Chapter 16: Phylogenetic Diversity of Bacteria

Although environmental sequencing studies reveal more than eighty bacterial phyla, only a subset has been extensively characterized in laboratory culture, with the majority of known species belonging to a few dominant groups such as Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Proteobacteria represent the largest and most metabolically diverse bacterial phylum, encompassing multiple classes including Alpha-, Beta-, Gamma-, Delta-, Epsilon-, and Zetaproteobacteria, whose members exhibit a wide range of metabolic strategies such as chemolithotrophy, chemoorganotrophy, and phototrophy as well as diverse ecological roles including symbiosis and pathogenicity. Additional major lineages include Firmicutes and Actinobacteria, both composed largely of gram-positive bacteria but distinguished by genomic GC content and physiological traits; these groups include lactic acid bacteria important in food fermentation, endospore-forming Bacillus and Clostridium species, filamentous actinomycetes that produce many antibiotics, and acid-fast Mycobacterium species responsible for diseases such as tuberculosis. The phylum Tenericutes contains wall-less bacteria such as Mycoplasma that possess reduced genomes and often live as parasites within host organisms. The chapter also surveys gram-negative phyla such as Bacteroidetes, which include important intestinal microbes specialized in polysaccharide degradation, as well as related groups including Chlamydiae, Planctomycetes, and Verrucomicrobia that display unusual cellular structures and life cycles, including obligate intracellular parasitism and compartmentalized cell organization. Additional phylogenetically distinct bacterial groups inhabit extreme environments, including hyperthermophilic phyla such as Thermotogae, Aquificae, and Thermodesulfobacteria that grow optimally at very high temperatures and often rely on chemolithotrophic metabolisms. The chapter concludes by highlighting other environmentally important bacterial lineages such as Deinococcus–Thermus, known for extreme radiation resistance and thermophily, Acidobacteria and Nitrospirae involved in soil and nitrogen cycling, and several anaerobic groups that participate in organic matter degradation. Together these diverse bacterial phyla illustrate the remarkable evolutionary breadth of the domain Bacteria and demonstrate how phylogenetic analysis integrates molecular genetics, physiology, and ecology to understand microbial diversity and evolutionary history.