16

Brock Biology of Microorganisms: Chapter 16 - Phylogenetic Diversity of Bacteria

Overview of Phylogenetic Diversity

• Major Lineages of Bacteria

  • More than 90 percent of characterized genera and species belong to four primary phyla:

  • Proteobacteria

  • Actinobacteria

  • Firmicutes

  • Bacteroidetes

Proteobacteria

General Characteristics

• Proteobacteria

  • Largest and most metabolically diverse phylum

  • Majority of significant bacteria in medical, industrial, and agricultural contexts

  • All members are gram-negative.

Subdivisions of Proteobacteria

1. Alphaproteobacteria

2. Betaproteobacteria

3. Gammaproteobacteria

   • Enterobacteriales

   • Pseudomonadales

   • Vibrionales

4. Deltaproteobacteria

5. Epsilonproteobacteria

6. Zetaproteobacteria

Alphaproteobacteria

Overview

• Nearly 1000 described species

• Most are obligate or facultative aerobes

• Many are oligotrophic (able to grow in low-nutrient environments)

• Ten orders with many species concentrated in six major orders:

  • Rhizobiales

  • Rickettsiales

  • Rhodobacterales

  • Rhodospirillales

  • Caulobacterales

  • Sphingomonadales

Rhizobiales Order

• Key Genera: Bartonella, Methylobacterium, Pelagibacter, Rhizobium, Agrobacterium

  • Largest and most metabolically diverse order

  • Contains various metabolic types: phototrophs, chemolithotrophs, nitrogen-fixing bacteria, and pathogens.

  • Agrobacterium tumefaciens induces crown gall disease and is closely related to related rhizobia (genera that fix nitrogen symbiotically).

  • Does not form nodules; genomic markers suggest gall formation genes are unrelated to nitrogen-fixing genes but reside on a plasmid.

Specific Genera from Rhizobiales

• Methylobacterium

  • Known as “pink-pigmented facultative methylotrophs,” found across various environments including aquatic systems, toilets, and baths.

• Bartonella

  • Intracellular human pathogens transmitted through arthropods.

• Pelagibacter

  • Species P. ubique is oligotrophic, aerobic, chemoorganotrophic; believed to be the most abundant bacterial species on Earth, thriving in ocean photic zones.

Rickettsiales Order

• Key Genera: Rickettsia, Wolbachia

  • Obligate intracellular parasites or mutualists associated mostly with arthropods.

• Rickettsia

  • Causes diseases like Typhus and Rocky Mountain spotted fever; transmitted via ticks, fleas, lice, and mites; dependent on metabolite uptake from the host.

• Wolbachia

  • Parasites of arthropods and some nematodes; can induce parthenogenesis (development of unfertilized eggs), conditional male mortality, and feminization of males.

Other Groups of Alphaproteobacteria

• Key Genera: Rhodobacter, Acetobacter, Caulobacter, Sphingomonas

  • Rhodobacterales and Rhodospirillales

  • Includes purple nonsulfur bacteria, aerobic anoxygenic phototrophs, nitrogen-fixing bacteria, denitrifiers, and magnetotactic bacteria.

  • Caulobacterales

  • Oligotrophic and strictly aerobic; form prosthecae and stalks, many divide asymmetrically, e.g., Caulobacter.

  • Sphingomonadales

  • Diverse group of aerobic and facultatively aerobic chemoorganotrophs; notable for the ability to metabolize organic contaminants, contributing to bioremediation efforts.

Betaproteobacteria

General Overview

• Approximately 500 described species; third-largest class of Proteobacteria.

• Exhibits significant functional diversity.

• Six major orders:

  • Burkholderiales

  • Hydrogenophilales

  • Methylophilales

  • Neisseriales

  • Nitrosomonadales

  • Rhodocyclales

Burkholderiales Order

• Key Genus: Burkholderia

  • Diverse metabolic and ecological characteristics.

  • Strict respiratory chemoorganotrophs, all aerobic, some capable of anaerobic growth and nitrogen fixation.

  • Burkholderia cepacia

  • Soil bacterium, opportunistic pathogen; possess antifungal and antinematodal properties; involved in nosocomial infections in humans.

Neisseriales Order

• Key Genera: Chromobacterium, Neisseria

  • Diverse group of chemoorganotrophs.

• Neisseria Genera

  • Commonly found on animals; pathogenic species include N. meningitides and N. gonorrhoeae; always cocci in shape.

• Chromobacterium

  • Rod-shaped, facultative aerobe; some species like C. violaceum produce the antimicrobial pigment violacein.

Gammaproteobacteria

Enterobacteriales

Key Characteristics

• Comprising key genera: Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, Serratia, Shigella.

• Largest and most diverse class of Proteobacteria with significant ecological and metabolic diversity.

Enteric Bacteria Characteristics

• Enterobacteriales are a relatively homogeneous phylogenetic group within Gammaproteobacteria.

  • Traits: facultative aerobic, gram-negative, nonsporulating rods; flagella often peritrichous.

  • Oxidase-negative and catalase-positive; relatively simple nutrient requirements; capable of fermenting sugars.

  • Includes many pathogens and industrially relevant bacteria such as Escherichia coli.

Fermentation Patterns in Enteric Bacteria

• Two broad fermentation types based on end products from glucose fermentation:

  • Mixed-Acid Fermentation: Produces significant amounts of acetic, lactic, and succinic acids, along with ethanol.

  • Genera: Escherichia, Salmonella, Shigella, Citrobacter, Proteus, Yersinia.

  • 2,3-butanediol Fermentation: Major products include butanediol and ethanol; minor acids produced.

  • Genera: Enterobacter, Klebsiella, Erwinia, Serratia.

Specific Genera in Mixed-Acid Fermentation

• Escherichia

  • Universal inhabitants of the intestinal tract, synthesizing vitamins K for their hosts; includes pathogenic strains causing gastrointestinal infections.

• Salmonella

  • Pathogenic, linked to typhoid fever and gastroenteritis; found in various animal hosts.

• Shigella

  • Typically pathogenic causing bacillary dysentery.

• Proteus

  • Notable for motility and urease production; contributing to urinary tract infections.

Butanediol Fermenters

• Genera: Enterobacter, Klebsiella, Serratia

  • Species more closely related to each other than mixed-acid fermenters.

• Enterobacter aerogenes

  • Commonly found in various environments including water and sewage; may cause urinary tract infections.

• Klebsiella pneumoniae

  • Found mainly in soil and water; sometimes pathogenic.

• Serratia marcescens

  • Capable of producing red pigments and associated with various infections.

Pseudomonadales and Vibrionales

Pseudomonadales

• Key Genera: Aliivibrio, Pseudomonas, Vibrio

  • Aerobic respiratory chemoorganotrophs; variable metabolic capacities; some can respire anaerobically.

• Genera like Pseudomonas aeruginosa are opportunistic pathogens linked to urinary and respiratory diseases, while others act as plant pathogens.

Vibrionales

• Facultatively aerobic and often pathogenic; genera include Vibrio and Aliivibrio.

  • Vibrio cholera

  • Causes cholera in humans, primarily affecting water systems, not other hosts.

  • Vibrio parahaemolyticus

  • Causes gastroenteritis, found in aquatic environments.

Deltaproteobacteria and Epsilonproteobacteria

Deltaproteobacteria

• Predominantly associated with sulfate-reducing, sulfur-reducing, and as bacterial predators.

• Key Genera: Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter, Syntrophobacter.

  • Active in a variety of metabolic processes including iron and sulfur reduction.

Epsilonproteobacteria

• Key Genera: Campylobacter, Helicobacter

  • Gram-negative, oxidase-positive, motile spirilla; many species are pathogenic.

• Campylobacter jejuni

  • Known for acute gastroenteritis causing bloody diarrhea.

• Helicobacter pylori

  • Linked to chronic gastritis and peptic ulcers; capable of colonizing the human stomach.

Sulfur-Metabolizing Epsilonproteobacteria

• Ubiquitous in sulfur-rich environments; commonly found in deep-sea hydrothermal vents and sediments.

• Exhibit chemolithotrophy, utilizing inorganic compounds as electron donors, contributing to sulfur cycling, critical for ecosystems reliant on sulfur.