Classification and Diversity of Prokaryotes: Bacteria and Archaea

Classification of Prokaryotes

Overview

Prokaryotes are classified into two domains: Bacteria and Archaea. Bacteria are further divided into multiple phyla based on genetic, morphological, and physiological characteristics. This section summarizes key groups of bacteria and archaea, their properties, and their medical, industrial, and ecological significance.

Gram-Negative Bacteria

Alphaproteobacteria

• Rickettsia: Obligate intracellular parasites; cause spotted fevers and typhus. Transmitted by insects and ticks. Damages blood capillaries, leading to spotted rash.

• Bartonella: Human pathogens; Bartonella henselae causes cat-scratch disease. Not intracellular.

• Brucella: Small coccobacilli; cause brucellosis. Survive phagocytosis, allowing persistence in host.

• Acetobacter and Gluconobacter: Aerobic, industrially important; convert ethanol to acetic acid (vinegar).

• Rhizobium and Bradyrhizobium: Nitrogen-fixing bacteria; form symbiotic root nodules in legumes.

• Wolbachia: Intracellular endosymbionts in insects; alter reproduction and egg development. Used in mosquito control to reduce viral transmission.

Deltaproteobacteria

• Bdellovibrio: Predatory bacterium; attacks other gram-negative bacteria by penetrating their cell wall and reproducing inside the periplasm.

Campylobacterota

• Campylobacter: Slender, helical rods; microaerophilic; cause foodborne intestinal disease (C. jejuni).

• Helicobacter: Curved rods; microaerophilic; H. pylori causes peptic ulcers and stomach cancer.

Other Gram-Negative Bacteria

• Bacteroides: Anaerobic rods; abundant in human gut; cause peritonitis after bowel perforation.

• Treponema: Spirochetes; move by axial filaments; T. pallidum causes syphilis.

• Borrelia: Spirochetes; transmitted by ticks/lice; cause relapsing fever and Lyme disease.

• Leptospira: Tightly coiled spirochetes; cause leptospirosis; transmitted via contaminated water.

Gammaproteobacteria

• Francisella: Small, pleomorphic; F. tularensis causes tularemia.

• Pseudomonas: Aerobic rods; metabolically versatile; P. aeruginosa causes opportunistic infections and is resistant to many antibiotics.

• Legionella: Grows in aquatic environments; causes Legionnaires' disease; survives in amoebae.

• Vibrio: Slightly curved rods; aquatic; V. cholerae causes cholera.

• Yersinia: Straight rods; Y. pestis causes plague; transmitted by fleas.

• Enterobacter: Straight rods; cause urinary tract and healthcare-associated infections.

• Pasteurella: Rods; animal pathogens; can infect humans via animal bites.

• Escherichia: E. coli is a common gut inhabitant; indicator of fecal contamination; causes UTIs and foodborne disease.

• Salmonella: Intestinal pathogens; cause typhoid fever and salmonellosis; many serovars.

• Shigella: Human-only pathogen; causes bacillary dysentery.

• Klebsiella: Soil/water; some fix nitrogen; K. pneumoniae causes pneumonia.

• Serratia: Red pigment; hospital contaminant; causes UTIs and respiratory infections.

• Proteus: Highly motile; swarming growth; causes UTIs and wound infections.

Betaproteobacteria

• Spirillum: Large spiral-shaped; moves by polar flagella; freshwater habitats.

• Bordetella: Rod-shaped; nonmotile; B. pertussis causes whooping cough.

• Neisseria: Diplococci; inhabit mucous membranes; N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis).

Gram-Positive Bacteria

Low G+C Gram-Positive Bacteria (Phylum Bacillota)

• Clostridium: Obligate anaerobes; endospore-forming rods; cause tetanus, botulism, gas gangrene, foodborne diarrhea.

• Bacillus: Aerobic/facultative anaerobes; endospore-forming rods; B. anthracis (anthrax), B. thuringiensis (insecticide), B. cereus (food poisoning).

• Staphylococcus: Cocci in clusters; facultative anaerobes; S. aureus causes many diseases; yellow pigment protects from sunlight.

• Lactobacillus: Aerotolerant; lactic acid producers; important in food fermentation (yogurt, sauerkraut).

• Streptococcus: Chains of cocci; complex taxonomy; pathogenic (S. pyogenes, S. agalactiae, S. pneumoniae, S. mutans); hemolytic properties used for classification.

• Enterococcus: Facultative anaerobes; hardy; cause healthcare-associated infections; highly antibiotic-resistant.

• Listeria: Facultative anaerobes; L. monocytogenes contaminates food, grows at refrigeration temperatures; dangerous in pregnancy.

Low G+C Wall-Less Bacteria (Phylum Mycoplasmatota)

• Mycoplasma: Wall-less, highly pleomorphic; smallest self-replicating organisms; M. pneumoniae causes mild pneumonia; colonies have "fried egg" appearance.

High G+C Gram-Positive Bacteria (Phylum Actinomycetota)

• General Characteristics: Pleomorphic; many grow as branching filaments (actinomycetes); resemble fungi morphologically but are prokaryotes.

• Mycobacterium: Acid-fast rods; waxy cell wall with mycolic acids; slow growth; M. tuberculosis (tuberculosis), M. leprae (leprosy).

• Nocardia: Acid-fast; forms filaments; N. asteroides causes pulmonary infection and mycetoma.

• Corynebacterium: Highly pleomorphic; C. diphtheriae causes diphtheria.

• Frankia: Nitrogen-fixing; forms nodules on alder roots.

• Streptomyces: Branching filaments; produce conidiospores; major source of antibiotics; produce geosmin (soil odor).

• Actinomyces: Branching filaments; facultative anaerobes; A. israelii causes actinomycosis (tissue destruction).

High G+C Gram-Positive Bacteria (Phylum Deinococcota)

• General Characteristics: Gram-positive; cell wall differs chemically; includes species resistant to environmental extremes.

Domain Archaea

General Characteristics

• Cell walls lack peptidoglycan.

• rRNA sequences distinct from Bacteria and Eukarya.

• Adapted to extreme environments.

Major Groups

• Thermoproteota: Thermophiles and hyperthermophiles; grow at high/extremely high temperatures.

• Euryarchaeota: Methanogens (produce methane); halophiles (require high salt concentrations).

Microbial Diversity and the Microbiome

Microbial Diversity

• Earth hosts an enormous number of microbial species (estimated at one trillion).

• Many cannot be cultivated by conventional methods.

• Molecular techniques (e.g., iChip) allow identification without culturing.

• Microorganisms are ubiquitous and inhabit diverse, dynamic ecosystems.

Microbiome in Space

• Astronauts carry their microbiome into space; spaceflight alters microbial growth and virulence.

• Microgravity and increased radiation suppress immune function and change bacterial behavior.

• Salmonella Typhimurium and Pseudomonas aeruginosa become more virulent in space.

• Bacteria form unique biofilm structures in microgravity.

• Microbiome studies on the ISS show changes in abundance and antibiotic resistance, which return to normal after return to Earth.

Summary Table: Key Bacterial Groups and Their Properties

Group	Gram Reaction	Morphology	Oxygen Requirement	Key Features/Diseases
Rickettsia	Negative	Rod/coccobacilli	Obligate intracellular	Spotted fevers, typhus
Clostridium	Positive	Rod	Obligate anaerobe	Tetanus, botulism, gas gangrene
Bacillus	Positive	Rod	Aerobic/facultative	Anthrax, insecticide, food poisoning
Staphylococcus	Positive	Cocci (clusters)	Facultative anaerobe	Skin infections, food poisoning
Streptococcus	Positive	Cocci (chains)	Facultative anaerobe	Pharyngitis, pneumonia, dental caries
Mycobacterium	Positive (acid-fast)	Rod	Aerobic	Tuberculosis, leprosy
Escherichia	Negative	Rod	Facultative anaerobe	UTIs, diarrhea, indicator organism
Salmonella	Negative	Rod	Facultative anaerobe	Typhoid fever, salmonellosis
Neisseria	Negative	Diplococci	Aerobic	Gonorrhea, meningitis
Archaea (Methanogens)	None	Varied	Anaerobic	Produce methane
Archaea (Halophiles)	None	Varied	Aerobic/anaerobic	Require high salt

Key Terms and Definitions

• Gram Reaction: Laboratory staining technique distinguishing bacteria by cell wall structure (Gram-positive: thick peptidoglycan; Gram-negative: thin peptidoglycan and outer membrane).

• Endospore: Highly resistant, dormant structure formed by some bacteria for survival under adverse conditions.

• Obligate Intracellular Parasite: Organism that can only reproduce inside host cells.

• Facultative Anaerobe: Organism that can grow with or without oxygen.

• Actinomycetes: Filamentous, branching bacteria resembling fungi; important in soil and antibiotic production.

• Acid-Fast: Bacteria with waxy cell walls (mycolic acids) that resist decolorization by acid alcohol after staining.

• Microbiome: The collection of microorganisms living in a particular environment, such as the human body.

• Biofilm: Structured community of microorganisms attached to a surface and embedded in a self-produced matrix.

Additional info:

• Many bacteria are classified by their G+C content (guanine-cytosine content in DNA), which affects their genetic and physiological properties.

• Beta-hemolytic and alpha-hemolytic streptococci are distinguished by their effects on blood agar: beta-hemolysis (clear zone), alpha-hemolysis (green zone).

• Microbial diversity is continually expanding as new identification methods (e.g., molecular sequencing) reveal previously uncultivable species.

• Archaea are not known to cause disease in humans but play important roles in environmental processes (e.g., methane production, salt tolerance).