[6] Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation.

Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas.

[9] Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example.

Instead they are often mutualists or commensals, such as the methanogens (methane-producing strains) that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers facilitate digestion.

Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.

Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing.

To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains known as the three-domain system: the Eukarya, the Bacteria and the Archaea,[2] in what is now known as the Woesian Revolution.

[19] This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes.

[24] A new phylum "Korarchaeota" has also been proposed, containing a small group of unusual thermophilic species sharing features of both the main phyla, but most closely related to the Thermoproteota.

[25][26] Other detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006[27] and are some of the smallest organisms known.

kingdom Nanobdellati) was proposed to group "Nanoarchaeota", "Nanohaloarchaeota", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising "Micrarchaeota" and "Parvarchaeota"), and other similar archaea.

This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities.

[31][3] According to Tom A. Williams et al. 2017,[32] Castelle & Banfield (2018)[33] and GTDB release 09-RS220 (24 April 2024):[34][35][36] "Altarchaeales" "Diapherotrites" "Micrarchaeota" "Aenigmarchaeota" "Nanohaloarchaeota" "Nanoarchaeota" "Pavarchaeota" "Mamarchaeota" "Woesarchaeota" "Pacearchaeota" Thermococci Pyrococci Methanococci Methanobacteria Methanopyri Archaeoglobi Methanocellales Methanosarcinales Methanomicrobiales Halobacteria Thermoplasmatales Methanomassiliicoccales Aciduliprofundum boonei Thermoplasma volcanium "Korarchaeota" Thermoproteota "Aigarchaeota" "Geoarchaeota" Nitrososphaerota "Bathyarchaeota" "Odinarchaeota" "Thorarchaeota" "Lokiarchaeota" "Helarchaeota"[37] "Heimdallarchaeota" Eukaryota "Undinarchaeota" "Huberarchaeaota" "Aenigmarchaeota" "Nanohalarchaeota" Nanobdellota "Altarchaeota" "Iainarchaeota" "Micrarchaeota" "Methanococcia" "Hadarchaeia" Thermococci "Hydrothermarchaeia" "Methanopyria" "Methanobacteriia" "Izemarchaea" (MBG-D, E2) "Poseidoniia" (MGII & MGIII) "Thermoplasmatia" "Methanomicrobia" "Methanoliparia" "Archaeoglobia" "Syntropharchaeia" Methanocellia Methanosarcinia Methanonatronarchaeia Halobacteria "Thorarchaeia" (MBG-B) "Njordarchaeia" "Sifarchaeia" "Wukongarchaeia" "Heimdallarchaeia" (inc. Eukaryota) "Odinarchaeia" "Jordarchaeia" "Baldrarchaeia" "Hermodarchaeia" "Promethearchaeia"

[59] Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago,[60] though such data have since been questioned.

[63] Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.

Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations.

[81] Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer[82] and usually contain a thick sacculus (exoskeleton) of varying chemical composition.

[90] This proposal is also supported by other work investigating protein structural relationships[91] and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.

[99] A lineage of archaea discovered in 2015, Lokiarchaeum (of the proposed new phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time.

[107] Other morphologies in the Thermoproteota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.

[115] Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration.

[128] Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes.

The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.

Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses.

[173] While the reproductive cycles and genomic mechanisms of archaea-specific species may be similar to other viruses, they bear unique characteristics that were specifically developed due to the morphology of host cells they infect.

Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing.

[199] Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well.

[204] Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.

[213] In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes, and sewage-treatment works.

In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey.