Chapter 11: The Prokaryotes: Domains Bacteria and Archaea

The Prokaryotes: Domains Bacteria and Archaea introduces the use of rRNA sequencing, especially 16S rRNA, as a molecular method to classify prokaryotes and construct phylogenetic relationships. The domain Bacteria is presented first, divided into phyla such as Proteobacteria (Gram-negative), Firmicutes and Actinobacteria (Gram-positive), Cyanobacteria (photosynthetic), and others. The Proteobacteria are subdivided into classes—alpha, beta, gamma, delta, and epsilon—each associated with characteristic genera and ecological roles. Highlights include nitrogen-fixing Rhizobium, pathogenic Neisseria, facultative anaerobes like Escherichia and Salmonella, myxobacteria with social motility, and Helicobacter linked to peptic ulcers. Gram-positive bacteria are divided into Firmicutes (low G+C content, including Clostridium, Bacillus, Staphylococcus, and Streptococcus) and Actinobacteria (high G+C, such as Mycobacterium and Streptomyces, known for antibiotics and acid-fast cell walls). Cyanobacteria are recognized for oxygenic photosynthesis and ecological importance in aquatic environments, while Chlamydiae, Spirochaetes, and Bacteroidetes are covered as unique phyla with distinct pathogenic representatives. The chapter also reviews Planctomycetes and Deinococcus-Thermus, with attention to their unusual cellular features and radiation resistance. The Archaea domain is discussed in terms of its distinct evolutionary lineage and environmental niches. Key groups include extreme halophiles (e.g., Halobacterium), thermophiles (e.g., Sulfolobus), and methanogens (e.g., Methanobacterium), which are crucial in anaerobic digestion and greenhouse gas production. The structural and genetic differences between bacteria and archaea—such as cell wall composition, membrane lipids, and ribosomal RNA sequences—are emphasized. This chapter highlights the vast metabolic, structural, and ecological diversity within prokaryotic life and underscores the importance of molecular tools in uncovering relationships that traditional morphology cannot resolve.