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

Bacteria and Archaea

Overview

Bacteria and Archaea are two of the three domains of life, representing the prokaryotic organisms. They are highly diverse, ancient, and play essential roles in ecosystems and human health. This guide summarizes their characteristics, diversity, metabolism, and significance.

The Three Domains of Life

Characteristics of Domains

• Bacteria, Archaea, and Eukarya are the three domains.

• Most members of Bacteria and Archaea are unicellular prokaryotes (no membrane-bound organelles, DNA not in nucleus).

• Distinguished by types of molecules in membranes/cell walls and cellular processes.

Prokaryote vs. Eukaryote:

• Prokaryotes: DNA in a single circular chromosome, no nucleus.

• Eukaryotes: DNA in several chromosomes, inside a nucleus.

Table: Comparison of the Three Domains of Life

Characteristic	Bacteria	Archaea	Eukarya
Nuclear envelope	Absent	Absent	Present
Membrane-bound organelles	Absent	Absent	Present
Peptidoglycan in cell wall	Present	Absent	Absent
Membrane lipids	Unbranched hydrocarbons	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
Response to antibiotics streptomycin and chloramphenicol	Growth usually inhibited	Growth not inhibited	Growth not inhibited
Histones associated with DNA	Absent	Present in some species	Present
Circular chromosome	Present	Present	Absent
Growth at temperatures >100°C	Some species	Some species	No

Prokaryotic Diversity and Abundance

Numbers and Distribution

• Only a small fraction of Bacteria and Archaea have been described; millions likely exist.

• Estimated 5 × 1030 prokaryotic cells living on Earth now.

• Prokaryotes live almost everywhere, including extreme environments (deep Earth, Antarctic ice).

• More prokaryotic cells than human cells in/on the human body.

Distinguishing Different Prokaryotes

Morphological Diversity

• Prokaryotes vary in size, shape, and motility.

• Bacterial cell walls are classified as Gram-positive or Gram-negative based on Gram stain.

Gram-Positive vs. Gram-Negative Bacteria

• Gram-positive: Appear purple, have thick peptidoglycan layer.

• Gram-negative: Appear pink, thin peptidoglycan layer, outer phospholipid bilayer.

• Many antibiotics (e.g., penicillin) target peptidoglycan; Gram-negative bacteria are more resistant due to their outer membrane.

Other Cell Features and Structures

Cell Defenses

• Capsule: Polysaccharide or protein layer that allows adherence and protection.

• Endospore: Inactive, highly stable structure that allows survival in harsh conditions.

• Fimbriae: Hair-like structures that help cells stick to surfaces or each other (similar to sex pili).

Motility

• Many prokaryotes exhibit taxis (directed movement toward/away from stimuli).

• Most use flagella for movement; prokaryotic and eukaryotic flagella are analogous, not homologous.

• Motility proteins are often modified from other cellular structures.

Internal Cell Structure

Specialized Membranes

• Prokaryotes lack complex internal organization but may have infolded membranes for metabolic functions (e.g., respiration, photosynthesis).

DNA Organization

• Prokaryotes have less DNA than eukaryotes.

• DNA is organized in a single circular chromosome and additional small rings called plasmids.

• Chromosome is located in the nucleoid region, not surrounded by a membrane.

Genetic Diversity in Prokaryotes

Factors Contributing to Diversity

• Rapid reproduction: Binary fission every 1-3 hours produces clones.

• Mutation: High reproduction rates lead to many mutations.

• Genetic recombination: DNA from two sources is combined.

Genetic Recombination Mechanisms

• Transformation: Uptake of DNA from the environment.

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

• Conjugation: DNA transfer between cells via sex pilus (one-way transfer).

Nutrition and Metabolism

Energy Sources for ATP Production

• Light (photosynthetic pigments)

• Organic molecules (e.g., glucose)

• Inorganic molecules (e.g., hydrogen sulfide, iron)

Prokaryotes can be autotrophs (make their own food) or heterotrophs (consume organic compounds).

Table: Types of Nutrition in Prokaryotes

Source of Energy	Source of Carbon	Type
Light	CO2	Photoautotroph
Light	Organic compounds	Photoheterotroph
Chemicals (organic)	CO2	Chemoautotroph
Chemicals (organic)	Organic compounds	Chemoheterotroph
Chemicals (inorganic)	CO2	Chemolithoautotroph
Chemicals (inorganic)	Organic compounds	Chemolithoheterotroph

Additional info: Only two of these nutritional types are found in eukaryotes; all six are found in prokaryotes.

Oxygen Metabolism

Types of Respiration

• Cyanobacteria were the first organisms to perform photosynthesis that produced O2.

• Obligate anaerobes: Poisoned by O2; use fermentation or anaerobic respiration.

• Obligate aerobes: Require O2 for respiration.

• Facultative anaerobes: Can use O2 or not.

ATP Yield:

• Aerobic respiration: Yields 32 ATP per glucose.

• Fermentation: Yields 2 ATP per glucose.

Nitrogen Metabolism

Importance and Fixation

• Nitrogen is required for proteins and DNA.

• Most atmospheric nitrogen (N2) is unusable by eukaryotes.

• Nitrogen fixation is performed by certain prokaryotes (e.g., cyanobacteria, bacteria associated with plant roots).

• Anabaena species cooperate to photosynthesize and fix nitrogen using specialized cells called heterocysts.

Prokaryote Diversity

Bacteria

• Monophyletic group (descended from a common ancestor).

• Cyanobacteria (formerly blue-green algae): All perform photosynthesis.

• α-proteobacteria: May have given rise to mitochondria.

Archaea

• Live in virtually all habitats, including extreme environments.

• No known parasitic species.

• More closely related to Eukaryotes than to Bacteria.

Extremophiles

• Extreme halophiles: Thrive in highly saline environments.

• Extreme thermophiles: Thrive in very hot environments.

• Methanogens: Release methane as a metabolic byproduct.

Additional info: Studying extremophiles may help us understand the origins of life on Earth.

Prokaryotes in the Environment

Ecological Roles

• Some are decomposers (chemoheterotrophic), breaking down dead organic matter.

• Prokaryotes make nitrogen, phosphorus, and potassium more available for plant growth.

• Can form symbioses with other organisms (e.g., bioluminescent bacteria in flashlight fish).

• Used in bioremediation to degrade pollutants (e.g., oil spills).

Prokaryotes and Disease

Pathogenic Prokaryotes

• Some prokaryotes are human pathogens, but only a small fraction are pathogenic.

• Examples include Streptococcus pyogenes, Staphylococcus aureus, Clostridium botulinum, Borrelia burgdorferi (causes Lyme disease).

• Diseases caused by bacteria include food poisoning, flesh-eating disease, and Lyme disease.

Table: Examples of Pathogenic Bacteria

Species	Tissues Affected	Disease
Clostridium botulinum	Gastrointestinal tract, nervous system	Food poisoning (botulism)
Streptococcus pyogenes	Skin, respiratory tract	Flesh-eating disease, strep throat
Borrelia burgdorferi	Blood, skin	Lyme disease
Staphylococcus aureus	Skin, wounds	Abscesses, toxic shock syndrome
Escherichia coli	Gastrointestinal tract	Food poisoning
Additional info: Other species may cause pneumonia, plague, and other diseases.

Koch's Postulates

Establishing Disease Causation

• Microbe must be present in diseased individuals and absent from healthy ones.

• Organism must be isolated and grown in pure culture.

• Pure culture injected into healthy animal should cause disease symptoms.

• Organism should be re-isolated from diseased animal and grown in pure culture.

• Microbe must be demonstrated to be the same as the original organism.

Koch's postulates confirm causative links between specific infectious diseases and specific microbes.

Review/Important Concepts

• What are the three domains of life and their characteristics?

• How are different types of prokaryotes identified?

• What causes large genetic diversity in prokaryotes?

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

• Are all prokaryotes beneficial? Do some cause diseases in humans?

• If they don't cause disease, what are some examples of beneficial prokaryotes?