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The Archaea ( or or ) constitute a domain and kingdom of single-celled microorganisms. These microbes (archaea; singular archaeon) are prokaryotes, meaning they have no cell nucleus or any other membrane-bound organelles in their cells. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is outdated. Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla. Classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores. Archaea were initially viewed as extremophiles living in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, and marshlands. They are also part of the human microbiota, found in the colon, oral cavity, and skin. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.


New domain

s. Pictured here is Grand Prismatic Spring of Yellowstone National Park.]] For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. For example, microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume.{{ cite journal |author=Staley, J.T. |title=The bacterial species dilemma and the genomic-phylogenetic species concept |journal=Philosophical Transactions of the Royal Society B |volume=361 |issue=1475 |pages=1899–909 |date=2006 |pmid=17062409 |doi=10.1098/rstb.2006.1914 |pmc=1857736}} In 1965, Emile Zuckerkandl and Linus Pauling{{ cite journal |author=Zuckerkandl, E. |author2=Pauling, L. |title=Molecules as documents of evolutionary history |journal=J. Theor. Biol. |volume=8 |issue=2 |pages=357–66 |date=1965 |pmid=5876245 |doi=10.1016/0022-5193(65)90083-4}} proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other. This approach, known as phylogenetics, is the main method used today. Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes. These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms 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, Woese later proposed a new natural system of organisms with three separate Domains: the Eukarya, the Bacteria and the Archaea, in what is now known as "The Woesian Revolution". The word archaea comes from the Ancient Greek , meaning "ancient things", Archaea. (2008). In Merriam-Webster Online Dictionary. Retrieved , 2008 as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity. For a long time, archaea were seen as extremophiles that only exist in extreme habitats such as hot springs and salt lakes. However, as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were also included in the Archaea. By the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms that are widely distributed in nature and are common in all habitats. This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.{{ cite journal |author=Theron, J. |author2=Cloete, T.E. |title=Molecular techniques for determining microbial diversity and community structure in natural environments |journal=Crit. Rev. Microbiol. |volume=26 |issue=1 |pages=37–57 |date=2000 |pmid=10782339 |doi=10.1080/10408410091154174}}{{ cite journal |author=Schmidt, T.M. |title=The maturing of microbial ecology |journal=Int. Microbiol. |volume=9 |issue=3 |pages=217–23 |date=2006 |pmid=17061212 |url=http://www.im.microbios.org/0903/0903217.pdf |format=PDF |deadurl=yes |archiveurl=https://web.archive.org/web/20080911074811/http://www.im.microbios.org/0903/0903217.pdf |archivedate=11 September 2008 |df=dmy }}

Current classification

are a new group of archaea recently discovered in acid mine drainage.]] 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.{{ cite journal |author=Gevers, D. |author2=Dawyndt, P. |author3=Vandamme, P. |title=Stepping stones towards a new prokaryotic taxonomy |journal=Philosophical Transactions of the Royal Society B |volume=361 |issue=1475 |pages=1911–6 |date=November 29, 2006 |pmid=17062410 |doi=10.1098/rstb.2006.1915 |pmc=1764938 |displayauthors=etal }} These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms ( molecular phylogenetics). Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, the Nanoarchaeota. 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.{{ cite journal |author=Barns, S.M. |author2=Delwiche, C.F. |author3=Palmer, J.D. |author4= Pace NR |title=Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=93 |issue=17 |pages=9188–93 |date=1996 |pmid=8799176 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=8799176 |doi=10.1073/pnas.93.17.9188 |pmc=38617|bibcode = 1996PNAS...93.9188B }}{{ cite journal |author=Elkins, J.G. |author2=Podar, M. |author3=Graham, D.E. |title=A korarchaeal genome reveals insights into the evolution of the Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=23 |pages=8102–7 |date=June 2008 |pmid=18535141 |doi=10.1073/pnas.0801980105 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=18535141 |pmc=2430366 |bibcode=2008PNAS..105.8102E|displayauthors=1 |last4=Makarova |first4=KS |last5=Wolf |first5=Y |last6=Randau |first6=L |last7=Hedlund |first7=BP |last8=Brochier-Armanet |first8=C |last9=Kunin |first9=V |last10=Anderson |first10=I |last11=Lapidus|first11=A |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 }} Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known. A superphylum – TACK – has been proposed that includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota. This superphylum may be related to the origin of eukaryotes. More recently, the superphylum Asgard has been named and proposed to be more closely related to the original eukaryote and a sister group to TACK.

Concept of species

The classification of archaea into species is also controversial. Biology defines a species as a group of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but not with others) is of no help here because archaea reproduce asexually. Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. A second concern is to what extent such species designations have practical meaning. Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure. The Bacteria also contain many uncultured microbes with similar implications for characterization.

Origin and evolution

The age of the Earth is about 4.54 billion years.{{cite web | date=1997 | title=Age of the Earth | url=http://pubs.usgs.gov/gip/geotime/age.html | publisher=U.S. Geological Survey | accessdate=2006-01-10 | archiveurl= https://web.archive.org/web/20051223072700/http://pubs.usgs.gov/gip/geotime/age.html| archivedate= 23 December 2005 | deadurl= no}}{{cite journal | last=Dalrymple | first=G. Brent | title=The age of the Earth in the twentieth century: a problem (mostly) solved | journal=Special Publications, Geological Society of London | date=2001 | volume=190 | issue=1 | pages=205–221 | doi=10.1144/GSL.SP.2001.190.01.14 |bibcode = 2001GSLSP.190..205D }} Although probable prokaryotic cell fossils date to almost 3.5  billion years ago, most prokaryotes do not have distinctive morphologies and fossil shapes cannot be used to identify them as archaea.{{ cite journal |author=Schopf J |title=Fossil evidence of Archaean life |url= |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=361 |issue=1470 |pages=869–85 |date=2006 |pmid=16754604 |doi=10.1098/rstb.2006.1834 |format=PDF |pmc=1578735 }} Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms.{{ cite journal |author=Chappe B |author2=Albrecht P |author3=Michaelis W |title=Polar Lipids of Archaebacteria in Sediments and Petroleums |journal=Science |volume=217 |issue=4554 |pages=65–66 |date=July 1982 |pmid=17739984 |doi=10.1126/science.217.4554.65|bibcode = 1982Sci...217...65C }} Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago;{{ cite journal |author=Brocks JJ |author2=Logan GA |author3=Buick R |author4=Summons RE |title=Archean molecular fossils and the early rise of eukaryotes |journal=Science |volume=285 |issue=5430 |pages=1033–6 |date=1999 |pmid=10446042 |doi=10.1126/science.285.5430.1033|citeseerx= }} such data have since been questioned.{{ cite journal |author=Rasmussen B |author2=Fletcher IR |author3=Brocks JJ |author4=Kilburn MR |title=Reassessing the first appearance of eukaryotes and cyanobacteria |journal=Nature |volume=455 |issue=7216 |pages=1101–4 |date=October 2008 |pmid=18948954 |doi=10.1038/nature07381|bibcode = 2008Natur.455.1101R }} Such lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which include Earth's oldest known sediments, formed 3.8 billion years ago.{{ cite journal |last=Hahn |first=Jürgen |author2=Pat Haug |date=1986 |title=Traces of Archaebacteria in ancient sediments |journal=System Applied Microbiology |volume=7 |issue=Archaebacteria '85 Proceedings |pages=178–83 |doi=10.1016/S0723-2020(86)80002-9}} The archaeal lineage may be the most ancient that exists on Earth.{{ cite journal |author=Wang M |author2=Yafremava LS |author3=Caetano-Anollés D |author4=Mittenthal JE |author5=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=1572–85 |date=2007 |pmid=17908824 |doi=10.1101/gr.6454307 |pmc=2045140}} Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.{{ cite journal |author=Woese CR |author2= Gupta R |title=Are archaebacteria merely derived 'prokaryotes'? |journal=Nature |volume=289 |issue=5793 |pages=95–6 |date=1981 |pmid=6161309 |doi=10.1038/289095a0|bibcode = 1981Natur.289...95W }} One possibilityKandler O. The early diversification of life and the origin of the three domains: A proposal. In: Wiegel J, Adams WW, editors. Thermophiles: The keys to molecular evolution and the origin of life? Athens: Taylor and Francis, 1998: 19-31. is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. 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 only later.{{ cite journal |author=Gribaldo S |author2=Brochier-Armanet C |title=The origin and evolution of Archaea: a state of the art |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=361 |issue=1470 |pages=1007–22 |date=2006 |pmid=16754611 |url= |doi=10.1098/rstb.2006.1841 |pmc=1578729 }} Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote's only surviving meaning is "not a eukaryote", limiting its value.{{ 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=1–9 |date=1 March 1994|pmid=8177167 |pmc=372949 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8177167 }}

Comparison to other domains

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.Information is from Willey JM, Sherwood LM, Woolverton CJ. Microbiology 7th ed. (2008), Ch. 19 pp. 474–475, except where noted. Many of these characteristics are also discussed below. Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA molecule sequenced, known as 16s rRNA, is present in all organisms and always has the same vital function, the production of proteins. Because this function is so central to life, organisms with mutations of their 16s rRNA are unlikely to survive, leading to great stability in the structure of this nucleotide over many generations. 16s rRNA is also large enough to retain organism-specific information, but small enough to be sequenced in a manageable amount of time. In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that involved splitting the RNA into fragments that could be sorted and compared to other fragments from other organisms. The more similar the patterns between species were, the more closely related the organisms. Woese used his new rRNA comparison method to categorize and contrast different organisms. He sequenced a variety of different species and happened upon a group of methanogens that had vastly different patterns than any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than they were to other organisms sequenced, leading Woese to propose the new domain of Archaea. His experiments showed that the Archaea were more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. This led to the conclusion that Archaea and Eukarya shared a more recent common ancestor than Eukarya and Bacteria in general. The development of the nucleus occurred after the split between Bacteria and this common ancestor. Although Archaea are prokaryotic, they are more closely related to Eukarya and thus cannot be placed within either the Bacteria or Eukarya domains. One property unique to Archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in Bacteria and Eukarya, which may be a contributing factor to the ability of many Archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Comparative analysis of archaeal genomes has also identified several molecular signatures in the form of conserved signature indels and signature proteins which are uniquely present in either all Archaea or different main groups within Archaea. Another unique feature of Archaea is that no other known organisms are capable of methanogenesis (the metabolic production of methane). Methanogenic Archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are Bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas.

Relationship to bacteria

"green air" © 2007 - Ingo Malchow, Webdesign Neustrelitz
This article based upon the http://en.wikipedia.org/wiki/Archaea, the free encyclopaedia Wikipedia and is licensed under the GNU Free Documentation License.
Further informations available on the list of authors and history: http://en.wikipedia.org/w/index.php?title=Archaea&action=history
presented by: Ingo Malchow, Mirower Bogen 22, 17235 Neustrelitz, Germany