Bacterial Phylogenetic Diversity — Proteobacteria, Actinobacteria, and Deep Lineages Explained | Chapter 16 from Brock Biology of Microorganisms

Chapter 16 of Brock Biology of Microorganisms shifts the lens from ecological and metabolic diversity to evolutionary relationships, offering a panoramic view of bacterial phylogeny. By analyzing 16S rRNA gene sequences, microbiologists have uncovered more than 80 bacterial phyla. This chapter highlights the most well-studied groups—such as Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes—while also introducing lesser-known and deeply branching lineages that expand our understanding of the microbial tree of life.

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Proteobacteria: The Largest and Most Diverse Bacterial Phylum

All Proteobacteria are gram-negative and exhibit extensive metabolic diversity, encompassing phototrophs, chemolithotrophs, pathogens, and nitrogen fixers. This phylum is divided into six major classes:

• Alphaproteobacteria: Includes Rhizobium, Agrobacterium, Rickettsia, and Wolbachia; known for nitrogen fixation, plant symbiosis, and intracellular parasitism.
• Betaproteobacteria: Examples include Burkholderia and Nitrosomonas; diverse in metabolism and include pathogens and chemolithotrophs.
• Gammaproteobacteria: Contains Escherichia, Salmonella, Pseudomonas, and marine bacteria; includes enterics and sulfur oxidizers.
• Deltaproteobacteria: Home to sulfate and iron reducers like Geobacter, and predators like Bdellovibrio and Myxococcus.
• Epsilonproteobacteria: Includes Campylobacter and Helicobacter; often inhabit extreme or host-associated niches.
• Zetaproteobacteria: Represented by Mariprofundus ferrooxydans, a marine iron oxidizer.

Gram-Positive Bacteria: Firmicutes, Tenericutes, and Actinobacteria

Firmicutes (Low GC Gram-Positives)

• Includes Lactobacillus, Streptococcus, Bacillus, and Clostridium.
• Many form endospores and are important in fermentation, pathogenesis, and biotechnology.

Tenericutes

These are cell wall-less bacteria such as Mycoplasma and Spiroplasma, often parasites with the smallest genomes among free-living organisms.

Actinobacteria (High GC Gram-Positives)

• Includes Streptomyces, Corynebacterium, and Mycobacterium.
• Notable for antibiotic production, filamentous growth, and acid-fast cell walls with mycolic acids.

Bacteroidetes and the CPV Superphylum

Bacteroidetes

• Bacteroides: Key gut microbiota; specialize in breaking down complex polysaccharides.
• Cytophaga: Exhibit gliding motility and decompose cellulose and chitin.
• Flavobacterium and Sphingobacterium: Aquatic or soil bacteria with diverse metabolisms.

Chlamydiae, Planctomycetes, and Verrucomicrobia (CPV Superphylum)

• Chlamydiae: Obligate intracellular parasites like Chlamydia trachomatis; unique life cycle with elementary and reticulate bodies.
• Planctomycetes: Compartmentalized cells with internal membranes and protein stalks; some perform anaerobic ammonium oxidation (anammox).
• Verrucomicrobia: Prosthecate bacteria; includes methanotrophs such as Methylacidiphilum.

Deeply Branching and Thermophilic Lineages

• Thermotogae: Fermentative anaerobes with outer sheaths; thrive in extreme heat.
• Aquificae: Among the most thermophilic organisms known; obligate chemolithoautotrophs.
• Thermodesulfobacteria: Sulfate reducers with unique ether-linked lipids.

Other Noteworthy Phyla

• Deinococcus–Thermus: Includes Deinococcus radiodurans (radiation-resistant) and Thermus aquaticus (source of Taq polymerase).
• Acidobacteria: Acidophilic and widespread; challenging to culture.
• Nitrospirae: Includes Nitrospira (nitrifiers) and Leptospirillum (iron oxidizers).
• Fusobacteria: Anaerobic biofilm-formers found in the gut and oral microbiome.
• Fibrobacteres: Cellulose-degrading anaerobes in herbivore intestines.
• Synergistetes: Protein-degrading bacteria found in anaerobic wounds and guts.
• Deferribacteres: Anaerobes that reduce iron and nitrate; thermophilic environments.
• Chrysiogenetes: Use arsenate as a terminal electron acceptor.

Glossary of Key Concepts

• Actinomycetes: Filamentous, antibiotic-producing members of Actinobacteria.
• 16S rRNA gene: Standard marker for reconstructing bacterial phylogeny.
• Comammox: Complete ammonia oxidation by a single organism.
• Prosthecae: Cellular appendages in Planctomycetes and Verrucomicrobia.
• Mycolic acids: Long-chain lipids in the acid-fast walls of Mycobacterium.
• Endospore: Dormant, heat-resistant cell produced by Bacillus and Clostridium.
• Elementary/Reticulate Body: Infectious/living forms in the life cycle of Chlamydiae.
• Thermophiles: Microorganisms that grow optimally above 80°C.
• Sphingolipids: Specialized lipids produced by some Bacteroidetes.
• Horizontal Gene Transfer (HGT): Exchange of genes across lineages; crucial in bacterial evolution.

Conclusion: The Tree of Bacterial Life

The phylogenetic diversity of bacteria is nothing short of astounding. Chapter 16 of Brock Biology of Microorganisms presents a structured view of bacterial evolution based on molecular data, revealing not only the relationships among familiar groups but also the hidden branches of microbial life that remain poorly understood. This framework enhances our grasp of microbial ecology, evolution, and the development of modern classification systems.

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