient Cycling

• Prokaryotes are essential for cycling nutrients between living and nonliving systems.

• Nitrogen fixation: Conversion of atmospheric N2 to ammonia (NH3), making nitrogen available to other organisms.

• Decomposition: Breaking down organic matter and recycling nutrients.

Symbiotic Relationships

• Many prokaryotes form mutualistic associations with larger organisms (e.g., human gut microbiome).

• Some are commensal or pathogenic.

Prokaryotes and Human Health

Pathogenic Bacteria

• Some bacteria cause diseases (e.g., cholera, tuberculosis, syphilis).

• Gram-negative bacteria often have endotoxins that can trigger strong immune responses.

Antibiotics and Resistance

• Antibiotics target prokaryote-specific features (e.g., peptidoglycan synthesis, ribosomal proteins).

• Examples:

  • Penicillin: Inhibits peptidoglycan synthesis (affects Gram-positive bacteria).

  • Tetracycline: Inhibits bacterial ribosomes.

• Antibiotic resistance can arise through mutations or acquisition of resistance genes (often on plasmids).

Beneficial Uses of Bacteria

• Food production: Cheese, yogurt, and other fermented foods.

• Bioremediation: Using bacteria to break down sewage, oil spills, and other pollutants.

• Genetic engineering: Harnessing bacterial machinery to produce chemicals, medicines, and antibiotics.

Summary Table: Key Differences Between Bacteria and Archaea

Feature	Bacteria	Archaea
Cell Wall	Contains peptidoglycan	No peptidoglycan; unique molecules
Membrane Lipids	Ester-linked	Ether-linked
RNA Polymerase	One type	Several types, similar to eukaryotes
Habitat	Wide range, including moderate environments	Often extreme environments

Additional info: Some details about the diversity of prokaryotes and their evolutionary relationships were inferred from standard biology textbooks to provide a complete and coherent study guide.