Archaeal Ecology

Abstract The Archaea represent one of the three domains of life and are distinguished from the Bacteria and Eukarya both phylogenetically and biochemically. As a group, the Archaea are physiologically diverse and inhabit a wide range of ecosystems, including the most extreme environments on Earth. While traditionally thought to be restricted to just a few phyla and primarily inhabiting extreme environments, Archaea are now known to be globally distributed across many environments and of significant importance in multiple biogeochemical cycles. The Archaea also comprise a phylogenetically and metabolically diverse group of organisms in several recognised phyla and many more recently proposed phylum‐level lineages representing uncultivated organisms. The use of environmental genomics to understand uncultured archaeal diversity has recently shed light on many new potential lineages of Archaea and continues to expand and revise our understanding of Archaea in natural environments. Key Concepts The archaeal domain consists of numerous metabolically diverse phyla which are ubiquitously distributed among both extreme and mesic environments. Many proposed new archaeal phyla have been discovered with the use of environmental genomic techniques and remain uncultured. These include the proposed ‘Woesearchaeaota’, ‘Bathyarchaeota’, ‘Pacearchaeota’, ‘Thorarchaeaota’ and ‘Lokiarchaeota’ among others. Archaea inhabit the most extreme habitats known, including hypersaline, hyperacidic and high‐temperature environments. While not restricted only to extreme habitats, there is a significant amount of archaeal diversity in thermal and acidic habitats, where they are often dominant members of microbial communities there. In addition to surface hydrothermal features such as hot springs and deep‐sea vents, Archaea are also abundant in subsurface environments, an area of on going research interest. Methanogens, thus far only known from the Euryarchaeota, are responsible for the terminal step in carbon cycling (the production of CH 4 ) and are important members of anaerobic environments, including animal digestive tracts. Members of the Thaumarchaeota phylum play a critical role in global nitrogen cycling through nitrification (i.e. ammonia oxidation) in soils and oceans. Genomes of the uncultivated members of the proposed ‘Bathyarchaeota’ phylum suggest that these organisms may be key members in global carbon cycling and have been implicated in acetogenesis.