|
Initially, archaea were seen as [[extremophile]]s that lived in harsh environments, such as [[hot spring]]s and [[salt lake]]s, but they have since been found in a broad range of [[habitat]]s, such as [[soil]]s, [[ocean]]s, 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 now recognized as a major part of life on Earth and may play an important role in both the [[carbon cycle]] and [[nitrogen cycle]]. No clear examples of archaeal [[pathogen]]s or [[parasite]]s are known, but they are often [[mutualism|mutualists]] or [[commensalism|commensals]]. One example are the [[methanogen]]ic archaea that inhabit the gut of humans and [[ruminant]]s, where they are present in vast numbers and aid in the [[digestion]] of food. Archaea have some importance in technology, with methanogens used to produce [[biogas]] and as part of [[sewage treatment]], and enzymes from extremophile archaea that can resist high temperatures and organic solvents are exploited in [[biotechnology]].
== Classification ==
=== A new domain ===
Early in the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their [[biochemistry]], [[morphology (biology)|morphology]] and [[metabolism]]. For example, microbiologists tried to classify microorganisms based on the structures of their [[cell wall]]s, their shapes, and the substances they consume.<ref>{{cite journal |author=Staley JT |title=The bacterial species dilemma and the genomic-phylogenetic species concept |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1475 |pages=1899–909 |year=2006 |pmid=17062409 |url=http://journals.royalsociety.org/openurl.asp?genre=article&doi=10.1098/rstb.2006.1914 |doi=10.1098/rstb.2006.1914}}</ref> However, a new approach was proposed in 1965,<ref>{{cite journal |author=Zuckerkandl E, Pauling L |title=Molecules as documents of evolutionary history |journal=J. Theor. Biol. |volume=8 |issue=2 |pages=357–66 |year=1965 |pmid=5876245 |doi=10.1016/0022-5193(65)90083-4}}</ref> using the sequences of the [[gene]]s in these organisms to work out which prokaryotes are genuinely related to each other. This approach, known as [[phylogenetics]], is the main method used today.
[[Imageගොනුව:Grand prismatic spring.jpg|thumb|right|250px|Archaea were first detected in extreme environments, such as volcanic [[hot spring]]s.]]
Archaea were first classified as a separate group of prokaryotes in 1977 by [[Carl Woese]] and [[George E. Fox]] in [[phylogenetic tree]]s based on the sequences of [[ribosomal RNA]] (rRNA) genes.<ref>{{cite journal|author=Woese C, Fox G |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proc Natl Acad Sci USA |volume=74 |issue=11 |pages=5088–90 |year=1977 |pmid=270744 |pmc=432104 |doi=10.1073/pnas.74.11.5088}}</ref> These two groups were originally named the Archaebacteria and Eubacteria and treated as [[kingdom (biology)|kingdomkingdoms]]s or subkingdoms, which Woese and Fox termed ''Urkingdoms''. Woese argued that this group of prokaryotes is a fundamentally different sort of life. To emphasize this difference, these two domains were later renamed Archaea and Bacteria.<ref>{{cite journal |author=Woese CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=87 |issue=12 |pages=4576–9 |year=1990 |pmid=2112744 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=2112744 |doi=10.1073/pnas.87.12.4576}}</ref> The word ''archaea'' comes from the [[Ancient Greek]] {{Polytonic|[[wikt:ἀρχαῖος|ἀρχαῖα]]}}, meaning "ancient things".<ref>archaea. (2008). In ''Merriam-Webster Online Dictionary''. Retrieved July 1, 2008, from http://www.merriam-webster.com/dictionary/archaea</ref>
At first, only the [[methanogen]]s were placed in this new domain, and the archaea were seen as extremophiles that exist only in habitats such as [[hot spring]]s and [[salt lake]]s. By the end of the 20th century, microbiologists realized that the archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans.<ref name=DeLong>{{cite journal |author=DeLong EF |title=Everything in moderation: archaea as 'non-extremophiles' |journal=Curr. Opin. Genet. Dev. |volume=8 |issue=6 |pages=649–54 |year=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 the [[polymerase chain reaction]] to detect prokaryotes in samples of water or soil from their [[nucleic acid]]s alone. This allows the detection and identification of organisms that cannot be [[microbiological culture|cultured]] in the laboratory, which is often difficult.<ref>{{cite journal |author=Theron J, Cloete TE |title=Molecular techniques for determining microbial diversity and community structure in natural environments |journal=Crit. Rev. Microbiol. |volume=26 |issue=1 |pages=37–57 |year=2000 |pmid=10782339 |doi=10.1080/10408410091154174}}</ref><ref>{{cite journal |author=Schmidt TM |title=The maturing of microbial ecology |journal=Int. Microbiol. |volume=9 |issue=3 |pages=217–23 |year=2006 |pmid=17061212 |url=http://www.im.microbios.org/0903/0903217.pdf|format=PDF}}</ref>
=== Current classification ===
{{Further|[[Biological classification]] and [[Systematics]]}}
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 |author=Gevers D, Dawyndt P, Vandamme P, ''et al.'' |title=Stepping stones towards a new prokaryotic taxonomy |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1475 |pages=1911–61911–6 |year=2006 |pmid=17062410 |doi=10.1098/rstb.2006.1915 |url=http://journals.royalsociety.org/openurl.asp?genre=article&doi=10.1098/rstb.2006.1915}}</ref> These classifications rely heavily on the use of the sequence of [[ribosomal RNA]] genes to reveal relationships between organisms ([[molecular phylogeny|molecular phylogenetics]]).<ref name=Robertson/> Most of the culturable and well-investigated species of archaea are members of two main [[phylum|phyla]], the [[Euryarchaeota]] and [[Crenarchaeota]]. Other groups have been tentatively created. For example, the peculiar species ''[[Nanoarchaeum|Nanoarchaeum equitans]]'', which was discovered in 2003, has been given its own phylum, the [[Nanoarchaeota]].<ref>{{cite journal |author=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=27–827–8 |year=2002 |pmid=11986665 |doi=10.1038/417063a}}</ref> A new phylum [[Korarchaeota]] has also been proposed, it contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota.<ref>{{cite journal |author=Barns SM, Delwiche CF, Palmer JD, Pace NR |title=Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=93 |issue=17 |pages=9188–939188–93 |year=1996 |pmid=8799176 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=8799176 |doi=10.1073/pnas.93.17.9188}}</ref><ref>{{cite journal |author=Elkins JG, Podar M, Graham DE, ''et al.'' |title=A korarchaeal genome reveals insights into the evolution of the Archaea |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=105 |issue=23 |pages=8102–7 |year=2008 |month=June |pmid=18535141 |doi=10.1073/pnas.0801980105 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=18535141 |last12=Goltsman |first12=E |last13=Barry |first13=K |last14=Koonin |first14=EV |last15=Hugenholtz |first15=P |last16=Kyrpides |first16=N |last17=Wanner |first17=G |last18=Richardson |first18=P |last19=Keller |first19=M |last20=Stetter |first20=KO}}</ref> Other recently detected species of archaea are only distantly related to any of these groups, such as the [[Archaeal Richmond Mine Acidophilic Nanoorganisms]] (ARMAN), which were discovered in 2006.<ref>{{cite journal |author=Baker, B.J., Tyson, G.W., Webb, R.I., Flanagan, J., Hugenholtz, P. and Banfield, J.F. |title=Lineages of acidophilic Archaea revealed by community genomic analysis. Science |journal=Science |volume=314 |issue=6884 |pages=1933 – 1935 |year=2006 |doi=10.1126/science.1132690 |pmid=17185602}}</ref>
[[Imageගොනුව:Rio tinto river CarolStoker NASA Ames Research Center.jpg|thumb|200px|left|The [[archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN]] are a new group of archaea recently discovered in [[acid mine drainage]].]]
The classification of archaea into species is also controversial. In biology, a [[species]] is a group of related organisms. A popular definition of a species in [[animal]]s is a set of organisms that can breed with each other and are [[reproductive isolation|reproductively isolated]] from other groups of organisms (''i.e.'' they cannot breed with other species).<ref>{{cite journal |author=de Queiroz K |title=Ernst Mayr and the modern concept of species |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 Suppl 1 |pages=6600–76600–7 |year=2005 |pmid=15851674 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=15851674 |doi =10.1073/pnas.0502030102}}</ref> However, efforts to classify prokaryotes such as archaea into species are complicated by the fact that they are asexual and show high levels of [[horizontal gene transfer]] between lineages. The area is contentious; with, for example, some data suggesting that in archaea such as the genus ''[[Ferroplasma]]'', individual cells can be grouped into populations that have highly similar genomes and rarely transfer genes with more divergent groups of cells.<ref>{{cite journal |author=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=407–16407–16 |year=2007 |pmid=17603112 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=17603112 |doi =10.1534/genetics.107.072892}}</ref> These groups of cells are argued to be analogous to species. On the other hand, studies in ''[[Halorubrum]]'' found significant genetic exchange between such populations.<ref>{{cite journal |author=Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF |title=Searching for species in haloarchaea |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=104 |issue=35 |pages=14092–714092–7 |year=2007 |pmid=17715057 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=17715057 |doi =10.1073/pnas.0706358104 }}</ref> Such results have led to the argument that classifying these groups of organisms as species would have little practical meaning.<ref>{{cite journal |author=Kunin V, Goldovsky L, Darzentas N, Ouzounis CA |title=The net of life: reconstructing the microbial phylogenetic network |journal=Genome Res. |volume=15 |issue=7 |pages=954–9954–9 |year=2005 |pmid=15965028 |url=http://www.genome.org/cgi/pmidlookup?view=long&pmid=15965028 |doi =10.1101/gr.3666505}}</ref>
Current knowledge on the diversity of archaea is fragmentary and the total number of archaean species cannot be estimated with any accuracy.<ref name=Robertson>{{cite journal |author=Robertson CE, Harris JK, Spear JR, Pace NR |title=Phylogenetic diversity and ecology of environmental Archaea |journal=Curr. Opin. Microbiol. |volume=8 |issue=6 |pages=638–42638–42 |year=2005 |pmid=16236543 |doi=10.1016/j.mib.2005.10.003}}</ref> Even estimates of the total number of phyla in the archaea range from 18 to 23, of which only 8 phyla have representatives that have been grown in culture and studied directly. Many of these hypothetical groups are known from only a single rRNA sequence, indicating that the vast majority of the diversity among these organisms remains completely unknown.<ref>{{cite journal |author=Hugenholtz P |title=Exploring prokaryotic diversity in the genomic era |journal=Genome Biol. |volume=3 |issue=2 |pages=REVIEWS0003 |year=2002 |pmid=11864374 |url=http://genomebiology.com/1465-6906/3/REVIEWS0003 |doi =10.1186/gb-2002-3-2-reviews0003 }}</ref> The problem of how to study and classify uncultured microbes is also encountered in the Bacteria.<ref>{{cite journal |author=Rappé MS, Giovannoni SJ |title=The uncultured microbial majority |journal=Annu. Rev. Microbiol. |volume=57 |pages=369–94369–94 |year=2003 |pmid=14527284 |doi=10.1146/annurev.micro.57.030502.090759}}</ref>
== Origin and evolution ==
{{further|[[Timeline of evolution]]}}
Although probable [[fossils]] of prokaryotic cells have been dated to almost 3.5 [[bya|billion years ago]], most prokaryotes do not have distinctive morphologies and the shapes of fossils cannot be used to identify them as Archaea.<ref>{{cite journal |author=Schopf J |title=Fossil evidence of Archaean life |url=http://www.journals.royalsoc.ac.uk/content/g38537726r273422/fulltext.pdf |journal=Philos Trans R Soc Lond B Biol Sci |volume=361 |issue=1470 |pages=869–85869–85 |year=2006 |pmid=16754604 |doi=10.1098/rstb.2006.1834|format=PDF}}</ref> Instead, chemical fossils, in the form of the unique [[lipid]]s found in archaea, are more informative because such compounds do not occur in other groups of organisms.<ref>{{cite journal |author=Chappe B, Albrecht P, Michaelis W |title=Polar Lipids of Archaebacteria in Sediments and Petroleums |journal=Science |volume=217 |issue=4554 |pages=65–66 |year=1982 |month=July |pmid=17739984 |doi=10.1126/science.217.4554.65}}</ref> Some publications have suggested that the remains of lipids that may be either archaean or eukaryotic were present in [[shale]]s dating from 2.7 billion years ago;<ref>{{cite journal |author=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=1033–61033–6 |year=1999 |pmid=10446042 |doi=10.1126/science.285.5430.1033}}</ref> these data have since been questioned.<ref>{{cite journal |author=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 |year=2008 |month=October |pmid=18948954 |doi=10.1038/nature07381}}</ref> Such lipids have also been detected in rocks dating back to the [[Precambrian]]. The oldest known traces of these isoprene lipids come from the [[Isua greenstone belt|Isua district]] of west [[Greenland]], which include sediments formed 3.8 billion years ago and are the oldest on Earth.<ref>{{cite journal |last=Hahn |first=Jürgen |coauthors=Pat Haug |year=1986 |title=Traces of Archaebacteria in ancient sediments |journal=System Applied Microbiology |volume=7 |issue=Archaebacteria '85 Proceedings |pages=178–83178–83}}</ref> The origin of Archaea appears very old indeed and the archaeal lineage may be the most ancient that exists on earth.<ref name=Wang>{{cite journal |author=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 Res. |volume=17 |issue=11 |pages=1572–851572–85 |year=2007 |pmid=17908824 |doi=10.1101/gr.6454307}}</ref>
{{PhylomapA|size=400px||caption=[[Phylogenetic tree]] showing the relationship between the archaea and other forms of life. [[Eukaryote]]s are colored red, archaea green and [[bacteria]] blue. Adapted from Ciccarelli ''et al.''<ref>{{cite journal|author=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |title=Toward automatic reconstruction of a highly resolved tree of life |journal=Science |volume=311 |issue=5765 |pages=1283–71283–7 |year=2006 |pmid=16513982 |doi=10.1126/science.1123061}}</ref>}}
Woese argued that the bacteria, archaea, and eukaryotes each represent a separate line of descent that diverged early on from an ancestral colony of organisms.<ref>{{cite journal |author=Woese CR, Gupta R |title=Are archaebacteria merely derived 'prokaryotes'? |journal=Nature |volume=289 |issue=5793 |pages=95–695–6 |year=1981 |pmid=6161309 |doi=10.1038/289095a0}}</ref><ref>{{cite journal |author=Woese C |title=The universal ancestor |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=95 |issue=12 |pages=6854–96854–9 |year=1998 |pmid=9618502 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9618502 |doi=10.1073/pnas.95.12.6854}}</ref> A few biologists, however, have argued that the Archaea and Eukaryota arose from a group of bacteria.<ref>{{cite journal |author=Gupta RS |title=The natural evolutionary relationships among prokaryotes |journal=Crit. Rev. Microbiol. |volume=26 |issue=2 |pages=111–31111–31 |year=2000 |pmid=10890353 |doi=10.1080/10408410091154219}}</ref> It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared later in the history of life on Earth.<ref>{{cite journal |author=Gribaldo S, Brochier-Armanet C |title=The origin and evolution of Archaea: a state of the art |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1470 |pages=1007–221007–22 |year=2006 |pmid=16754611 |url=http://www.journals.royalsoc.ac.uk/content/q74671t476444mq5/ |doi =10.1098/rstb.2006.1841}}</ref> Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, this has led to the argument that the term ''prokaryote'' has no real evolutionary meaning and should be discarded entirely.<ref name=PMID8177167>{{cite journal |author=Woese CR |title=There must be a prokaryote somewhere: microbiology's search for itself |journal=Microbiol. Rev. |volume=58 |issue=1 |pages=1–91–9 |year=1994 |month=March |pmid=8177167 |pmc=372949 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8177167 |day=01}}</ref>
The relationship between archaea and eukaryotes remains an important problem. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two together. Some early analyses even suggested that the relationship between eukaryotes and the archaeal phylum [[Euryarchaeota]] is closer than the relationship between the Euryarchaeota and the phylum [[Crenarchaeota]].<ref>{{cite journal |author=Lake JA |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184–6184–6 |year=1988 |month=January |pmid=3340165 |doi=10.1038/331184a0}}</ref> However, it is now considered more likely that the ancestor of the eukaryotes diverged early from the Archaea.<ref>{{cite journal |author=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=145–7145–7 |year=1989 |month=May |pmid=2497353 |doi=10.1038/339145a0}}</ref><ref>{{cite journal |author=Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV |title=The deep archaeal roots of eukaryotes |journal=Mol. Biol. Evol. |year=2008 |month=May |pmid=18463089 |doi=10.1093/molbev/msn108 |url=http://mbe.oxfordjournals.org/cgi/reprint/msn108v1 |volume=25 |pages=1619 |issue=8}}</ref> The discovery of archaean-like genes in certain bacteria, such as ''[[Thermotogae|Thermotoga maritima]]'', makes these relationships difficult to determine, since [[horizontal gene transfer]] has occurred.<ref>{{cite journal |author=Nelson KE, Clayton RA, Gill SR, ''et al.'' |title=Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima |journal=Nature |volume=399 |issue=6734 |pages=323–9323–9 |year=1999 |pmid=10360571 |doi=10.1038/20601 |last12=Utterback |first12=TR |last13=Malek |first13=JA |last14=Linher |first14=KD |last15=Garrett |first15=MM |last16=Stewart |first16=AM |last17=Cotton |first17=MD |last18=Pratt |first18=MS |last19=Phillips |first19=CA |last20=Richardson |first20=D |last21=Heidelberg |first21=J |last22=Sutton |first22=GG |last23=Fleischmann |first23=RD |last24=Eisen |first24=JA |last25=White |first25=O |last26=Salzberg |first26=SL |last27=Smith |first27=HO |last28=Venter |first28=JC |last29=Fraser |first29=CM}}</ref> Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and [[cytoplasm]]; this accounts for various genetic similarities but runs into difficulties explaining cell structure.<ref>{{cite journal |author=Lake JA. |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184–6184–6 |year=1988 |pmid=3340165 |doi=10.1038/331184a0}}</ref>
== Morphology ==
[[Imageගොනුව:Relative scale.svg|thumb|250px|left|The sizes of prokaryotic cells relative to other cells and biomolecules.]]
Individual archaeans range from 0.1 [[Micrometre|micrometermicrometers]]s (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.<ref name=Bergey/> Other morphologies in the [[Crenarchaeota]] include irregularly shaped lobed cells in ''[[Sulfolobus]]'', thin needle-like filaments that are less than half a micrometer in diameter in ''[[Thermofilum]]'', and almost perfectly rectangular rods in ''[[Thermoproteus]]'' and ''[[Pyrobaculum]]''.<ref>Barns, Sue and Burggraf, Siegfried. (1997) [http://tolweb.org/Crenarchaeota/9 Crenarchaeota]. Version 01 January 1997. in ''The Tree of Life Web Project''</ref> There is even a species of flat, square archaea called ''[[Haloquadra|Haloquadra walsbyi]]'' that lives in hypersaline pools.<ref name=Walsby1980>{{cite journal |author=Walsby, A.E. |year=1980 |title=A square bacterium |journal=Nature |volume=283 |issue=5742 |pages=69–7169–71 |doi=10.1038/283069a0}}</ref> These unusual shapes are probably maintained both by their cell walls and a [[prokaryotic cytoskeleton]]. Proteins related to the cytoskeleton components of other organisms exist in the archaea,<ref>{{cite journal |author=Hara F, Yamashiro K, Nemoto N, ''et al.'' |title=An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin |journal=J. Bacteriol. |volume=189 |issue=5 |pages=2039–452039–45 |year=2007 |pmid=17189356 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=17189356 |doi =10.1128/JB.01454-06}}</ref> and filaments are formed within their cells,<ref>{{cite journal |author=Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ |title=Chaperonin filaments: the archaeal cytoskeleton? |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=94 |issue=10 |pages=5383–85383–8 |year=1997 |pmid=9144246 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9144246 |doi=10.1073/pnas.94.10.5383}}</ref> but in contrast to other organisms, these cellular structures are poorly understood in archaea.<ref>{{cite journal |author=Hixon WG, Searcy DG |title=Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts |journal=BioSystems |volume=29 |issue=2–3 |pages=151–60151–60 |year=1993 |pmid=8374067 |doi=10.1016/0303-2647(93)90091-P}}</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 of archaea form aggregates or filaments of cells up to 200 μm long,<ref name=Bergey/> and these organisms can be prominent members of the communities of microbes that make up [[biofilm]]s.<ref>{{cite journal |author=Hall-Stoodley L, Costerton JW, Stoodley P |title=Bacterial biofilms: from the natural environment to infectious diseases |journal=Nat. Rev. Microbiol. |volume=2 |issue=2 |pages=95–10895–108 |year=2004 |pmid=15040259 |doi=10.1038/nrmicro821}}</ref> An extreme example is ''[[Thermococcus]] coalescens'', as aggregates of these cells fuse together in culture, forming single giant cells.<ref>{{cite journal |author=Kuwabara T, Minaba M, Iwayama Y, ''et al.'' |title=Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount |journal=Int. J. Syst. Evol. Microbiol. |volume=55 |issue=Pt 6 |pages=2507–142507–14 |year=2005 |month=November |pmid=16280518 |doi=10.1099/ijs.0.63432-0 |url=http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=16280518 |last12=Kamekura |first12=M}}</ref> A particularly elaborate form of multicellular colony is produced by archaea in the genus ''[[Pyrodictium]]''. Here, the cells produce arrays of long, thin hollow tubes called ''cannulae'' that stick out from the cells' surfaces and connect them together into a dense bush-like colony.<ref>{{cite journal |author=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=J. Struct. Biol. |volume=141 |issue=1 |pages=34–4234–42 |year=2003 |pmid=12576018 |url=http://linkinghub.elsevier.com/retrieve/pii/S1047847702005816 |doi=10.1016/S1047-8477(02)00581-6}}</ref> The function of these cannulae is not known, but they may allow the cells to communicate or exchange nutrients with their neighbors.<ref>{{cite journal |author=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=J. Bacteriol. |volume=181 |issue=16 |pages=5114–85114–8 |year=1999 |pmid=10438790 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=10438790 |month=Aug |day=15}}</ref> Colonies can also be produced by an association between different species. For example, in the "string-of-pearls" community that was discovered in 2001 in a German swamp, round whitish colonies of a novel species of archaea in the phylum Euryarchaeota are spaced along thin filaments that can be up to {{convert|15|cm}} long; these filaments are made of a particular species of bacteria.<ref>{{cite journal |author=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=Appl. Environ. Microbiol. |volume=67 |issue=5 |pages=2336–44 |year=2001 |month=May |pmid=11319120 |pmc=92875 |doi=10.1128/AEM.67.5.2336-2344.2001 }}</ref>
== Cell structure ==
Archaea are similar to bacteria in their general [[Cell (biology)|cell]] structure, but the composition and organization of some of these structures set the archaea apart. Like bacteria, archaea lack interior membranes so their cells do not contain [[organelle]]s.<ref name=PMID8177167/> They also resemble bacteria in that their cell membrane is usually bounded by a [[cell wall]] and they swim by the use of one or more [[flagella]].<ref name=Thomas/> In overall structure the archaea are most similar to [[gram-positive bacteria]], as most have a single plasma membrane and cell wall, and lack a [[periplasmic space]]; the exception to this general rule is the archaean ''[[Ignicoccus]]'', which possess a particularly large periplasm that contains membrane-bound [[vesicle (biology)|vesicles]] and is enclosed by an outer membrane.<ref>{{cite journal |author=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=9–189–18 |year=2002 |month=March |pmid=15803654 |url=http://archaea.ws/archive/freetext/1-9.pdf|format=PDF |doi=10.1155/2002/307480}}</ref>
=== Cell membranes ===
[[Imageගොනුව:Archaea membrane.svg|thumb|right|300px|Membrane structures. '''Top''': an archaeal phospholipid, '''1''' isoprene sidechain, '''2''' ether linkage, '''3''' L-glycerol, '''4''' phosphate moieties. '''Middle''': a bacterial and eukaryotic phospholipid: '''5''' fatty acid, '''6''' ester linkage, '''7''' D-glycerol, '''8''' phosphate moieties. '''Bottom''': '''9''' lipid bilayer of bacteria and eukaryotes, '''10''' lipid monolayer of some archaea.]]
Archaeal membranes are made of molecules that differ strongly from those in other forms of life, which is evidence 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 will dissolve in water (the [[phosphate]] "head"), and a "greasy" non-polar part that will not dissolve in water (the lipid tail). These dissimilar parts are connected by a [[glycerol]] group. In water, phospholipids cluster together, with the polar phosphate heads facing the water and the non-polar lipid tails facing away from the water. This causes them to assemble into layers. The major structure in cell membranes is a double layer of these phospholipids, which is called a [[lipid bilayer]].
The phospholipids in the membranes of archaea are unusual in four ways. Firstly, bacteria and eukaryotes have membranes composed mainly of glycerol-[[ester]] [[lipid]]s, whereas archaea have membranes composed of glycerol-[[ether lipid]]s.<ref>{{cite journal |author=De Rosa M, Gambacorta A, Gliozzi A |title=Structure, biosynthesis, and physicochemical properties of archaebacterial lipids |journal=Microbiol. Rev. |volume=50 |issue=1 |pages=70–8070–80 |year=1986 |pmid=3083222 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=3083222 |month=Mar |day=01}}</ref> The difference between these two types of phospholipid is the type of bond that joins the lipids to the glycerol group; these two types of bonds 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]]. Ether bonds are chemically more resistant then ester bonds, which might contribute to the ability of some archaea to survive at extremes of temperature and in very acidic or alkaline environments.<ref>{{cite journal |author=Albers SV, van de Vossenberg JL, Driessen AJ, Konings WN |title=Adaptations of the archaeal cell membrane to heat stress |journal=Front. Biosci. |volume=5 |issue= |pages=D813–20D813–20 |year=2000 |month=September |pmid=10966867 |url=http://www.bioscience.org/2000/v5/d/albers/list.htm |doi=10.2741/albers}}</ref> Bacteria and eukaryotes do contain some ether lipids, but in contrast to archaea these lipids are not a major part of their membranes.
Secondly, archaeal lipids are unique because the [[stereochemistry]] of the glycerol group is the reverse of that found in other organisms. The glycerol group can occur in two forms that are mirror images of one another, which may be called the right-handed and left-handed forms; in chemical terms these forms are called ''[[enantiomer]]s''. Just as a right hand does not fit easily into a left-handed glove, a right-handed glycerol molecule generally cannot be used or made by [[enzyme]]s adapted for the left-handed form. This suggests that archaea use entirely different enzymes for synthesizing their phospholipids than do bacteria and eukaryotes; since such enzymes developed very early in life's history, this in turn suggests that the archaea split off very early from the other two domains.<ref name=Koga>{{cite journal |author=Koga Y, Morii H |title=Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations |journal=Microbiol. Mol. Biol. Rev. |volume=71 |issue=1 |pages=97–12097–120 |year=2007 |pmid=17347520 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=17347520 |doi =10.1128/MMBR.00033-06}}</ref>
Thirdly, the lipid tails of the phospholipids of archaea are chemically different from those in other organisms. Archaeal lipids are based upon the [[isoprene|isoprenoid]] sidechain and are long chains with multiple side-branches and sometimes even [[cyclopropane]] or [[cyclohexane]] rings.<ref>{{cite journal |author=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=J. Lipid Res. |volume=43 |issue=10 |pages=1641–511641–51 |year=2002 |month=October |pmid=12364548 |url=http://www.jlr.org/cgi/pmidlookup?view=long&pmid=12364548 |doi=10.1194/jlr.M200148-JLR200}}</ref> This is in contrast to the [[fatty acid]]s found in other organisms' membranes, which have straight chains with no 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 archaean membranes from becoming leaky at high temperatures.<ref>{{cite journal |author=Koga Y, Morii H |title=Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects |journal=Biosci. Biotechnol. Biochem. |volume=69 |issue=11 |pages=2019–342019–34 |year=2005 |month=November |pmid=16306681 |url=http://www.jstage.jst.go.jp/article/bbb/69/11/2019/_pdf |doi=10.1271/bbb.69.2019}}</ref>
Finally, in some archaea the phospholipid bilayer is replaced by a single monolayer. In effect, the archaea have fused the tails of two independent phospholipid molecules into a single molecule with two polar heads; this fusion may make their membranes more rigid and better able to resist harsh environments.<ref>{{cite journal |author=Hanford MJ, Peeples TL |title=Archaeal tetraether lipids: unique structures and applications |journal=Appl. Biochem. Biotechnol. |volume=97 |issue=1 |pages=45–62 |year=2002 |month=January |pmid=11900115 |doi=10.1385/ABAB:97:1:45}}</ref> For example, all the lipids in ''[[Ferroplasma]]'' are of this type, which is thought to aid this organism's survival in the extraordinarily acidic environments in which it thrives.<ref>{{cite journal |author=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=411–9 |year=2004 |month=October |pmid=15258835 |doi=10.1007/s00792-004-0404-5}}</ref>
=== Cell wall and flagella ===
{{further|[[Cell wall#Archaeal cell walls|Cell wall]]}}
Most archaea possess a cell wall—the exceptions being ''[[Thermoplasma]]'' and ''[[Ferroplasma]]''.<ref name=Golyshina>{{cite journal |author=Golyshina OV, Pivovarova TA, Karavaiko GI, ''et al.'' |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=Int. J. Syst. Evol. Microbiol. |volume=50 Pt 3 |pages=997–1006997–1006 |year=2000 |month=May |pmid=10843038 |url=http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=10843038 |issue=3 |day=01}}</ref> In most archaea the wall is assembled from surface-layer proteins, which form an [[S-layer]].<ref>{{cite journal |author=Sára M, Sleytr UB |title=S-Layer proteins |journal=J. Bacteriol. |volume=182 |issue=4 |pages=859–68859–68 |year=2000 |pmid=10648507 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=10648507 |doi=10.1128/JB.182.4.859-868.2000}}</ref> An S-layer is made of a rigid array of protein molecules that cover the outside of the cell like chain mail.<ref>{{cite journal |author=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=J Struct Biol |volume=124 |issue=2–32–3 |pages=276–302 |year=1998|pmid = 10049812 |doi=10.1006/jsbi.1998.4070}}</ref> This layer provides both chemical and physical protection, and can act as a barrier preventing [[macromolecule]]s from coming into contact with the cell membrane.<ref name=Kandler1998>{{cite journal |year=1998 |title=Cell wall polymers in Archaea (Archaebacteria) |journal=Cellular and Molecular Life Sciences (CMLS) |volume=54 |issue=4 |pages=305–308305–308 |doi=10.1007/s000180050156 |url=http://www.springerlink.com/index/PXMTKQ8WH8X650ED.pdf|format=PDF |author1=Kandler, O |author2=König, H}}</ref> In contrast to bacteria, most archaea lack [[peptidoglycan]] in their cell walls.<ref name="Howland">{{cite book |last=Howland |first=John L. |year=2000 |title=The Surprising Archaea: Discovering Another Domain of Life |pages=32 |location=Oxford |publisher=Oxford University Press |isbn=0-19-511183-4 }}</ref> The exception is [[pseudopeptidoglycan]], which is found in [[Methanobacteriales]], but this polymer is different from the peptidoglycan of bacteria since it lacks [[amino acid|D-amino acids]] and [[N-acetylmuramic acid]].<ref name=Kandler1998>{{cite journal |year=1998 |title=Cell wall polymers in Archaea (Archaebacteria) |journal=Cellular and Molecular Life Sciences (CMLS) |volume=54 |issue=4 |pages=305–308305–308 |doi=10.1007/s000180050156 |url=http://www.springerlink.com/index/PXMTKQ8WH8X650ED.pdf|format=PDF |author1=Kandler, O |author2=König, H}}</ref>
Archaea also have [[flagellum|flagella]], and these operate in a similar way to bacterial flagella—theyflagella—they are long stalks that are driven by rotatory motors at the base of the flagella. These motors are powered by the [[electrochemical gradient|proton gradient]] across the membrane. However, archaeal flagella are notably different in their composition and development.<ref name=Thomas>{{cite journal |author=Thomas NA, Bardy SL, Jarrell KF |title=The archaeal flagellum: a different kind of prokaryotic motility structure |journal=FEMS Microbiol. Rev. |volume=25 |issue=2 |pages=147–74147–74 |year=2001 |pmid=11250034 |doi=10.1111/j.1574-6976.2001.tb00575.x}}</ref> The two types of flagella evolved from different ancestors, the bacterial flagellum shares a common ancestor with the [[Type_III_secretion_systemType III secretion system#Type_III_secretion_system_Type III secretion system .28T3SS.29|type III secretion system]],<ref>{{cite journal |author=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 |issue= |pages=151–63 |year=2003 |month=July |pmid=12909351 |doi= 10.1016/S0378-1119(03)00612-7|url=http://linkinghub.elsevier.com/retrieve/pii/S0378111903006127}}</ref><ref>{{cite journal |author=Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH |title=Phylogenetic analyses of the constituents of Type III protein secretion systems |journal=J. Mol. Microbiol. Biotechnol. |volume=2 |issue=2 |pages=125–44 |year=2000 |month=April |pmid=10939240}}</ref> while archaeal flagella appear to have evolved from the bacterial type IV [[Pilus|pili]].<ref>{{cite journal |author=Ng SY, Chaban B, Jarrell KF |title=Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications |journal=J. Mol. Microbiol. Biotechnol. |volume=11 |issue=3–5 |pages=167–91167–91 |year=2006 |pmid=16983194 |doi=10.1159/000094053}}</ref> In contrast to the bacterial flagellum, which is a hollow stalk and is assembled by subunits moving up the central pore and then adding onto the tip of the flagella, archaeal flagella are synthesized by adding subunits onto their base.<ref>{{cite journal |author=Bardy SL, Ng SY, Jarrell KF |title=Prokaryotic motility structures |journal=Microbiology (Reading, Engl.) |volume=149 |issue=Pt 2 |pages=295–304295–304 |year=2003 |month=February |pmid=12624192 |url=http://mic.sgmjournals.org/cgi/pmidlookup?view=long&pmid=12624192 |doi=10.1099/mic.0.25948-0}}</ref>
== Metabolism ==
{{further|[[Microbial metabolism]]}}
Archaea exhibit a great variety of chemical reactions in their [[metabolism]] and use many different sources of energy. These forms of metabolism are classified into [[primary nutritional groups|nutritional groups]], depending on the source of energy and the source of carbon. Some archaea obtain their energy from [[inorganic compound]]s such as [[sulfur]] or [[ammonia]] (they are [[lithotroph]]s). These archaea include [[nitrifying bacteria|nitrifiernitrifiers]]s, [[methanogen]]s and [[anaerobic]] [[methane]] [[oxidiser]]s.<ref name=valentine>{{cite journal |author=Valentine DL |title=Adaptations to energy stress dictate the ecology and evolution of the Archaea |journal=Nat. Rev. Microbiol. |volume=5 |issue=4 |pages=316–23316–23 |year=2007 |pmid=17334387 |doi=10.1038/nrmicro1619}}</ref> In these reactions one compound passes electrons to another (in a [[redox]] reaction), releasing energy that is then used to fuel the cell's activities. One compound acts as an [[electron donor]] and one as an [[electron acceptor]]. A common feature of all these reactions is that the energy released is used to generate [[adenosine triphosphate]] (ATP) through [[chemiosmosis]], which is the same basic process that happens in the [[mitochondrion]] of animal cells.<ref name=Schafer>{{cite journal |author=Schäfer G, Engelhard M, Müller V |title=Bioenergetics of the Archaea |journal=Microbiol. Mol. Biol. Rev. |volume=63 |issue=3 |pages=570–620570–620 |year=1999 |month=September |pmid=10477309 |pmc=103747 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=10477309 |day=01}}</ref>
Other groups of archaea use sunlight as a source of energy (they are [[phototroph]]s). However, oxygen-generating [[photosynthesis]] does not occur in any of these organisms.<ref name=Schafer/> Many basic [[metabolic pathway]]s are shared between 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 |author=Zillig W |title=Comparative biochemistry of Archaea and Bacteria |journal=Curr. Opin. Genet. Dev. |volume=1 |issue=4 |pages=544–51544–51 |year=1991 |month=December |pmid=1822288 |doi=10.1016/S0959-437X(05)80206-0}}</ref> These similarities with other organisms probably reflect both the early evolution of these parts of metabolism in the history of life and their high level of efficiency.<ref>{{cite journal |author=Romano A, Conway T |title=Evolution of carbohydrate metabolic pathways |journal=Res Microbiol |volume=147 |issue=6–7 |pages=448–55448–55 |year=1996 |pmid=9084754 |doi=10.1016/0923-2508(96)83998-2}}</ref>
{|class="wikitable" style="margin-left: auto; margin-right: auto;"
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Some Euryarchaeota are [[methanogen]]s and produce methane gas 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 journal |author=Koch A |title=How did bacteria come to be? |journal=Adv Microb Physiol |volume=40 |pages=353–99353–99 |year=1998 |pmid=9889982 |doi=10.1016/S0065-2911(08)60135-6}}</ref> A common reaction in these organisms 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 |author=DiMarco AA, Bobik TA, Wolfe RS |title=Unusual coenzymes of methanogenesis |journal=Annu. Rev. Biochem. |volume=59 |pages=355–94355–94 |year=1990 |pmid=2115763 |doi=10.1146/annurev.bi.59.070190.002035}}</ref> Other organic compounds such as [[alcohol]]s, [[acetic acid]] or [[formic acid]] are used as alternative [[electron acceptor]]s by methanogens. These reactions are common in [[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 |author=Klocke M, Nettmann E, Bergmann I, ''et al.'' |title=Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass |journal=Syst. Appl. Microbiol. |year=2008 |month=May |pmid=18501543 |doi=10.1016/j.syapm.2008.02.003 |volume=31 |pages=190 |issue=3}}</ref>
[[Imageගොනුව:Bacteriorhodopsin.png|thumb|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 |author=Subramaniam S, Henderson R |title=Molecular mechanism of vectorial proton translocation by bacteriorhodopsin |journal=Nature |volume=406 |issue=6796 |pages=653–7 |year=2000 |month=August |pmid=10949309 |doi=10.1038/35020614}}</ref>]]
Other archaea use CO<sub>2</sub> in the atmosphere as a source of carbon, in a process called [[carbon fixation]] (they are [[autotroph]]s). In the archaea, this process involves either a highly modified form of the [[Calvin cycle]],<ref>{{cite journal |author=Mueller-Cajar O, Badger MR |title=New roads lead to Rubisco in archaebacteria |journal=Bioessays |volume=29 |issue=8 |pages=722–4722–4 |year=2007 |month=August |pmid=17621634 |doi=10.1002/bies.20616}}</ref> or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle.<ref>{{cite journal |author=Berg IA, Kockelkorn D, Buckel W, Fuchs G |title=A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea |journal=Science (journal) |volume=318 |issue=5857 |pages=1782–61782–6 |year=2007 |month=December |pmid=18079405 |doi=10.1126/science.1149976}}</ref> The Crenarchaeota also use the [[reverse Krebs cycle]] and the Euryarchaeota also use the [[reductive acetyl-CoA pathway]].<ref>{{cite journal |author=Thauer RK |title=Microbiology. A fifth pathway of carbon fixation |journal=Science (journal) |volume=318 |issue=5857 |pages=1732–31732–3 |year=2007 |month=December |pmid=18079388 |doi=10.1126/science.1152209}}</ref> In these organisms, carbon-fixation is powered by inorganic sources of energy, rather than by capturing sunlight as in plants and [[cyanobacteria]]. There are no known archaea that carry out [[photosynthesis]], which is when light is used by [[photoautotroph]]s as a source of energy as well as driving the fixation of carbon dioxide.<ref name=Bryant>{{cite journal |author=Bryant DA, Frigaard NU |title=Prokaryotic photosynthesis and phototrophy illuminated |journal=Trends Microbiol. |volume=14 |issue=11 |pages=488–96488–96 |year=2006 |month=November |pmid=16997562 |doi=10.1016/j.tim.2006.09.001}}</ref> The energy sources used by archaea to fix carbon are extremely diverse, and range from the oxidation of [[ammonia]] by the [[Nitrosopumilales]]<ref>{{cite journal |author=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=543–6543–6 |year=2005 |month=September |pmid=16177789 |doi=10.1038/nature03911}}</ref><ref>{{cite journal |author=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=ISME J |volume=1 |issue=1 |pages=19–2719–27 |year=2007 |month=May |pmid=18043610 |doi=10.1038/ismej.2007.8}}</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 the ions out of 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 structure and function of these light-driven pumps has been studied in great detail, which has revealed that their ability 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 |author=Lanyi JK |title=Bacteriorhodopsin |journal=Annu. Rev. Physiol. |volume=66 |pages=665–88665–88 |year=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/> the size of which may be as great as 5,751,492 [[base pair]]s in ''[[Methanosarcina acetivorans]]'',<ref>{{cite journal |author=Galagan JE, Nusbaum C, Roy A, ''et al.'' |title=The genome of M. acetivorans reveals extensive metabolic and physiological diversity |journal=Genome Res. |volume=12 |issue=4 |pages=532–42 |year=2002 |month=April |pmid=11932238 |pmc=187521 |doi=10.1101/gr.223902 |last12=Allen |first12=N |last13=Naylor |first13=J |last14=Stange-Thomann |first14=N |last15=Dearellano |first15=K |last16=Johnson |first16=R |last17=Linton |first17=L |last18=Mcewan |first18=P |last19=Mckernan |first19=K |last20=Talamas |first20=J |last21=Tirrell |first21=A |last22=Ye |first22=W |last23=Zimmer |first23=A |last24=Barber |first24=RD |last25=Cann |first25=I |last26=Graham |first26=DE |last27=Grahame |first27=DA |last28=Guss |first28=AM |last29=Hedderich |first29=R |last30=Ingram-Smith |first30=C |last31=Kuettner |first31=HC |last32=Krzycki |first32=JA |last33=Leigh |first33=JA |last34=Li |first34=W |last35=Liu |first35=J |last36=Mukhopadhyay |first36=B |last37=Reeve |first37=JN |last38=Smith |first38=K |last39=Springer |first39=TA |last40=Umayam |first40=LA |last41=White |first41=O |last42=White |first42=RH |last43=Conway De Macario |first43=E |last44=Ferry |first44=JG |last45=Jarrell |first45=KF |last46=Jing |first46=H |last47=Macario |first47=AJ |last48=Paulsen |first48=I |last49=Pritchett |first49=M |last50=Sowers |first50=KR |last51=Swanson |first51=RV |last52=Zinder |first52=SH |last53=Lander |first53=E |last54=Metcalf |first54=WW |last55=Birren |first55=B }}</ref> the largest archaean genome sequenced to date. At one-tenth of this size is the tiny 490,885 base-pair genome of ''[[Nanoarchaeum equitans]]'', which is the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes.<ref>{{cite journal |author=Waters E, ''et al.'' |title=The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=100 |issue=22 |pages=12984–812984–8 |year=2003 |pmid=14566062 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=14566062
|doi =10.1073/pnas.1735403100 |last12=Lin |first12=X |last13=Mathur |first13=E |last14=Ni |first14=J |last15=Podar |first15=M |last16=Richardson |first16=T |last17=Sutton |first17=GG |last18=Simon |first18=M |last19=Soll |first19=D |last20=Stetter |first20=KO |last21=Short |first21=JM |last22=Noordewier |first22=M}}</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 |author=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=J. Bacteriol. |volume=177 |issue=15 |pages=4417–264417–26 |year=1995 |pmid=7635827 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=7635827 |month=Aug |day=01}}</ref><ref name=SotaTop>{{cite book |chapterurl=http://www.horizonpress.com/pla|author=Sota M; Top EM|year=2008|chapter=Horizontal Gene Transfer Mediated by Plasmids|title=Plasmids: Current Research and Future Trends|publisher=Caister Academic Press|id=[http://www.horizonpress.com/pla ISBN 978-1-904455-35-6]}}</ref>
[[Imageගොනුව:RT8-4.jpg|thumb|200px|left|''[[Sulfolobus]]'' infected with the DNA virus STSV1.<ref>{{cite journal |author=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=J. Virol. |volume=79 |issue=14 |pages=8677–868677–86 |year=2005 |pmid=15994761 |url=http://jvi.asm.org/cgi/pmidlookup?view=long&pmid=15994761 |doi =10.1128/JVI.79.14.8677-8686.2005}}</ref> Bar is 1 [[Micrometre|micrometer]].]]
Archaea can be infected by double-stranded [[DNA viruses]] that are unrelated to any other form of virus and have a variety of unusual shapes, with some resembling bottles, hooked rods, or teardrops.<ref>{{cite journal |author=Prangishvili D, Forterre P, Garrett RA |title=Viruses of the Archaea: a unifying view |journal=Nat. Rev. Microbiol. |volume=4 |issue=11 |pages=837–48837–48 |year=2006 |pmid=17041631 |doi=10.1038/nrmicro1527}}</ref> These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.<ref>{{cite journal |author=Prangishvili D, Garrett RA |title=Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses |journal=Biochem. Soc. Trans. |volume=32 |issue=Pt 2 |pages=204–8204–8 |year=2004 |pmid=15046572 |url=http://www.biochemsoctrans.org/bst/032/0204/bst0320204.htm |doi=10.1042/BST0320204}}</ref> However, one example of a single-stranded DNA virus that infects halophilic archaea was identified in 2009.<ref>{{cite journal |author=Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH |title=An ssDNA virus infecting archaea; A new lineage of viruses with a membrane envelope |journal=Mol. Microbiol. |volume=72 |issue=2 |pages=307–19 |year=2009 |month=March |pmid=19298373 |doi=10.1111/j.1365-2958.2009.06642.x}}</ref> Defenses against these viruses may involve [[RNA interference]] from [[repetitive DNA]] sequences within archaean genomes that are related to the genes of the viruses.<ref>{{cite journal |author=Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E |title=Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements |journal=J. Mol. Evol. |volume=60 |issue=2 |pages=174–82174–82 |year=2005 |pmid=15791728 |doi=10.1007/s00239-004-0046-3}}</ref><ref>{{cite journal |author=Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV |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=Biol. Direct |volume=1 |pages=7 |year=2006 |pmid=16545108 |doi=10.1186/1745-6150-1-7}}</ref>
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 Archaea, although most of these unique genes have no known function.<ref>{{cite journal |author=Graham DE, Overbeek R, Olsen GJ, Woese CR |title=An archaeal genomic signature |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=97 |issue=7 |pages=3304–83304–8 |year=2000 |pmid=10716711 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=10716711 |doi =10.1073/pnas.050564797}}</ref> Of the remainder of the genes unique to archaea that have an identified function, most are involved in methanogenesis. The genes that are shared between archaea, bacteria and eukaryotes 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 features of archaean genomes are the organization of genes of related function—such as enzymes catalysing 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 |author=Gaasterland T |title=Archaeal genomics |journal=Curr. Opin. Microbiol. |volume=2 |issue=5 |pages=542–7542–7 |year=1999 |pmid=10508726 |doi=10.1016/S1369-5274(99)00014-4}}</ref>
Transcription and translation in archaea are more similar to these processes in eukaryotes than in bacteria, with the archaean [[RNA polymerase]] and [[ribosome]]s being very close to their equivalents in eukaryotes.<ref name=Allers>{{cite journal |author=Allers T, Mevarech M |title=Archaeal genetics - the third way |journal=Nat. Rev. Genet. |volume=6 |issue=1 |pages=58–7358–73 |year=2005 |pmid=15630422 |doi=10.1038/nrg1504}}</ref> Although archaea only have 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 assemblies of proteins (the [[general transcription factor]]s) directing the binding of the RNA polymerase to a gene's [[promoter]].<ref>{{cite journal |author=Werner F |title=Structure and function of archaeal RNA polymerases |journal=Mol. Microbiol. |volume=65 |issue=6 |pages=1395–4041395–404 |year=2007 |month=September |pmid=17697097 |doi=10.1111/j.1365-2958.2007.05876.x}}</ref> However, other archaean [[transcription factor]]s are closer to those found in bacteria.<ref>{{cite journal |author=Aravind L, Koonin EV |title=DNA-binding proteins and evolution of transcription regulation in the archaea |journal=Nucleic Acids Res. |volume=27 |issue=23 |pages=4658–704658–70 |year=1999 |pmid=10556324 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10556324 |doi=10.1093/nar/27.23.4658}}</ref> [[Post-transcriptional modification]] is simpler than in eukaryotes, since most archaean genes lack [[intron]]s, although there are many introns in their [[transfer RNA]] and [[ribosomal RNA]] genes,<ref>{{cite journal |author=Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA |title=Archaeal introns: splicing, intercellular mobility and evolution |journal=Trends Biochem. Sci. |volume=22 |issue=9 |pages=326–31326–31 |year=1997 |month=September |pmid=9301331 |doi=10.1016/S0968-0004(97)01113-4}}</ref> and introns may occur in a few of their protein-encoding genes.<ref>{{cite journal |author=Watanabe Y, Yokobori S, Inaba T, ''et al.'' |title=Introns in protein-coding genes in Archaea |journal=FEBS Lett. |volume=510 |issue=1-2 |pages=27–3027–30 |year=2002 |month=January |pmid=11755525 |doi=10.1016/S0014-5793(01)03219-7}}</ref><ref>{{cite journal |author=Yoshinari S, Itoh T, Hallam SJ, ''et al.'' |title=Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease |journal=Biochem. Biophys. Res. Commun. |volume=346 |issue=3 |pages=1024–321024–32 |year=2006 |month=August |pmid=16781672 |doi=10.1016/j.bbrc.2006.06.011}}
</ref>
== Reproduction ==
{{Further|[[Asexual reproduction]]}}
Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; [[meiosis]] does not occur, so if a species of archaea exists in more than one form, these will all have the same genetic material.<ref name=Bergey>{{cite book |title=Bergey’s Manual of Systematic Bacteriology |last=Krieg |first=Noel |year=2005 |publisher=Springer |location=USA |isbn=978-0-387-24143-2 |pages=21–621–6}}</ref> [[Cell division]] is controlled in the archaea in a [[cell cycle]]; after the cell's [[chromosome]] is replicated and the two daughter chromosomes are separated, the cell divides.<ref name=Bernander>{{cite journal |author=Bernander R |title=Archaea and the cell cycle |journal=Mol. Microbiol. |volume=29 |issue=4 |pages=955–61955–61 |year=1998 |pmid=9767564 |doi=10.1046/j.1365-2958.1998.00956.x}}</ref> The details of the archaeal cell cycle have only been investigated in the genus ''[[Sulfolobus]]'', but here it has characters that are similar to both bacterial and eukaryotic systems. In this archaean, the chromosomes are replicated from multiple starting-points ([[origin of replication|origins of replication]]) using [[DNA polymerase]]s that resemble the equivalent eukaryotic enzymes.<ref>{{cite journal |author=Kelman LM, Kelman Z |title=Multiple origins of replication in archaea |journal=Trends Microbiol. |volume=12 |issue=9 |pages=399–401399–401 |year=2004 |pmid=153371581 |doi=10.1016/j.tim.2004.07.001}}</ref> However, the proteins that direct cell division, such as the 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/>
[[Spore]]s are made by both bacteria and eukaryotes, but are not formed in any of the known archaea.<ref>{{cite journal |author=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=Arch. Microbiol. |volume=182 |issue=2–3 |pages=182–92182–92 |year=2004 |pmid=15340788 |doi=10.1007/s00203-004-0696-y}}</ref> Some species of [[Haloarchaea]] undergo [[phenotypic switching]] and grow as several different types of cell, including thick-walled structures that are resistant to [[osmotic shock]] and allow the archaea to survive in water at low concentrations of salt, but these are not reproductive structures and may instead help them disperse to new habitats.<ref>{{cite journal |author=Kostrikina NA, Zvyagintseva IS, Duda VI. |title=Cytological peculiarities of some extremely halophilic soil archaeobacteria |journal=Arch. Microbiol. |volume=156 |issue=5 |pages=344–49344–49 |year=1991 |doi=10.1007/BF00248708}}</ref>
== Ecology ==
=== Habitats ===
Archaea exist in a broad range of [[habitat]]s, and are a major part of global [[ecosystem]]s,<ref name=DeLong/> and may contribute up to 20% of the total [[Biomass (ecology)|biomass]] on Earth.<ref>{{cite journal |author=DeLong EF, Pace NR |title=Environmental diversity of bacteria and archaea |journal=Syst. Biol. |volume=50 |issue=4 |pages=470–8470–8 |year=2001 |pmid=12116647 |doi=10.1080/106351501750435040}}</ref> Multiple archaeans are [[extremophile]]s, and historically this was seen as their [[ecological niche]].<ref name=valentine/> Indeed, some archaea survive high temperatures, often above 100 [[Celsius|°C]], as found in [[geyser]]s, [[black smoker]]s, and oil wells. Others are found in very cold habitats and others in highly [[salt|saline]], [[acid]]ic, or [[alkaline]] water. However, other archaea are [[mesophile]]s that grow in much milder conditions, in [[marsh]]land, [[sewage]], the [[ocean]]s, and [[soil]]s.<ref name=DeLong/>
[[Imageගොනුව:Plankton satellite image.jpg|thumb|left|300px|Image of [[plankton]] (light green) in the [[ocean]]s; archaea form a major part of oceanic life.]]
Extremophile archaea are members of four main [[physiological]] groups. These are the [[halophile]]s, [[thermophile]]s, [[alkaliphile]]s, and [[Acidophile (organisms)|acidophileacidophiles]]s.<ref name=Pikuta/> These groups are not comprehensive or related to which phylum the organisms belong to, nor are they mutually exclusive, since some archaea belong to several of these groups. Nonetheless, they are a useful starting point for classification.
Halophiles, including the genus ''[[Halobacterium]]'', live in extremely saline environments such as [[salt lake]]s and start outnumbering their bacterial counterparts at salinities greater than 20–25%.<ref name=valentine/> Thermophiles grow best at temperatures above 45 °C, in places such as hot springs; ''hyperthermophilic'' archaea are defined as those that grow optimally at temperatures greater than 80 °C.<ref>{{cite book |title=Brock Biology of Microorganisms | year=2006| author=Madigan MT, Martino JM | edition=11th |pages=136 |publisher=Pearson |isbn=0-13-196893-9}}</ref> The archaeal ''[[Methanopyrus kandleri]]'' Strain 116 grows at 122 °C, which is the highest recorded temperature at which any organism will grow.<ref>{{cite journal | author = 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 °C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation | journal = Proc Natl Acad Sci USA | year = 2008 | volume = 105 | issue = 31| pages = 10949–54 | doi = 10.1073/pnas.0712334105 | pmid = 18664583}}</ref> Other archaea exist in very acidic or alkaline conditions.<ref name=Pikuta>{{cite journal |author=Pikuta EV, Hoover RB, Tang J |title=Microbial extremophiles at the limits of life |journal=Crit. Rev. Microbiol. |volume=33 |issue=3 |pages=183–209183–209 |year=2007 |pmid=17653987 |doi=10.1080/10408410701451948}}</ref> For example, one of the most extreme archaean acidophiles is ''Picrophilus torridus'', which grows at pH 0, which is equivalent to thriving in 1.2 [[Molar concentration|Molar]] [[sulfuric acid]].<ref>{{cite journal |author=Ciaramella M, Napoli A, Rossi M |title=Another extreme genome: how to live at pH 0 |journal=Trends Microbiol. |volume=13 |issue=2 |pages=49–5149–51 |year=2005 |month=February |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 |author=Javaux EJ |title=Extreme life on Earth—past, present and possibly beyond |journal=Res. Microbiol. |volume=157 |issue=1 |pages=37–4837–48 |year=2006 |pmid=16376523 |doi=10.1016/j.resmic.2005.07.008}}</ref> This has focused on the possibility that microbial life may exist on [[Mars]],<ref>{{cite journal |author=Nealson KH |title=Post-Viking microbiology: new approaches, new data, new insights |journal=Orig Life Evol Biosph |volume=29 |issue=1 |pages=73–9373–93 |year=1999 |month=January |pmid=11536899 |url=http://www.kluweronline.com/art.pdf?issn=0169-6149&volume=29&page=73 |doi=10.1023/A:1006515817767}}</ref> and has even led to the suggestion that viable microbes could be transferred between planets in [[meteorite]]s.<ref>{{cite journal |author=Davies PC |title=The transfer of viable microorganisms between planets |journal=Ciba Found. Symp. |volume=202 |pages=304–14304–14; discussion 314–7 |year=1996 |pmid=9243022}}</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 |author=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 Microbiol. Ecol. |volume=36 |issue=2–3 |pages=193–202193–202 |year=2001 |month=July |pmid=11451524}}</ref> Even more significant are the large numbers of archaea found throughout the world's oceans in the [[plankton]] community (as part of the [[picoplankton]]).<ref name=Karner>{{cite journal |author=Karner MB, DeLong EF, Karl DM |title=Archaeal dominance in the mesopelagic zone of the Pacific Ocean |journal=Nature |volume=409 |issue=6819 |pages=507–10507–10 |year=2001 |pmid=11206545 |doi=10.1038/35054051}}</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 |author=Giovannoni SJ, Stingl U. |title=Molecular diversity and ecology of microbial plankton |journal=Nature |volume=427 |issue=7057 |pages=343–8343–8 |year=2005 |pmid=16163344 |doi=10.1038/nature04158 }}</ref> Consequently, our understanding of the role of archaea in the ecology of the oceans is rudimentary, so their full influence on global [[biogeochemistry|biogeochemical]] cycles remains largely unexplored.<ref>{{cite journal |author=DeLong EF, Karl DM |title=Genomic perspectives in microbial oceanography |journal=Nature |volume=437 |issue=7057 |pages=336–42336–42 |year=2005 |month=September |pmid=16163343 |doi=10.1038/nature04157}}</ref> Some marine Crenarchaeota are capable of [[nitrification]], suggesting these organisms may be important in the oceanic [[nitrogen cycle]],<ref>{{cite journal |author =Konneke 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=7057 |pages=543–6543–6 |year=2005 |pmid=16177789 |doi=10.1038/nature03911 }}</ref> although these oceanic Crenarchaeota may also use other sources of energy.<ref>{{cite journal |author=Agogué H, Maaike B, 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=788–791 |year=2008|doi=10.1038/nature07535 |pmid=19037244 |last1=Agogué |first1=H |last2=Brink |first2=M |last3=Dinasquet |first3=J |last4=Herndl |first4=GJ}}</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 into this sediment.<ref>{{cite journal |author=Teske A, Sørensen KB |title=Uncultured archaea in deep marine subsurface sediments: have we caught them all? |journal=ISME J |volume=2 |issue=1 |pages=3–183–18 |year=2008 |month=January |pmid=18180743 |doi=10.1038/ismej.2007.90}}</ref><ref>{{cite journal |author=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|year=2008 |month=July |pmid=18641632 |doi=10.1038/nature07174}}</ref>
=== Role in chemical cycling ===
{{Further|[[Biogeochemical cycle]]}}
Archaea are part of the systems on Earth that recycle elements such as [[carbon]], [[nitrogen]] and [[sulfur]] through the various habitats in [[ecosystem]]s. Although these activities are vital for the normal function of ecosystems, archaea can also contribute to the changes that humans have made in the environment, and even cause [[pollution]].
Archaea carry out many steps in the [[nitrogen cycle]], this includes both dissimilatory reactions that remove nitrogen from ecosystems, such as [[nitrate]]-based respiration and [[denitrification]]: as well as assimilatory processes that introduce nitrogen, such as nitrate assimilation and [[nitrogen fixation]].<ref>{{cite journal |author=Cabello P, Roldán MD, Moreno-Vivián C |title=Nitrate reduction and the nitrogen cycle in archaea |journal=Microbiology (Reading, Engl.) |volume=150 |issue=Pt 11 |pages=3527–463527–46 |year=2004 |month=November |pmid=15528644 |doi=10.1099/mic.0.27303-0 |url=http://mic.sgmjournals.org/cgi/content/full/150/11/3527?view=long&pmid=15528644}}</ref><ref>{{cite journal |author=Mehta MP, Baross JA |title=Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon |journal=Science (journal) |volume=314 |issue=5806 |pages=1783–6 |year=2006 |month=December |pmid=17170307 |doi=10.1126/science.1134772}}</ref> The involvement of archaea in [[ammonia]] oxidation reactions was recently discovered; these being particularly important in the oceans.<ref>{{cite journal |author=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=ISME J |volume=1 |issue=1 |pages=19–27 |year=2007 |month=May |pmid=18043610 |doi=10.1038/ismej.2007.8}}</ref><ref>{{cite journal |author=Coolen MJ, Abbas B, van Bleijswijk J, ''et al.'' |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=Environ. Microbiol. |volume=9 |issue=4 |pages=1001–16 |year=2007 |month=April |pmid=17359272 |doi=10.1111/j.1462-2920.2006.01227.x}}</ref> The archaea also appear to be crucial for ammonia oxidation in soils, this produces [[nitrite]], which is then oxidized to [[nitrate]] by other microbes, and then taken up by plants and other organisms.<ref>{{cite journal |author=Leininger S, Urich T, Schloter M, ''et al.'' |title=Archaea predominate among ammonia-oxidizing prokaryotes in soils |journal=Nature |volume=442 |issue=7104 |pages=806–9806–9 |year=2006 |month=August |pmid=16915287 |doi=10.1038/nature04983}}</ref>
In the [[sulfur cycle]], archaea that grow by oxidizing [[sulfur]] compounds are important as they release this element from rocks, making it available to other organisms. However, the archaea that do this, such as ''Sulfolobus'', can cause environmental damage since they produce [[sulfuric acid]] as a waste product, and the growth of these organisms in abandoned mines can contribute to [[acid mine drainage]].<ref name=Baker2003>{{Cite journal | year = 2003 | title = Microbial communities in acid mine drainage | journal = FEMS Microbiology Ecology | volume = 44 | issue = 2 | pages = 139–152 | doi = 10.1016/S0168-6496(03)00028-X | url = http://www.blackwell-synergy.com/doi/abs/10.1016/S0168-6496(03)00028-X | author1 = Baker, B. J | author2 = Banfield, J. F}}</ref>
In the [[carbon cycle]], methanogen archaea are significant as methane producers. The ability of these archaea to remove hydrogen is important in the degradation of organic matter by the populations of microorganisms that act as [[decomposer]]s in anaerobic ecosystems, such as sediments, marshes and [[sewage treatment]] works.<ref>{{cite journal |author=Schimel J |title=Playing scales in the methane cycle: from microbial ecology to the globe |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=101 |issue=34 |pages=12400–112400–1 |year=2004 |month=August |pmid=15314221 |pmc=515073 |doi=10.1073/pnas.0405075101 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=15314221}}</ref> However, methane is one of the most abundant [[greenhouse gas]]es in Earth's atmosphere, constituting 18% of the global total.<ref>{{cite web | title= EDGAR 3.2 Fast Track 2000 | url= http://www.mnp.nl/edgar/model/v32ft2000edgar/ | accessdate= 2008-06-26 }}</ref> It is 25 times more potent as a greenhouse gas than carbon dioxide.<ref>{{cite web | date= 2008-04-23 | title = Annual Greenhouse Gas Index (AGGI) Indicates Sharp Rise in Carbon Dioxide and Methane in 2007 | url=http://www.esrl.noaa.gov/media/2008/aggi.html | accessdate= 2008-06-26 }}</ref> Methanogens are the primary source of [[atmospheric methane]], and are responsible for most of the world's yearly [[Methane#missions of methane|methane emissions]].<ref name="Trace Gases">{{cite web|url=http://www.grida.no/climate/ipcc_tar/wg1/134.htm#4211|title=Trace Gases: Current Observations, Trends, and Budgets|work=Climate Change 2001|publisher=United Nations Environment Programme}}</ref> As a consequence, these archaea contribute to global greenhouse gas emissions and [[global warming]].
=== Interactions with other organisms ===
{{Further|[[Biological interaction]]}}
[[Imageගොනුව:Coptotermes formosanus shiraki USGov k8204-7.jpg|thumb|right|Methanogenic archaea form a [[symbiosis]] with [[termite]]s.]]
The well-characterized interactions between archaea and other organisms are either [[mutualistic|mutualism]] or [[commensalism|commensal]]. As of 2007, no clear examples of archaeal [[pathogen]]s or [[parasite]]s are known.<ref>{{cite journal |author=Eckburg P, Lepp P, Relman D |title=Archaea and their potential role in human disease |journal=Infect Immun |volume=71 |issue=2 |pages=591–6591–6 |year=2003 |pmid=12540534 |doi=10.1128/IAI.71.2.591-596.2003}}</ref><ref>{{cite journal |author=Cavicchioli R, Curmi P, Saunders N, Thomas T |title=Pathogenic archaea: do they exist? |journal=Bioessays |volume=25 |issue=11 |pages=1119–281119–28 |year=2003 |pmid=14579252 |doi=10.1002/bies.10354}}</ref> However, a relationship has been proposed between the presence of some species of methanogens and [[periodontal disease|infections in the mouth]],<ref>{{cite journal |author=Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D |title=Methanogenic Archaea and human periodontal disease |journal=Proc Natl Acad Sci USA |volume=101 |issue=16 |pages=6176–816176–81 |year=2004 |pmid=15067114 |doi=10.1073/pnas.0308766101}}</ref><ref>{{cite journal |author=Vianna ME, Conrads G, Gomes BP, Horz HP |title=Identification and quantification of archaea involved in primary endodontic infections |journal=J. Clin. Microbiol. |volume=44 |issue=4 |pages=1274–821274–82 |year=2006 |month=April |pmid=16597851 |pmc=1448633 |doi=10.1128/JCM.44.4.1274-1282.2006 |url=http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=16597851}}</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>{{cite journal |author=Waters E, Hohn MJ, Ahel I, ''et al.'' |title=The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=100 |issue=22 |pages=12984–812984–8 |year=2003 |month=October |pmid=14566062 |pmc=240731 |doi=10.1073/pnas.1735403100 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=14566062 |last12=Lin |first12=X |last13=Mathur |first13=E |last14=Ni |first14=J |last15=Podar |first15=M |last16=Richardson |first16=T |last17=Sutton |first17=GG |last18=Simon |first18=M |last19=Soll |first19=D |last20=Stetter |first20=KO |last21=Short |first21=JM |last22=Noordewier |first22=M}}</ref> and appears to offer no benefit to its [[host (biology)|host]].<ref>{{cite journal |author=Jahn U, Gallenberger M, Paper W, ''et al.'' |title=Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea |journal=J. Bacteriol. |volume=190 |issue=5 |pages=1743–501743–50 |year=2008 |month=March |pmid=18165302 |doi=10.1128/JB.01731-07 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=18165302}}</ref>
One well-understood example of mutualism is the interaction between protozoa and [[methanogen]]ic archaea in the digestive tracts of animals that digest [[cellulose]], such as [[ruminant]]s and [[termite]]s.<ref name=Chaban>{{cite journal |author=Chaban B, Ng SY, Jarrell KF |title=Archaeal habitats—from the extreme to the ordinary |journal=Can. J. Microbiol. |volume=52 |issue=2 |pages=73–11673–116 |year=2006 |month=February |pmid=16541146 |doi=10.1139/w05-147}}</ref> In these anaerobic environments, [[protozoa]] break down [[cellulose]] from plant material to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen will reduce the energy released by this reaction. When methanogens convert the hydrogen to methane, the protozoa benefit as they will gain more energy from breaking down cellulose.<ref>{{cite journal |author=Schink B |title=Energetics of syntrophic cooperation in methanogenic degradation |journal=Microbiol. Mol. Biol. Rev. |volume=61 |issue=2 |pages=262–80262–80 |year=1997 |month=June |pmid=9184013 |pmc=232610 }}</ref>
These associations between methanogens and protozoa are taken a step further in several species of anaerobic protozoa, such as ''Plagiopyla frontata''; here the archaea actually reside inside the protozoa and consume the hydrogen produced in their [[hydrogenosome]]s.<ref name=Lange2005>{{cite journal |year=2005 |title=Archaea in protozoa and metazoa |journal=Applied Microbiology and Biotechnology |volume=66 |issue=5 |pages=465–474465–474 |doi=10.1007/s00253-004-1790-4 |pmid=15630514 |last1=Lange |first1=M |last2=Westermann |first2=P |last3=Ahring |first3=BK |author1=Lange, M |author2=Westermann, P |author3=Ahring, B.K}}</ref><ref>{{cite journal |author=van Hoek AH, van Alen TA, Sprakel VS, ''et al.'' |title=Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates |journal=Mol. Biol. Evol. |volume=17 |issue=2 |pages=251–8251–8 |year=2000 |month=February |pmid=10677847 |url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10677847 |day=01}}</ref> Similar associations with larger organisms are now being found, with the discovery that the marine archaean ''[[Cenarchaeum|Cenarchaeum symbiosum]]'' lives within (it is an [[endosymbiont]] of) the [[sponge]] ''Axinella mexicana''.<ref name=Preston1996>{{cite journal |year=1996 |title=A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov |journal=Proc Natl Acad Sci USA |volume=93 |issue=13 |pages=6241–6 |pmc=39006 |doi =10.1073/pnas.93.13.6241 |pmid =8692799 |author1=Preston, C.M |author2=Wu, K.Y |author3=Molinski, T.F |author4=Delong, E.F}}</ref>
Archaea can also be 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]], with this species making up about one in ten of all the prokaryotes in the human gut.<ref>{{cite journal |author=Eckburg PB, Bik EM, Bernstein CN, ''et al.'' |title=Diversity of the human intestinal microbial flora |journal=Science |volume=308 |issue=5728 |pages=1635–8 |year=2005 |month=June |pmid=15831718 |pmc=1395357 |doi=10.1126/science.1110591 }}</ref> As in termites, these methanogens may in fact be mutualists in humans, interacting with other microbes in the gut to aid the digestion of food.<ref>{{cite journal |author=Samuel BS, Gordon JI |title=A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=26 |pages=10011–610011–6 |year=2006 |month=June |pmid=16782812 |pmc=1479766 |doi=10.1073/pnas.0602187103}}</ref> Communities of archaea are also associated with a range of other organisms, such as on the surface of [[coral]]s,<ref>{{cite journal |year =2004 |title =Coral-associated Archaea |journal =Marine Ecology Progress Series |volume =273 |pages =89–96 |url =http://www.marine.usf.edu/genomics/PDFs%20of%20papers/wegleyetal2004.pdf |doi=10.3354/meps273089|format=PDF |author1 =Wegley, L |author2 =Yu, Y |author3 =Breitbart, M |author4 =Casas, V |author5 =Kline, D.I |author6 =Rohwer, F |last1 =Wegley |first1 =L |last2 =Yu |last3 =Breitbart |last4 =Casas |last5 =Kline |last6 =Rohwer}}</ref> and in the region of soil that surrounds plant roots (the [[Rhizosphere (ecology)|rhizosphere]]).<ref>{{cite journal |author=Chelius MK, Triplett EW |title=The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L |journal=Microb. Ecol. |volume=41 |issue=3 |pages=252–63252–63 |year=2001 |month=April |pmid=11391463 |doi=10.1007/s002480000087}}</ref><ref>{{cite journal |author=Simon HM, Dodsworth JA, Goodman RM |title=Crenarchaeota colonize terrestrial plant roots |journal=Environ. Microbiol. |volume=2 |issue=5 |pages=495–505495–505 |year=2000 |month=October |pmid=11233158 |doi=10.1046/j.1462-2920.2000.00131.x}}</ref>
== Significance in technology and industry ==
{{further|[[Biotechnology]]}}
A new class of potentially useful [[antibiotic]]s has been discovered in archaea. A few of these [[archaeocin]]s have been characterized, but hundreds more are believed to exist, especially within ''[[Haloarchaea]]'' and ''[[Sulfolobus]]''.<ref>{{cite journal |author=O'Connor EM, Shand RF |title=Halocins and sulfolobicins: the emerging story of archaeal protein and peptide antibiotics |journal=J. Ind. Microbiol. Biotechnol. |volume=28 |issue=1 |pages=23–31 |year=2002 |month=January |pmid=11938468 |doi=10.1038/sj/jim/7000190}}</ref> These compounds are important since they are different in structure to 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. The discovery of new archaeocins depends on successful recovery and cultivation of new species of archaea from the environment.<ref>{{cite book | author = Shand RF; Leyva KJ | chapter = Archaeal Antimicrobials: An Undiscovered Country | editor = Blum P (ed.) | title = Archaea: New Models for Prokaryotic Biology | publisher = Caister Academic Press | year = 2008 | isbn = 978-1-904455-27-1}}</ref>
== See also ==
* [[List of Archaea genera]]
* [[List of sequenced archeal genomes]]
* ''[[The Surprising Archaea]]'' (book)
== References ==
{{Reflist|2}}
== Further reading ==
* {{cite book |author=Howland, John L. |title=The Surprising Archaea: Discovering Another Domain of Life |location=Oxford |publisher=Oxford University Press |year=2000 |isbn=0-19-511183-4}}
* {{cite book |author=Martinko JM, Madigan MT |title=Brock Biology of Microorganisms |edition=11th |publisher=Prentice Hall |location=Englewood Cliffs, N.J |year=2005 |isbn=0-13-144329-1}}
* {{cite book |author=Lipps G |year=2008 |chapter=Archaeal Plasmids|title=Plasmids: Current Research and Future Trends |publisher=Caister Academic Press |isbn=978-1-904455-35-6}}
== External links ==
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