Chapter 27: Bacteria and Archaea

Prokaryotes encompass two distinct domains, Bacteria and Archaea, whose structural organization, genetic mechanisms, and metabolic versatility enable them to occupy nearly every terrestrial and aquatic environment on Earth. These organisms lack membrane-bound organelles and a true nucleus, instead organizing their genetic material within a nucleoid region and maintaining rapid growth through binary fission, a form of asexual reproduction that generates genetically identical offspring with remarkable speed. A defining characteristic of prokaryotes is their capacity for horizontal gene transfer, occurring through transformation (uptake of naked deoxyribonucleic acid from the environment), transduction (transfer of genes via viral vectors), and conjugation (direct cell-to-cell transfer through a pilus), mechanisms that accelerate genetic diversity and adaptive evolution independently of vertical inheritance. Bacterial cells are enclosed by peptidoglycan-containing cell walls that provide structural support and protection, while archaeal cell walls employ distinct polysaccharide or protein compositions, reflecting their evolutionary separation from bacteria and their adaptation to extreme environments including hypersaline, thermophilic, and acidic niches where few other organisms survive. Prokaryotic metabolic diversity is extraordinary, encompassing photoautotrophs that harness light energy, chemoautotrophs that oxidize inorganic compounds, and heterotrophs that consume organic substrates; additionally, organisms demonstrate flexibility in respiration, utilizing aerobic pathways when oxygen is available and switching to anaerobic processes in its absence, with some bacteria performing nitrogen fixation to convert atmospheric nitrogen into biologically accessible forms. Archaea represent a domain fundamentally distinct from Bacteria at the molecular level, possessing unique ribosomal ribonucleic acid sequences that served as evidence for the three-domain system of classification and establishing their profound evolutionary divergence. Ecologically, prokaryotes drive essential biogeochemical cycles by decomposing organic matter, cycling nutrients, and forming critical microbiome communities within soil, water, and animal digestive systems; simultaneously, certain prokaryotic species engage in pathogenic interactions with humans, causing disease while others provide essential metabolic services supporting broader ecosystem function and stability.