Archaea

{{Taxobox
| color = #F3E0E0
| name = Archaea
| fossil_range = [[Archean]] - Recent
| image = Halobacteria.jpg
| image_width = 200px
| image_caption = ''[[Halobacteria]]'' sp. strain NRC-1, each cell about 5 μm in length.
| superdomain = [[Neomura]]
| domain = '''Archaea'''
| domain_authority = [[Carl Woese|Woese]], [[Otto Kandler|Kandler]] & [[Mark Wheelis|Wheelis]], 1990
| subdivision_ranks = Phyla
| subdivision =
[[Crenarchaeota]] 
[[Euryarchaeota]] 
[[Korarchaeota]] 
[[Nanoarchaeota]] 
[[Archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN]]
}}
[[Image:Colourful Thermophilic Archaebacteria Stain in Midway Geyser Basin.jpg|thumb|right|200px|Yellowstone hot springs harbour archaea]]
The '''Archaea''' ({{pronEng|ɑrˈkiːə}}) are a major group of [[microorganism]]s. Originally named and sometimes still colloquially called '''archaebacteria''', this latter term is deprecated since archaea are not bacteria.

Like [[bacteria]], archaea are single-celled organisms that lack [[cell nucleus|nuclei]] and are therefore [[prokaryote]]s, classified in [[kingdom (biology)|kingdom]] [[Monera]] in the traditional five-kingdom [[Linnaean taxonomy|taxonomy]]. Although there is still uncertainty in the [[phylogeny]], Archaea, [[Eukaryota]] and Bacteria are the fundamental classifications of what is called the [[three-domain system]]. Although their prokaryotic features are diagnostic of that clade, archaea are more closely related to eukaryotes than to bacteria. To account for this, archaeans and eukaryotes are grouped together in the [[clade]] [[Neomura]], which is thought to have arisen from [[gram-positive]] bacteria. A recent genomic study suggested however that Archaea may be the most ancient organismal lineage in the world.<ref name=Wang>{{cite journal|author=Wang M, Yafremava LS, Caetano-Anolles D, Mittenthal JE, caetano-Anolles G|title=Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world|journal=Genome Res|volume=17|pages=1572-85|year=2007|pmid = 17908824}}</ref>

Archaea were originally described in [[extremophile|extreme]] environments, but have since been found in all [[habitat]]s and may contribute up to 20% of total [[Biomass (ecology)|biomass]].<ref>{{cite journal
|author=DeLong EF, Pace NR|year=2001|title=Environmental diversity of bacteria and archaea|journal=Syst. Biol.|volume=50|pages=470-478}}</ref> A single individual or species from this domain is called an ''archaeon'' (sometimes spelled "archeon"),<ref name=valentine>{{cite journal|author=David L. Valentine|month=Apr|year=2007
|title=Adaptations to energy stress dictate the ecology and evolution of the Archaea|journal=Nat. Rev. Microbiol.|volume=5|issue=4|pages=316-323|doi=10.1038/nrmicro1619}}</ref> while the [[Adjective|adjectival]] form is ''archaeal'' or ''archaean''. The [[etymology]] is [[Greek language|Greek]], from αρχαία meaning "ancient ones".

==Habitats==
Multiple archaeans are [[extremophile]]s, and some would say this is their [[ecological niche]].<ref name=valentine/> They can survive high temperatures, often above 100°C, as found in [[geyser]]s, [[black smoker]]s, and oil wells. Some are found in very cold habitats and others in highly [[salt|saline]], [[acid]]ic, or [[alkaline]] water. [[Mesophile]]s favor milder conditions in [[marsh]]land, [[sewage]] and [[soil]]. Many [[methanogen]]ic archaea are found in the digestive tracts of animals such as [[ruminant]]s, [[termite]]s, and humans. As of 2007, no clear examples of archaeal [[pathogen]]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=591-6 |year=2003 |id=PMID 12540534}}</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=1119-28 |year=2003 |id=PMID 14579252}}</ref> although a relationship has been proposed between the presence of some methanogens and human [[periodontal disease]].<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 U S A |volume=101 |issue=16 |pages=6176-81 |year=2004 |id=PMID 15067114}}</ref>

Archaea are commonly placed into three [[physiological]] groups. These are the [[halophile]]s, [[thermophile]]s and [[Acidophile (organisms)|acidophile]]s. These groups are not necessarily comprehensive or [[monophyletic]], nor even mutually exclusive. Nonetheless, they are a useful starting point for ecological studies. Halophiles, including the [[genus]] ''[[Halobacterium]]'', live in extremely saline environments and start outnumbering their bacterial counterparts at salinities greater than 20-25%.<ref name=valentine/> These can be found in sediments or in the intestines of animals.<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 |pmid=15831718}}</ref> Thermophiles live in places that have high temperatures, such as hot springs. Where optimal growth occurs at greater than 80°C, the archaeon is a ''hyperthermophyle'', and the highest recorded temperature survived was 121°C. Although thermophilic bacteria predominate at some high temperatures, archaea generally have the edge when [[acid]]ity exceeds pH 5. True acidophiles withstand pH 0 and below.<ref name=valentine/>

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. It is increasingly becoming recognised that [[methanogen]]s are commonly present in low-temperature environments such as cold [[sediment]]s. Some studies have even suggested that at these temperatures the pathway by which [[methanogenesis]] occurs may change due to the [[thermodynamic]] constraints imposed by low temperatures. Perhaps even more significant are the large numbers of archaea found throughout most of the world's oceans, a predominantly cold environment. These archaea, which belong to several deeply branching lineages unrelated to those previously known, can be present in extremely high numbers (up to 40% of the microbial biomass) although almost none have been isolated 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 = 343-8 | year = 2005 | pmid = 16163344 }}</ref> Currently we have almost no information regarding the physiology of these organisms, meaning that their effects on global [[biogeochemistry|biogeochemical]] cycles remain unknown. One recent study has shown, however, that one group of marine [[crenarchaeota]] are capable of [[nitrification]], a trait previously unknown among the archaea.<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 = 543-6 | year = 2005 | pmid = 16177789 }}</ref>

==History of archaean microbiology==
Archaea were identified in 1977 by [[Carl Woese]] and [[George E. Fox]] as being a separate branch based on their separation from other prokaryotes on 16S [[rRNA]] [[phylogenetic tree]]s.<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}}</ref> These two groups were originally named the Archaebacteria and Eubacteria, treated as [[kingdom (biology)|kingdom]]s or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and [[Bacteria]] to emphasize this, and argued that together with [[Eukaryota|Eukarya]] they compose [[three-domain system|three Domains]] of living organisms.<ref>{{cite journal |quotes=no | author = Woese, Carl R., Kandler, Otto, Wheelis, Mark L | title = Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences | year = 1990 | issue = 12 | volume = 87 | pages = 4576 – 4579}}</ref>

== Morphology and physiology ==

[[Image:Relative scale.svg|thumb|300px|The sizes of prokaryotes relative to other organisms and biomolecules.]]

=== Size and shape ===
Individual archaeans range from 0.1 μm to over 15 μm in diameter, and some form aggregates or filaments up to 200 μm in length. They occur in various shapes, such as spherical, rod-shape, spiral, lobed, or rectangular. Recently, a species of flat, square archaean that lives in hypersaline pools has been discovered.<ref>{{cite journal | author = Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. | title = Cultivation of Walsby's square haloarchaeon. | journal = FEMS Microbiol Lett. | | volume = 238| issue = 2 | pages = 469-73 | year = 2004 | pmid = 15358434 | url = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15358434&query_hl=36&itool=pubmed_docsum}}</ref>

=== Comparison of archaeal, bacterial and eukaryotic cells ===
Archaea are similar to other [[prokaryote]]s in most aspects of [[Cell (biology)|cell]] structure and [[metabolism]]. However, their genetic [[transcription (genetics)|transcription]] and [[translation (genetics)|translation]] — the two central processes in [[molecular biology]] — do not show many typical bacterial features, and are in many aspects similar to those of [[eukaryote]]s. For instance, archaeal translation uses eukaryotic-like initiation and elongation factors, and their transcription involves [[TATA Binding Protein]]s and [[TFIIB]] as in eukaryotes. Many archaeal tRNA and rRNA genes harbor unique archaeal [[introns]] which are neither like eukaryotic introns, nor like bacterial (type I and type II etc which can "home") introns.

Several other characteristics also set the Archaea apart. Like bacteria and eukaryotes, archaea possess [[glycerol]]-based [[phospholipids]]. However, three features of the archaeal lipids are unusual:<ref>White, David. (1995) ''The Physiology and Biochemistry of Prokaryotes'', pages 6-7. (Oxford: Oxford University Press). ISBN 0-19-508439-X.</ref>
* The archaeal lipids are unique because the [[stereochemistry]] of the glycerol is the reverse of that found in bacteria and eukaryotes. This is strong evidence for a different biosynthetic pathway.
* Most bacteria and eukaryotes have membranes composed mainly of glycerol-[[ester]] [[lipid]]s, whereas archaea have membranes composed of glycerol-[[ether lipid]]s. Even when bacteria have ether-linked lipids, the stereochemistry of the glycerol is the bacterial form. These differences may be an adaptation on the part of Archaea to [[hyperthermophile|hyperthermophily]]. However, it is worth noting that even mesophilic archaea have ether-linked lipids.
* Archaeal lipids are based upon the [[isoprene|isoprenoid]] sidechain. This is a five-carbon unit that is also common in rubber and as a component of some bacterial and eukaryotic vitamins. However, only the archaea incorporate these compounds into their cellular lipids, frequently as C-20 (four monomers) or C-40 (eight monomers) side-chains. In some archaea, the C-40 isoprenoid side-chain is long enough to span the membrane, forming a monolayer for a [[cell membrane]] with glycerol phosphate [[Functional group|moieties]] on both ends. Although dramatic, this adaptation is most common in the extremely [[thermophilic]] archaea.

=== Cell wall and flagella ===
{{further|[[Cell wall#Archaeal cell walls|Cell wall]]}}
Although not unique, archaeal cell walls are also unusual. For instance, in most archaea they are formed by surface-layer proteins or an S-layer. S-layers are common in bacteria, where they serve as the sole cell-wall component in some organisms (like the Planctomyces) or an outer layer in many organisms with [[peptidoglycan]]. With the exception of one group of methanogens, archaea lack a peptidoglycan wall (and in the case of the exception, the peptidoglycan is very different from the type found in bacteria).<ref name="Howland 2000">Howland, John L. (2000) ''The Surprising Archaea: Discovering Another domain of Life'', pages 69-71. (Oxford: Oxford University Press). ISBN 0-19-511183-4.</ref>

Archaeans also have [[flagellum|flagella]] that are notably different in composition and development from the superficially similar flagella of bacteria. The bacterial flagellum is a modified type III secretion system, while archeal flagella resemble type IV pilli which use a sec dependent secretion system somewhat similar to but different from type II secretion system.

== Metabolism ==

Archaea exhibit a variety of different types of [[metabolism]]; there are [[nitrifying bacteria|nitrifier]]s, methanogens and anaerobic methane oxidisers.<ref name=valentine/> Methanogens live in [[anaerobic environment]]s and produce methane. Of note are the [[halobacteria]], which use light to produce energy. Although no archaea conduct [[photosynthesis]] with an [[electron transport chain]], light-activated ion pumps like [[bacteriorhodopsin]] and [[halorhodopsin]] play a role in generating ion gradients, which are harnessed into [[adenosine triphosphate]] (ATP).

== Genetics and propagation ==

Archaea have one circular [[chromosome]] although up to 30% of their genetic material may be contained in [[plasmid]]s, as evidenced by comparisons of [[GC content]]. Archaea can reproduce by binary and multiple fission, fragmentation, and budding.

== Phylogeny ==
[[Image:Phylogenetic tree.svg|thumb|right|320px|A phylogenetic tree based on [[rRNA]] data, showing the separation of bacteria, archaea, and eukaryote.]]
[[Image:Neomuratree.svg|thumb|right|320px|An alternative tree based on the model of neomuran evolution from eubacteria. [[Last universal ancestor|LUCA]]: '''L'''ast '''U'''niversal '''C'''ommon '''A'''ncestor]]
Archaea are divided into two main groups based on rRNA trees, the [[Euryarchaeota]] and [[Crenarchaeota]]. Three other groups have been tentatively created for certain environmental samples, the peculiar species ''[[Nanoarchaeum|Nanoarchaeum equitans]]'', discovered in 2002 by [[Karl Stetter]],<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 – 8 | year = 2002| pmid = 11986665}}</ref> and the [[Archael Richmond Mine Acidophilic Nanoorganisms]] (ARMAN) groups discovered by [[Brett Baker]], but their affinities are uncertain.<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}}</ref>

Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral ''progenote'' with poorly developed genetic machinery. Later he treated these groups formally as [[three-domain system|domain]]s, each comprising several kingdoms. This division has become very popular, although the idea of the progenote itself is not generally supported. Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria. The relationship between Archaea and Eukarya remains an important problem. Aside from the similarities noted above, many genetic trees group the two together. Some place eukaryotes closer to Euryarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise. However, the discovery of archaean-like genes in certain bacteria, such as ''Thermotoga'', makes their relationship difficult to determine, as [[horizontal gene transfer]] may have occurred.<ref>{{cite journal | author = Nelson KE. 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 = 323-9 | year = 1999 | pmid = 10360571}}</ref> Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which 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 = 184-6 | year = 1988 | pmid = 3340165}}</ref> However, a recent large scale phylogenetic analysis of the structure of proteins encoded in almost 200 completely sequenced genomes showed that the origin of Archaea is much more ancient and that the archaeal lineage may represent the most ancient that exists on earth.<ref name=Wang> In fact, the study shows that the ancestor of all life had a proteome with a rather complex collection of protein structures, many of which are widely spread in modern metabolism. Single gene [[sequencing]] for [[systematics]] has led to whole [[genome sequencing]]; by January, 2007, 31 archaeal genomes have been completed with 29 partially completed.<ref>http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi</ref>

===Origin and early evolution===
The Archaea should not be confused with the [[geological]] term ''[[Archean]] eon'', also known as the ''Archeozoic era''. This refers to the primordial period of [[earth]] history when Archaea and Bacteria were the only [[Cell (biology)|cellular]] organisms living on the planet.<ref>{{cite journal |author=Altermann W, Kazmierczak J |title=Archean microfossils: a reappraisal of early life on Earth |journal=Res Microbiol |volume=154 |issue=9 |pages=611-7 |year=2003 |pmid=14596897}}</ref><ref>{{cite journal |author=Cavalier-Smith T |title=Cell evolution and Earth history: stasis and revolution |url=http://www.journals.royalsoc.ac.uk/content/0164755512w92302/fulltext.pdf |journal=Philos Trans R Soc Lond B Biol Sci |volume=361 |issue=1470 |pages=969-1006 |year=2006 |pmid=16754610}}</ref> Probable [[fossils]] of these [[microorganism|microbes]] have been dated to almost 3.5 billion years ago,<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=869-85 |year=2006 |pmid=16754604}}</ref> and the remains of lipids that may be either archaean or eukaryotic have been detected in shales 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=1033-6 |year=1999 |pmid=10446042}}</ref>

The last common ancestor of Bacteria and Archaea was probably a non-methanogenic thermophile, raising the possibility that lower temperatures are extreme environments in archaeal terms, and organisms that can survive in cooler environments evolved later on.<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=1007-22 |year=2006 |pmid=16754611 |url=http://www.journals.royalsoc.ac.uk/content/q74671t476444mq5/}}</ref>

== See also ==
*[[Anaerobic digestion]]
*[[List of Archaea genera]]
*[[List of sequenced archeal genomes]]
 
== 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}}

==External links==
{{wiktionary}}
{{wikispecies}}
* [http://www.microbe.org/microbes/archaea.asp Archaea]
* [http://www.archaea.unsw.edu.au/ ArchaeaWeb - by UNSW - Information about Archaea]
* [http://tellapallet.com/tree_of_life.htm Tree of Life illustration showing how Archaea relates to other lifeforms]
* [http://www.ucmp.berkeley.edu/archaea/archaea.html Introduction to the Archaea, ecology, systematics and morphology]
* [http://www.daviddarling.info/encyclopedia/A/archaea.html Archaea at The Encyclopedia of Astrobiology, Astronomy, & Spaceflight]
* [http://news.bbc.co.uk/1/hi/sci/tech/399972.stm BBC News July 21, 1999: Toughest bug reveals genetic secrets] Citat: "...It [''Pyrococcus abyssi''] likes conditions that the vast majority of other organisms would find impossible to live in. It thrives best at temperatures of about 103 degrees [Celsius] and under pressures of about 200 atmospheres...."
* [http://opm.phar.umich.edu/localization.php?localization=Archaebacterial%20membrane 3D structures of proteins from archaebacterial membranes]
* [http://www.genoscope.cns.fr/Pab/ Pyrococcus abyssi Home page at Genoscope]
* [http://archaea.ucsc.edu/ Browse any completed archaeal genome at UCSC]
* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonList&page=lineageMicrobes&domain=Archaea Comparative Analysis of Archaeal Genomes] (at [[United_States_Department_of_Energy|DOE's]] [[Integrated_Microbial_Genomes_System|IMG system]])

{{Extremophile}}

[[Category:Archaea| ]]
[[Category:Extremophiles]]
[[Category:Microbiology]]

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