Chapter 20: Archaea – Structure, Function & Ecological Roles

The domain Archaea encompasses a remarkably diverse group of prokaryotic microbes exhibiting unique physiological characteristics, thriving not only in extreme environments, such as high heat, salt, or acidity (extremophiles), but also in mundane habitats like marine plankton and the human digestive tract. Archaeal taxonomy recognizes three main phyla—Euryarchaeota, Crenarchaeota, and Thaumarchaeota—though numerous additional phyla, including the evolutionarily significant Asgard archaea, have been proposed based on metagenomic evidence. Metabolism in Archaea is unique; autotrophic species fix carbon using the energetically favorable reductive acetyl-CoA pathway (used by methanogens) or the HP/HB and DC/HB cycles, while chemoorganotrophs employ modified Embden-Meyerhof and Entner-Doudoroff pathways that often differ from bacterial versions in net ATP yield. The phylum Euryarchaeota includes the strictly anaerobic methanogens, which are vital for energy production and global carbon cycling by generating methane using unique cofactors, as well as anaerobic methanotrophs (ANME) that oxidize methane by running this pathway in reverse, often symbiotically with sulfate-reducing bacteria. Euryarchaeota also contains the extreme halophiles (Haloarchaea) that require high concentrations of NaCl, coping with osmotic stress through a "salt-in" mechanism and sometimes generating energy via light-driven proton pumping using archaerhodopsin. Within the TACK superphylum, Crenarchaeota often consists of sulfur-dependent thermophiles and thermoacidophiles, while Thaumarchaeota comprises mesophilic ammonia oxidizers crucial for global nitrogen cycling, identified partly by the presence of the lipid thaumarchaeol.