The Prokaryotes: Domains Bacteria and Archaea – Classification, Structure, and Diversity

Chapter 11: The Prokaryotes – Domains Bacteria and Archaea

Overview of Prokaryotic Diversity

This chapter explores the classification, structure, and ecological roles of prokaryotes, focusing on the domains Bacteria and Archaea. Prokaryotes are the most abundant and diverse group of organisms on Earth, occupying a wide range of environments and playing essential roles in biogeochemical cycles, health, and disease.

Classification of Prokaryotes

Major Taxonomic Groups

• Bacteria: Includes multiple phyla, classified by Gram reaction, metabolic properties, and genetic characteristics.

• Archaea: Distinct from bacteria, often extremophiles, lacking peptidoglycan in their cell walls.

Prokaryotes are classified into phyla, classes, and genera based on genetic, morphological, and physiological traits. The following table summarizes selected groups:

Domain	Phylum	Selected Classes	Key Features
Bacteria (Gram-Negative)	Pseudomonadota (Proteobacteria)	Alpha-, Beta-, Gamma-, Delta-, Epsilonproteobacteria	Largest group; diverse metabolism
Bacteria (Gram-Negative)	Cyanobacteria	Cyanobacteria	Oxygenic photosynthesis
Bacteria (Gram-Positive)	Bacillota (Firmicutes)	Bacilli, Clostridia	Low G+C content; endospore formers
Archaea	Thermoproteota, Euryarchaeota	Thermoprotei, Methanobacteria, Halobacteria	Extremophiles: thermophiles, halophiles, methanogens

Additional info: Classification is continually updated with advances in molecular phylogenetics.

Gram-Negative Bacteria

Pseudomonadota (Proteobacteria)

The largest and most diverse group of Gram-negative bacteria, divided into five classes based on genetic and metabolic differences.

• Alphaproteobacteria: Adapted to low-nutrient environments; often have prosthecae (stalks or buds).

• Betaproteobacteria: Diverse group, includes important pathogens and environmental bacteria.

• Gammaproteobacteria: Includes many medically and ecologically significant genera.

• Deltaproteobacteria: Includes bacteria with unique predatory or sulfur-reducing lifestyles.

• Campylobacterota: Helical or curved rods, often microaerophilic.

Key Genera and Their Roles

Alphaproteobacteria

• Pelagibacter: Among the most abundant marine bacteria; crucial in the carbon cycle.

• Azospirillum: Nitrogen-fixing, associates with plant roots.

• Acetobacteraceae (Acetobacter, Gluconobacter): Convert ethanol to acetic acid.

• Rickettsia: Obligate intracellular parasites; cause spotted fevers (e.g., epidemic typhus, Rocky Mountain spotted fever).

• Ehrlichia: Tick-borne pathogens causing ehrlichiosis.

• Rhizobium and Bradyrhizobium: Nitrogen-fixing symbionts in legume roots.

• Agrobacterium: Plant pathogen causing crown gall disease by inserting a plasmid into plant cells.

• Nitrobacter and Nitrosomonas: Chemoautotrophs involved in nitrification.

Betaproteobacteria

• Spirillum: Motile freshwater bacteria with polar flagella.

• Sphaerotilus: Forms protective sheaths; found in freshwater and sewage.

• Burkholderia: Degrades diverse organic molecules; includes pathogens (e.g., B. pseudomallei).

• Bordetella: Nonmotile rods; B. pertussis causes whooping cough.

• Neisseria: Pathogens causing gonorrhea and meningococcal meningitis.

• Zoogloea: Important in wastewater treatment (activated sludge).

Gammaproteobacteria

• Acidithiobacillus: Oxidizes sulfur compounds for energy.

• Beggiatoa: Oxidizes hydrogen sulfide in aquatic sediments.

• Francisella: F. tularensis causes tularemia.

• Pseudomonas: Metabolically diverse, opportunistic pathogens; common in soil and water.

• Legionella: Found in water systems; causes legionellosis.

• Coxiella: C. burnetii causes Q fever; transmitted by aerosols or contaminated milk.

• Vibrio: Aquatic; V. cholerae causes cholera, V. parahaemolyticus causes gastroenteritis.

• Enterobacteriales (Enterics): Facultative anaerobes, ferment carbohydrates, peritrichous flagella.

• Escherichia: E. coli is an indicator of fecal contamination; some strains cause disease.

• Salmonella: Many serovars; causes foodborne illness and typhoid fever.

• Shigella: Causes bacillary dysentery.

• Klebsiella: K. pneumoniae causes pneumonia.

• Serratia: Produces red pigment; nosocomial infections.

• Proteus: Swarming motility; forms concentric rings on agar.

• Yersinia: Y. pestis causes plague; flea-borne.

• Erwinia: Plant pathogens.

Campylobacterota

• Campylobacter: Microaerophilic, curved rods; C. jejuni causes foodborne illness.

• Helicobacter: Microaerophilic, multiple flagella; causes peptic ulcers and stomach cancer.

Photosynthetic Bacteria

Photosynthetic bacteria are classified by their pigments, electron donors, and oxygen production.

Common Name	Example	Phylum	Electron Donor	Oxygenic?
Cyanobacteria	Anabaena	Cyanobacteria	H2O	Yes
Green nonsulfur bacteria	Chloroflexus	Chloroflexi	Organic compounds	No
Green sulfur bacteria	Chlorobium	Chlorobi	H2S	No
Purple nonsulfur bacteria	Rhodospirillum	Proteobacteria	Organic compounds	No
Purple sulfur bacteria	Chromatium	Proteobacteria	H2S	No

Other Gram-Negative Bacteria

• Chlamydiae: Intracellular pathogens; lack peptidoglycan; form infectious elementary bodies.

• Bacteroidota: Anaerobes; abundant in the gut and mouth; degrade complex molecules.

• Fusobacteria: Anaerobes; cause dental abscesses.

• Spirochaetes: Helical, motile via axial filaments; includes Treponema (syphilis), Borrelia (Lyme disease), Leptospira (leptospirosis).

Gram-Positive Bacteria

Classification by G+C Content

• High G+C: e.g., Streptomyces, Mycobacterium

• Low G+C: e.g., Streptococcus, Clostridium

Bacillota (Low G+C Gram-Positive Bacteria)

• Bacillus: Endospore-forming rods; includes B. anthracis (anthrax), B. cereus (food poisoning).

• Staphylococcus: Grape-like clusters; S. aureus causes wound infections, is often antibiotic-resistant.

• Streptococcus: Chains of cocci; diverse pathogens.

Domain Archaea

Diversity and Adaptations

• Halophiles: Require high salt concentrations (>25%).

• Thermophiles: Grow at temperatures >80°C.

• Acidophiles: Grow at very low pH (approaching 0).

• Methanogens: Anaerobic; produce methane; some are part of the human microbiota.

Additional info: Archaea lack peptidoglycan and have unique membrane lipids.

Microbial Diversity and Detection

Limits of Microbial Knowledge

• Many microbes cannot be cultured in the laboratory.

• Molecular techniques (e.g., PCR, metagenomics) are used to detect unculturable bacteria.

Example: Detection of environmental bacteria by sequencing 16S rRNA genes.