Chapter 11: The Prokaryotes – Domains Bacteria and Archaea

Overview of Prokaryotic Classification

This chapter explores the diversity, classification, and unique characteristics of prokaryotes, focusing on the domains Bacteria and Archaea. Prokaryotes are classified based on genetic, biochemical, and morphological features, with significant medical, ecological, and industrial importance.

• Domains: Bacteria and Archaea

• Major Groups: Gram-negative and Gram-positive bacteria, and Archaea

• Classification: Based on phyla, classes, and physiological traits

Table: Classification of Selected Prokaryotes

Additional info: Table summarizes main taxonomic groups and their notable features.

Gram-Negative Bacteria: Phylum Pseudomonadota (Proteobacteria)

General Features

• Gram-negative cell wall structure

• Chemoheterotrophic metabolism

• Largest and most diverse bacterial phylum

• Divided into five classes: Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria

Alphaproteobacteria

Alphaproteobacteria are notable for their ecological roles and associations with plants and animals. Many are oligotrophic, thriving in low-nutrient environments.

• Pelagibacter: Extremely abundant in oceans; important in the carbon cycle.

• Azospirillum: Nitrogen-fixing bacteria associated with plant roots.

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

• Rickettsia: Obligate intracellular parasites causing spotted fevers; transmitted by arthropods.

• Ehrlichia: Tick-borne pathogens causing ehrlichiosis.

• Caulobacter and Hyphomicrobium: Aquatic bacteria with stalks or hyphae; reproduce by budding.

• Rhizobium and Bradyrhizobium: Nitrogen-fixing symbionts of legumes (rhizobia).

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

• Bartonella: Human pathogen; B. henselae causes cat-scratch disease.

• Brucella: Obligate parasite of mammals; causes brucellosis.

Betaproteobacteria

Betaproteobacteria include important environmental and pathogenic genera.

• Spirillum: Freshwater bacteria with polar flagella.

• Sphaerotilus: Sheathed bacteria found in freshwater and sewage; aid in nutrient gathering.

• Burkholderia: Metabolically versatile; B. cepacia degrades organic molecules; B. pseudomallei causes melioidosis.

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

• Neisseria: Gram-negative cocci; N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis).

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

Gammaproteobacteria

This class contains many medically and environmentally significant bacteria.

• Acidithiobacillus: Sulfur-oxidizing bacteria.

• Thiotrichales (Beggiatoa): Oxidize hydrogen sulfide for energy.

• Francisella: F. tularensis causes tularemia.

• Pseudomonadales (Pseudomonas): Opportunistic pathogens, highly versatile, form biofilms, and are antibiotic-resistant.

• Azotobacter, Azomonas: Nitrogen-fixing bacteria.

• Moraxella: M. lacunata causes conjunctivitis.

• Acinetobacter: A. baumannii is a respiratory pathogen, often antibiotic-resistant.

• Legionellales (Legionella, Coxiella): Legionella causes legionellosis; Coxiella burnetii causes Q fever.

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

• Enterobacteriales (Enterics): Facultative anaerobes inhabiting the intestinal tract; ferment carbohydrates; peritrichous flagella.

• Key genera: Escherichia (E. coli), Salmonella, Shigella, Klebsiella, Serratia, Proteus, Yersinia, Erwinia, Enterobacter, Cronobacter

Deltaproteobacteria

Deltaproteobacteria include bacteria with unique predatory or sulfur-reducing lifestyles.

• Bdellovibrio: Predatory bacteria that attack other Gram-negative bacteria.

• Desulfovibrionales: Use sulfate as a terminal electron acceptor; found in anaerobic environments.

• Myxococcales: Gliding bacteria that form fruiting bodies and myxospores.

Campylobacterota

Campylobacterota are slender, helical, or curved Gram-negative rods, often microaerophilic.

• Campylobacter: C. jejuni causes foodborne intestinal disease.

• Helicobacter: H. pylori causes peptic ulcers and stomach cancer.

Cyanobacteria (Oxygenic Photosynthetic Bacteria)

Cyanobacteria perform oxygenic photosynthesis, contributing significantly to Earth's oxygen supply. Many have specialized cells called heterocysts for nitrogen fixation.

• Unicellular, colonial, and filamentous forms

• Gas vesicles for buoyancy

• Major contributors to atmospheric oxygen

Table: Selected Characteristics of Photosynthesizing Bacteria

Chlamydiae

Chlamydiae are obligate intracellular bacteria lacking peptidoglycan in their cell walls. They have a unique developmental cycle involving infectious elementary bodies and replicative reticulate bodies.

• Chlamydia trachomatis: Causes trachoma and urethritis.

• Chlamydophila psittaci: Causes respiratory psittacosis.

• Chlamydophila pneumoniae: Causes mild pneumonia in young adults.

Spirochaetes

Spirochaetes are coiled bacteria that move via axial filaments, producing a corkscrew motion.

• Treponema pallidum: Causes syphilis.

• Borrelia: Causes relapsing fever and Lyme disease.

• Leptospira: Excreted in animal urine; causes leptospirosis.

Gram-Positive Bacteria

Classification by G+C Content

• High G+C Gram-Positive Bacteria: Actinomycetota (e.g., Streptomyces, Mycobacterium)

• Low G+C Gram-Positive Bacteria: Bacillota (e.g., Streptococcus, Clostridium)

Bacillota (Low G+C Gram-Positive Bacteria)

• Clostridiales (Clostridium, Clostridioides): Endospore-forming obligate anaerobes; cause tetanus, botulism, gas gangrene, and C. difficile infections.

• Bacillales (Bacillus, Staphylococcus): Endospore-forming rods and cocci; B. anthracis (anthrax), B. thuringiensis (insect pathogen), B. cereus (food poisoning), S. aureus (wound infections, enterotoxin production).

• Lactobacillales (Lactobacillus, Streptococcus, Enterococcus, Listeria): Aerotolerant anaerobes; important in food production and as pathogens.

Actinomycetota (High G+C Gram-Positive Bacteria)

• Mycobacterium: Waxy, acid-fast cell wall; causes tuberculosis and leprosy.

• Nocardia: Acid-fast, filamentous; causes pulmonary infections.

• Corynebacterium: C. diphtheriae causes diphtheria.

• Streptomyces: Soil bacteria producing antibiotics; filamentous morphology.

• Actinomyces: Filamentous, found in mouth and throat.

Deinococcota (High G+C Gram-Positive Bacteria)

• Deinococcus radiodurans: Extremely radiation-resistant due to unique DNA repair mechanisms.

• Thermus aquaticus: Thermophilic; source of Taq polymerase for PCR.

Domain Archaea

General Features

• Lack peptidoglycan in cell walls

• Often extremophiles (halophiles, thermophiles, acidophiles)

• Methanogens produce methane anaerobically; some are part of human microbiota

Microbial Diversity

Microbial diversity is vast, with millions of species yet to be discovered. Bacteria vary greatly in size, genome content, and ecological roles. Many cannot be cultured in the laboratory, limiting our understanding of their biology.

• Size range: From nanobacteria (0.02–0.08 μm) to large bacteria like Thiomargarita magnifica (up to 1 cm)

• Genome size: Carsonella ruddii has one of the smallest known genomes (182 genes)

• Environmental diversity: PCR studies reveal thousands of species per gram of soil

Additional info: Many bacteria are part of complex food webs and require other microbes for growth.