View source for Archaea

{{Short description|Domain of organisms}}
{{Pp-move}}
{{Redirect|Archea|the geologic time period|Archaean (disambiguation){{!}}Archaean|the rhythm game|Arcaea|text=For other uses, see [[Archaea (disambiguation)]].}}{{Featured article}}
{{Use dmy dates|date=June 2020}}
{{Automatic taxobox
| fossil_range = {{long fossil range|3420|0}} [[Paleoarchean]] – present
| image = Archaea.png
| image_caption = Composite image to illustrate the morphological diversity of Archaea. Left column, from top to bottom: ''[[w:Methanosarcina barkeri|Methanosarcina barkeri]]''; [[w:Ignicoccus|''Ignicoccus hospitalis'']] with two smaller ''[[w:Nanoarchaeum equitans|Nanoarchaeum equitans]]''; an [[w:Archaeal Richmond Mine acidophilic nanoorganisms|Archaeal Richmond Mine acidophilic nanoorganism]] (ARMAN); ''[[w:Haloquadratum walsbyi|Haloquadratum walsbyi]]''. Right column, from top to bottom: ''[[w:Methanohalophilus mahii|Methanohalophilus mahii]]''; an artist's rendering of ''[[w:Pyrococcus furiosus|Pyrococcus furiosus]]''; a model of ''[[w:Promethearchaeum syntrophicum|Promethearchaeum syntrophicum]]''; ''[[w:Halobacterium|Halobacterium]]'' species NRC-1.
| taxon = Archaea
| authority = [[Carl Woese|Woese]] ''et al.'' 2024<ref name="valid-dom-kingdom">{{Cite journal |last1=Göker |first1=Markus |last2=Oren |first2=Aharon |title=Valid publication of names of two domains and seven kingdoms of prokaryotes |journal=International Journal of Systematic and Evolutionary Microbiology |date=22 January 2024 |volume=74 |issue=1 |doi=10.1099/ijsem.0.006242|pmid=38252124 |doi-access=free }} &ndash; this article represents the valid publication of the name Archaea. Although Woese proposed the name in 1990, the name was not valid until this article from 2024, hence the date.</ref>
| type_genus = ''[[Methanobacterium]]''
| type_genus_authority = Kluyver and van Niel 1936 (Approved Lists 1980)<ref name=":1" />
| subdivision_ranks = Kingdoms
| subdivision_ref = <ref name=Petitjean>{{Cite journal |vauthors=Petitjean C, Deschamps P, López-García P, Moreira D |title=Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota |journal=Genome Biology and Evolution |volume=7 |issue=1 |pages=191–204 |date=December 2014 |pmid=25527841 |pmc=4316627 |doi=10.1093/gbe/evu274}}</ref><ref name="valid-dom-kingdom"/><ref name=":1" />
| subdivision = * [[Nanobdellati]] (monophyletic?)
* [[Methanobacteriati]] (monophyletic?)
*'''[[Proteoarchaeota]]'''
** [[Asgard (Archaea)|Promethearchaeati]] (cladistically includes eukaryotes)
** [[Thermoproteati]] (monophyletic?)
And see [[#Prokaryotic phyla|text]]
| synonyms = * "Archaebacteria" <small>Woese & Fox 1977</small>
* "Archaeobacteria" <small>Murray 1988</small>
* "Mendocutes" <small>Gibbons & Murray 1978</small>
* "Mendosicutes" <small>Murray 1984</small>
* "Metabacteria" <small>Hori and Osawa 1979</small>
* "Neomura" <small>Cavalier-Smith 2002</small>
* "Archaebiota" <small>Luketa 2012</small>
* "Arkarya" <small>Forterre 2015</small>
}}

'''Archaea''' ({{IPAc-en|audio=en-us-Archaea.ogg|ɑr|ˈ|k|iː|ə}} {{respell|ar|KEE|ə}}) is a [[Domain (biology)|domain]] of [[organism]]s. Traditionally, Archaea only included its [[Prokaryote|prokaryotic]] members, but this has since been found to be [[paraphyletic]], as [[eukaryote]]s are known to have evolved from archaea. Even though the domain Archaea [[Cladistics|cladistically]] includes eukaryotes, the term "archaea" ({{singular}}: archaeon {{IPAc-en|ɑr|ˈ|k|iː|Q|n}} {{respell|ar|KEE|on}}, from the Greek "ἀρχαῖον", which means ancient) in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially [[Taxonomy (biology)|classified]] as [[bacteria]], receiving the name archaebacteria ({{IPAc-en|ˌ|ɑ:r|k|i|b|æ|k|ˈ|t|ɪər|i|ə}}, in the Archaebacteria [[Kingdom (biology)|kingdom]]), but this term has fallen out of use.<ref>{{cite journal |vauthors=Pace NR |title=Time for a change |journal=Nature |volume=441 |issue=7091 |pages=289 |date=May 2006 |pmid=16710401 |doi=10.1038/441289a |bibcode=2006Natur.441..289P |s2cid=4431143 |doi-access=free }}</ref> Archaeal cells have unique properties separating them from [[Bacteria]] and [[Eukaryote|Eukaryota]]. <!-- This paragraph should state what the "unique properties" are. -->Archaea are further divided into multiple recognized [[phylum|phyla]]. Classification is difficult because most have not been [[Isolation (microbiology)|isolated]] in a laboratory and have been detected only by their [[Gene|gene sequences]] in environmental samples. It is unknown if they can produce [[endospore]]s.

Archaea are often similar to bacteria in size and shape, although a few have very different shapes, such as the flat, square cells of ''[[Haloquadratum walsbyi]]''.<ref>{{cite journal |vauthors=Stoeckenius W |title=Walsby's square bacterium: fine structure of an orthogonal procaryote |journal=Journal of Bacteriology |volume=148 |issue=1 |pages=352–60 |date=October 1981 |pmid=7287626 |pmc=216199 |doi=10.1128/JB.148.1.352-360.1981 }}</ref> Despite this, archaea possess [[gene]]s and several [[metabolic pathway]]s that are more closely related to those of eukaryotes, notably for the [[enzyme]]s involved in [[transcription (genetics)|transcription]] and [[translation (biology)|translation]]. Other aspects of archaeal biochemistry are unique, such as their reliance on [[ether lipid]]s in their [[cell membrane]]s,<ref>{{cite web |title=Archaea Basic Biology |date=March 2018 |url=https://basicbiology.net/micro/microorganisms/archaea }}</ref> including [[archaeol]]s. Archaea use more diverse energy sources than eukaryotes, ranging from [[organic compounds]] such as sugars, to [[ammonia]], [[ion|metal ions]] or even [[hydrogen|hydrogen gas]]. The [[Halophile|salt-tolerant]] [[Haloarchaea]] use sunlight as an energy source, and other species of archaea [[carbon fixation|fix carbon]] (autotrophy), but unlike [[cyanobacteria]], no known species of archaea does both. Archaea [[asexual reproduction|reproduce asexually]] by [[binary fission]], [[Fragmentation (reproduction)|fragmentation]], or [[budding]]; unlike bacteria, no known species of Archaea form [[endospore]]s. The first observed archaea were [[extremophile]]s, living in extreme environments such as [[hot spring]]s and [[salt lake]]s with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every [[habitat]], including soil,<ref name="Chow_2022">{{cite journal |vauthors=Chow C, Padda KP, Puri A, Chanway CP |title=An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture |journal=Current Microbiology |volume=79 |issue=11 |pages=322 |date=September 2022 |pmid=36125558 |doi=10.1007/s00284-022-03016-y |s2cid=252376815 }}</ref> oceans, and [[marshland]]s. Archaea are particularly numerous in the oceans, and the archaea in [[plankton]] may be one of the most abundant groups of organisms on the planet.

Archaea are a major part of [[Life|Earth's life]]. They are part of the [[microbiota]] of all organisms. In the [[human microbiome]], they are important in the [[Colon (anatomy)|gut]], mouth, and on the skin.<ref name=Bang2015>{{cite journal |vauthors=Bang C, Schmitz RA |title=Archaea associated with human surfaces: not to be underestimated |journal=FEMS Microbiology Reviews |volume=39 |issue=5 |pages=631–48 |date=September 2015 |pmid=25907112 |doi=10.1093/femsre/fuv010 |doi-access=free }}</ref> Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; [[Nitrogen cycle|nitrogen cycling]]; organic compound turnover; and maintaining microbial [[Symbiosis|symbiotic]] and [[Syntrophy|syntrophic]] communities, for example.<ref name="Chow_2022" /><ref>{{cite journal |vauthors=Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA |title=Archaea Are Interactive Components of Complex Microbiomes |journal=Trends in Microbiology |volume=26 |issue=1 |pages=70–85 |date=January 2018 |pmid=28826642 |doi=10.1016/j.tim.2017.07.004 }}</ref> No archaea are known to be [[pathogen]]s or [[parasite]]s; many are [[Mutualism (biology)|mutualists]] or [[commensalism|commensals]], such as the [[methanogen]]s (methane-producers) that inhabit the [[gastrointestinal tract]] in humans and [[ruminant]]s, where their vast numbers facilitate [[digestion]]. Methanogens are used in [[biogas]] production and [[sewage treatment]], while [[biotechnology]] exploits enzymes from extremophile archaea that can endure high temperatures and organic [[solvents]].

==Discovery and classification==
{{anchor|A new domain}}

===Early concept===
[[File:Aerial image of Grand Prismatic Spring (view from the south).jpg|thumb|left|Archaea were discovered in volcanic [[hot spring]]s. Pictured here is [[Grand Prismatic Spring]] of [[Yellowstone National Park]].]]

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their [[biochemistry]], [[morphology (biology)|morphology]] and [[metabolism]]. Microbiologists tried to classify microorganisms based on the structures of their [[cell wall]]s, their shapes, and the substances they consume.<ref>{{cite journal |vauthors=Staley JT |title=The bacterial species dilemma and the genomic-phylogenetic species concept |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=361 |issue=1475 |pages=1899–909 |date=November 2006 |pmid=17062409 |pmc=1857736 |doi=10.1098/rstb.2006.1914 }}</ref> In 1965, [[Emile Zuckerkandl]] and [[Linus Pauling]]<ref>{{cite journal |vauthors=Zuckerkandl E, Pauling L |title=Molecules as documents of evolutionary history |journal=Journal of Theoretical Biology |volume=8 |issue=2 |pages=357–66 |date=March 1965 |pmid=5876245 |doi=10.1016/0022-5193(65)90083-4 |bibcode=1965JThBi...8..357Z }}</ref> instead proposed using the sequences of the [[gene]]s in different prokaryotes to work out how they are related to each other. This [[phylogenetics|phylogenetic]] approach is the main method used today.<ref name="pmid30148503">{{cite journal |vauthors=Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P |title=A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life |journal=Nature Biotechnology |volume=36 |issue=10 |pages=996–1004 |date=November 2018 |pmid=30148503 |doi=10.1038/nbt.4229 |s2cid=52093100 }}</ref>

Archaea were first classified separately from bacteria in 1977 by [[Carl Woese]] and [[George E. Fox]], based on their [[ribosomal RNA]] (rRNA) genes.<ref name="ReferenceA"/> (At that time only the [[methanogen]]s were known). They called these groups the ''Urkingdoms'' of Archaebacteria and Eubacteria, though other researchers treated them as [[kingdom (biology)|kingdoms]] or subkingdoms. 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 then thought to be natural [[Domain (biology)|domains]] known as the [[three-domain system]]: the [[Eukarya]], the [[Bacteria]] and the Archaea,<ref name="Woese">{{cite journal |vauthors=Woese CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=87 |issue=12 |pages=4576–9 |date=June 1990 |pmid=2112744 |pmc=54159 |doi=10.1073/pnas.87.12.4576 |bibcode=1990PNAS...87.4576W |doi-access=free }}</ref> in what is now known as the [[Woeseian revolution|Woesian Revolution]].<ref>{{Cite book|url=https://books.google.com/books?id=d7zOviXnbSYC&q=Jan+Sapp|title=The new foundations of evolution: on the tree of life |vauthors=Sapp J |publisher=Oxford University Press|year=2009|isbn=978-0-19-973438-2|location=New York}}</ref>

The word ''archaea'' comes from the [[Ancient Greek]] {{lang|grc|[[wikt:ἀρχαῖος|ἀρχαῖα]]}}, meaning "ancient things",<ref>{{cite web |url=http://www.merriam-webster.com/dictionary/archaea |title=Archaea |date=2008 |work=Merriam-Webster Online Dictionary |access-date=1 July 2008 }}</ref> as the first representatives of the domain Archaea were [[methanogen]]s and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme [[halophilic]]<ref name=Magrum>{{cite journal |vauthors=Magrum LJ, Luehrsen KR, Woese CR |title=Are extreme halophiles actually "bacteria"? |journal=Journal of Molecular Evolution |volume=11 |issue=1 |pages=1–8 |date=May 1978 |pmid=660662 |doi=10.1007/bf01768019 |bibcode=1978JMolE..11....1M |s2cid=1291732 }}</ref> and [[hyperthermophilic]] microbes<ref name=Stetter>{{cite journal |vauthors=Stetter KO |author-link=Karl Stetter|title=Hyperthermophiles in the history of life |journal=Ciba Foundation Symposium |volume=202 |pages=1–10; discussion 11–8 |date=1996 |pmid=9243007 }}</ref> were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as [[hot spring]]s and [[salt lake]]s, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature.<ref name=DeLong>{{cite journal |vauthors=DeLong EF |title=Everything in moderation: archaea as 'non-extremophiles' |journal=Current Opinion in Genetics & Development |volume=8 |issue=6 |pages=649–54 |date=December 1998 |pmid=9914204 |doi=10.1016/S0959-437X(98)80032-4 }}</ref> 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. This allows the detection and identification of organisms that have not been [[microbiological culture|cultured]] in the laboratory.<ref>{{cite journal |vauthors=Theron J, Cloete TE |title=Molecular techniques for determining microbial diversity and community structure in natural environments |journal=Critical Reviews in Microbiology |volume=26 |issue=1 |pages=37–57 |date=2000 |pmid=10782339 |doi=10.1080/10408410091154174 |s2cid=5829573 }}</ref><ref>{{cite journal |vauthors=Schmidt TM |title=The maturing of microbial ecology |journal=International Microbiology |volume=9 |issue=3 |pages=217–23 |date=September 2006 |pmid=17061212 |url=http://www.im.microbios.org/0903/0903217.pdf |archive-url=https://web.archive.org/web/20080911074811/http://www.im.microbios.org/0903/0903217.pdf|url-status=dead |archive-date=11 September 2008 }}</ref>

===Classification===
{{Further|Biological classification|Systematics}}
[[File:Rio tinto river CarolStoker NASA Ames Research Center.jpg|thumb|left|The [[Archaeal Richmond Mine acidophilic nanoorganisms|ARMAN]] are a group of archaea discovered in [[acid mine drainage]] in the early 2000s.]]
The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors.<ref name=Gevers>{{cite journal |vauthors=Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, De Vos P |title=Stepping stones towards a new prokaryotic taxonomy |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=361 |issue=1475 |pages=1911–16 |date=November 2006 |pmid=17062410 |pmc=1764938 |doi=10.1098/rstb.2006.1915 |display-authors=6 }}</ref> These classifications rely heavily on the use of the sequence of [[ribosomal RNA]] genes to reveal relationships among organisms ([[molecular phylogeny|molecular phylogenetics]]).<ref name=Robertson/> Most of the culturable and well-investigated species of archaea are members of two main kingdoms, the [[Methanobacteriati]] and the [[Thermoproteati]] (formerly TACK). Other groups have been tentatively created, such as the peculiar species ''[[Nanoarchaeum equitans]]'' — discovered in 2003 and assigned its own phylum, the Nanoarchaeota (reassigned to [[Nanobdellota]] in 2023<ref>{{Cite journal |last=Göker |first=Markus |last2=Oren |first2=Aharon |date=2023 |title=Valid publication of four additional phylum names |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006024 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=73 |issue=9 |pages=006024 |doi=10.1099/ijsem.0.006024 |issn=1466-5034 |pmid=37695645 |doi-access=free}}</ref>).<ref>{{cite journal |vauthors=Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO |title=A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont |journal=Nature |volume=417 |issue=6884 |pages=63–67 |date=May 2002 |pmid=11986665 |doi=10.1038/417063a |bibcode=2002Natur.417...63H |s2cid=4395094 }}</ref> A new phylum "[[Korarchaeota|''Candidatus'' Korarchaeota]]" (now [[Thermoproteota]])<ref name=":1" /> has also been proposed, containing a small group of unusual thermophilic species sharing features of both the main phyla.<ref>{{cite journal |vauthors=Barns SM, Delwiche CF, Palmer JD, Pace NR |title=Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=93 |issue=17 |pages=9188–93 |date=August 1996 |pmid=8799176 |pmc=38617 |doi=10.1073/pnas.93.17.9188 |bibcode=1996PNAS...93.9188B |doi-access=free }}</ref><ref>{{cite journal |vauthors=Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO |title=A korarchaeal genome reveals insights into the evolution of the Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=23 |pages=8102–07 |date=June 2008 |pmid=18535141 |pmc=2430366 |doi=10.1073/pnas.0801980105 |bibcode=2008PNAS..105.8102E |display-authors=6 |doi-access=free }}</ref> 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<ref>{{cite journal |vauthors=Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF |s2cid=26033384 |title=Lineages of acidophilic archaea revealed by community genomic analysis |journal=Science |volume=314 |issue=5807 |pages=1933–35 |date=December 2006 |pmid=17185602 |doi=10.1126/science.1132690 |bibcode=2006Sci...314.1933B }}</ref> and are some of the smallest organisms known.<ref>{{cite journal |vauthors=Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF |title=Enigmatic, ultrasmall, uncultivated Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=107 |issue=19 |pages=8806–11 |date=May 2010 |pmid=20421484 |pmc=2889320 |doi=10.1073/pnas.0914470107 |bibcode=2010PNAS..107.8806B |display-authors=6 |doi-access=free }}</ref>

A [[Phylum|superphylum]] – "TACK" (now kingdom [[Thermoproteati]])– which includes the Thaumarchaeota (now [[Nitrososphaerota]]), "[[Augarchaeota]]", Crenarchaeota (now Thermoproteota), and "[[Korarchaeota|''Candidatus'' Korarchaeota]]" (now Thermoproteota)<ref name=":1" /> was proposed in 2011 to be related to the origin of eukaryotes.<ref name=Guy2011>{{cite journal |vauthors=Guy L, Ettema TJ |title=The archaeal 'TACK' superphylum and the origin of eukaryotes |journal=Trends in Microbiology |volume=19 |issue=12 |pages=580–87 |date=December 2011 |pmid=22018741 |doi=10.1016/j.tim.2011.09.002 }}</ref> In 2017, the newly discovered and newly named "Asgard" (now kingdom [[Asgard (Archaea)|Promethearchaeati]]) superphylum was proposed to be more closely related to the original eukaryote and a sister group to Thermoproteati / "TACK".<ref name="ZN_Asgard2017">{{cite journal |vauthors=Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ |title=Asgard archaea illuminate the origin of eukaryotic cellular complexity |journal=Nature |volume=541 |issue=7637 |pages=353–58 |date=January 2017 |pmid=28077874 |doi=10.1038/nature21031 |bibcode=2017Natur.541..353Z |osti=1580084 |s2cid=4458094 |display-authors=6 |url=https://escholarship.org/content/qt0qh5400s/qt0qh5400s.pdf?t=pgp8bj }}</ref>

In 2013, the superphylum "DPANN" (now 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. Therefore, Nanobdellati/"DPANN" may include members obligately dependent on symbiotic interactions, and may even include novel parasites. However, other phylogenetic analyses found that Nanobdellati/"DPANN" does not form a [[Monophyly|monophyletic]] group, and that the apparent grouping is caused by [[long branch attraction]] (LBA), suggesting that all these lineages belong to Methanobacteriati.<ref>Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). [https://academic.oup.com/femsle/article/366/2/fnz008/5281434 Genomic diversity, lifestyles and evolutionary origins of DPANN archaea]. Nature.</ref><ref name=Petitjean/>
{{clear}}

===Phylogeny===

According to Tom A. Williams ''et al.'' 2017,<ref name="WT2017">{{cite journal|display-authors=6|vauthors=Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJ, Embley TM|date=June 2017|title=Integrative modeling of gene and genome evolution roots the archaeal tree of life|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=114|issue=23|pages=E4602–E4611|doi=10.1073/pnas.1618463114|pmc=5468678|pmid=28533395|bibcode=2017PNAS..114E4602W |doi-access=free}}</ref> Castelle & Banfield (2018)<ref name="CCBJ2018">{{cite journal|vauthors=Castelle CJ, Banfield JF|year=2018|title=Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life|journal=Cell|volume=172|issue=6|pages=1181–1197|doi=10.1016/j.cell.2018.02.016|pmid=29522741|doi-access=free}}</ref> and [[GTDB]] release 10-RS226 (16th April 2025).<ref name="about">{{cite web |title=GTDB release 10-RS226 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]]|access-date=1 May 2025}}</ref><ref name="tree">{{cite web |title=ar53_r226.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/ar53_r226.sp_labels.tree |website=[[Genome Taxonomy Database]]|access-date=1 May 2025}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]]|access-date=1 May 2025}}</ref>

{|class="wikitable"
|-
! colspan=1 |Tom A. Williams ''et al.'' 2017<ref name="WT2017"/> and Castelle & Banfield 2018<ref name="CCBJ2018"/>
! colspan=1 |10-RS226 (16th April 2025)<ref name="about" /><ref name="tree" /><ref name="taxon_history" />
|- 
|style="vertical-align:top|
{{Clade|style=font-size:90%; line-height:80%
|label1='''Archaea'''
|1={{Clade
  |1={{Clade
    |label1=[[Nanobdellati]]
    |1={{Clade
      |1={{Clade
        |1="Altarchaeales"
        |2={{Clade
          |1="[[Diapherotrites]]"
          |2="[[Micrarchaeota]]"
           }}
         }}
      |2={{Clade
        |1="[[Aenigmarchaeota]]"
        |2={{Clade
          |1="[[Nanohaloarchaeota]]"
          |2={{Clade
            |1={{Clade
              |1="[[Nanoarchaeota]]"
              |2="Pavarchaeota"
               }}
            |2={{Clade
              |1="Mamarchaeota"
              |2={{Clade
                |1="Woesarchaeota"
                |2="[[Pacearchaeota]]"
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
  |2={{Clade
    |label1=[[Methanobacteriati]]
    |1={{Clade
      |1={{Clade
        |1=[[Thermococci]]
        |2=[[Pyrococcus|Pyrococci]]
         }}
      |2={{Clade
        |1={{Clade
          |1=[[Methanococci]]
          |2={{Clade
            |1=[[Methanobacteria]]
            |2=[[Methanopyri]]
             }}
           }}
        |2={{Clade
          |1={{Clade
            |1=[[Archaeoglobi]]
            |2={{Clade
              |1={{Clade
                |1=[[Methanocellales]]
                |2=[[Methanosarcinales]]
                 }}
              |2={{Clade
                |1=[[Methanomicrobiales]]
                |2=[[Halobacteria]]
                 }}
               }}
             }}
          |2={{Clade
            |1=[[Thermoplasmatales]]
            |2={{Clade
              |1=[[Methanomassiliicoccales]]
              |2={{Clade
                |1=''[[Aciduliprofundum boonei]]''
                |2=''[[Thermoplasma]] volcanium''
                 }}
               }}
             }}
           }}
         }}
       }}
    |label2=[[Proteoarchaeota]]
    |2={{Clade
      |label1=[[Thermoproteati]]
      |1={{Clade
        |1="[[Korarchaeota]]"
        |2={{Clade
          |1=[[Thermoproteota]]
          |2={{Clade
            |1={{Clade
              |1="[[Aigarchaeota]]"
              |2="[[Geoarchaeota]]"
               }}
            |2={{Clade 
              |1=[[Nitrososphaerota]] 
              |2="[[Bathyarchaeota]]"
               }}
             }}
           }}
         }}
      |label2="[[Eukaryomorpha]]"
      |2={{Clade
        |1={{Clade
          |label1=[[Asgard (Archaea)|Promethearchaeati]]
          |1={{Clade
            |1={{Clade
              |1="[[Odinarchaeota]]"
              |2="[[Thorarchaeota]]"
               }}
            |2={{Clade 
              |1="[[Lokiarchaeota]]"
              |2="Helarchaeota"<ref name=SK2018>{{cite journal |vauthors=Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, Teske AP, Ettema TJ, Baker BJ |display-authors=6 |title=Asgard archaea capable of anaerobic hydrocarbon cycling |journal=Nature Communications |volume=10 |issue=1 |pages=1822 |date=April 2019 |pmid=31015394 |doi=10.1038/s41467-019-09364-x |pmc=6478937 |bibcode=2019NatCo..10.1822S }}</ref>
               }}
             }}
           }}
        |2={{Clade 
          |1="[[Heimdallarchaeota]]"
          |2=[[Eukaryote|Eukaryota]]
           }} 
         }}
       }}
     }}
   }}
}}
|
{{barlabel|size=3|at2=14|label2=[[Methanobacteriati]] /<br/>"Euryarchaeota"
|cladogram={{Clade|style=font-size:90%; line-height:80%
|label1='''Archaea'''
|1={{Clade
  |1={{Clade
  |label1=[[Nanobdellati]]
  |1={{Clade
    |1={{clade
      |1={{clade
      |label1="[[Altarchaeota]]"
      |1="Altarchaeia"
         }}
      |2={{clade
        |label1="[[Iainarchaeota]]"
        |1="Iainarchaeia"
        |label2="[[Micrarchaeota]]"
        |2="Micrarchaeia"
         }}
       }}
    |2={{Clade
      |1={{clade
      |label1="[[Undinarchaeota]]"
      |1="Undinarchaeia"
         }}
      |2={{clade
        |1={{clade
          |1={{clade
          |label1="[[Huberarchaeaota]]"
          |1="Huberarchaeia"
             }}
          |2={{clade
            |label1="[[Aenigmarchaeota]]"
            |1="Aenigmatarchaeia"
            |label2="[[Nanohaloarchaeota|Nanohalarchaeota]]"
            |2="Nanohalobiia"
             }}
           }}
        |2={{clade
        |label1=[[Nanoarchaeota|Nanobdellota]]
        |1=Nanobdellia
           }}
         }}
       }}
     }}
     }}
  |2={{clade
    |1={{clade
      |1={{Clade
      |label1=[[Proteoarchaeota]]
      |1={{Clade
        |1={{Clade
        |label1="[[Korarchaeota]]"
        |1="Korarchaeia"
           }}
        |2={{Clade
          |label2=Thermoproteati:
          |sublabel2=[[Thermoproteota]]
          |2={{Clade
            |label1="BAT"
            |1={{Clade
              |1="[[Bathyarchaeia]]"
              |2={{Clade
                |1=Nitrososphaeria_A
                |2=[[Nitrososphaeria]]
                 }}
               }}
            |label2="Sulfobacteria"
            |2={{Clade
              |2="[[Sulfolobia]]"
              |1={{Clade
                |1="[[Methanomethylicia]]"
                |2="[[Thermoprotei|Thermoproteia]]"
                 }}
               }}
             }}
          |label1=Promethearchaeati:
          |sublabel1=[[Asgard (archaea)|Promethearchaeota]]
          |1={{Clade
            |1="[[Asgardarchaeia]]"
            |2={{Clade
              |1="[[Atabeyarchaeia]]"
              |2={{Clade
                |1={{Clade
                  |1={{Clade
                    |1="[[Odinarchaeia]]"
                    |2="[[Jordarchaeia]]"
                     }}
                  |2={{Clade
                    |1={{Clade
                      |1="[[Baldrarchaeia]]"
                      |2="[[Thorarchaeia]]" (MBG-B)
                       }}
                    |2={{Clade
                      |1="[[Hermodarchaeia]]"
                      |2="[[Lokiarchaeia|Promethearchaeia]]"
                       }}
                     }}
                   }}
                |2={{Clade
                  |1="[[Sifarchaeia]]"
                  |2={{Clade
                    |1="[[Wukongarchaeia]]"
                    |2={{Clade
                      |1="[[Njordarchaeia]]"
                      |2="[[Heimdallarchaeia]]" (inc. [[Eukaryota]])
                       }}
                     }}
                   }}
                 }}
               }}
             }}
           }}
         }}
         }}
      |2={{clade
        |label1=[[Thermoplasmatota]]
        |1={{Clade
          |1="[[Izemarchaea]]" (MBG-D, E2)|barbegin1=red
          |2={{Clade
            |1="[[Poseidoniia]]" (MGII & MGIII)|bar1=red
            |2="[[Thermoplasmata|Thermoplasmatia]]"|bar2=red
             }}
           }}
        |label2=[[Halobacteriota]]
        |2={{Clade
          |1=[[Methanonatronarchaeia]]|bar1=red
          |2={{Clade
            |1={{Clade
              |1={{Clade
                |1="[[Methanoliparia]]"|bar1=red
                |2="[[Archaeoglobi|Archaeoglobia]]"|bar2=red
                 }}
              |2={{Clade
                |1="[[Syntropharchaeia]]"|bar1=red
                |2={{Clade
                  |1=[[Methanocellia]]|bar1=red
                  |2=[[Methanosarcinia]]|bar2=red
                   }}
                 }}
               }}
            |2={{Clade
              |1="[[Methanomicrobia]]"|bar1=red
              |2=[[Halobacteria]]|bar2=red
               }}
             }}
           }}
         }}
       }}
    |2={{clade
    |label1="Methanomada"
    |1={{clade
      |1={{clade
        |label1="[[Hadarchaeota]]"
        |1="Hadarchaeia"|bar1=red
        |label2=Methanobacteriota_B
        |2="[[Thermococci|Thermococcia]]"|bar2=red
         }}
      |2={{clade
        |label1="[[Hydrothermarchaeota]]"
        |1="Hydrothermarchaeia"|bar1=red
        |label2=[[Methanobacteriota]]
        |2={{clade
          |1="[[Methanococci|Methanococcia]]"|bar1=red
          |2={{clade
            |1="[[Methanopyri|Methanopyria]]"|bar1=red
            |2="[[Methanobacteria|Methanobacteriia]]"|barend2=red
             }}
           }}
         }}
       }}
       }}
     }}
   }}
}}
}}
|}

===Concept of species===
The classification of archaea into species is also controversial. [[Ernst Mayr]]'s [[species]] definition — a [[reproductive isolation|reproductively isolated]] group of interbreeding organisms — does not apply, as archaea reproduce only asexually.<ref>{{cite journal |vauthors=de Queiroz K |title=Ernst Mayr and the modern concept of species |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=102 |issue=Supplement 1 |pages=6600–6007 |date=May 2005 |pmid=15851674 |pmc=1131873 |doi=10.1073/pnas.0502030102 |bibcode=2005PNAS..102.6600D |doi-access=free }}</ref>

Archaea show high levels of [[horizontal gene transfer]] between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus ''[[Ferroplasma]]''.<ref>{{cite journal |vauthors=Eppley JM, Tyson GW, Getz WM, Banfield JF |title=Genetic exchange across a species boundary in the archaeal genus ferroplasma |journal=Genetics |volume=177 |issue=1 |pages=407–16 |date=September 2007 |pmid=17603112 |pmc=2013692 |doi=10.1534/genetics.107.072892 }}</ref> On the other hand, studies in ''[[Halorubrum]]'' found significant genetic transfer to/from less-related populations, limiting the criterion's applicability.<ref>{{cite journal |vauthors=Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF |title=Searching for species in haloarchaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=104 |issue=35 |pages=14092–97 |date=August 2007 |pmid=17715057 |pmc=1955782 |doi=10.1073/pnas.0706358104 |bibcode=2007PNAS..10414092P |doi-access=free }}</ref> Some researchers question whether such species designations have practical meaning.<ref>{{cite journal |vauthors=Kunin V, Goldovsky L, Darzentas N, Ouzounis CA |title=The net of life: reconstructing the microbial phylogenetic network |journal=Genome Research |volume=15 |issue=7 |pages=954–59 |date=July 2005 |pmid=15965028 |pmc=1172039 |doi=10.1101/gr.3666505 }}</ref>

Current knowledge on genetic diversity in archaeans is fragmentary, so the total number of species cannot be estimated with any accuracy.<ref name=Robertson>{{cite journal |vauthors=Robertson CE, Harris JK, Spear JR, Pace NR |title=Phylogenetic diversity and ecology of environmental Archaea |journal=Current Opinion in Microbiology |volume=8 |issue=6 |pages=638–642 |date=December 2005 |pmid=16236543 |doi=10.1016/j.mib.2005.10.003 }}</ref> Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, so the level of diversity remains obscure.<ref>{{cite journal |vauthors=Hugenholtz P |title=Exploring prokaryotic diversity in the genomic era |journal=Genome Biology |volume=3 |issue=2 |pages=REVIEWS0003 |date=2002 |pmid=11864374 |pmc=139013 |doi=10.1186/gb-2002-3-2-reviews0003 |doi-access=free }}</ref> This situation is also seen in the Bacteria; many uncultured microbes present similar issues with characterization.<ref>{{cite journal |vauthors=Rappé MS, Giovannoni SJ |s2cid=10781051 |title=The uncultured microbial majority |journal=Annual Review of Microbiology |volume=57 |pages=369–94 |date=2003 |pmid=14527284 |doi=10.1146/annurev.micro.57.030502.090759 |url=http://pdfs.semanticscholar.org/b762/aceb7d94a73637fb761f9168fc8dc3601bf6.pdf |archive-url=https://web.archive.org/web/20190302145243/http://pdfs.semanticscholar.org/b762/aceb7d94a73637fb761f9168fc8dc3601bf6.pdf |url-status=dead |archive-date=2019-03-02 }}</ref>

==Prokaryotic phyla==
===Valid phyla===
The following phyla have been validly published according to the [[International Code of Nomenclature of Prokaryotes|Prokaryotic Code]]; belonging to the four kingdoms of archaea:<ref>{{cite journal |vauthors=Oren A, Garrity GM |title=Valid publication of the names of forty-two phyla of prokaryotes |journal=Int J Syst Evol Microbiol |year=2021 |volume=71 |issue=10 |pages=5056 |doi=10.1099/ijsem.0.005056 |pmid=34694987 |s2cid=239887308 |doi-access=free }}</ref><ref>{{cite journal |last1=Göker |first1=Markus |last2=Oren |first2=Aharon |title=Valid publication of four additional phylum names |journal=International Journal of Systematic and Evolutionary Microbiology |date=11 September 2023 |volume=73 |issue=9 |doi=10.1099/ijsem.0.006024|pmid=37695645 |doi-access=free }}</ref><ref name=":1">{{Cite journal |last1=Parte |first1=Aidan C. |last2=Sardà Carbasse |first2=Joaquim |last3=Meier-Kolthoff |first3=Jan P. |last4=Reimer |first4=Lorenz C. |last5=Göker |first5=Markus |date=2020-11-01 |title=List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=70 |issue=11 |pages=5607–5612 |doi=10.1099/ijsem.0.004332 |issn=1466-5026 |pmc=7723251 |pmid=32701423}}</ref>
* [[Methanobacteriota]]
* [[Microcaldota]]
* [[Nanoarchaeota|Nanobdellota]]
* [[Promethearchaeota]]
* [[Thermoproteota]]

===Candidate phyla===
The following phyla have been proposed, but have not been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in '''bold''':<ref>{{Cite journal |last=Xie |first=Ruize |last2=Wang |first2=Yinzhao |last3=Huang |first3=Danyue |last4=Hou |first4=Jialin |last5=Li |first5=Liuyang |last6=Hu |first6=Haining |last7=Zhao |first7=Xiaoxiao |last8=Wang |first8=Fengping |date=2021-08-06 |title=Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes |url=https://doi.org/10.1007/s11427-021-1969-6 |journal=Science China Life Sciences |language=en |volume=65 |issue=4 |pages=818–829 |doi=10.1007/s11427-021-1969-6 |issn=1869-1889|url-access=subscription }}</ref><ref name=":1" /><ref>{{Cite journal |last1=Liu |first1=Yang |last2=Makarova |first2=Kira S. |last3=Huang |first3=Wen-Cong |last4=Wolf |first4=Yuri I. |last5=Nikolskaya |first5=Anastasia N. |last6=Zhang |first6=Xinxu |last7=Cai |first7=Mingwei |last8=Zhang |first8=Cui-Jing |last9=Xu |first9=Wei |last10=Luo |first10=Zhuhua |last11=Cheng |first11=Lei |last12=Koonin |first12=Eugene V. |last13=Li |first13=Meng |date=2021-04-28 |title=Expanded diversity of Asgard archaea and their relationships with eukaryotes |journal=Nature |language=en |volume=593 |issue=7860 |pages=553–557 |bibcode=2021Natur.593..553L |doi=10.1038/s41586-021-03494-3 |issn=1476-4687 |pmc=11165668 |pmid=33911286}}</ref><ref>{{Cite journal |last=Imachi |first=Hiroyuki |last2=Nobu |first2=Masaru K. |last3=Kato |first3=Shingo |last4=Takaki |first4=Yoshihiro |last5=Miyazaki |first5=Masayuki |last6=Miyata |first6=Makoto |last7=Ogawara |first7=Miyuki |last8=Saito |first8=Yumi |last9=Sakai |first9=Sanae |last10=Tahara |first10=Yuhei O. |last11=Takano |first11=Yoshinori |last12=Tasumi |first12=Eiji |last13=Uematsu |first13=Katsuyuki |last14=Yoshimura |first14=Toshihiro |last15=Itoh |first15=Takashi |date=2024 |title=Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov. |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006435 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=74 |issue=7 |pages=006435 |doi=10.1099/ijsem.0.006435 |issn=1466-5034 |pmc=11316595 |pmid=38967634}}</ref>

{{div col|colwidth=250px}}
*"[[Candidatus Aenigmatarchaeum|''Ca.'' Aenigmatarchaeota]]"
*"[[Candidatus Altarchaeota|''Ca.'' Altarchaeota]]"
*"[[Aigarchaeota|''Ca.'' Augarchaeota]]"
*"[[Candidatus Freyrarchaeota|''Ca.'' Freyrarchaeota]]"
*'''"[[Candidatus Geoarchaeota|''Ca.'' Geoarchaeota]]"'''
*"[[Hadesarchaea|''Ca.'' Hadarchaeota]]"
*"[[Candidatus Hodarchaeum|''Ca.'' Hodarchaeota]]"
*"[[Candidatus Huberarchaeum|''Ca.'' Huberarchaeota]]"
*"[[Candidatus Hydrothermarchaeota|''Ca.'' Hydrothermarchaeota]]"
*"[[Candidatus Iainarchaeota|''Ca.'' Iainarchaeota]]"
*'''"[[Candidatus Kariarchaeota|''Ca.'' Kariarchaeota]]"'''
*"[[Candidatus Micrarchaeota|''Ca.'' Micrarchaeota]]"
*"[[Nanohaloarchaea|''Ca.'' Nanohalarchaeota]]"
*"[[Candidatus Nezhaarchaeota|''Ca.'' Nezhaarchaeota]]"
*"[[Candidatus Parvarchaeota|''Ca.'' Parvarchaeota]]"
*"[[Candidatus Poseidoniota|''Ca.'' Poseidoniota]]"
*"[[Candidatus Undinarchaeota|''Ca.'' Undinarchaeota]]"
*'''"[[Candidatus Sigynarchaeota|''Ca.'' Sigynarchaeota]]"'''{{div col end}}

==Origin and evolution==
{{Further|Timeline of evolution}}

The [[age of the Earth]] is about 4.54&nbsp;billion years.<ref name="USGS1997">{{cite web |date=1997 |title=Age of the Earth |url=http://pubs.usgs.gov/gip/geotime/age.html |publisher=U.S. Geological Survey |access-date=2006-01-10 |archive-url=https://web.archive.org/web/20051223072700/http://pubs.usgs.gov/gip/geotime/age.html|archive-date=23 December 2005 |url-status=live}}</ref><ref>{{cite journal |vauthors=Dalrymple GB |title=The age of the Earth in the twentieth century: a problem (mostly) solved |journal=Special Publications, Geological Society of London |date=2001 |volume=190 |issue=1 |pages=205–21 |doi=10.1144/GSL.SP.2001.190.01.14 |bibcode=2001GSLSP.190..205D |s2cid=130092094 }}</ref><ref>{{cite journal |vauthors=Manhesa G, Allègre CJ, Dupréa B, Hamelin B |title=Lead isotope study of basic-ultrabasic layered complexes: Speculations about the age of the earth and primitive mantle characteristics |journal=[[Earth and Planetary Science Letters]] |date=1980 |volume=47 |issue=3 |pages=370–82 |doi=10.1016/0012-821X(80)90024-2 |bibcode=1980E&PSL..47..370M }}</ref> Scientific evidence suggests that [[Abiogenesis|life began]] on Earth at least 3.5&nbsp;[[billion years ago]].<ref name="AmSci">{{cite journal |vauthors=de Duve C |author-link=Christian de Duve |title=The Beginnings of Life on Earth |url=http://www.americanscientist.org/issues/pub/the-beginnings-of-life-on-earth/1 |journal=[[American Scientist]] |date=October 1995 |access-date=15 January 2014 |archive-date=6 June 2017 |archive-url=https://web.archive.org/web/20170606074801/http://www.americanscientist.org/issues/pub/the-beginnings-of-life-on-earth/1 |url-status=dead }}</ref><ref name="AT-20120904">{{cite web |vauthors=Timmer J |title=3.5 billion year old organic deposits show signs of life|url=https://arstechnica.com/science/2012/09/3-5-billion-year-old-organic-deposts-show-signs-of-life/ |date=4 September 2012 |work=[[Ars Technica]] |access-date=15 January 2014 }}</ref> The earliest evidence for [[life|life on Earth]] is [[graphite]] found to be [[Biogenic substance|biogenic]] in 3.7-billion-year-old [[Metasediment|metasedimentary rocks]] discovered in [[Western Greenland]]<ref name="NG-20131208">{{Cite journal |vauthors=Ohtomo Y, Kakegawa T, Ishida A, Nagase T, Rosingm MT|title=Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks |journal=[[Nature Geoscience]] |volume=7|issue=1|page=25|doi=10.1038/ngeo2025|date=8 December 2013|bibcode=2014NatGe...7...25O}}</ref> and [[microbial mat]] [[fossils]] found in 3.48-billion-year-old [[sandstone]] discovered in [[Western Australia]].<ref name="AP-20131113">{{cite news |vauthors=Borenstein S |title=Oldest fossil found: Meet your microbial mom|url=http://apnews.excite.com/article/20131113/DAA1VSC01.html |date=13 November 2013 |agency=Associated Press|access-date=15 November 2013 }}</ref><ref name="AST-20131108">{{cite journal |vauthors=[[Nora Noffke|Noffke N]], Christian D, Wacey D, Hazen RM |title=Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia |journal=Astrobiology |volume=13 |issue=12 |pages=1103–24 |date=December 2013 |pmid=24205812 |pmc=3870916 |doi=10.1089/ast.2013.1030 |bibcode=2013AsBio..13.1103N }}</ref> In 2015, possible remains of [[Biotic material|biotic matter]] were found in 4.1-billion-year-old rocks in Western Australia.<ref name="AP-20151019">{{cite news |vauthors=Borenstein S |title=Hints of life on what was thought to be desolate early Earth |url=http://apnews.excite.com/article/20151019/us-sci--earliest_life-a400435d0d.html |date=19 October 2015 |work=[[Excite (web portal)|Excite]] |location=Yonkers, NY |publisher=[[Mindspark Interactive Network]] |agency=[[Associated Press]] |access-date=2015-10-20}}</ref><ref name="PNAS-20151014-pdf">{{cite journal |vauthors=Bell EA, Boehnke P, Harrison TM, [[Wendy Mao|Mao WL]] |title=Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=112 |issue=47 |pages=14518–21 |date=November 2015 |pmid=26483481 |pmc=4664351 |doi=10.1073/pnas.1517557112 |url=http://www.pnas.org/content/early/2015/10/14/1517557112.full.pdf |publisher=National Academy of Sciences |bibcode=2015PNAS..11214518B |doi-access=free }}</ref>

Although probable prokaryotic cell [[fossils]] date to almost 3.5&nbsp;[[bya|billion years ago]], most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea.<ref>{{cite journal |vauthors=Schopf JW |title=Fossil evidence of Archaean life |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=361 |issue=1470 |pages=869–85 |date=June 2006 |pmid=16754604 |pmc=1578735 |doi=10.1098/rstb.2006.1834 }}</ref> Instead, [[chemical fossil]]s of unique [[lipid]]s are more informative because such compounds do not occur in other organisms.<ref>{{cite journal |vauthors=Chappe B, Albrecht P, Michaelis W |title=Polar lipids of archaebacteria in sediments and petroleums |journal=Science |volume=217 |issue=4554 |pages=65–66 |date=July 1982 |pmid=17739984 |doi=10.1126/science.217.4554.65 |bibcode=1982Sci...217...65C |s2cid=42758483 }}</ref> Some publications suggest that archaeal or eukaryotic lipid remains are present in [[shale]]s dating from 2.7&nbsp;billion years ago,<ref>{{cite journal |vauthors=Brocks JJ, Logan GA, Buick R, Summons RE |title=Archean molecular fossils and the early rise of eukaryotes |journal=Science |volume=285 |issue=5430 |pages=1033–36 |date=August 1999 |pmid=10446042 |doi=10.1126/science.285.5430.1033 |bibcode=1999Sci...285.1033B |citeseerx=10.1.1.516.9123 }}</ref> though such data have since been questioned.<ref>{{cite journal |vauthors=Rasmussen B, Fletcher IR, Brocks JJ, Kilburn MR |title=Reassessing the first appearance of eukaryotes and cyanobacteria |journal=Nature |volume=455 |issue=7216 |pages=1101–4 |date=October 2008 |pmid=18948954 |doi=10.1038/nature07381 |bibcode=2008Natur.455.1101R |s2cid=4372071 }}</ref> These lipids have also been detected in even older rocks from west [[Greenland]]. The oldest such traces come from the [[Isua greenstone belt|Isua district]], which includes Earth's oldest known sediments, formed 3.8&nbsp;billion years ago.<ref>{{cite journal |vauthors=Hahn J, Haug P |date=1986 |title=Traces of Archaebacteria in ancient sediments |journal=System Applied Microbiology |volume=7 |issue=Archaebacteria '85 Proceedings |pages=178–83 |doi=10.1016/S0723-2020(86)80002-9|bibcode=1986SyApM...7..178H }}</ref> The archaeal lineage may be the most ancient that exists on Earth.<ref name=Wang>{{cite journal |vauthors=Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G |title=Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world |journal=Genome Research |volume=17 |issue=11 |pages=1572–85 |date=November 2007 |pmid=17908824 |pmc=2045140 |doi=10.1101/gr.6454307 }}</ref>

Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.<ref>{{cite journal |vauthors=Woese CR, Gupta R |title=Are archaebacteria merely derived 'prokaryotes'? |journal=Nature |volume=289 |issue=5793 |pages=95–96 |date=January 1981 |pmid=6161309 |doi=10.1038/289095a0 |bibcode=1981Natur.289...95W |s2cid=4343245 }}</ref><ref name="Woese1">{{cite journal |vauthors=Woese C |title=The universal ancestor |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=95 |issue=12 |pages=6854–59 |date=June 1998 |pmid=9618502 |pmc=22660 |doi=10.1073/pnas.95.12.6854 |bibcode=1998PNAS...95.6854W |doi-access=free }}</ref> One possibility<ref name=Woese1 /><ref name=Kandler>{{cite book |vauthors=Kandler OT |chapter=The early diversification of life and the origin of the three domains: a proposal. |veditors=Wiegel J, Adams WW |title=Thermophiles: the keys to molecular evolution and the origin of life. |date=August 1998 |pages=19–31 |location=Athens |publisher=Taylor and Francis |chapter-url=https://books.google.com/books?id=c0ZZDwAAQBAJ&pg=PA19|isbn=978-1-4822-7304-5 }}</ref> is that this occurred before the [[evolution of cells]], when the lack of a typical cell membrane allowed unrestricted [[lateral gene transfer]], and that the common ancestors of the three domains arose by fixation of specific subsets of genes.<ref name=Woese1 /><ref name=Kandler/> It is possible that the [[Last universal common ancestor|last common ancestor]] of bacteria and archaea was a [[thermophile]], which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later.<ref>{{cite journal |vauthors=Gribaldo S, Brochier-Armanet C |title=The origin and evolution of Archaea: a state of the art |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=361 |issue=1470 |pages=1007–22 |date=June 2006 |pmid=16754611 |pmc=1578729 |doi=10.1098/rstb.2006.1841 }}</ref> Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term ''prokaryote'' may suggest a false similarity between them.<ref name=PMID8177167>{{cite journal |vauthors=Woese CR |title=There must be a prokaryote somewhere: microbiology's search for itself |journal=Microbiological Reviews |volume=58 |issue=1 |pages=1–9 |date=March 1994 |pmid=8177167 |pmc=372949 |doi=10.1128/MMBR.58.1.1-9.1994 }}</ref> However, structural and functional similarities between lineages often occur because of shared ancestral traits or [[Convergent evolution|evolutionary convergence]]. These similarities are known as a ''grade'', and [[prokaryote]]s are best thought of as a grade of life, characterized by such features as an absence of membrane-bound organelles.

===Comparison with other domains===
The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.<ref>Information is from Willey JM, Sherwood LM, Woolverton CJ. ''Microbiology'' 7th ed. (2008), Ch. 19 pp.&nbsp;474–475, except where noted.</ref>

{|class="wikitable plainrowheaders"
|-
! Property
! Archaea
!width="27%"|Bacteria
! Eukaryota
|-
! scope=row |'''[[Cell membrane]]'''
|[[Ether]]-linked [[lipids]]
|[[Ester]]-linked lipids
|Ester-linked lipids
|-
! scope=row |'''[[Cell wall]]'''
|[[Glycoprotein]], or [[S-layer]]; rarely [[pseudopeptidoglycan]]
|[[Peptidoglycan]], S-layer, or no cell wall
|Various structures
|-
! scope=row |'''[[Gene]] structure'''
|[[Circular chromosome]]s, similar [[Translation (biology)|translation]] and [[Transcription (biology)|transcription]] to Eukaryota
|Circular chromosomes, unique translation and transcription
|Multiple, linear chromosomes, but translation and transcription similar to Archaea
|-
! scope=row |'''Internal [[Cell (biology)|cell]] structure'''
|No membrane-bound [[organelle]]s (?<ref>{{cite journal |vauthors=Heimerl T, Flechsler J, Pickl C, Heinz V, Salecker B, Zweck J, Wanner G, Geimer S, Samson RY, Bell SD, Huber H, Wirth R, Wurch L, Podar M, Rachel R |title=A Complex Endomembrane System in the Archaeon ''Ignicoccus hospitalis'' Tapped by ''Nanoarchaeum equitans'' |journal=Frontiers in Microbiology |volume=8 |pages=1072 |date=13 June 2017 |pmid=28659892 |pmc=5468417 |doi=10.3389/fmicb.2017.01072 |doi-access=free }}</ref>) or [[nucleus (biology)|nucleus]]
|No membrane-bound organelles or nucleus
|Membrane-bound organelles and nucleus
|-
! scope=row |'''[[Metabolism]]<ref>{{cite book |vauthors=Jurtshuk P |chapter=Bacterial Metabolism |title=Medical Microbiology |date=1996 |publisher=University of Texas Medical Branch at Galveston |location=Galveston (TX) |pmid=21413278 |edition=4th |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK7919/ |ref=Medical Microbiology |isbn=9780963117212 }}</ref>'''
|Various, including [[diazotrophy]], with [[methanogenesis]] unique to Archaea
|Various, including [[photosynthesis]], [[aerobic respiration|aerobic]] and [[anaerobic respiration]], [[fermentation]], diazotrophy, and [[autotroph]]y
|Photosynthesis, cellular respiration, and fermentation; no diazotrophy
|-
! scope=row |'''[[Reproduction]]'''
|[[Asexual reproduction]], [[horizontal gene transfer]]
|Asexual reproduction, horizontal gene transfer
|[[Sexual reproduction|Sexual]] and asexual reproduction
|-
! scope=row |{{nowrap|'''Protein synthesis initiation'''}}
|[[Methionine]]
|[[Formylmethionine]]
|Methionine
|-
! scope=row |'''[[RNA polymerase]]'''
|One
|One
|Many
|-
! scope=row |'''[[EEF2|EF-2]]/[[EF-G]]'''
|Sensitive to [[diphtheria toxin]]
|Resistant to diphtheria toxin
|Sensitive to diphtheria toxin
|}

Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule [[16S rRNA]] is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S&nbsp;rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations. 16S&nbsp;rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms.<ref name="ReferenceA">{{cite journal |vauthors=Woese CR, Fox GE |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=74 |issue=11 |pages=5088–90 |date=November 1977 |pmid=270744 |pmc=432104 |doi=10.1073/pnas.74.11.5088 |bibcode=1977PNAS...74.5088W |doi-access=free }}</ref> The more similar the patterns between species, the more closely they are related.<ref>{{ cite book |vauthors=Howland JL |date=2000 |title=The Surprising Archaea: Discovering Another Domain of Life |pages=25–30 |location=Oxford |publisher=Oxford University Press |isbn=978-0-19-511183-5 |url=https://books.google.com/books?id=cWae0vGkX4QC&pg=PA25}}</ref>

Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes.<ref name="ReferenceA"/> These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea.<ref name="ReferenceA"/> His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure.<ref name="nature.com">{{cite journal |vauthors=Cavicchioli R |title=Archaea—timeline of the third domain |journal=Nature Reviews. Microbiology |volume=9 |issue=1 |pages=51–61 |date=January 2011 |pmid=21132019 |doi=10.1038/nrmicro2482 |s2cid=21008512 }}</ref> This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria.<ref name="nature.com"/> The development of the nucleus occurred after the split between Bacteria and this common ancestor.<ref name="nature.com"/><ref name=Woese />

One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and [[salinity]]. Comparative analysis of archaeal genomes has also identified several molecular [[conserved signature indels]] and signature proteins uniquely present in either all archaea or different main groups within archaea.<ref>{{cite journal |vauthors=Gupta RS, Shami A |title=Molecular signatures for the Crenarchaeota and the Thaumarchaeota |journal=Antonie van Leeuwenhoek |volume=99 |issue=2 |pages=133–57 |date=February 2011 |pmid=20711675 |doi=10.1007/s10482-010-9488-3 |s2cid=12874800 }}</ref><ref>{{cite journal |vauthors=Gao B, Gupta RS |title=Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis |journal=BMC Genomics |volume=8 |pages=86 |date=March 2007 |pmid=17394648 |pmc=1852104 |doi=10.1186/1471-2164-8-86 |doi-access=free }}</ref><ref>{{cite journal |vauthors=Gupta RS, Naushad S, Baker S |title=Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov |journal=International Journal of Systematic and Evolutionary Microbiology |volume=65 |issue=Pt 3 |pages=1050–69 |date=March 2015 |pmid=25428416 |doi=10.1099/ijs.0.070136-0 |doi-access=free }}</ref> Another unique feature of archaea, found in no other organisms, is [[methanogenesis]] (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. [[Methanogen]]s also play a critical role in the [[carbon cycle]], breaking down organic carbon into methane, which is also a major greenhouse gas.<ref>{{cite book |vauthors=Deppenmeier U |title=The unique biochemistry of methanogenesis |volume=71 |pages=223–83 |date=2002 |pmid=12102556 |doi=10.1016/s0079-6603(02)71045-3 |isbn=978-0-12-540071-8 |series=Progress in Nucleic Acid Research and Molecular Biology }}</ref>

This difference in the biochemical structure of Bacteria and Archaea has been explained by researchers through evolutionary processes.{{vague|date=October 2024}} It is theorized that both [[Domain (biology)|domains]] originated at deep sea alkaline [[Hydrothermal vent microbial communities|hydrothermal vents]]. At least twice, microbes evolved lipid biosynthesis and cell wall biochemistry. It has been suggested that the [[last universal common ancestor]] was a non-free-living organism.<ref>{{cite journal |vauthors=Martin W, Russell MJ |title=On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=358 |issue=1429 |pages=59–85 |date=January 2003 |pmid=12594918 |pmc=1693102 |doi=10.1098/rstb.2002.1183}}</ref> It may have had a permeable membrane composed of bacterial simple chain amphiphiles (fatty acids), including archaeal simple chain amphiphiles (isoprenoids). These stabilize fatty acid membranes in seawater; this property may have driven the divergence of bacterial and archaeal membranes, "with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".<ref>{{cite journal |vauthors=Jordan SF, Nee E, Lane N |title=Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide |journal=Interface Focus |volume=9 |issue=6 |pages=20190067 |date=December 2019 |pmid=31641436 |pmc=6802135 |doi=10.1098/rsfs.2019.0067}}</ref>

===Relationship to bacteria===
{{PhylomapA|size=350px|caption=[[Phylogenetic tree]] showing the relationship between the Archaea and other domains of life. [[Eukaryote]]s are colored red, archaea green and [[bacteria]] blue. Adapted from {{harvp|Ciccarelli|Doerks|von Mering|Creevey|Snel|Bork|2006}}<ref name=Cicc06>{{cite journal |vauthors=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |date=March 2006 |title=Toward automatic reconstruction of a highly resolved tree of life |journal=[[Science (journal)|Science]] |volume=311 |issue=5765 |pages=1283–1287 |pmid=16513982 |doi=10.1126/science.1123061 |bibcode=2006Sci...311.1283C |citeseerx=10.1.1.381.9514 |s2cid=1615592 }}</ref>}}
The relationships among the [[three-domain system|three domains]] are of central importance for understanding the origin of life. Most of the [[metabolic pathway]]s, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in [[gene expression]] are common between Archaea and Eukarya.<ref>{{cite journal |vauthors=Koonin EV, Mushegian AR, Galperin MY, Walker DR |date=August 1997 |title=Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea |journal=[[Molecular Microbiology]] |volume=25 |issue=4 |pages=619–637 |pmid=9379893 |doi=10.1046/j.1365-2958.1997.4821861.x |doi-access=free |s2cid=36270763 }}</ref> Within prokaryotes, archaeal cell structure is most similar to that of [[Gram-positive]] bacteria, largely because both have a single lipid bilayer<ref name=Gupta-1>{{cite journal |vauthors=Gupta RS |date=December 1998 |title=Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes |journal=[[Microbiology and Molecular Biology Reviews]] |volume=62 |issue=4 |pages=1435–1491 |pmid=9841678 |pmc=98952 |doi=10.1128/MMBR.62.4.1435-1491.1998 }}</ref> and usually contain a thick sacculus (exoskeleton) of varying chemical composition.<ref>{{cite journal |vauthors=Koch AL |date=April 2003 |title=Were Gram-positive rods the first bacteria? |journal=[[Trends in Microbiology]] |volume=11 |issue=4 |pages=166–170 |pmid=12706994 |doi=10.1016/S0966-842X(03)00063-5 }}</ref> In some phylogenetic trees based upon different gene / protein sequences of prokaryotic [[Homology (biology)|homologs]], the archaeal homologs are more closely related to those of gram-positive bacteria.<ref name=Gupta-1/> Archaea and gram-positive bacteria also share conserved [[indels]] in a number of important proteins, such as [[Hsp70]] and [[glutamine synthetase]]&nbsp;I;<ref name=Gupta-1/><ref name=Gupta-2>{{cite journal |vauthors=Gupta RS |date=August 1998 |title=What are archaebacteria: Life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms |journal=[[Molecular Microbiology]] |volume=29 |issue=3 |pages=695–707 |pmid=9723910 |doi=10.1046/j.1365-2958.1998.00978.x |doi-access=free |s2cid=41206658 }}</ref> but the phylogeny of these genes was interpreted to reveal inter-domain gene transfer,<ref>{{cite journal |vauthors=Gogarten JP |date=November 1994 |title=Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages |journal=[[Journal of Molecular Evolution]] |volume=39 |issue=5 |pages=541–543 |pmid=7807544 |doi=10.1007/bf00173425 |bibcode=1994JMolE..39..541G |s2cid=44922755 }}</ref><ref>{{cite journal |vauthors=Brown JR, Masuchi Y, Robb FT, Doolittle WF |title=Evolutionary relationships of bacterial and archaeal glutamine synthetase genes |journal=[[Journal of Molecular Evolution]] |volume=38 |issue=6 |pages=566–576 |date=June 1994 |pmid=7916055 |doi=10.1007/BF00175876 |bibcode=1994JMolE..38..566B |s2cid=21493521 }}</ref> and might not reflect the organismal relationship(s).<ref name=pmid26323756>{{cite journal |vauthors=Katz LA |date=September 2015 |title=Recent events dominate inter-domain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=370 |issue=1678 |page=20140324 |pmid=26323756 |pmc=4571564 |doi=10.1098/rstb.2014.0324 }}</ref>

It has been proposed that the archaea evolved from Gram-positive bacteria in response to antibiotic [[evolutionary pressure|selection pressure]].<ref name=Gupta-1/><ref name=Gupta-2/><ref name=Gupta-3>{{cite journal |vauthors=Gupta RS |year=2000 |title=The natural evolutionary relationships among prokaryotes |journal=[[Critical Reviews in Microbiology]] |volume=26 |issue=2 |pages=111–131 |pmid=10890353 |doi=10.1080/10408410091154219 |citeseerx=10.1.1.496.1356 |s2cid=30541897 }}</ref> This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by Gram-positive bacteria,<ref name=Gupta-1/><ref name=Gupta-2/> and that these antibiotics act primarily on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea.<ref name=Gupta-3/> The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms;<ref name=Gupta-3/><ref>{{cite book |vauthors=Gupta RS |year=2005 |chapter=Molecular sequences and the early history of life |veditors=Sapp J |title=Microbial Phylogeny and Evolution: Concepts and controversies |place=New York, NY |publisher=Oxford University Press |pages=160–183 }}</ref> [[Thomas Cavalier-Smith|Cavalier-Smith]] has made a similar suggestion, the [[Neomura]] hypothesis.<ref>{{cite journal |vauthors=Cavalier-Smith T |date=January 2002 |title=The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification |journal=[[International Journal of Systematic and Evolutionary Microbiology]] |volume=52 |issue=Pt&nbsp;1 |pages=7–76 |pmid=11837318 |doi=10.1099/00207713-52-1-7 |doi-access=free }}</ref> This proposal is also supported by other work investigating protein structural relationships<ref>{{cite journal |vauthors=Valas RE, Bourne PE |date=February 2011 |title=The origin of a derived superkingdom: How a gram-positive bacterium crossed the desert to become an archaeon |journal=[[Biology Direct]] |volume=6 |pages=16 |pmid=21356104 |pmc=3056875 |doi=10.1186/1745-6150-6-16 |doi-access=free }}</ref> and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.<ref>{{cite journal |vauthors=Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA |date=September 2006 |title=Evidence that the root of the tree of life is not within the Archaea |journal=[[Molecular Biology and Evolution]] |volume=23 |issue=9 |pages=1648–1651 |pmid=16801395 |doi=10.1093/molbev/msl046 |doi-access=free }}</ref>

===Relation to eukaryotes===
{{further|Symbiogenesis}}

[[File:Symbiogenesis 2 mergers.svg|thumb|upright=1.8|In the theory of [[symbiogenesis]], a merger of an Promethearchaeati / "Asgard" archaean and an aerobic bacterium created the [[eukaryote]]s, with aerobic [[Mitochondrion|mitochondria]]; a second merger added [[chloroplast]]s, creating the [[Viridiplantae|green plants]].<ref name=latorre>{{cite book |vauthors=Latorre A, Durban A, Moya A, Pereto J |chapter-url=https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |chapter=The role of symbiosis in eukaryotic evolution |title=Origins and Evolution of Life: An astrobiological perspective |veditors=Gargaud M, López-Garcìa P, Martin H |year=2011 |location=Cambridge |publisher=Cambridge University Press |pages=326–339 |isbn=978-0-521-76131-4 |access-date=27 August 2017 |archive-date=24 March 2019 |archive-url=https://web.archive.org/web/20190324055723/https://books.google.com/books?id=m3oFebknu1cC&pg=PA326 |url-status=live }}</ref>]]

The evolutionary relationship between archaea and [[eukaryote]]s remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.<ref name="pmid29123225">{{cite journal |vauthors=Eme L, Spang A, Lombard J, Stairs CW, ((Ettema TJG)) |title=Archaea and the origin of eukaryotes |journal=Nature Reviews. Microbiology |volume=15 |issue=12 |pages=711–723 |date=November 2017 |pmid=29123225 |doi=10.1038/nrmicro.2017.133 |s2cid=8666687 }}</ref>

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum [[Thermoproteota]] is closer than the relationship between the [[Methanobacteriati]] and the phylum Thermoproteota<ref name="ReferenceC">{{cite journal |vauthors=Lake JA |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184–86 |date=January 1988 |pmid=3340165 |doi=10.1038/331184a0 |bibcode=1988Natur.331..184L |s2cid=4368082 }}</ref> and the presence of archaea-like genes in certain bacteria, such as ''[[Thermotoga maritima]]'', from [[horizontal gene transfer]].<ref>{{cite journal |vauthors=Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM |title=Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima |journal=Nature |volume=399 |issue=6734 |pages=323–29 |date=May 1999 |pmid=10360571 |doi=10.1038/20601 |display-authors=6 |bibcode=1999Natur.399..323N |s2cid=4420157 }}</ref> The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea,<ref>{{cite journal |vauthors=Gouy M, Li WH |title=Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree |journal=Nature |volume=339 |issue=6220 |pages=145–47 |date=May 1989 |pmid=2497353 |doi=10.1038/339145a0 |bibcode=1989Natur.339..145G |s2cid=4315004 }}</ref><ref>{{cite journal |vauthors=Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV |title=The deep archaeal roots of eukaryotes |journal=Molecular Biology and Evolution |volume=25 |issue=8 |pages=1619–30 |date=August 2008 |pmid=18463089 |pmc=2464739 |doi=10.1093/molbev/msn108 }}</ref> and that eukaryotes arose through [[symbiogenesis]], the fusion of an archaean and a eubacterium, which formed the [[mitochondrion|mitochondria]]; this hypothesis explains the genetic similarities between the groups.<ref name=latorre/> The [[eocyte hypothesis]] instead posits that [[Eukaryota]] emerged relatively late from the Archaea.<ref name=2domains>{{cite journal |vauthors=Williams TA, Foster PG, Cox CJ, Embley TM |title=An archaeal origin of eukaryotes supports only two primary domains of life |journal=Nature |volume=504 |issue=7479 |pages=231–36 |date=December 2013 |pmid=24336283 |doi=10.1038/nature12779 |bibcode=2013Natur.504..231W |s2cid=4461775 |url=https://eprint.ncl.ac.uk/fulltext.aspx?url=199146/704E71B4-8D68-4F3C-93BA-E73C50449593.pdf&pub_id=199146 }}</ref>

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. It has been called a transitional organism between prokaryotes and eukaryotes.<ref name="NYT-20150506">{{cite news |vauthors=Zimmer C |author-link=Carl Zimmer |title=Under the Sea, a Missing Link in the Evolution of Complex Cells |url=https://www.nytimes.com/2015/05/07/science/under-the-sea-a-missing-link-in-the-evolution-of-complex-cells.html |date=6 May 2015 |work=[[The New York Times]] |access-date=6 May 2015}}</ref><ref>{{cite journal |vauthors=Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ |title=Complex archaea that bridge the gap between prokaryotes and eukaryotes |journal=Nature |volume=521 |issue=7551 |pages=173–179 |date=May 2015 |pmid=25945739 |pmc=4444528 |doi=10.1038/nature14447 |bibcode=2015Natur.521..173S }}</ref>

Several sister phyla of "Lokiarchaeota" have since been found ("[[Thorarchaeota]]", "[[Odinarchaeota]]", "[[Heimdallarchaeota]]"), all together comprising a newly proposed [[Supergroup (biology)|supergroup]] "Asgard".<ref name="ZN_Asgard2017"/><ref name="NCBI taxonomy page on Archaea">{{citation |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?webmode=Undef&id=2157&lvl=5&lin=f&keep=1&srchmode=1&unlock |title=NCBI taxonomy page on Archaea }}</ref><ref>{{cite journal |vauthors=Seitz KW, Lazar CS, Hinrichs KU, Teske AP, Baker BJ |title=Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction |journal=The ISME Journal |volume=10 |issue=7 |pages=1696–705 |date=July 2016 |pmid=26824177 |pmc=4918440 |doi=10.1038/ismej.2015.233 |bibcode=2016ISMEJ..10.1696S }}</ref>

Details of the relation of Promethearchaeati / "Asgard" members and eukaryotes are still under consideration,<ref name="pmid31384702">{{cite journal |vauthors=MacLeod F, Kindler GS, Wong HL, Chen R, Burns BP |title=Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes |journal=AIMS Microbiology |volume=5 |issue=1 |pages=48–61 |date=2019 |pmid=31384702 |pmc=6646929 |doi=10.3934/microbiol.2019.1.48 }}</ref> although, in January 2020, scientists reported that ''[[Candidatus Prometheoarchaeum syntrophicum]]'', a type of Promethearchaeati / "Asgard" archaea, may be a possible link between simple [[prokaryotic]] and complex [[eukaryotic]] microorganisms about two billion years ago.<ref name="NYT-2020115">{{cite news |vauthors=Zimmer C |title=This Strange Microbe May Mark One of Life's Great Leaps – A organism living in ocean muck offers clues to the origins of the complex cells of all animals and plants. |url=https://www.nytimes.com/2020/01/15/science/cells-eukaryotes-archaea.html |date=15 January 2020 |work=[[The New York Times]] |access-date=16 January 2020 }}</ref><ref name="NAT-20200115">{{cite journal |vauthors=Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K |display-authors=6 |title=Isolation of an archaeon at the prokaryote-eukaryote interface |journal=Nature |volume=577 |issue=7791 |pages=519–525 |date=January 2020 |pmid=31942073 |pmc=7015854 |doi=10.1038/s41586-019-1916-6 |bibcode=2020Natur.577..519I |doi-access=free }}</ref><ref name="ARC-200929">{{cite journal |vauthors=Tirumalai MR, Sivaraman RV, Kutty LA, Song EL, Fox GE|title=Ribosomal Protein Cluster Organization in Asgard Archaea|journal=Archaea|volume=2023|date=September 2023 |pages=1–16 |doi=10.1155/2023/5512414 |doi-access=free |pmid=38314098 |pmc=10833476|bibcode=2023Archa202312414T }}</ref>

==Morphology==
Individual archaea range from 0.1&nbsp;[[Micrometre|micrometers]] (μm) to over 15&nbsp;μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.<ref name=Bergey/> 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]]''.<ref>{{cite web|vauthors=Barns S, Burggraf S |date=1997 |url=http://tolweb.org/Crenarchaeota/9 |title=Crenarchaeota |series=Version 01 January 1997 |work=The Tree of Life Web Project}}</ref> Archaea in the genus ''[[Haloquadratum]]'' such as ''[[Haloquadratum walsbyi]]'' are flat, square specimens that live in hypersaline pools.<ref name=Walsby1980>{{cite journal|vauthors=Walsby AE|date=1980|title=A square bacterium|journal=Nature|volume=283|issue=5742|pages=69–71|doi=10.1038/283069a0|bibcode=1980Natur.283...69W |s2cid=4341717}}</ref> These unusual shapes are probably maintained by both their cell walls and a [[prokaryotic cytoskeleton]]. Proteins related to the cytoskeleton components of other organisms exist in archaea,<ref>{{cite journal |vauthors=Hara F, Yamashiro K, Nemoto N, Ohta Y, Yokobori S, Yasunaga T, Hisanaga S, Yamagishi A |title=An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin |journal=Journal of Bacteriology |volume=189 |issue=5 |pages=2039–45 |date=March 2007 |pmid=17189356 |pmc=1855749 |doi=10.1128/JB.01454-06 |display-authors=6 }}</ref> and filaments form within their cells,<ref>{{cite journal |vauthors=Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ |title=Chaperonin filaments: the archaeal cytoskeleton? |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=94 |issue=10 |pages=5383–88 |date=May 1997 |pmid=9144246 |pmc=24687 |doi=10.1073/pnas.94.10.5383 |bibcode=1997PNAS...94.5383T |doi-access=free }}</ref> but in contrast with other organisms, these cellular structures are poorly understood.<ref>{{cite journal |vauthors=Hixon WG, Searcy DG |title=Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts |journal=Bio Systems |volume=29 |issue=2–3 |pages=151–60 |date=1993 |pmid=8374067 |doi=10.1016/0303-2647(93)90091-P |bibcode=1993BiSys..29..151H }}</ref> In ''[[Thermoplasma]]'' and ''[[Ferroplasma]]'' the lack of a [[cell wall]] means that the cells have irregular shapes, and can resemble [[Amoeboid|amoebae]].<ref name=Golyshina/>

Some species form aggregates or filaments of cells up to 200&nbsp;μm long.<ref name=Bergey/> These organisms can be prominent in [[biofilm]]s.<ref>{{cite journal |vauthors=Hall-Stoodley L, Costerton JW, Stoodley P |title=Bacterial biofilms: from the natural environment to infectious diseases |journal=Nature Reviews. Microbiology |volume=2 |issue=2 |pages=95–108 |date=February 2004 |pmid=15040259 |doi=10.1038/nrmicro821 |s2cid=9107205 }}</ref> Notably, aggregates of ''[[Thermococcus]] coalescens'' cells fuse together in culture, forming single giant cells.<ref>{{cite journal |vauthors=Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M, Marumo K, Maruyama A, Sugai A, Itoh T, Ishibashi J, Urabe T, Kamekura M |title=Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount |journal=International Journal of Systematic and Evolutionary Microbiology |volume=55 |issue=Pt 6 |pages=2507–14 |date=November 2005 |pmid=16280518 |doi=10.1099/ijs.0.63432-0 |display-authors=6 |doi-access=free }}</ref> 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.<ref>{{cite journal |vauthors=Nickell S, Hegerl R, Baumeister W, Rachel R |title=Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography |journal=Journal of Structural Biology |volume=141 |issue=1 |pages=34–42 |date=January 2003 |pmid=12576018 |doi=10.1016/S1047-8477(02)00581-6 }}</ref> The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.<ref>{{cite journal |vauthors=Horn C, Paulmann B, Kerlen G, Junker N, Huber H |title=In vivo observation of cell division of anaerobic hyperthermophiles by using a high-intensity dark-field microscope |journal=Journal of Bacteriology |volume=181 |issue=16 |pages=5114–18 |date=August 1999 |pmid=10438790 |pmc=94007 |doi=10.1128/JB.181.16.5114-5118.1999 }}</ref> Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Methanobacteriati species are spaced along thin filaments that can range up to {{convert|15|cm}} long; these filaments are made of a particular bacteria species.<ref>{{cite journal |vauthors=Rudolph C, Wanner G, Huber R |title=Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology |journal=Applied and Environmental Microbiology |volume=67 |issue=5 |pages=2336–44 |date=May 2001 |pmid=11319120 |pmc=92875 |doi=10.1128/AEM.67.5.2336-2344.2001 |bibcode=2001ApEnM..67.2336R }}</ref>

==Structure, composition development, and operation==
Archaea and bacteria have generally similar [[Cell (biology)|cell]] structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and [[organelle]]s.<ref name=PMID8177167/> Like bacteria, the [[cell membrane]]s of archaea are usually bounded by a [[cell wall]] and they swim using one or more [[flagella]].<ref name=Thomas/> Structurally, archaea are most similar to [[gram-positive bacteria]]. Most have a single plasma membrane and cell wall, and lack a [[periplasmic space]]; the exception to this general rule is ''[[Ignicoccus]]'', which possess a particularly large periplasm that contains membrane-bound [[vesicle (biology)|vesicles]] and is enclosed by an outer membrane.<ref>{{cite journal |vauthors=Rachel R, Wyschkony I, Riehl S, Huber H |title=The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon |journal=Archaea |volume=1 |issue=1 |pages=9–18 |date=March 2002 |pmid=15803654 |pmc=2685547 |doi=10.1155/2002/307480 |doi-access=free }}</ref>

===Cell wall and archaella===
{{Further|Cell wall#Archaeal cell walls}}

Most archaea (but not ''[[Thermoplasma]]'' and ''[[Ferroplasma]]'') possess a cell wall.<ref name=Golyshina>{{cite journal |vauthors=Golyshina OV, Pivovarova TA, Karavaiko GI, Kondratéva TF, Moore ER, Abraham WR, Lünsdorf H, Timmis KN, Yakimov MM, Golyshin PN |title=Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea |journal=International Journal of Systematic and Evolutionary Microbiology |volume=50 |issue=3 |pages=997–1006 |date=May 2000 |pmid=10843038 |doi=10.1099/00207713-50-3-997 |display-authors=6 |doi-access=free }}</ref> In most archaea, the wall is assembled from surface-layer proteins, which form an [[S-layer]].<ref>{{cite journal |vauthors=Sára M, Sleytr UB |title=S-Layer proteins |journal=Journal of Bacteriology |volume=182 |issue=4 |pages=859–68 |date=February 2000 |pmid=10648507 |pmc=94357 |doi=10.1128/JB.182.4.859-868.2000 }}</ref> An S-layer is a rigid array of protein molecules that cover the outside of the cell (like [[chain mail]]).<ref>{{cite journal |vauthors=Engelhardt H, Peters J |title=Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions |journal=Journal of Structural Biology |volume=124 |issue=2–3 |pages=276–302 |date=December 1998 |pmid=10049812 |doi=10.1006/jsbi.1998.4070 }}</ref> This layer provides both chemical and physical protection, and can prevent [[macromolecule]]s from contacting the cell membrane.<ref name=Kandler1998>{{cite journal |vauthors=Kandler O, König H |title=Cell wall polymers in Archaea (Archaebacteria) |journal=Cellular and Molecular Life Sciences |volume=54 |issue=4 |pages=305–08 |date=April 1998 |pmid=9614965 |doi=10.1007/s000180050156|s2cid=13527169 |pmc=11147200 }}</ref> Unlike bacteria, archaea lack [[peptidoglycan]] in their cell walls.<ref name="Howland">{{cite book |vauthors=Howland JL |date=2000 |title=The Surprising Archaea: Discovering Another Domain of Life |page=32 |location=Oxford |publisher=Oxford University Press |isbn=978-0-19-511183-5 }}</ref> [[Methanobacteriales]] do have cell walls containing [[pseudopeptidoglycan]], which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks [[D-amino acids]] and [[N-acetylmuramic acid]], substituting the latter with [[N-Acetyltalosaminuronic acid]].<ref name="Kandler1998"/>

Archaeal flagella are known as [[archaellum|archaella]], that operate like bacterial [[flagellum|flagella]] – their long stalks are driven by rotatory motors at the base. These motors are powered by a [[electrochemical gradient|proton gradient]] across the membrane, but archaella are notably different in composition and development.<ref name=Thomas>{{cite journal |vauthors=Thomas NA, Bardy SL, Jarrell KF |title=The archaeal flagellum: a different kind of prokaryotic motility structure |journal=FEMS Microbiology Reviews |volume=25 |issue=2 |pages=147–74 |date=April 2001 |pmid=11250034 |doi=10.1111/j.1574-6976.2001.tb00575.x |doi-access=}}</ref> The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the [[type III secretion system]],<ref>{{cite journal |vauthors=Gophna U, Ron EZ, Graur D |title=Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events |journal=Gene |volume=312 |pages=151–63 |date=July 2003 |pmid=12909351 |doi=10.1016/S0378-1119(03)00612-7 }}</ref><ref>{{cite journal |vauthors=Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH |title=Phylogenetic analyses of the constituents of Type III protein secretion systems |journal=Journal of Molecular Microbiology and Biotechnology |volume=2 |issue=2 |pages=125–44 |date=April 2000 |pmid=10939240 }}</ref> while archaeal flagella appear to have evolved from bacterial [[type IV pili]].<ref>{{cite journal |vauthors=Ng SY, Chaban B, Jarrell KF |title=Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications |journal=Journal of Molecular Microbiology and Biotechnology |volume=11 |issue=3–5 |pages=167–91 |date=2006 |pmid=16983194 |doi=10.1159/000094053 |s2cid=30386932 }}</ref> In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.<ref>{{cite journal |vauthors=Bardy SL, Ng SY, Jarrell KF |title=Prokaryotic motility structures |journal=Microbiology |volume=149 |issue=Pt 2 |pages=295–304 |date=February 2003 |pmid=12624192 |doi=10.1099/mic.0.25948-0 |doi-access=free |s2cid=20751743 }}</ref>

===Membranes===
[[File:Archaea membrane.svg|thumb|right|upright=1.5|Membrane structures. '''Top''',&nbsp;an archaeal phospholipid: '''1''',&nbsp;isoprene chains; '''2''',&nbsp;ether linkages; '''3''',&nbsp;[[Levorotation and dextrorotation|L-glycerol]] [[Moiety (chemistry)|moiety]]; '''4''',&nbsp;phosphate group. '''Middle''',&nbsp;a bacterial or eukaryotic phospholipid: '''5''',&nbsp;fatty acid chains; '''6''',&nbsp;ester linkages; '''7''',&nbsp;[[Levorotation and dextrorotation|D-glycerol]] moiety; '''8''',&nbsp;phosphate group. '''Bottom''': '''9''',&nbsp;lipid bilayer of bacteria and eukaryotes; '''10''',&nbsp;lipid monolayer of some archaea.]]
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.<ref name=Koga/> In all organisms, [[cell membrane]]s are made of molecules known as [[phospholipid]]s. These molecules possess both a [[chemical polarity|polar]] part that dissolves in water (the [[phosphate]] "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a [[glycerol]] moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a [[lipid bilayer]].<ref name="pmid29739208">{{cite journal |vauthors=Youssefian S, Rahbar N, Van Dessel S |title=Thermal conductivity and rectification in asymmetric archaeal lipid membranes |journal=The Journal of Chemical Physics |volume=148 |issue=17 |pages=174901 |date=May 2018 |pmid=29739208 |doi=10.1063/1.5018589 |bibcode=2018JChPh.148q4901Y }}</ref>

The phospholipids of archaea are unusual in four ways:
* They have membranes composed of glycerol-[[ether lipid]]s, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-[[ester]] [[lipid]]s.<ref>{{cite journal |vauthors=De Rosa M, Gambacorta A, Gliozzi A |title=Structure, biosynthesis, and physicochemical properties of archaebacterial lipids |journal=Microbiological Reviews |volume=50 |issue=1 |pages=70–80 |date=March 1986 |pmid=3083222 |pmc=373054 |doi=10.1128/MMBR.50.1.70-80.1986 }}</ref> The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids, this is an [[ester|ester bond]], whereas in ether lipids this is an [[ether|ether bond]].<ref name="pmid25229144">{{cite journal |vauthors=Balleza D, Garcia-Arribas AB, Sot J, Ruiz-Mirazo K, Goñi FM |title=Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains |journal=Biophysical Journal |volume=107 |issue=6 |pages=1364–74 |date=September 2014 |pmid=25229144 |pmc=4167531 |doi=10.1016/j.bpj.2014.07.036 |bibcode=2014BpJ...107.1364B }}</ref>
* The [[stereochemistry]] of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called ''[[enantiomer]]s''. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by [[enzyme]]s adapted for the other. The archaeal phospholipids are built on a backbone of ''sn''-glycerol-1-phosphate, which is an enantiomer of ''sn''-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains.<ref name=Koga>{{cite journal |vauthors=Koga Y, Morii H |title=Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations |journal=Microbiology and Molecular Biology Reviews |volume=71 |issue=1 |pages=97–120 |date=March 2007 |pmid=17347520 |pmc=1847378 |doi=10.1128/MMBR.00033-06 }}</ref>
* Archaeal lipid tails differ from those of other organisms in that they are based upon long [[isoprene|isoprenoid]] chains with multiple side-branches, sometimes with [[cyclopropane]] or [[cyclohexane]] rings.<ref>{{cite journal |vauthors=Damsté JS, Schouten S, Hopmans EC, van Duin AC, Geenevasen JA |title=Crenarchaeol: The characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota |journal=Journal of Lipid Research |volume=43 |issue=10 |pages=1641–51 |date=October 2002 |pmid=12364548 |doi=10.1194/jlr.M200148-JLR200 |doi-access=free }}</ref> By contrast, the [[fatty acid]]s in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.<ref>{{cite journal |vauthors=Koga Y, Morii H |s2cid=42237252 |title=Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects |journal=Bioscience, Biotechnology, and Biochemistry |volume=69 |issue=11 |pages=2019–34 |date=November 2005 |pmid=16306681 |doi=10.1271/bbb.69.2019 |doi-access=free }}</ref>
* In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a [[bolaamphiphile]]); this fusion may make their membranes more rigid and better able to resist harsh environments.<ref>{{cite journal |vauthors=Hanford MJ, Peeples TL |title=Archaeal tetraether lipids: unique structures and applications |journal=Applied Biochemistry and Biotechnology |volume=97 |issue=1 |pages=45–62 |date=January 2002 |pmid=11900115 |doi=10.1385/ABAB:97:1:45 |s2cid=22334666 }}</ref> For example, the lipids in ''[[Ferroplasma]]'' are of this type, which is thought to aid this organism's survival in its highly acidic habitat.<ref>{{cite journal |vauthors=Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF |title=Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid |journal=Extremophiles |volume=8 |issue=5 |pages=411–19 |date=October 2004 |pmid=15258835 |doi=10.1007/s00792-004-0404-5 |s2cid=15702103 }}</ref>

==Metabolism==
{{Further|Microbial metabolism}}
Archaea exhibit a great variety of chemical reactions in their [[metabolism]] and use many sources of energy. These reactions are classified into [[primary nutritional groups|nutritional groups]], depending on energy and carbon sources. Some archaea obtain energy from [[inorganic compound]]s such as [[sulfur]] or [[ammonia]] (they are [[chemotroph]]s). These include [[nitrifying bacteria|nitrifiers]], [[methanogen]]s and [[anaerobic organism|anaerobic]] [[methane]] [[oxidiser]]s.<ref name=valentine>{{cite journal |vauthors=Valentine DL |title=Adaptations to energy stress dictate the ecology and evolution of the Archaea |journal=Nature Reviews. Microbiology |volume=5 |issue=4 |pages=316–23 |date=April 2007 |pmid=17334387 |doi=10.1038/nrmicro1619 |s2cid=12384143 }}</ref> In these reactions, one compound passes electrons to another (in a [[redox]] reaction), releasing energy to fuel the cell's activities. One compound acts as an [[electron donor]] and one as an [[electron acceptor]]. The energy released is used to generate [[adenosine triphosphate]] (ATP) through [[chemiosmosis]], the same basic process that happens in the [[mitochondrion]] of eukaryotic cells.<ref name=Schafer>{{cite journal |vauthors=Schäfer G, Engelhard M, Müller V |title=Bioenergetics of the Archaea |journal=Microbiology and Molecular Biology Reviews |volume=63 |issue=3 |pages=570–620 |date=September 1999 |pmid=10477309 |pmc=103747 |doi=10.1128/MMBR.63.3.570-620.1999 }}</ref>

Other groups of archaea use sunlight as a source of energy (they are [[phototroph]]s), but oxygen–generating [[photosynthesis]] does not occur in any of these organisms.<ref name=Schafer/> Many basic [[metabolic pathway]]s are shared among all forms of life; for example, archaea use a modified form of [[glycolysis]] (the [[Entner–Doudoroff pathway]]) and either a complete or partial [[citric acid cycle]].<ref name=Zillig>{{cite journal |vauthors=Zillig W |title=Comparative biochemistry of Archaea and Bacteria |journal=Current Opinion in Genetics & Development |volume=1 |issue=4 |pages=544–51 |date=December 1991 |pmid=1822288 |doi=10.1016/S0959-437X(05)80206-0 }}</ref> These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.<ref>{{cite journal |vauthors=Romano AH, Conway T |title=Evolution of carbohydrate metabolic pathways |journal=Research in Microbiology |volume=147 |issue=6–7 |pages=448–55 |date=1996 |pmid=9084754 |doi=10.1016/0923-2508(96)83998-2 |doi-access=free }}</ref>

{|class="wikitable" style="margin-left: auto; margin-right: auto;"
|+ Nutritional types in archaeal metabolism
|-
!Nutritional type
!Source of energy
!Source of carbon
!Examples
|-
|&nbsp;[[Phototroph]]s&nbsp;
|style="text-align:center;"|&nbsp;Sunlight&nbsp;
|style="text-align:center;"|&nbsp;Organic compounds&nbsp;
|&nbsp;''[[Halobacterium]]''&nbsp;
|-
|&nbsp;[[Lithotroph]]s
|style="text-align:center;"|&nbsp;Inorganic compounds
|style="text-align:center;"|&nbsp;Organic compounds or [[carbon fixation]]
|&nbsp;''[[Ferroglobus]]'', ''[[Methanobacteria]]'' or ''[[Pyrolobus]]''&nbsp;
|-
|&nbsp;[[Organotroph]]s
|style="text-align:center;"|&nbsp;Organic compounds&nbsp;
|style="text-align:center;"|&nbsp;Organic compounds or [[carbon fixation]]&nbsp;
|&nbsp;''[[Pyrococcus]]'', ''[[Sulfolobus]]'' or ''[[Methanosarcinales]]''&nbsp;
|}

Some Methanobacteriati are [[methanogen]]s (archaea that produce methane as a result of metabolism) living in [[anaerobic environment]]s, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen.<ref>{{cite book |vauthors=Koch AL |title=How did bacteria come to be? |volume=40 |pages=353–99 |date=1998 |pmid=9889982 |doi=10.1016/S0065-2911(08)60135-6 |isbn=978-0-12-027740-7 |series=Advances in Microbial Physiology }}</ref> A common reaction involves the use of [[carbon dioxide]] as an electron acceptor to oxidize [[hydrogen]]. Methanogenesis involves a range of [[coenzyme]]s that are unique to these archaea, such as [[coenzyme M]] and [[methanofuran]].<ref>{{cite journal |vauthors=DiMarco AA, Bobik TA, Wolfe RS |title=Unusual coenzymes of methanogenesis |journal=Annual Review of Biochemistry |volume=59 |pages=355–94 |date=1990 |pmid=2115763 |doi=10.1146/annurev.bi.59.070190.002035 }}</ref> Other organic compounds such as [[Alcohol (chemistry)|alcohol]]s, [[acetic acid]] or [[formic acid]] are used as alternative [[electron acceptor]]s by methanogens. These reactions are common in [[Gut (zoology)|gut]]-dwelling archaea. [[Acetic acid]] is also broken down into methane and carbon dioxide directly, by ''acetotrophic'' archaea. These acetotrophs are archaea in the order [[Methanosarcinales]], and are a major part of the communities of microorganisms that produce [[biogas]].<ref>{{cite journal |vauthors=Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B |title=Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass |journal=Systematic and Applied Microbiology |volume=31 |issue=3 |pages=190–205 |date=August 2008 |pmid=18501543 |doi=10.1016/j.syapm.2008.02.003 |bibcode=2008SyApM..31..190K |display-authors=6 }}</ref>

[[File:Bacteriorhodopsin.png|thumb|upright|right|Bacteriorhodopsin from ''[[Halobacterium salinarum]]''. The retinol [[cofactor (biochemistry)|cofactor]] and residues involved in proton transfer are shown as [[ball-and-stick model]]s.<ref>
Based on [http://www.rcsb.org/pdb/explore.do?structureId=1FBB PDB 1FBB]. Data published in {{cite journal |vauthors=Subramaniam S, Henderson R |title=Molecular mechanism of vectorial proton translocation by bacteriorhodopsin |journal=Nature |volume=406 |issue=6796 |pages=653–57 |date=August 2000 |pmid=10949309 |doi=10.1038/35020614 |bibcode=2000Natur.406..653S |s2cid=4395278 }}</ref>]]
Other archaea use {{chem|CO|2}} in the [[atmosphere]] as a source of carbon, in a process called [[carbon fixation]] (they are [[autotroph]]s). This process involves either a highly modified form of the [[Calvin cycle]]<ref>{{cite journal |vauthors=Mueller-Cajar O, Badger MR |title=New roads lead to Rubisco in archaebacteria |journal=BioEssays |volume=29 |issue=8 |pages=722–24 |date=August 2007 |pmid=17621634 |doi=10.1002/bies.20616 }}</ref> or another metabolic pathway called the 3-hydroxypropionate/&thinsp;4-hydroxybutyrate cycle.<ref>{{cite journal |vauthors=Berg IA, Kockelkorn D, Buckel W, Fuchs G |s2cid=13218676 |title=A 3-hydroxypropionate/&thinsp;4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea |journal=Science |volume=318 |issue=5857 |pages=1782–86 |date=December 2007 |pmid=18079405 |doi=10.1126/science.1149976 |bibcode=2007Sci...318.1782B }}</ref> The Thermoproteota also use the [[reverse Krebs cycle]] while the Methanobacteriati also use the [[reductive acetyl-CoA pathway]].<ref>{{cite journal |vauthors=Thauer RK |title=Microbiology. A fifth pathway of carbon fixation |journal=Science |volume=318 |issue=5857 |pages=1732–33 |date=December 2007 |pmid=18079388 |doi=10.1126/science.1152209 |s2cid=83805878 }}</ref> Carbon fixation is powered by inorganic energy sources. No known archaea carry out [[photosynthesis]].<ref name=Bryant>{{cite journal |vauthors=Bryant DA, Frigaard NU |title=Prokaryotic photosynthesis and phototrophy illuminated |journal=Trends in Microbiology |volume=14 |issue=11 |pages=488–96 |date=November 2006 |pmid=16997562 |doi=10.1016/j.tim.2006.09.001 }}</ref> Archaeal energy sources are extremely diverse, and range from the oxidation of [[ammonia]] by the [[Nitrosopumilales]]<ref name="ReferenceD">{{cite journal |vauthors=Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA |title=Isolation of an autotrophic ammonia-oxidizing marine archaeon |journal=Nature |volume=437 |issue=7058 |pages=543–46 |date=September 2005 |pmid=16177789 |doi=10.1038/nature03911 |bibcode=2005Natur.437..543K |s2cid=4340386 }}</ref><ref name="ReferenceB">{{cite journal |vauthors=Francis CA, Beman JM, Kuypers MM |title=New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation |journal=The ISME Journal |volume=1 |issue=1 |pages=19–27 |date=May 2007 |pmid=18043610 |doi=10.1038/ismej.2007.8 |doi-access=free |bibcode=2007ISMEJ...1...19F }}</ref> to the oxidation of [[hydrogen sulfide]] or elemental [[sulfur]] by species of ''[[Sulfolobus]]'', using either oxygen or metal ions as electron acceptors.<ref name=Schafer/>

[[Phototroph]]ic archaea use light to produce chemical energy in the form of ATP. In the [[Halobacteria]], light-activated ion pumps like [[bacteriorhodopsin]] and [[halorhodopsin]] generate ion gradients by pumping ions out of and into the cell across the [[plasma membrane]]. The energy stored in these [[electrochemical gradient]]s is then converted into ATP by [[ATP synthase]].<ref name=Bergey/> This process is a form of [[photophosphorylation]]. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a [[retinol]] [[Cofactor (biochemistry)|cofactor]] buried in the center of the protein.<ref>{{cite journal |vauthors=Lanyi JK |title=Bacteriorhodopsin |journal=Annual Review of Physiology |volume=66 |pages=665–88 |date=2004 |pmid=14977418 |doi=10.1146/annurev.physiol.66.032102.150049 }}</ref>

==Genetics==
{{Further|Plasmid|Genome}}
Archaea usually have a single [[circular chromosome]],<ref name=Allers/> but many euryarchaea have been shown to bear multiple copies of this chromosome.<ref>{{cite journal |vauthors=Hildenbrand C, Stock T, Lange C, Rother M, Soppa J |title=Genome copy numbers and gene conversion in methanogenic archaea |journal=Journal of Bacteriology |volume=193 |issue=3 |pages=734–43 |date=February 2011 |pmid=21097629|pmc=3021236 |doi=10.1128/JB.01016-10 }}</ref> The largest known archaeal genome as of 2002 was 5,751,492&nbsp;[[base pair]]s in ''[[Methanosarcina acetivorans]]''.<ref>{{cite journal |vauthors=Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B |display-authors=6 |title=The genome of M. acetivorans reveals extensive metabolic and physiological diversity |journal=Genome Research |volume=12 |issue=4 |pages=532–42 |date=April 2002 |pmid=11932238 |pmc=187521 |doi=10.1101/gr.223902 }}</ref> The tiny 490,885&nbsp;base-pair genome of ''[[Nanoarchaeum equitans]]'' is one-tenth of this size and the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes.<ref name="pnas.org">{{cite journal |vauthors=Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M |title=The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=100 |issue=22 |pages=12984–88 |date=October 2003 |pmid=14566062 |pmc=240731 |doi=10.1073/pnas.1735403100 |display-authors=6 |bibcode=2003PNAS..10012984W |doi-access=free }}</ref> Smaller independent pieces of DNA, called ''[[plasmid]]s'', are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to [[bacterial conjugation]].<ref>{{cite journal |vauthors=Schleper C, Holz I, Janekovic D, Murphy J, Zillig W |title=A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating |journal=Journal of Bacteriology |volume=177 |issue=15 |pages=4417–26 |date=August 1995 |pmid=7635827 |pmc=177192 |doi=10.1128/jb.177.15.4417-4426.1995 }}</ref><ref name=SotaTop>{{cite book |chapter-url=http://www.horizonpress.com/pla |vauthors=Sota M, Top EM |date=2008|chapter=Horizontal Gene Transfer Mediated by Plasmids|title=Plasmids: Current Research and Future Trends|publisher=Caister Academic Press|isbn=978-1-904455-35-6}}</ref>

[[File:RT8-4.jpg|thumb|upright|left|''[[Sulfolobus]]'' infected with the [[DNA virus]] [[STSV-1|STSV1]].<ref>{{cite journal |vauthors=Xiang X, Chen L, Huang X, Luo Y, She Q, Huang L |title=Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features |journal=Journal of Virology |volume=79 |issue=14 |pages=8677–86 |date=July 2005 |pmid=15994761 |pmc=1168784 |doi=10.1128/JVI.79.14.8677-8686.2005 }}</ref> Bar is 1&nbsp;[[Micrometre|micrometer]].]]

Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function.<ref>{{cite journal |vauthors=Graham DE, Overbeek R, Olsen GJ, Woese CR |title=An archaeal genomic signature |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=97 |issue=7 |pages=3304–08 |date=March 2000 |pmid=10716711 |pmc=16234 |doi=10.1073/pnas.050564797 |bibcode=2000PNAS...97.3304G |doi-access=free }}</ref> Of the remainder of the unique proteins that have an identified function, most belong to the Methanobacteriati and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to [[Transcription (genetics)|transcription]], [[Translation (biology)|translation]], and [[nucleotide|nucleotide metabolism]].<ref name="Gaasterland" /> Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same [[metabolic pathway]] into novel [[operon]]s, and large differences in [[tRNA]] genes and their [[aminoacyl tRNA synthetase]]s.<ref name="Gaasterland">{{cite journal |vauthors=Gaasterland T |title=Archaeal genomics |journal=Current Opinion in Microbiology |volume=2 |issue=5 |pages=542–47 |date=October 1999 |pmid=10508726 |doi=10.1016/S1369-5274(99)00014-4 }}</ref>

Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal [[RNA polymerase]] being very close to its equivalent in eukaryotes,<ref name=Allers>{{cite journal |vauthors=Allers T, Mevarech M |title=Archaeal genetics – the third way |journal=Nature Reviews Genetics |volume=6 |issue=1 |pages=58–73 |date=January 2005 |pmid=15630422 |doi=10.1038/nrg1504 |s2cid=20229552 |url=http://eprints.nottingham.ac.uk/45896/1/Allers%20%26%20Mevarech%20%282005%29.pdf |access-date=12 September 2019 |archive-date=20 July 2018 |archive-url=https://web.archive.org/web/20180720020131/http://eprints.nottingham.ac.uk/45896/1/Allers%20%26%20Mevarech%20%282005%29.pdf |url-status=dead }}</ref> while archaeal translation shows signs of both bacterial and eukaryotic equivalents.<ref name=Dennis>{{cite journal |vauthors=Dennis PP |title=Ancient ciphers: translation in Archaea |journal=Cell |volume=89 |issue=7 |pages=1007–10 |date=June 1997 |pmid=9215623 |doi=10.1016/S0092-8674(00)80288-3 |s2cid=18862794 |doi-access=free }}</ref> Although archaea have only one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic [[RNA polymerase II]], with similar protein assemblies (the [[general transcription factor]]s) directing the binding of the RNA polymerase to a gene's [[promoter (biology)|promoter]],<ref>{{cite journal |vauthors=Werner F |title=Structure and function of archaeal RNA polymerases |journal=Molecular Microbiology |volume=65 |issue=6 |pages=1395–404 |date=September 2007 |pmid=17697097 |doi=10.1111/j.1365-2958.2007.05876.x |s2cid=28078184 |doi-access=free }}</ref> but other archaeal [[transcription factor]]s are closer to those found in bacteria.<ref>{{cite journal |vauthors=Aravind L, Koonin EV |title=DNA-binding proteins and evolution of transcription regulation in the archaea |journal=Nucleic Acids Research |volume=27 |issue=23 |pages=4658–70 |date=December 1999 |pmid=10556324 |pmc=148756 |doi=10.1093/nar/27.23.4658 }}</ref> [[Post-transcriptional modification]] is simpler than in eukaryotes, since most archaeal genes lack [[intron]]s, although there are many introns in their [[transfer RNA]] and [[ribosomal RNA]] genes,<ref>{{cite journal |vauthors=Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA |title=Archaeal introns: splicing, intercellular mobility and evolution |journal=Trends in Biochemical Sciences |volume=22 |issue=9 |pages=326–31 |date=September 1997 |pmid=9301331 |doi=10.1016/S0968-0004(97)01113-4 }}</ref> and introns may occur in a few protein-encoding genes.<ref>{{cite journal |vauthors=Watanabe Y, Yokobori S, Inaba T, Yamagishi A, Oshima T, Kawarabayasi Y, Kikuchi H, Kita K |title=Introns in protein-coding genes in Archaea |journal=FEBS Letters |volume=510 |issue=1–2 |pages=27–30 |date=January 2002 |pmid=11755525 |doi=10.1016/S0014-5793(01)03219-7 |s2cid=27294545 |display-authors=6 |doi-access=free |bibcode=2002FEBSL.510...27W }}</ref><ref>{{cite journal |vauthors=Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, Oshima T, Kita K, Watanabe Y |title=Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease |journal=Biochemical and Biophysical Research Communications |volume=346 |issue=3 |pages=1024–32 |date=August 2006 |pmid=16781672 |doi=10.1016/j.bbrc.2006.06.011 |bibcode=2006BBRC..346.1024Y |display-authors=6 }}
</ref>

===Gene transfer and genetic exchange===
''[[Haloferax volcanii]]'', an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.<ref>{{cite journal |vauthors=Rosenshine I, Tchelet R, Mevarech M |title=The mechanism of DNA transfer in the mating system of an archaebacterium |journal=Science |volume=245 |issue=4924 |pages=1387–89 |date=September 1989 |pmid=2818746 |doi=10.1126/science.2818746 |bibcode=1989Sci...245.1387R }}</ref>

When the hyperthermophilic archaea ''[[Sulfolobus solfataricus]]''<ref name=Frols2008>{{cite journal |vauthors=Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV |title=UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation |journal=Molecular Microbiology |volume=70 |issue=4 |pages=938–52 |date=November 2008 |pmid=18990182 |doi=10.1111/j.1365-2958.2008.06459.x |s2cid=12797510 |display-authors=6 |url=https://www.rug.nl/research/portal/en/publications/uvinducible-cellular-aggregation-of-the-hyperthermophilic-archaeon-sulfolobus-solfataricus-is-mediated-by-pili-formation(0dd2a8eb-0f4b-4382-805d-158a870be95e).html |doi-access=free }}</ref> and ''[[Sulfolobus acidocaldarius]]''<ref name=Ajon>{{cite journal |vauthors=Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C |title=UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili |journal=Molecular Microbiology |volume=82 |issue=4 |pages=807–17 |date=November 2011 |pmid=21999488 |doi=10.1111/j.1365-2958.2011.07861.x |s2cid=42880145 |display-authors=6 |url=https://pure.rug.nl/ws/files/6771142/2011MolMicrobiolAjon.pdf |doi-access=free }}</ref> are exposed to DNA-damaging UV irradiation or to the agents [[bleomycin]] or [[mitomycin C]], species-specific cellular aggregation is induced. Aggregation in ''S.&nbsp;solfataricus'' could not be induced by other physical stressors, such as pH or temperature shift,<ref name=Frols2008 /> suggesting that aggregation is induced specifically by [[DNA damage]]. Ajon et al.<ref name=Ajon /> showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in ''S.&nbsp;acidocaldarius''. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al.<ref name=Frols2008 /><ref>{{cite journal |vauthors=Fröls S, White MF, Schleper C |title=Reactions to UV damage in the model archaeon Sulfolobus solfataricus |journal=Biochemical Society Transactions |volume=37 |issue=Pt 1 |pages=36–41 |date=February 2009 |pmid=19143598 |doi=10.1042/BST0370036 }}</ref> and Ajon et al.<ref name=Ajon /> hypothesized that cellular aggregation enhances species-specific DNA transfer between ''Sulfolobus'' cells in order to provide increased repair of damaged DNA by means of [[homologous recombination]]. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.<ref>{{cite book |chapter=Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis |vauthors=Bernstein H, Bernstein C |title=Biocommunication of Archaea |veditors=Witzany G |publisher=[[Springer Nature]] |year=2017|isbn=978-3-319-65535-2|pages=301–117|doi=10.1007/978-3-319-65536-9_7}}</ref>

===Archaeal viruses===
Archaea are the target of a number of [[virus]]es in a diverse virosphere distinct from bacterial and eukaryotic viruses. They have been organized into 15–18 DNA-based families so far, but multiple species remain un-isolated and await classification.<ref name=":0">{{cite encyclopedia |vauthors=Blohs M, Moissl-Eichinger C, Mahnert A, Spang A, Dombrowski N, Krupovic M, Klingl A |title=Archaea – An Introduction|date=January 2019 |encyclopedia=Encyclopedia of Microbiology |edition=Fourth |pages=243–252|veditors=Schmidt TM |publisher=Academic Press|language=en|isbn=978-0-12-811737-8 |doi=10.1016/B978-0-12-809633-8.20884-4|s2cid=164553336 }}</ref><ref name="Krupovic_2018">{{cite journal |vauthors=Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV |title=Viruses of archaea: Structural, functional, environmental and evolutionary genomics |journal=Virus Research |volume=244 |pages=181–193 |date=January 2018 |pmid=29175107 |pmc=5801132 |doi=10.1016/j.virusres.2017.11.025 }}</ref><ref>{{cite journal |vauthors=Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH |title=Archaeal viruses and bacteriophages: comparisons and contrasts |journal=Trends in Microbiology |volume=22 |issue=6 |pages=334–44 |date=June 2014 |pmid=24647075 |doi=10.1016/j.tim.2014.02.007 |url=http://www.sciencedirect.com/science/article/pii/S0966842X14000419 |url-access=subscription }}</ref> These families can be informally divided into two groups: archaea-specific and cosmopolitan. Archaeal-specific viruses target only archaean species and currently include 12 families. Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses.<ref name="Krupovic_2018" /> 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.<ref name=":0" /> Their virus release mechanisms differ from that of other phages. [[Bacteriophage]]s generally undergo either [[Lytic cycle|lytic]] pathways, [[Lysogenic cycle|lysogenic]] pathways, or (rarely) a mix of the two.<ref>{{cite journal |vauthors=Principi N, Silvestri E, Esposito S |title=Advantages and Limitations of Bacteriophages for the Treatment of Bacterial Infections |language=en |journal=Frontiers in Pharmacology |volume=10 |pages=513 |date=2019 |pmid=31139086 |doi=10.3389/fphar.2019.00513 |pmc=6517696 |doi-access=free }}</ref> Most archaea-specific viral strains maintain a stable, somewhat lysogenic, relationship with their hosts – appearing as a chronic infection. This involves the gradual, and continuous, production and release of [[Virus|virions]] without killing the host cell.<ref>{{cite encyclopedia |vauthors=Prangishvili D |title=Brenner's Encyclopedia of Genetics|chapter=Viruses of the Archaea|date=2013-01-01 |chapter-url=http://www.sciencedirect.com/science/article/pii/B9780123749840016272|encyclopedia=Brenner's Encyclopedia of Genetics (Second Edition)|pages=295–298|veditors=Maloy S, Hughes K |publisher=Academic Press |language=en|isbn=978-0-08-096156-9|access-date=2020-03-16|doi=10.1016/B978-0-12-374984-0.01627-2}}</ref> Prangishyili (2013) noted that it has been hypothesized that tailed archaeal phages originated from bacteriophages capable of infecting [[haloarchaea]]l species. If the hypothesis is correct, it can be concluded that other [[double-stranded DNA viruses]] that make up the rest of the archaea-specific group are their own unique group in the global viral community. Krupovic et al. (2018) states that the high levels of [[horizontal gene transfer]], rapid mutation rates in viral genomes, and lack of universal gene sequences have led researchers to perceive the evolutionary pathway of archaeal viruses as a network. The lack of similarities among [[phylogenetic marker]]s in this network and the global virosphere, as well as external linkages to non-viral elements, may suggest that some species of archaea specific viruses evolved from non-viral [[mobile genetic elements]] (MGE).<ref name="Krupovic_2018"/>

These viruses have been studied in most detail in thermophilics, particularly the orders [[Sulfolobales]] and [[Thermoproteales]].<ref>{{cite journal|vauthors=Prangishvili D, Garrett RA|date=April 2004|title=Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses|url=https://curis.ku.dk/ws/files/51497971/0320204.pdf|journal=Biochemical Society Transactions|volume=32|issue=Pt 2|pages=204–08|doi=10.1042/BST0320204|pmid=15046572|s2cid=20018642 }}</ref> Two groups of [[single-stranded DNA viruses]] that infect archaea have been recently isolated. One group is exemplified by the ''[[Halorubrum pleomorphic virus 1]]'' (''[[Pleolipoviridae]]'') infecting halophilic archaea,<ref>{{cite journal|vauthors=Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH|date=April 2009|title=An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope|journal=Molecular Microbiology|volume=72|issue=2|pages=307–19|doi=10.1111/j.1365-2958.2009.06642.x|pmid=19298373|s2cid=24894269|doi-access=free}}</ref> and the other one by the ''[[Aeropyrum coil-shaped virus]]'' (''[[Spiraviridae]]'') infecting a hyperthermophilic (optimal growth at 90–95&nbsp;°C) host.<ref>{{cite journal|vauthors=Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D|date=August 2012|title=Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=109|issue=33|pages=13386–91|bibcode=2012PNAS..10913386M|doi=10.1073/pnas.1203668109|pmc=3421227|pmid=22826255|doi-access=free}}</ref> Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve [[RNA interference]] from [[repetitive DNA]] sequences that are related to the genes of the viruses.<ref>{{cite journal|vauthors=Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E|date=February 2005|title=Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements|journal=Journal of Molecular Evolution|volume=60|issue=2|pages=174–82|bibcode=2005JMolE..60..174M|doi=10.1007/s00239-004-0046-3|pmid=15791728|s2cid=27481111}}</ref><ref>{{cite journal|vauthors=Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV|date=March 2006|title=A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action|journal=Biology Direct|volume=1|pages=7|doi=10.1186/1745-6150-1-7|pmc=1462988|pmid=16545108 |doi-access=free }}</ref>

==Reproduction==
{{Further|Asexual reproduction}}

Archaea reproduce asexually by binary or multiple [[fission (biology)|fission]], fragmentation, or [[budding]]; [[mitosis]] and [[meiosis]] do not occur, so if a species of archaea exists in more than one form, all have the same genetic material.<ref name=Bergey>{{cite book |title=Bergey's Manual of Systematic Bacteriology |vauthors=Krieg N |date=2005 |publisher=Springer |location=US |isbn=978-0-387-24143-2 |pages=21–26}}</ref> [[Cell division]] is controlled in a [[cell cycle]]; after the cell's [[chromosome]] is replicated and the two daughter chromosomes separate, the cell divides.<ref name=Bernander>{{cite journal |vauthors=Bernander R |title=Archaea and the cell cycle |journal=Molecular Microbiology |volume=29 |issue=4 |pages=955–61 |date=August 1998 |pmid=9767564 |doi=10.1046/j.1365-2958.1998.00956.x |s2cid=34816545 }}</ref> In the genus ''[[Sulfolobus]]'', the cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting points ([[origin of replication|origins of replication]]) using [[DNA polymerase]]s that resemble the equivalent eukaryotic enzymes.<ref>{{cite journal |vauthors=Kelman LM, Kelman Z |title=Multiple origins of replication in archaea |journal=Trends in Microbiology |volume=12 |issue=9 |pages=399–401 |date=September 2004 |pmid=15337158 |doi=10.1016/j.tim.2004.07.001 }}</ref>

In Methanobacteriati the cell division protein [[FtsZ]], which forms a contracting ring around the cell, and the components of the [[septum]] that is constructed across the center of the cell, are similar to their bacterial equivalents.<ref name=Bernander/> In cren-<ref>
{{cite journal |vauthors=Lindås AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R |title=A unique cell division machinery in the Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=48 |pages=18942–46 |date=December 2008 |pmid=18987308 |pmc=2596248 |doi=10.1073/pnas.0809467105 |bibcode=2008PNAS..10518942L |doi-access=free }}</ref><ref>{{cite journal |vauthors=Samson RY, Obita T, Freund SM, Williams RL, Bell SD |title=A role for the ESCRT system in cell division in archaea |journal=Science |volume=322 |issue=5908 |pages=1710–13 |date=December 2008 |pmid=19008417 |pmc=4121953 |doi=10.1126/science.1165322 |bibcode=2008Sci...322.1710S }}</ref> and thaumarchaea,<ref>{{cite journal |vauthors=Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R |title=Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus |journal=Molecular Microbiology |volume=82 |issue=3 |pages=555–66 |date=November 2011 |pmid=21923770 |doi=10.1111/j.1365-2958.2011.07834.x |s2cid=1202516 |doi-access=free }}</ref> the cell division machinery Cdv fulfills a similar role. This machinery is related to the eukaryotic ESCRT-III machinery which, while best known for its role in cell sorting, also has been seen to fulfill a role in separation between divided cell, suggesting an ancestral role in cell division.<ref name="pmid29551994">{{cite journal |vauthors=Caspi Y, Dekker C |title=Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery |journal=Frontiers in Microbiology |volume=9 |pages=174 |date=2018 |pmid=29551994 |pmc=5840170 |doi=10.3389/fmicb.2018.00174 |doi-access=free }}</ref>

Both bacteria and eukaryotes, but not archaea, make [[spore]]s.<ref>{{cite journal |vauthors=Onyenwoke RU, Brill JA, Farahi K, Wiegel J |title=Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes) |journal=Archives of Microbiology |volume=182 |issue=2–3 |pages=182–92 |date=October 2004 |pmid=15340788 |doi=10.1007/s00203-004-0696-y |bibcode=2004ArMic.182..182O |s2cid=34339306 }}</ref> Some species of [[Haloarchaea]] undergo [[phenotypic switching]] and grow as several different cell types, including thick-walled structures that are resistant to [[osmotic shock]] and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.<ref>{{
cite journal |vauthors=Kostrikina NA, Zvyagintseva IS, Duda VI |title=Cytological peculiarities of some extremely halophilic soil archaeobacteria |journal=Arch. Microbiol. |volume=156 |issue=5 |pages=344–49 |date=1991 |doi=10.1007/BF00248708|bibcode=1991ArMic.156..344K |s2cid=13316631 }}</ref>

==Behavior==

===Communication===
[[Quorum sensing]] was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. 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.<ref>{{cite journal |vauthors=Rajput A, Kumar M |title=Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing |language=English |journal=Frontiers in Microbiology |volume=8 |pages=798 |date=2017 |pmid=28515720 |pmc=5413776 |doi=10.3389/fmicb.2017.00798 |doi-access=free }}</ref>

==Ecology==

===Habitats===
[[File:Morning-Glory Hotspring.jpg|thumb|Archaea that grow in the hot water of the Morning Glory [[Hot Spring]] in [[Yellowstone National Park]] produce a bright colour]]
Archaea exist in a broad range of [[habitat]]s, are recognized as a major part of global [[ecosystem]]s,<ref name=DeLong/> and may represent about 20% of microbial cells in the oceans.<ref>{{cite journal |vauthors=DeLong EF, Pace NR |title=Environmental diversity of bacteria and archaea |journal=Systematic Biology |volume=50 |issue=4 |pages=470–78 |date=August 2001 |pmid=12116647 |doi=10.1080/106351501750435040 |citeseerx=10.1.1.321.8828 }}</ref> However, the first-discovered archaeans were [[extremophile]]s.<ref name=valentine/> Indeed, some archaea survive high temperatures, often above {{convert|100|C|F}}, as found in [[geyser]]s, [[black smoker]]s, and oil wells. Other common habitats include very cold habitats and highly [[salt|saline]], [[acid]]ic, or [[alkaline]] water, but archaea include [[mesophile]]s that grow in mild conditions, in [[swamp]]s and [[marsh]]land, [[sewage]], the [[ocean]]s, the [[intestinal tract]] of animals, and [[soil]]s.<ref name="Chow_2022" /><ref name=DeLong/> Similar to [[Plant growth-promoting rhizobacteria|PGPR]], Archaea are considered a source of plant growth promotion as well.<ref name="Chow_2022" />

Extremophile archaea are members of four main [[physiological]] groups. These are the [[halophile]]s, [[thermophile]]s, [[alkaliphile]]s, and [[Acidophile (organisms)|acidophiles]].<ref name=Pikuta/> These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.<ref name="pmid28777382">{{cite journal |vauthors=Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S |title=The growing tree of Archaea: new perspectives on their diversity, evolution and ecology |journal=The ISME Journal |volume=11 |issue=11 |pages=2407–2425 |date=November 2017 |pmid=28777382 |pmc=5649171 |doi=10.1038/ismej.2017.122 |bibcode=2017ISMEJ..11.2407A }}</ref>

Halophiles, including the genus ''[[Halobacterium]]'', live in extremely saline environments such as [[salt lake]]s and outnumber their bacterial counterparts at salinities greater than 20–25%.<ref name=valentine/> Thermophiles grow best at temperatures above {{convert|45|C|F}}, in places such as hot springs; ''hyperthermophilic'' archaea grow optimally at temperatures greater than {{convert|80|C}}.<ref>{{cite book |title=Brock Biology of Microorganisms |date=2006|vauthors=Madigan MT, Martino JM |edition=11th |page=136 |publisher=Pearson |isbn=978-0-13-196893-6}}</ref> The archaeal ''[[Methanopyrus kandleri]]'' Strain 116 can even reproduce at {{convert|122|C}}, the highest recorded temperature of any organism.<ref>{{cite journal |vauthors=Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K |title=Cell proliferation at 122&nbsp;°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=31 |pages=10949–54 |date=August 2008 |pmid=18664583 |pmc=2490668 |doi=10.1073/pnas.0712334105 |bibcode=2008PNAS..10510949T |doi-access=free}}</ref>

Other archaea exist in very acidic or alkaline conditions.<ref name=Pikuta>{{cite journal |vauthors=Pikuta EV, Hoover RB, Tang J |title=Microbial extremophiles at the limits of life |journal=Critical Reviews in Microbiology |volume=33 |issue=3 |pages=183–209 |date=2007 |pmid=17653987 |doi=10.1080/10408410701451948 |s2cid=20225471}}</ref> For example, one of the most extreme archaean acidophiles is ''[[Picrophilus|Picrophilus torridus]]'', which grows at pH&nbsp;0, which is equivalent to thriving in 1.2&nbsp;[[Molar concentration|molar]] [[sulfuric acid]].<ref>{{cite journal |vauthors=Ciaramella M, Napoli A, Rossi M |title=Another extreme genome: how to live at pH 0 |journal=Trends in Microbiology |volume=13 |issue=2 |pages=49–51 |date=February 2005 |pmid=15680761 |doi=10.1016/j.tim.2004.12.001}}</ref>

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of [[extraterrestrial life]].<ref>{{cite journal |vauthors=Javaux EJ |title=Extreme life on Earth--past, present and possibly beyond |journal=Research in Microbiology |volume=157 |issue=1 |pages=37–48 |date=2006 |pmid=16376523 |doi=10.1016/j.resmic.2005.07.008 |doi-access=free}}</ref> Some extremophile habitats are not dissimilar to those on [[Mars]],<ref>{{cite journal |vauthors=Nealson KH |title=Post-Viking microbiology: new approaches, new data, new insights |journal=Origins of Life and Evolution of the Biosphere |volume=29 |issue=1 |pages=73–93 |date=January 1999 |pmid=11536899 |doi=10.1023/A:1006515817767 |bibcode=1999OLEB...29...73N |url=http://www.kluweronline.com/art.pdf?issn=0169-6149&volume=29&page=73 |s2cid=12289639 |access-date=24 June 2008 |archive-date=16 October 2019 |archive-url=https://web.archive.org/web/20191016200314/http://www.kluweronline.com/art.pdf?issn=0169-6149&volume=29&page=73}}</ref> leading to the suggestion that viable microbes could be transferred between planets in [[meteorite]]s.<ref>{{cite book |vauthors=Davies PC |veditors=Bock GR, Goode JA |title=Ciba Foundation Symposium 202 – Evolution of Hydrothermal Ecosystems on Earth (And Mars?) |chapter=The Transfer of Viable Microorganisms Between Planets |pages=304–14; discussion 314–17 |date=1996 |pmid=9243022 |doi=10.1002/9780470514986.ch16 |series=Novartis Foundation Symposia |volume=202 |isbn=9780470514986}}</ref>

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. For example, archaea are common in cold oceanic environments such as polar seas.<ref>{{cite journal |vauthors=López-García P, López-López A, Moreira D, Rodríguez-Valera F |title=Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front |journal=FEMS Microbiology Ecology |volume=36 |issue=2–3 |pages=193–202 |date=July 2001 |pmid=11451524 |doi=10.1016/s0168-6496(01)00133-7 |doi-broken-date=17 June 2025 |bibcode=2001FEMME..36..193L }}</ref> Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the [[plankton]] community (as part of the [[picoplankton]]).<ref name=Karner>{{cite journal |vauthors=Karner MB, DeLong EF, Karl DM |title=Archaeal dominance in the mesopelagic zone of the Pacific Ocean |journal=Nature |volume=409 |issue=6819 |pages=507–10 |date=January 2001 |pmid=11206545 |doi=10.1038/35054051 |bibcode=2001Natur.409..507K |s2cid=6789859 }}</ref> Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in [[pure culture]].<ref>{{cite journal |vauthors=Giovannoni SJ, Stingl U |title=Molecular diversity and ecology of microbial plankton |journal=Nature |volume=437 |issue=7057 |pages=343–48 |date=September 2005 |pmid=16163344 |doi=10.1038/nature04158 |bibcode=2005Natur.437..343G |s2cid=4349881 }}</ref> Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global [[biogeochemistry|biogeochemical]] cycles remains largely unexplored.<ref>{{cite journal |vauthors=DeLong EF, Karl DM |title=Genomic perspectives in microbial oceanography |journal=Nature |volume=437 |issue=7057 |pages=336–42 |date=September 2005 |pmid=16163343 |doi=10.1038/nature04157 |bibcode=2005Natur.437..336D |s2cid=4400950 }}</ref> Some marine Thermoproteota are capable of [[nitrification]], suggesting these organisms may affect the oceanic [[nitrogen cycle]],<ref name="ReferenceD"/> although these oceanic Thermoproteota may also use other sources of energy.<ref>{{cite journal |vauthors=Agogué H, Brink M, Dinasquet J, Herndl GJ |title=Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic |journal=Nature |volume=456 |issue=7223 |pages=788–91 |date=December 2008 |pmid=19037244 |doi=10.1038/nature07535 |bibcode=2008Natur.456..788A |s2cid=54566989 |url=https://hal.archives-ouvertes.fr/hal-01086735/file/Nature%2C%20HAL.pdf }}</ref>

Vast numbers of archaea are also found in the [[sediment]]s that cover the [[sea floor]], with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.<ref>{{cite journal |vauthors=Teske A, Sørensen KB |title=Uncultured archaea in deep marine subsurface sediments: have we caught them all? |journal=The ISME Journal |volume=2 |issue=1 |pages=3–18 |date=January 2008 |pmid=18180743 |doi=10.1038/ismej.2007.90 |hdl=10379/14139 |doi-access=free |bibcode=2008ISMEJ...2....3T |hdl-access=free }}</ref><ref>{{cite journal |vauthors=Lipp JS, Morono Y, Inagaki F, Hinrichs KU |title=Significant contribution of Archaea to extant biomass in marine subsurface sediments |journal=Nature |volume=454 |issue=7207 |pages=991–94 |date=August 2008 |pmid=18641632 |doi=10.1038/nature07174 |bibcode=2008Natur.454..991L |s2cid=4316347 }}</ref> It has been demonstrated that in all oceanic surface sediments (from 1,000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally.<ref>{{cite journal |vauthors=Danovaro R, Dell'Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D |title=Virus-mediated archaeal hecatomb in the deep seafloor |journal=Science Advances |volume=2 |issue=10 |pages=e1600492 |date=October 2016 |pmid=27757416 |pmc=5061471 |doi=10.1126/sciadv.1600492 |bibcode=2016SciA....2E0492D }}</ref>

===Role in chemical cycling===
{{Further|Biogeochemical cycle}}
Archaea recycle elements such as [[carbon]], [[nitrogen]], and [[sulfur]] through their various habitats.<ref name="pmid29753224">{{cite journal |vauthors=Liu X, Pan J, Liu Y, Li M, Gu JD |title=Diversity and distribution of Archaea in global estuarine ecosystems |journal=The Science of the Total Environment |volume=637–638 |pages=349–358 |date=October 2018 |pmid=29753224 |doi=10.1016/j.scitotenv.2018.05.016 |bibcode=2018ScTEn.637..349L |s2cid=21697690}}</ref> Archaea carry out many steps in the [[nitrogen cycle]]. This includes both reactions that remove nitrogen from ecosystems (such as [[nitrate]]-based respiration and [[denitrification]]) as well as processes that introduce nitrogen (such as nitrate assimilation and [[nitrogen fixation]]).<ref>{{cite journal |vauthors=Cabello P, Roldán MD, Moreno-Vivián C |title=Nitrate reduction and the nitrogen cycle in archaea |journal=Microbiology |volume=150 |issue=Pt 11 |pages=3527–46 |date=November 2004 |pmid=15528644 |doi=10.1099/mic.0.27303-0 |doi-access=free}}</ref><ref>{{cite journal |vauthors=Mehta MP, Baross JA |title=Nitrogen fixation at 92&nbsp;°C by a hydrothermal vent archaeon |journal=Science |volume=314 |issue=5806 |pages=1783–86 |date=December 2006 |pmid=17170307 |doi=10.1126/science.1134772 |bibcode=2006Sci...314.1783M |s2cid=84362603}}</ref>

Researchers recently discovered archaeal involvement in [[ammonia]] oxidation reactions. These reactions are particularly important in the oceans.<ref name="ReferenceB"/><ref>{{cite journal |vauthors=Coolen MJ, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MM, Wakeham SG, Sinninghe Damsté JS |title=Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: A basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids |journal=Environmental Microbiology |volume=9 |issue=4 |pages=1001–16 |date=April 2007 |pmid=17359272 |doi=10.1111/j.1462-2920.2006.01227.x |bibcode=2007EnvMi...9.1001C |display-authors=6 |hdl=1912/2034 |hdl-access=free }}</ref> The archaea also appear crucial for ammonia oxidation in soils. They produce [[nitrite]], which other microbes then oxidize to [[nitrate]]. Plants and other organisms consume the latter.<ref name=LeiningerUrich2006>{{cite journal |vauthors=Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C |title=Archaea predominate among ammonia-oxidizing prokaryotes in soils |journal=Nature |volume=442 |issue=7104 |pages=806–09 |date=August 2006 |pmid=16915287 |doi=10.1038/nature04983 |bibcode=2006Natur.442..806L |s2cid=4380804 |author-link7=James I. Prosser }}</ref>

In the [[sulfur cycle]], archaea that grow by oxidizing [[sulfur]] compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as ''Sulfolobus'', produce [[sulfuric acid]] as a waste product, and the growth of these organisms in abandoned mines can contribute to [[acid mine drainage]] and other environmental damage.<ref name=Baker2003>{{cite journal |vauthors=Baker BJ, Banfield JF |title=Microbial communities in acid mine drainage |journal=FEMS Microbiology Ecology |volume=44 |issue=2 |pages=139–52 |date=May 2003 |pmid=19719632 |doi=10.1016/S0168-6496(03)00028-X |doi-access=free |bibcode=2003FEMME..44..139B }}</ref>

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 [[decomposer]]s in anaerobic ecosystems, such as sediments, marshes, and [[sewage treatment|sewage-treatment]] works.<ref>{{cite journal |vauthors=Schimel J |title=Playing scales in the methane cycle: from microbial ecology to the globe |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=101 |issue=34 |pages=12400–01 |date=August 2004 |pmid=15314221 |pmc=515073 |doi=10.1073/pnas.0405075101 |bibcode=2004PNAS..10112400S |doi-access=free }}</ref>

===Interactions with other organisms===
{{Further|Biological interaction}}

[[File:Coptotermes formosanus shiraki USGov k8204-7.jpg|thumb|upright|Methanogenic archaea form a [[symbiosis]] with [[termite]]s, living in their gut and helping to digest cellulose.]]

The well-characterized interactions between archaea and other organisms are either [[Mutualism (biology)|mutual]] or [[commensalism|commensal]]. There are no clear examples of known archaeal [[pathogen]]s or [[parasite]]s,<ref>{{cite journal |vauthors=Eckburg PB, Lepp PW, Relman DA |title=Archaea and their potential role in human disease |journal=Infection and Immunity |volume=71 |issue=2 |pages=591–96 |date=February 2003 |pmid=12540534 |pmc=145348 |doi=10.1128/IAI.71.2.591-596.2003 }}</ref><ref>{{cite journal |vauthors=Cavicchioli R, Curmi PM, Saunders N, Thomas T |title=Pathogenic archaea: do they exist? |journal=BioEssays |volume=25 |issue=11 |pages=1119–28 |date=November 2003 |pmid=14579252 |doi=10.1002/bies.10354 |doi-access=free |hdl=1959.4/39571 |hdl-access=free }}</ref> but some species of methanogens have been suggested to be involved in [[periodontal disease|infections in the mouth]],<ref>{{cite journal |vauthors=Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA |title=Methanogenic Archaea and human periodontal disease |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=101 |issue=16 |pages=6176–81 |date=April 2004 |pmid=15067114 |pmc=395942 |doi=10.1073/pnas.0308766101 |bibcode=2004PNAS..101.6176L |doi-access=free }}</ref><ref>{{cite journal |vauthors=Vianna ME, Conrads G, Gomes BP, Horz HP |title=Identification and quantification of archaea involved in primary endodontic infections |journal=Journal of Clinical Microbiology |volume=44 |issue=4 |pages=1274–82 |date=April 2006 |pmid=16597851 |pmc=1448633 |doi=10.1128/JCM.44.4.1274-1282.2006 }}</ref> and ''[[Nanoarchaeum equitans]]'' may be a parasite of another species of archaea, since it only survives and reproduces within the cells of the Crenarchaeon ''[[Ignicoccus|Ignicoccus hospitalis]]'',<ref name="pnas.org"/> and appears to offer no benefit to its [[host (biology)|host]].<ref>{{cite journal |vauthors=Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stetter KO, Rachel R, Huber H |title=Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea |journal=Journal of Bacteriology |volume=190 |issue=5 |pages=1743–50 |date=March 2008 |pmid=18165302 |pmc=2258681 |doi=10.1128/JB.01731-07 |display-authors=6 }}</ref>

====Mutualism====
Mutualism is an interaction between individuals of different species that results in positive (beneficial) effects on per capita reproduction and/or survival of the interacting populations. One well-understood example of [[mutualism (biology)|mutualism]] is the interaction between [[protozoa]] and [[methanogen|methanogenic archaea]] in the digestive tracts of animals that digest [[cellulose]], such as [[ruminant]]s and [[termite]]s.<ref name=Chaban>{{cite journal |vauthors=Chaban B, Ng SY, Jarrell KF |title=Archaeal habitats—from the extreme to the ordinary |journal=Canadian Journal of Microbiology |volume=52 |issue=2 |pages=73–116 |date=February 2006 |pmid=16541146 |doi=10.1139/w05-147 }}</ref> In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy.<ref>{{cite journal |vauthors=Schink B |title=Energetics of syntrophic cooperation in methanogenic degradation |journal=Microbiology and Molecular Biology Reviews |volume=61 |issue=2 |pages=262–80 |date=June 1997 |doi=10.1128/mmbr.61.2.262-280.1997 |pmid=9184013 |pmc=232610 }}</ref>

In anaerobic protozoa, such as ''Plagiopyla frontata'', ''Trimyema'', ''Heterometopus'' and ''Metopus contortus'', archaea reside inside the protozoa and consume hydrogen produced in their [[hydrogenosome]]s.<ref>{{cite journal |vauthors=Lewis WH, Sendra KM, Embley TM, Esteban GF |title=Morphology and Phylogeny of a New Species of Anaerobic Ciliate, ''Trimyema finlayi'' n. sp., with Endosymbiotic Methanogens |journal=Frontiers in Microbiology |volume=9 |pages=140 |year=2018 |pmid=29515525 |pmc=5826066 |doi=10.3389/fmicb.2018.00140 |doi-access=free }}</ref><ref>{{Cite thesis |title=Anaerobic ciliates as a model group for studying the biodiversityand symbioses in anoxic environments |url=https://dspace.cuni.cz/bitstream/handle/20.500.11956/119201/140085745.pdf?sequence=4&isAllowed=y |year=2020}}</ref><ref>{{cite journal |vauthors=Wrede C, Dreier A, Kokoschka S, Hoppert M |title=Archaea in symbioses |journal=Archaea |volume=2012 |pages=596846 |year=2012 |pmid=23326206 |pmc=3544247 |doi=10.1155/2012/596846 |doi-access=free }}</ref><ref name=Lange2005>{{cite journal |vauthors=Lange M, Westermann P, Ahring BK |title=Archaea in protozoa and metazoa |journal=Applied Microbiology and Biotechnology |volume=66 |issue=5 |pages=465–474 |date=February 2005 |pmid=15630514 |doi=10.1007/s00253-004-1790-4 |s2cid=22582800 }}</ref><ref>{{cite journal |vauthors=van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, Hackstein JH |title=Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates |journal=Molecular Biology and Evolution |volume=17 |issue=2 |pages=251–258 |date=February 2000 |pmid=10677847 |doi=10.1093/oxfordjournals.molbev.a026304 |doi-access=free }}</ref> Archaea associate with larger organisms, too. For example, the marine archaean ''[[Cenarchaeum|Cenarchaeum symbiosum]]'' is an [[endosymbiont]] of the [[sponge]] ''[[Axinella|Axinella mexicana]]''.<ref name=Preston1996>{{cite journal |vauthors=Preston CM, Wu KY, Molinski TF, DeLong EF |title=A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=93 |issue=13 |pages=6241–6246 |date=June 1996 |pmid=8692799 |pmc=39006 |doi=10.1073/pnas.93.13.6241 |doi-access=free |bibcode=1996PNAS...93.6241P }}</ref>

====Commensalism====
Some archaea are commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen ''[[Methanobrevibacter smithii]]'' is by far the most common archaean in the [[human flora]], making up about one in ten of the prokaryotes in the human gut.<ref>{{cite journal |vauthors=Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA |title=Diversity of the human intestinal microbial flora |journal=Science |volume=308 |issue=5728 |pages=1635–38 |date=June 2005 |pmid=15831718 |pmc=1395357 |doi=10.1126/science.1110591 |bibcode=2005Sci...308.1635E |display-authors=6 }}</ref> In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion.<ref>{{cite journal |vauthors=Samuel BS, Gordon JI |title=A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=103 |issue=26 |pages=10011–16 |date=June 2006 |pmid=16782812 |pmc=1479766 |doi=10.1073/pnas.0602187103 |bibcode=2006PNAS..10310011S |doi-access=free }}</ref> Archaean communities associate with a range of other organisms, such as on the surface of [[coral]]s,<ref>{{cite journal|date=2004 |title=Coral-associated Archaea |journal=Marine Ecology Progress Series |volume=273 |pages=89–96 |doi=10.3354/meps273089 |author-link3=Mya Breitbart |vauthors=Wegley L, Yu Y, Breitbart M, Casas V, Kline DI, Rohwer F |bibcode=2004MEPS..273...89W |doi-access=free }}</ref> and in the region of soil that surrounds plant roots (the [[Rhizosphere (ecology)|rhizosphere]]).<ref>{{cite journal |vauthors=Chelius MK, Triplett EW |title=The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L |journal=Microbial Ecology |volume=41 |issue=3 |pages=252–263 |date=April 2001 |pmid=11391463 |doi=10.1007/s002480000087 |jstor=4251818 |bibcode=2001MicEc..41..252C |s2cid=20069511 }}</ref><ref>{{cite journal |vauthors=Simon HM, Dodsworth JA, Goodman RM |title=Crenarchaeota colonize terrestrial plant roots |journal=Environmental Microbiology |volume=2 |issue=5 |pages=495–505 |date=October 2000 |pmid=11233158 |doi=10.1046/j.1462-2920.2000.00131.x |bibcode=2000EnvMi...2..495S }}</ref>

====Parasitism====
Although Archaea do not have a historical reputation of being pathogens, Archaea are often found with similar genomes to more common pathogens like ''E. coli,''<ref>{{cite journal |vauthors=Gophna U, Charlebois RL, Doolittle WF |title=Have archaeal genes contributed to bacterial virulence? |journal=Trends in Microbiology |volume=12 |issue=5 |pages=213–219 |date=May 2004 |pmid=15120140 |doi=10.1016/j.tim.2004.03.002 }}</ref> showing metabolic links and evolutionary history with today's pathogens. Archaea have been inconsistently detected in clinical studies because of the lack of categorization of Archaea into more specific species.<ref>{{Cite journal |vauthors=Shiffman ME, Charalambous BM |date=2012 |title=The search for archaeal pathogens |journal=Reviews in Medical Microbiology |volume=23 |issue=3 |pages=45–51 |doi=10.1097/MRM.0b013e328353c7c9 |s2cid=88300156 |issn=0954-139X}}</ref>

==Significance in technology and industry==
{{Further|Biotechnology}}
[[Extremophile]] archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of [[enzyme]]s that function under these harsh conditions.<ref>{{cite journal |vauthors=Breithaupt H |title=The hunt for living gold. The search for organisms in extreme environments yields useful enzymes for industry |journal=EMBO Reports |volume=2 |issue=11 |pages=968–71 |date=November 2001 |pmid=11713183 |pmc=1084137 |doi=10.1093/embo-reports/kve238 }}</ref><ref name=Egorova>{{cite journal |vauthors=Egorova K, Antranikian G |title=Industrial relevance of thermophilic Archaea |journal=Current Opinion in Microbiology |volume=8 |issue=6 |pages=649–55 |date=December 2005 |pmid=16257257 |doi=10.1016/j.mib.2005.10.015 }}</ref> These enzymes have found many uses. For example, thermostable [[DNA polymerase]]s, such as the [[Pfu DNA polymerase]] from ''[[Pyrococcus furiosus]]'', revolutionized [[molecular biology]] by allowing the [[polymerase chain reaction]] to be used in research as a simple and rapid technique for [[cloning]] DNA. In industry, [[amylase]]s, [[galactosidases]] and [[pullulanase]]s in other species of ''[[Pyrococcus]]'' that function at over {{convert|100|C|F}} allow [[food processing]] at high temperatures, such as the production of low [[lactose]] milk and [[whey]].<ref>{{cite journal |vauthors=Synowiecki J, Grzybowska B, Zdziebło A |title=Sources, properties and suitability of new thermostable enzymes in food processing |journal=Critical Reviews in Food Science and Nutrition |volume=46 |issue=3 |pages=197–205 |date=2006 |pmid=16527752 |doi=10.1080/10408690590957296 |s2cid=7208835 }}</ref> Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in [[green chemistry]] that synthesize organic compounds.<ref name=Egorova/> This stability makes them easier to use in [[structural biology]]. Consequently, the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.<ref>{{cite journal |vauthors=Jenney FE, Adams MW |title=The impact of extremophiles on structural genomics (and vice versa) |journal=Extremophiles |volume=12 |issue=1 |pages=39–50 |date=January 2008 |pmid=17563834 |doi=10.1007/s00792-007-0087-9 |s2cid=22178563 }}</ref>

In contrast with the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. [[Methanogen|Methanogenic archaea]] are a vital part of [[sewage treatment]], since they are part of the community of microorganisms that carry out [[anaerobic digestion]] and produce [[biogas]].<ref>{{cite journal |vauthors=Schiraldi C, Giuliano M, De Rosa M |title=Perspectives on biotechnological applications of archaea |journal=Archaea |volume=1 |issue=2 |pages=75–86 |date=September 2002 |pmid=15803645 |pmc=2685559 |doi=10.1155/2002/436561 |doi-access=free }}</ref> In [[mineral processing]], acidophilic archaea display promise for the extraction of metals from [[ore]]s, including [[gold]], [[cobalt]] and [[copper]].<ref>{{cite journal |vauthors=Norris PR, Burton NP, Foulis NA |title=Acidophiles in bioreactor mineral processing |journal=Extremophiles |volume=4 |issue=2 |pages=71–76 |date=April 2000 |pmid=10805560 |doi=10.1007/s007920050139 |s2cid=19985179 }}</ref>

Archaea host a new class of potentially useful [[antibiotic]]s. A few of these [[archaeocin]]s have been characterized, but hundreds more are believed to exist, especially within ''[[Haloarchaea]]'' and ''[[Sulfolobus]]''. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new [[selectable marker]]s for use in archaeal molecular biology.<ref>{{cite book |vauthors=Shand RF, Leyva KJ |chapter=Archaeal Antimicrobials: An Undiscovered Country |veditors=Blum P |title=Archaea: New Models for Prokaryotic Biology |publisher=Caister Academic Press |date=2008 |isbn=978-1-904455-27-1}}</ref>

==See also==
{{Div col|colwidth=27em}}
* [[Aerobic methane production]]
* [[Earliest known life forms]]
* [[List of Archaea genera]]
* [[List of sequenced archaeal genomes]]
* [[Nuclear localization sequence]]
* [[Stirrup protein domain]]
* ''[[The Surprising Archaea]]'' (book)
* [[Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya]]
* [[Unique properties of hyperthermophilic archaea]]
* [[Branching order of bacterial phyla (Genome Taxonomy Database, 2018)]]
{{div col end}}

==References==
{{Reflist}}

==Further reading==
{{Refbegin}}
* {{cite book|vauthors=Howland JL |title=The Surprising Archaea: Discovering Another Domain of Life|url={{google books |plainurl=y |id=25LQQRBJI8QC}}|date=2000|publisher=Oxford University|isbn=978-0-19-511183-5}}
* {{cite book |vauthors=Martinko JM, Madigan MT |title=Brock Biology of Microorganisms |edition=11th |publisher=Prentice Hall |location=Englewood Cliffs, N.J |date=2005 |isbn=978-0-13-144329-7}}
* {{cite book |vauthors=Garrett RA, Klenk H |title=Archaea: Evolution, Physiology and Molecular Biology |publisher=WileyBlackwell |date=2005 |isbn=978-1-4051-4404-9}}
* {{cite book |vauthors=Cavicchioli R |title=Archaea: Molecular and Cellular Biology |publisher=American Society for Microbiology |date=2007 |isbn=978-1-55581-391-8}}
* {{cite book |veditors=Blum P |title=Archaea: New Models for Prokaryotic Biology |publisher=Caister Academic Press |date=2008 |isbn=978-1-904455-27-1}}
* {{cite book |vauthors=Lipps G |date=2008 |chapter=Archaeal Plasmids|title=Plasmids: Current Research and Future Trends |publisher=Caister Academic Press |isbn=978-1-904455-35-6}}
* {{cite book |vauthors=Sapp J |date=2009 |title=The New Foundations of Evolution: On the Tree of Life |location=New York |publisher=Oxford University Press |isbn=978-0-19-538850-3}}
* {{cite book |vauthors=Schaechter M |date=2009 |title=Archaea (Overview) in The Desk Encyclopedia of Microbiology |edition=2nd |location=San Diego and London|publisher=Elsevier Academic Press |isbn=978-0-12-374980-2}}
{{Refend}}

==External links==
{{Spoken Wikipedia|En-Archaea-article.ogg|date=2020-05-29}}

===General===
* [http://www.ucmp.berkeley.edu/archaea/archaea.html Introduction to the Archaea, ecology, systematics and morphology]
* [http://www.cen.ulaval.ca/merge/pdf/OceansofArchaea.pdf Oceans of Archaea]&nbsp;– E.F. DeLong, ''ASM News'', 2003

===Classification===
* [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2157&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI taxonomy page on Archaea]
* [https://web.archive.org/web/20081128023142/http://www.bacterio.cict.fr/archaea.html Genera of the domain Archaea]&nbsp;– list of Prokaryotic names with Standing in Nomenclature
* [http://berkeley.edu/news/media/releases/2006/12/21_microbes.shtml Shotgun sequencing finds nanoorganisms]&nbsp;– discovery of the ARMAN group of archaea

===Genomics===
* [http://archaea.ucsc.edu/ Browse any completed archaeal genome at UCSC]
* [https://img.jgi.doe.gov/cgi-bin/edu/main.cgi?section=TaxonList&page=taxonListAlpha&domain=Archaea Comparative Analysis of Archaeal Genomes] {{Webarchive|url=https://web.archive.org/web/20130216090908/http://img.jgi.doe.gov/cgi-bin/edu/main.cgi?section=TaxonList&page=taxonListAlpha&domain=Archaea |date=16 February 2013 }} (at [[United States Department of Energy|DOE's]] [[Integrated Microbial Genomes System|IMG system]])

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[[Category:Archaea|Archaea]]
[[Category:Extremophiles]]
[[Category:Domains (biology)]]
[[Category:Systems of bacterial taxonomy]]
[[Category:Biology terminology]]