The classification of life on Earth underwent a significant revision in 1977 with the discovery of the Archaea, establishing them as the third domain of life alongside Bacteria and Eukarya. Prior to this finding, these single-celled organisms were mistakenly grouped with bacteria due to their similar appearance and lack of a cell nucleus. Microbiologist Carl Woese and his colleagues used ribosomal RNA sequencing to reveal that Archaea possess a distinct evolutionary lineage, making them as genetically different from Bacteria as they are from complex organisms like plants and animals. This domain is characterized by unique features, such as ether-linked lipids in their cell membranes, which often enable survival in extreme environments. The recognition of Archaea has illuminated their pervasive and often-overlooked influence on the planet’s fundamental processes and their intimate associations within other living systems.
Global Biogeochemical Cycling
Archaea play an extensive role in the transformation and recycling of elements across the globe, fundamentally influencing the availability of nutrients in both terrestrial and aquatic ecosystems. Their metabolic diversity allows them to drive several reactions necessary for sustaining the global nitrogen and sulfur cycles. A major contribution to the nitrogen cycle comes from the Thaumarchaeota, a widespread group of archaea that are the primary ammonia oxidizers (AOA). AOA convert ammonia into nitrite through nitrification. This step is a necessary intermediate in the nitrogen cycle, making nitrogen available for plants and other microbes.
AOA are particularly dominant in the vast, nutrient-poor regions of the open ocean and in many soils, thriving at very low ammonia concentrations. They also produce less nitrous oxide, a potent greenhouse gas, compared to their bacterial counterparts. Archaea also engage in the sulfur cycle through both oxidation and reduction processes, often associated with specialized environments. Some anaerobic archaea utilize sulfate as a terminal electron acceptor, generating hydrogen sulfide. Conversely, other chemoautotrophic archaea can oxidize hydrogen sulfide, converting it first to elemental sulfur and then to sulfate.
The metabolic activities of sulfur-dependent Archaea are notable in geothermal areas and acidic environments. Certain acidophilic archaea are capable of metal leaching, where they oxidize sulfur compounds associated with metal ores, demonstrating the domain’s influence on mineral cycling.
The Unique Role of Methanogens
A distinguishing feature of the Archaea domain is the exclusive ability of methanogens to produce methane gas. Methanogenesis is a strictly anaerobic metabolic process that serves as the final step in the decomposition of organic matter in environments devoid of oxygen. These organisms convert simple compounds like carbon dioxide and hydrogen, acetate, or various methylated compounds into methane. The terminal reaction in this pathway is catalyzed by the unique enzyme methyl-coenzyme M reductase (McrA).
Methanogens flourish in anoxic niches such as deep-sea sediments, waterlogged wetlands, rice paddies, and the digestive tracts of many animals. Their activity makes them a major natural source of methane, a gas with significant environmental consequences. Methane is a potent greenhouse gas, possessing a global warming potential approximately 30 times greater than that of carbon dioxide over a 100-year period. Consequently, the metabolic output of methanogenic archaea plays an immediate role in regulating the Earth’s atmospheric temperature, particularly through production in natural wetlands and ruminant livestock.
The methane produced by methanogens does not always reach the atmosphere, however, due to the action of methane-consuming Archaea. This process, known as anaerobic oxidation of methane (AOM), is performed by archaea often in partnership with sulfate-reducing bacteria. This syntrophic relationship consumes methane in anoxic environments like marine sediments, converting it back into carbon dioxide.
Interactions with Multicellular Life
Archaea frequently engage in complex symbiotic relationships with multicellular organisms, becoming integral components of host microbiomes. In the human gut, the methanogenic species Methanobrevibacter smithii is often a dominant archaeon. This archaeon maintains a mutualistic relationship by scavenging hydrogen gas produced by other bacteria during the fermentation of dietary fiber. By consuming this hydrogen, M. smithii keeps its concentration low, which thermodynamically favors the fermentation pathways of the bacterial community. This process allows the bacteria to break down complex carbohydrates more efficiently, ultimately releasing more energy and nutrients for the host.
A similar relationship occurs in the rumen of cattle and other ruminants, where methanogens are essential for the efficient digestion of tough plant matter. In marine ecosystems, Archaea form tight associations with invertebrates such as sponges and corals. Sponges host dense and diverse communities of Archaea, including ammonia-oxidizing Thaumarchaeota. These symbiotic archaea recycle nutrients within the sponge by oxidizing the host’s waste ammonia, providing a usable nitrogen source.
Archaea also colonize the rhizosphere, the soil zone directly influenced by plant roots. Ammonia-oxidizing archaea are abundant in this zone, contributing to the nitrogen nutrition of the plant. Some archaeal species in the rhizosphere may also contribute to plant growth by influencing the synthesis of phytohormones.