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

Bacteria and Archaea

Introduction

Bacteria and Archaea are two of the three domains of life, representing the prokaryotic organisms. They are highly diverse, occupy nearly every environment on Earth, and play essential roles in ecological and biological processes. This guide summarizes their characteristics, diversity, identification, metabolism, and significance to humans and ecosystems.

The Three Domains of Life

Overview of Domains

• Bacteria, Archaea, and Eukarya are the three domains of life, classified based on cellular structure and genetic differences.

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

• Eukaryotes (Eukarya) have a nucleus and organelles, and include animals, plants, fungi, and protists.

Key Differences:

• Bacteria and Archaea have DNA in a single, circular chromosome, while Eukaryotes have DNA in multiple, linear chromosomes within a nucleus.

• Prokaryotes are generally smaller, simpler, and more diverse in metabolic capabilities.

• Archaea are more closely related to Eukaryotes than to Bacteria, based on genetic and biochemical evidence.

Prokaryotic Diversity and Abundance

Distribution and Abundance

• Prokaryotes are ubiquitous, found in soil, water, extreme environments (hot springs, deep sea vents, salt flats), and within other organisms.

• There are more prokaryotic cells in and on the human body than human cells.

• Estimates suggest there are nonillions (1030) of prokaryotic cells on Earth.

Distinguishing Prokaryotes: Structure and Identification

Cell Wall Types

• Most Bacteria have a cell wall containing peptidoglycan, a polymer of sugars and amino acids.

• Gram-positive bacteria have a thick peptidoglycan layer and stain purple with Gram stain.

• Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane, staining pink/red. They are often more resistant to antibiotics.

Gram Stain: A laboratory technique used to differentiate bacterial species based on cell wall structure.

Other Cell Features

• Capsule: A polysaccharide or protein layer outside the cell wall, providing protection and aiding in attachment.

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

• Flagella: Structures for motility, allowing movement toward or away from stimuli (taxis).

• Internal membranes: Some prokaryotes have infolded membranes for metabolic functions (e.g., respiration, photosynthesis).

• Plasmids: Small, circular DNA molecules separate from the main chromosome, often carrying beneficial genes (e.g., antibiotic resistance).

Genetic Diversity in Prokaryotes

Sources of Diversity

• Rapid reproduction: Binary fission allows for quick population growth and accumulation of mutations.

• Mutation: Even with low mutation rates, rapid reproduction leads to genetic variation.

• Genetic recombination: Exchange of genetic material increases diversity.

Mechanisms of Genetic Recombination

• Transformation: Uptake of DNA from the environment.

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

• Conjugation: Direct transfer of DNA between cells via a sex pilus (one-way transfer from donor to recipient).

Nutrition and Metabolism

Energy and Carbon Sources

• Prokaryotes use diverse energy sources for ATP production:

  • Phototrophs: Use light energy (photosynthetic pigments).

  • Chemotrophs: Use chemical energy from organic or inorganic molecules (e.g., glucose, hydrogen sulfide).

• Classified by carbon source:

  • Autotrophs: Use CO2 as a carbon source.

  • Heterotrophs: Require organic compounds for carbon.

Oxygen Metabolism

• Obligate aerobes: Require oxygen for cellular respiration.

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

• Facultative anaerobes: Can survive with or without oxygen.

Nitrogen Metabolism

• All organisms need nitrogen for proteins and nucleic acids.

• Atmospheric nitrogen (N2) is unusable by most organisms.

• Nitrogen fixation: Conversion of N2 to ammonia (NH3) by certain prokaryotes (e.g., cyanobacteria, some symbiotic bacteria in plant roots).

• Some prokaryotes cooperate in colonies to perform both photosynthesis and nitrogen fixation (e.g., Anabaena with heterocysts).

Prokaryote Diversity

Bacteria

• Cyanobacteria: Formerly called blue-green algae; all perform photosynthesis and contribute to oxygen production.

• Proteobacteria: Large, diverse group; includes many pathogens and symbionts; mitochondria are thought to have evolved from this group.

Archaea

• Often found in extreme environments (extremophiles):

  • Extreme halophiles: Thrive in high-salt environments.

  • Extreme thermophiles: Thrive in very hot environments.

  • Methanogens: Produce methane as a metabolic byproduct; important in anaerobic environments.

• Archaea help us understand early Earth conditions and the evolution of life.

Prokaryotes in the Environment

Ecological Roles

• Decomposers: Break down dead organic matter, recycling nutrients.

• Nutrient cycling: Make elements like nitrogen, phosphorus, and potassium available for plant growth.

• Symbiosis: Form beneficial relationships with other organisms (e.g., bioluminescent bacteria in flashlight fish).

• Bioremediation: Used to degrade pollutants, such as oil spills.

Prokaryotes and Disease

Pathogenic Prokaryotes

• Only a small fraction of prokaryotes are pathogenic (disease-causing).

• Examples of bacterial diseases: Lyme disease (Borrelia burgdorferi), tuberculosis, strep throat.

Koch's Postulates

• Set of criteria to establish a causative link between a microbe and a disease:

  1. Microbe must be present in individuals suffering from the disease and absent from healthy individuals.

  2. Microbe must be isolated and grown in pure culture.

  3. Microbe from pure culture must cause disease when introduced into a healthy experimental animal.

  4. Microbe must be re-isolated from the experimentally infected animal and shown to be the same as the original organism.

Beneficial Prokaryotes

Positive Roles

• Most prokaryotes do not cause disease and are essential for health and the environment.

• Examples: Gut bacteria aid digestion, nitrogen-fixing bacteria support plant growth, and some are used in food production (e.g., yogurt, cheese).

Comparison of the Three Domains of Life

Table: Key Differences Among Bacteria, Archaea, and Eukarya

Characteristic	Bacteria	Archaea	Eukarya
Cell type	Prokaryotic	Prokaryotic	Eukaryotic
Cell wall	Contains peptidoglycan	No peptidoglycan	Varies; cellulose or chitin in some
Membrane lipids	Unbranched hydrocarbons	Some branched hydrocarbons	Unbranched hydrocarbons
RNA polymerase	One kind	Several kinds	Several kinds
Initiator amino acid for protein synthesis	Formyl-methionine	Methionine	Methionine
Introns in genes	Very rare	Present in some genes	Present in many genes
Response to antibiotics	Growth usually inhibited	Growth not inhibited	Growth not inhibited
Histones associated with DNA	Absent	Present in some species	Present
Chromosome structure	Circular	Circular	Linear

Review and Important Concepts

• What are the three domains of life?

• How are different types of prokaryotes identified?

• What causes the large genetic diversity in prokaryotes?

• What are the different types of metabolism found in prokaryotes?

• How are prokaryotes beneficial?

• What are some examples of beneficial prokaryotes?