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{{redirect|Archea|the geologic eon|Archean|the spider genus|Archaea (spider)|the spider family|Archaeidae|the prefix "archae-"|List of commonly used taxonomic affixes}}{{for|the journal|Archaea (journal)}}{{pp-move-indef}}{{short description|A domain of single-celled prokaryotic microorganisms}}{{Use dmy dates|date=August 2013}}{{Automatic taxobox|name = Archaea (Archaebacteria)! Property! Archaea! Bacteria! Eukarya| Cell membrane| Ether-linked lipids, pseudopeptidoglycan| Ester-linked lipids, peptidoglycan| Ester-linked lipids, various structures| Gene structure| Circular chromosomes, similar translation and transcription to Eukarya| Circular chromosomes, unique translation and transcription| Multiple, linear chromosomes, similar translation and transcription to Archaea| Reproduction| Asexual reproduction, horizontal gene transfer| Asexual reproduction, horizontal gene transfer
35003.5-0Ga|earliest=3800}}Paleoarchean or perhaps Eoarchean – recent|image = Halobacteria.jpg|image_caption = Halobacterium sp. strain NRC-1,each cell about 5 Î¼m long|taxon = ArchaeaCarl Woese>Woese, Otto Kandler & Mark Wheelis>Wheelis, 1990 JOURNAL = GENOME BIOLOGY AND EVOLUTION ISSUE = 1 DATE = DECEMBER 2014 PMC = 4316627 LAST-AUTHOR-AMP = YES, and phylaNCBI TAXONOMY PAGE ON ARCHAEA >URL=HTTPS://WWW.NCBI.NLM.NIH.GOV/TAXONOMY/BROWSER/WWWTAX.CGI?MODE=UNDEF&ID=2157&LVL=5&LIN=F&KEEP=1&SRCHMODE=1&UNLOCK, |subdivision = (TACK)"Filarchaeota" Cavalier-Smith, T. 2014* "Aigarchaeota" Nunoura et al. 2011 }}Archaea ({{IPAc-en|audio=en-us-Archaea.ogg|É‘r|ˈ|k|iː|É™}} or {{IPAc-en|É‘r|ˈ|k|eɪ|É™}} {{respell|ar|KEE|É™}} or {{respell|ar|KAY|É™}}) constitute a domain of single-celled microorganisms. These microbes (archaea; singular archaeon) are prokaryotes, meaning they have no cell nucleus.Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is outdated.JOURNAL, Pace NR, Time for a change, Nature, 441, 7091, 289, May 2006, 16710401, 10.1038/441289a, 2006Natur.441..289P, Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukarya. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and were only 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 shapes quite unlike that of bacteria, such as the flat and square-shaped cells of Haloquadratum walsbyi.JOURNAL, Stoeckenius W, Walsby's square bacterium: fine structure of an orthogonal procaryote, Journal of Bacteriology, 148, 1, 352–60, October 1981, 7287626, 216199,weblink Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. 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, but 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.The first archaea observed were extremophiles living in harsh environments such as hot springs and salt lakes with no other organisms, but improved detection tools led to the discovery of archaea in almost every habitat, including soils, oceans, and marshlands. They are also part of the human microbiota in the gut, mouth, and skin.JOURNAL, Bang C, Schmitz RA, Archaea associated with human surfaces: not to be underestimated, FEMS Microbiology Reviews, 39, 5, 631–48, September 2015, 25907112, 10.1093/femsre/fuv010, 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 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.

Classification

{{anchor|A new domain}}

Early concept

File:Grand prismatic spring.jpg|thumb|left| Archaea were found in volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National ParkYellowstone National ParkFor 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.JOURNAL, Staley JT, The bacterial species dilemma and the genomic-phylogenetic species concept, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1475, 1899–909, November 2006, 17062409, 1857736, 10.1098/rstb.2006.1914, In 1965, Emile Zuckerkandl and Linus PaulingJOURNAL, Zuckerkandl E, Pauling L, Molecules as documents of evolutionary history, Journal of Theoretical Biology, 8, 2, 357–66, March 1965, 5876245, 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 phylogenetic approach is the main method used today.Archaea – at that time only the methanogens were known – were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox based on their ribosomal RNA (rRNA) genes. They called these groups the Urkingdoms of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains: the Eukarya, the Bacteria and the Archaea,JOURNAL, Woese CR, Kandler O, Wheelis ML, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proceedings of the National Academy of Sciences of the United States of America, 87, 12, 4576–9, June 1990, 2112744, 54159, 10.1073/pnas.87.12.4576,weblink 1990PNAS...87.4576W, in what is now known as "The Woesian Revolution".BOOK,weblink The new foundations of evolution: on the tree of life, Sapp, Jan, Oxford University Press, 2009, 978-0-19-973438-2, New York, The word archaea comes from the Ancient Greek , meaning "ancient things",Archaea. (2008). In Merriam-Webster Online Dictionary. Retrieved {{Nowrap|July 1}}, 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, but as new habitats were studied, more organisms were discovered. Extreme halophilicJOURNAL, Magrum LJ, Luehrsen KR, Woese CR, Are extreme halophiles actually "bacteria"?, Journal of Molecular Evolution, 11, 1, 1–8, May 1978, 660662, 10.1007/bf01768019, 1978JMolE..11....1M, and hyperthermophilic microbesJOURNAL, Stetter KO, Karl Stetter, Hyperthermophiles in the history of life, Ciba Foundation Symposium, 202, 1–10; discussion 11–8, 1996, 9243007, were also included in Archaea. For a long time, archaea were seen as extremophiles that only exist in extreme habitats such as hot springs and salt lakes, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature.JOURNAL, DeLong EF, Everything in moderation: archaea as 'non-extremophiles', Current Opinion in Genetics & Development, 8, 6, 649–54, December 1998, 9914204, 10.1016/S0959-437X(98)80032-4, 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.JOURNAL, Theron J, Cloete TE, Molecular techniques for determining microbial diversity and community structure in natural environments, Critical Reviews in Microbiology, 26, 1, 37–57, 2000, 10782339, 10.1080/10408410091154174, JOURNAL, Schmidt TM, The maturing of microbial ecology, International Microbiology, 9, 3, 217–23, September 2006, 17061212,weblink PDF,weblink" title="web.archive.org/web/20080911074811weblink">weblink dmy, yes, 11 September 2008,

Current classification

{{further|Biological classification|Systematics}}(File:Archaeal tree.png|thumb|right|Phylogenetic tree of Archaea using conserved genes)File:Rio tinto river CarolStoker NASA Ames Research Center.jpg|thumb|left|The ARMAN are a new group of archaea recently discovered in acid mine drainageacid mine drainageThe 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.JOURNAL, Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, De Vos P, Stepping stones towards a new prokaryotic taxonomy, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1475, 1911–16, November 2006, 17062410, 1764938, 10.1098/rstb.2006.1915, 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.JOURNAL, Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO, A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont, Nature, 417, 6884, 63–67, May 2002, 11986665, 10.1038/417063a, 2002Natur.417...63H, 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.JOURNAL, Barns SM, Delwiche CF, Palmer JD, Pace NR, Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences, Proceedings of the National Academy of Sciences of the United States of America, 93, 17, 9188–93, August 1996, 8799176, 38617, 10.1073/pnas.93.17.9188,weblink 1996PNAS...93.9188B, JOURNAL, Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO, A korarchaeal genome reveals insights into the evolution of the Archaea, Proceedings of the National Academy of Sciences of the United States of America, 105, 23, 8102–07, June 2008, 18535141, 2430366, 10.1073/pnas.0801980105, 2008PNAS..105.8102E, 6, 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 2006JOURNAL, Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF, Lineages of acidophilic archaea revealed by community genomic analysis, Science, 314, 5807, 1933–35, December 2006, 17185602, 10.1126/science.1132690, yes, 2006Sci...314.1933B, and are some of the smallest organisms known.JOURNAL, Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF, Enigmatic, ultrasmall, uncultivated Archaea, Proceedings of the National Academy of Sciences of the United States of America, 107, 19, 8806–11, May 2010, 20421484, 2889320, 10.1073/pnas.0914470107, 2010PNAS..107.8806B, 1, A superphylum – TACK – has been proposed that includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota.JOURNAL, Guy L, Ettema TJ, The archaeal 'TACK' superphylum and the origin of eukaryotes, Trends in Microbiology, 19, 12, 580–87, December 2011, 22018741, 10.1016/j.tim.2011.09.002, 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.JOURNAL, Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ, Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, 541, 7637, 353–58, January 2017, 28077874, 10.1038/nature21031, 2017Natur.541..353Z, etal,

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 since archaea reproduce asexually.JOURNAL, de Queiroz K, Ernst Mayr and the modern concept of species, Proceedings of the National Academy of Sciences of the United States of America, 102 Suppl 1, Suppl 1, 6600–07, May 2005, 15851674, 1131873, 10.1073/pnas.0502030102,weblink 2005PNAS..102.6600D, 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.JOURNAL, Eppley JM, Tyson GW, Getz WM, Banfield JF, Genetic exchange across a species boundary in the archaeal genus ferroplasma, Genetics, 177, 1, 407–16, September 2007, 17603112, 2013692, 10.1534/genetics.107.072892,weblink On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability.JOURNAL, Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF, Searching for species in haloarchaea, Proceedings of the National Academy of Sciences of the United States of America, 104, 35, 14092–97, August 2007, 17715057, 1955782, 10.1073/pnas.0706358104,weblink 2007PNAS..10414092P, Some researchers question whether such species designations have practical meaning.JOURNAL, Kunin V, Goldovsky L, Darzentas N, Ouzounis CA, The net of life: reconstructing the microbial phylogenetic network, Genome Research, 15, 7, 954–59, July 2005, 15965028, 1172039, 10.1101/gr.3666505,weblink Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy.JOURNAL, Robertson CE, Harris JK, Spear JR, Pace NR, Phylogenetic diversity and ecology of environmental Archaea, Current Opinion in Microbiology, 8, 6, 638–42, December 2005, 16236543, 10.1016/j.mib.2005.10.003, 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.JOURNAL, Hugenholtz P, Exploring prokaryotic diversity in the genomic era, Genome Biology, 3, 2, REVIEWS0003, 2002, 11864374, 139013, 10.1186/gb-2002-3-2-reviews0003, The Bacteria also include many uncultured microbes with similar implications for characterization.JOURNAL, Rappé MS, Giovannoni SJ, The uncultured microbial majority, Annual Review of Microbiology, 57, 369–94, 2003, 14527284, 10.1146/annurev.micro.57.030502.090759, On average, archaeal genomes show higher levels of complexity than those of bacteria.JOURNAL, Pratas D, Pinho A, On the Approximation of the Kolmogorov Complexity for DNA Sequences., Iberian Conference on Pattern Recognition and Image Analysis. Springer, 10255, 259–66, June 20–23, 2017, 10.1007/978-3-319-58838-4_29, Lecture Notes in Computer Science, 978-3-319-58837-7,

Origin and evolution

{{further|Timeline of evolution}}The age of the Earth is about 4.54 billion years.WEB
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, Scientific evidence suggests that life began on Earth at least 3.5 billion years ago.JOURNAL, de Duve, Christian, Christian de Duve, The Beginnings of Life on Earth,weblink American Scientist, October 1995, 15 January 2014, WEB, Timmer, John, 3.5 billion year old organic deposits show signs of life,weblink 4 September 2012, Ars Technica, 15 January 2014, The earliest evidence for life on Earth is graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in Western GreenlandJOURNAL,weblink Ohtomo Y, Kakegawa T, Ishida A, Nagase T, Rosingm MT, Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks, Nature Geoscience, 7, 25, 10.1038/ngeo2025, 8 December 2013, 9 Dec 2013, 2014NatGe...7...25O, and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.NEWS, Borenstein, Seth, Oldest fossil found: Meet your microbial mom,weblink 13 November 2013, Associated Press, 15 November 2013, JOURNAL, Noffke N, Christian D, Wacey D, Hazen RM, Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia, Astrobiology, 13, 12, 1103–24, December 2013, 24205812, 3870916, 10.1089/ast.2013.1030,weblink 2013AsBio..13.1103N, In 2015, possible remains of biotic matter were found in 4.1 billion-year-old rocks in Western Australia.NEWS, Borenstein, Seth, Hints of life on what was thought to be desolate early Earth,weblink 19 October 2015, Excite, Yonkers, NY, Mindspark Interactive Network, Associated Press, 2015-10-20, JOURNAL, Bell EA, Boehnke P, Harrison TM, Mao WL, Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon, Proceedings of the National Academy of Sciences of the United States of America, 112, 47, 14518–21, November 2015, 26483481, 4664351, 10.1073/pnas.1517557112,weblink National Academy of Sciences, PDF, 2015PNAS..11214518B, 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.JOURNAL, Schopf JW, Fossil evidence of Archaean life, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1470, 869–85, June 2006, 16754604, 1578735, 10.1098/rstb.2006.1834, Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms.JOURNAL, Chappe B, Albrecht P, Michaelis W, Polar lipids of archaebacteria in sediments and petroleums, Science, 217, 4554, 65–66, July 1982, 17739984, 10.1126/science.217.4554.65, 1982Sci...217...65C, Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago;JOURNAL, Brocks JJ, Logan GA, Buick R, Summons RE, Archean molecular fossils and the early rise of eukaryotes, Science, 285, 5430, 1033–36, August 1999, 10446042, 10.1126/science.285.5430.1033, 10.1.1.516.9123, such data have since been questioned.JOURNAL, Rasmussen B, Fletcher IR, Brocks JJ, Kilburn MR, Reassessing the first appearance of eukaryotes and cyanobacteria, Nature, 455, 7216, 1101–4, October 2008, 18948954, 10.1038/nature07381, 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 includes Earth's oldest known sediments, formed 3.8 billion years ago.JOURNAL, Jürgen, Hahn, Pat, Haug, vanc, 1986, Traces of Archaebacteria in ancient sediments, System Applied Microbiology, 7, Archaebacteria '85 Proceedings, 178–83, 10.1016/S0723-2020(86)80002-9, The archaeal lineage may be the most ancient that exists on Earth.JOURNAL, Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G, Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world, Genome Research, 17, 11, 1572–85, November 2007, 17908824, 2045140, 10.1101/gr.6454307, Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.JOURNAL, Woese CR, Gupta R, Are archaebacteria merely derived 'prokaryotes'?, Nature, 289, 5793, 95–96, January 1981, 6161309, 10.1038/289095a0, 1981Natur.289...95W, JOURNAL, Woese C, The universal ancestor, Proceedings of the National Academy of Sciences of the United States of America, 95, 12, 6854–59, June 1998, 9618502, 22660, 10.1073/pnas.95.12.6854, 1998PNAS...95.6854W, 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 bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later.JOURNAL, Gribaldo S, Brochier-Armanet C, The origin and evolution of Archaea: a state of the art, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361, 1470, 1007–22, June 2006, 16754611, 1578729, 10.1098/rstb.2006.1841, Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term prokaryote suggests a false similarity between them.JOURNAL, Woese CR, There must be a prokaryote somewhere: microbiology's search for itself, Microbiological Reviews, 58, 1, 1–9, March 1994, 8177167, 372949,weblink

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.{| class="wikitable"
Internal Cell (biology)>cell structureorganelles (?HEIMERL T, FLECHSLER J, PICKL C, HEINZ V, SALECKER B, ZWECK J, WANNER G, GEIMER S, SAMSON RY, BELL SD, HUBER H, WIRTH R, WURCH L, PODAR M, RACHEL R JOURNAL = FRONTIERS IN MICROBIOLOGY PAGES = 1072 PMID = 28659892 nucleus (biology)>nucleus| No membrane-bound organelles or nucleus| Membrane-bound organelles and nucleus
MetabolismJURTSHUKTITLE=MEDICAL MICROBIOLOGYPUBLISHER=UNIVERSITY OF TEXAS MEDICAL BRANCH AT GALVESTONEDITION=4THACCESS-DATE=5 NOVEMBER 2014, Medical Microbiology, | Various, with methanogenesis unique to Archaea| Various, including photosynthesis, aerobic and anaerobic respiration, fermentation, and autotrophy| Photosynthesis, cellular respiration and fermentation
Sexual reproduction>Sexual and asexual reproduction
Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this nucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be sequenced quickly. 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.JOURNAL, Woese CR, Fox GE, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proceedings of the National Academy of Sciences of the United States of America, 74, 11, 5088–90, November 1977, 270744, 432104, 10.1073/pnas.74.11.5088, 1977PNAS...74.5088W, The more similar the patterns between species, the more closely they are related.Woese used his new rRNA comparison method to categorize and contrast different organisms. He sequenced a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than to other organisms sequenced, leading Woese to propose the new domain of Archaea. His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure.JOURNAL, Cavicchioli R, Archaea--timeline of the third domain, Nature Reviews. Microbiology, 9, 1, 51–61, January 2011, 21132019, 10.1038/nrmicro2482,weblink This led to the conclusion that Archaea and Eukarya shared a more recent common ancestor than Eukarya and Bacteria. The development of the nucleus occurred after the split between Bacteria and this common ancestor.One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea.JOURNAL, Gupta RS, Shami A, Molecular signatures for the Crenarchaeota and the Thaumarchaeota, Antonie van Leeuwenhoek, 99, 2, 133–57, February 2011, 20711675, 10.1007/s10482-010-9488-3, JOURNAL, Gao B, Gupta RS, Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis, BMC Genomics, 8, 86, March 2007, 17394648, 1852104, 10.1186/1471-2164-8-86, JOURNAL, Gupta RS, Naushad S, Baker S, Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov, International Journal of Systematic and Evolutionary Microbiology, 65, Pt 3, 1050–69, March 2015, 25428416, 10.1099/ijs.0.070136-0, Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas.JOURNAL, Deppenmeier U, The unique biochemistry of methanogenesis, Progress in Nucleic Acid Research and Molecular Biology, 71, 223–83, 2002, 12102556, 10.1016/s0079-6603(02)71045-3, 978-0-12-540071-8, Progress in Nucleic Acid Research and Molecular Biology,

Relationship to bacteria

{{PhylomapA|size=350px||caption=Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al. (2006)JOURNAL, Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P, Toward automatic reconstruction of a highly resolved tree of life, Science, 311, 5765, 1283–87, March 2006, 16513982, 10.1126/science.1123061, 2006Sci...311.1283C, }}The relationship between the three domains is of central importance for understanding the origin of life. Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya.JOURNAL, Koonin EV, Mushegian AR, Galperin MY, Walker DR, Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea, Molecular Microbiology, 25, 4, 619–37, August 1997, 9379893, 10.1046/j.1365-2958.1997.4821861.x, Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayerJOURNAL, Gupta RS, Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes, Microbiology and Molecular Biology Reviews, 62, 4, 1435–91, December 1998, 9841678, 98952, and usually contain a thick sacculus (exoskeleton) of varying chemical composition.JOURNAL, Koch AL, Were Gram-positive rods the first bacteria?, Trends in Microbiology, 11, 4, 166–70, April 2003, 12706994, 10.1016/S0966-842X(03)00063-5, In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I;,JOURNAL, Gupta RS, What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms, Molecular Microbiology, 29, 3, 695–707, August 1998, 9723910, 10.1046/j.1365-2958.1998.00978.x, but the phylogeny of these genes was interpreted to reveal interdomain gene transfer,JOURNAL, Gogarten JP, Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages, Journal of Molecular Evolution, 39, 5, 541–43, November 1994, 7807544, 10.1007/bf00173425, 1994JMolE..39..541G, JOURNAL, Brown JR, Masuchi Y, Robb FT, Doolittle WF, Evolutionary relationships of bacterial and archaeal glutamine synthetase genes, Journal of Molecular Evolution, 38, 6, 566–76, June 1994, 7916055, 10.1007/BF00175876, 1994JMolE..38..566B, and might not reflect the organismal relationship(s).It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure.JOURNAL, Gupta RS, The natural evolutionary relationships among prokaryotes, Critical Reviews in Microbiology, 26, 2, 111–31, 2000, 10890353, 10.1080/10408410091154219, This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are primarily produced by gram-positive bacteria, and that these antibiotics primarily act on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms;Gupta RS. Molecular Sequences and the Early History of Life. In: Sapp J, editor. Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press, 2005: 160-183. Cavalier-Smith has made a similar suggestion.JOURNAL, Cavalier-Smith T, The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, International Journal of Systematic and Evolutionary Microbiology, 52, Pt 1, 7–76, January 2002, 11837318, 10.1099/00207713-52-1-7, This proposal is also supported by other work investigating protein structural relationshipsJOURNAL, Valas RE, Bourne PE, The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon, Biology Direct, 6, 16, February 2011, 21356104, 3056875, 10.1186/1745-6150-6-16, and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.JOURNAL, Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA, Evidence that the root of the tree of life is not within the Archaea, Molecular Biology and Evolution, 23, 9, 1648–51, September 2006, 16801395, 10.1093/molbev/msl046,

Relation to eukaryotes

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum CrenarchaeotaJOURNAL, Lake JA, Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences, Nature, 331, 6152, 184–86, January 1988, 3340165, 10.1038/331184a0, 1988Natur.331..184L, and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.JOURNAL, Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM, Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima, Nature, 399, 6734, 323–29, May 1999, 10360571, 10.1038/20601, 6, 1999Natur.399..323N, The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea,JOURNAL, Gouy M, Li WH, Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree, Nature, 339, 6220, 145–47, May 1989, 2497353, 10.1038/339145a0, 1989Natur.339..145G, JOURNAL, Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV, The deep archaeal roots of eukaryotes, Molecular Biology and Evolution, 25, 8, 1619–30, August 2008, 18463089, 2464739, 10.1093/molbev/msn108,weblink and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure. An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea.JOURNAL, Williams TA, Foster PG, Cox CJ, Embley TM, An archaeal origin of eukaryotes supports only two primary domains of life, Nature, 504, 7479, 231–36, December 2013, 24336283, 10.1038/nature12779,weblink 2013Natur.504..231W, A lineage of archaea discovered in 2015, Lokiarchaeum (of proposed new Phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes.NEWS, Zimmer, Carl, Carl Zimmer, Under the Sea, a Missing Link in the Evolution of Complex Cells,weblink May 6, 2015, The New York Times, May 6, 2015, JOURNAL, Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, 521, 7551, 173–179, May 2015, 25945739, 4444528, 10.1038/nature14447, 2015Natur.521..173S, Several sister phyla of "Lokiarchaeota" have since been found ("Thorarchaeota", "Odinarchaeota", "Heimdallarchaeota"), all together comprising a newly proposed supergroup Asgard, which may appear as a sister taxon to TACK.JOURNAL, Seitz KW, Lazar CS, Hinrichs KU, Teske AP, Baker BJ, Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction, The ISME Journal, 10, 7, 1696–705, July 2016, 26824177, 4918440, 10.1038/ismej.2015.233, Details of the relation of Asgard members and eukaryotes are still under consideration.

Morphology

Individual archaea range from 0.1 micrometers (μm) to over 15 Î¼m in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.Barns, Sue and Burggraf, Siegfried. (1997) Crenarchaeota. Version 1 January 1997. in The Tree of Life Web Project Archaea in the genus Haloquadratum such as Haloquadratum walsbyi are flat, square archaea that live in hypersaline pools.JOURNAL, Walsby, A.E., 1980, A square bacterium, Nature, 283, 5742, 69–71, 10.1038/283069a0, 1980Natur.283...69W, 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 archaea,JOURNAL, Hara F, Yamashiro K, Nemoto N, Ohta Y, Yokobori S, Yasunaga T, Hisanaga S, Yamagishi A, An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin, Journal of Bacteriology, 189, 5, 2039–45, March 2007, 17189356, 1855749, 10.1128/JB.01454-06,weblink etal, and filaments form within their cells,JOURNAL, Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ, Chaperonin filaments: the archaeal cytoskeleton?, Proceedings of the National Academy of Sciences of the United States of America, 94, 10, 5383–88, May 1997, 9144246, 24687, 10.1073/pnas.94.10.5383,weblink 1997PNAS...94.5383T, but in contrast to other organisms, these cellular structures are poorly understood.JOURNAL, Hixon WG, Searcy DG, Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts, Bio Systems, 29, 2-3, 151–60, 1993, 8374067, 10.1016/0303-2647(93)90091-P, In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae.Some species form aggregates or filaments of cells up to 200 Î¼m long. These organisms can be prominent in biofilms.JOURNAL, Hall-Stoodley L, Costerton JW, Stoodley P, Bacterial biofilms: from the natural environment to infectious diseases, Nature Reviews. Microbiology, 2, 2, 95–108, February 2004, 15040259, 10.1038/nrmicro821, Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells.JOURNAL, Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M, Marumo K, Maruyama A, Sugai A, Itoh T, Ishibashi J, Urabe T, Kamekura M, Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount, International Journal of Systematic and Evolutionary Microbiology, 55, Pt 6, 2507–14, November 2005, 16280518, 10.1099/ijs.0.63432-0, M, Kamekura, etal, Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration.JOURNAL, Nickell S, Hegerl R, Baumeister W, Rachel R, Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography, Journal of Structural Biology, 141, 1, 34–42, January 2003, 12576018, 10.1016/S1047-8477(02)00581-6,weblink The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.JOURNAL, Horn C, Paulmann B, Kerlen G, Junker N, Huber H, In vivo observation of cell division of anaerobic hyperthermophiles by using a high-intensity dark-field microscope, Journal of Bacteriology, 181, 16, 5114–18, August 1999, 10438790, 94007,weblink Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to {{convert|15|cm}} long; these filaments are made of a particular bacteria species.JOURNAL, Rudolph C, Wanner G, Huber R, Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology, Applied and Environmental Microbiology, 67, 5, 2336–44, May 2001, 11319120, 92875, 10.1128/AEM.67.5.2336-2344.2001,

Structure, composition development, and operation

Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is Ignicoccus, which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.JOURNAL, Rachel R, Wyschkony I, Riehl S, Huber H, The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon, Archaea, 1, 1, 9–18, March 2002, 15803654, 2685547, 10.1155/2002/307480,

Cell wall and flagella

{{further|Cell wall#Archaeal cell walls}}Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.JOURNAL, Golyshina OV, Pivovarova TA, Karavaiko GI, Kondratéva TF, Moore ER, Abraham WR, Lünsdorf H, Timmis KN, Yakimov MM, Golyshin PN, 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, International Journal of Systematic and Evolutionary Microbiology, 50 Pt 3, 3, 997–1006, May 2000, 10843038, 10.1099/00207713-50-3-997, etal, In most archaea the wall is assembled from surface-layer proteins, which form an S-layer.JOURNAL, Sára M, Sleytr UB, S-Layer proteins, Journal of Bacteriology, 182, 4, 859–68, February 2000, 10648507, 94357, 10.1128/JB.182.4.859-868.2000,weblink An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail).JOURNAL, Engelhardt H, Peters J, Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions, Journal of Structural Biology, 124, 2-3, 276–302, December 1998, 10049812, 10.1006/jsbi.1998.4070, This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane.JOURNAL, Kandler O, König H, Cell wall polymers in Archaea (Archaebacteria), Cellular and Molecular Life Sciences, 54, 4, 305–08, April 1998, 9614965, 10.1007/s000180050156,weblink PDF, Unlike bacteria, archaea lack peptidoglycan in their cell walls.BOOK, Howland, John L., 2000, The Surprising Archaea: Discovering Another Domain of Life, 32, Oxford, Oxford University Press, 0-19-511183-4, Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid.Archaea flagella operate like bacterial flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by the proton gradient across the membrane, but archaeal flagella are notably different in composition and development.JOURNAL, Thomas NA, Bardy SL, Jarrell KF, The archaeal flagellum: a different kind of prokaryotic motility structure, FEMS Microbiology Reviews, 25, 2, 147–74, April 2001, 11250034, 10.1111/j.1574-6976.2001.tb00575.x, The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system,JOURNAL, Gophna U, Ron EZ, Graur D, Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events, Gene, 312, 151–63, July 2003, 12909351, 10.1016/S0378-1119(03)00612-7,weblink JOURNAL, Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH, Phylogenetic analyses of the constituents of Type III protein secretion systems, Journal of Molecular Microbiology and Biotechnology, 2, 2, 125–44, April 2000, 10939240, while archaeal flagella appear to have evolved from bacterial type IV pili.JOURNAL, Ng SY, Chaban B, Jarrell KF, Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications, Journal of Molecular Microbiology and Biotechnology, 11, 3-5, 167–91, 2006, 16983194, 10.1159/000094053, In contrast to the bacterial flagellum, which is hollow and is assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.JOURNAL, Bardy SL, Ng SY, Jarrell KF, Prokaryotic motility structures, Microbiology, 149, Pt 2, 295–304, February 2003, 12624192, 10.1099/mic.0.25948-0,

Membranes

File:Archaea membrane.svg|thumb|right|300px|Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, (Levorotation and dextrorotation|D-glycerol]] moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea.)Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. In all organisms, cell membranes are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer.The phospholipids of archaea are unusual in four ways:
  • They have membranes composed of glycerol-ether lipids, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids.JOURNAL, De Rosa M, Gambacorta A, Gliozzi A, Structure, biosynthesis, and physicochemical properties of archaebacterial lipids, Microbiological Reviews, 50, 1, 70–80, March 1986, 3083222, 373054,weblink The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are chemically more resistant than ester bonds.
  • The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called enantiomers. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by enzymes adapted for the other. The archaeal phospholipids are built on a backbone of sn-glycerol-1-phosphate, which is an enantiomer of sn-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eucaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids than do bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains.JOURNAL, Koga Y, Morii H, Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations, Microbiology and Molecular Biology Reviews, 71, 1, 97–120, March 2007, 17347520, 1847378, 10.1128/MMBR.00033-06,weblink
  • Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprenoid chains with multiple side-branches, sometimes with cyclopropane or cyclohexane rings.JOURNAL, Damsté JS, Schouten S, Hopmans EC, van Duin AC, Geenevasen JA, Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota, Journal of Lipid Research, 43, 10, 1641–51, October 2002, 12364548, 10.1194/jlr.M200148-JLR200,weblink By contrast, the fatty acids in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.JOURNAL, Koga Y, Morii H, Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects, Bioscience, Biotechnology, and Biochemistry, 69, 11, 2019–34, November 2005, 16306681, 10.1271/bbb.69.2019,
  • In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments.JOURNAL, Hanford MJ, Peeples TL, Archaeal tetraether lipids: unique structures and applications, Applied Biochemistry and Biotechnology, 97, 1, 45–62, January 2002, 11900115, 10.1385/ABAB:97:1:45, For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat.JOURNAL, Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF, Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid, Extremophiles, 8, 5, 411–19, October 2004, 15258835, 10.1007/s00792-004-0404-5,

Metabolism

{{further|Microbial metabolism}}Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers.JOURNAL, Valentine DL, Adaptations to energy stress dictate the ecology and evolution of the Archaea, Nature Reviews. Microbiology, 5, 4, 316–23, April 2007, 17334387, 10.1038/nrmicro1619, In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, the same basic process that happens in the mitochondrion of eukaryotic cells.JOURNAL, Schäfer G, Engelhard M, Müller V, Bioenergetics of the Archaea, Microbiology and Molecular Biology Reviews, 63, 3, 570–620, September 1999, 10477309, 103747,weblink Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways 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.JOURNAL, Zillig W, Comparative biochemistry of Archaea and Bacteria, Current Opinion in Genetics & Development, 1, 4, 544–51, December 1991, 1822288, 10.1016/S0959-437X(05)80206-0, These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.JOURNAL, Romano AH, Conway T, Evolution of carbohydrate metabolic pathways, Research in Microbiology, 147, 6-7, 448–55, 1996, 9084754, 10.1016/0923-2508(96)83998-2, {|class="wikitable" style="margin-left: auto; margin-right: auto;"|+ Nutritional types in archaeal metabolism!Nutritional type!Source of energy!Source of carbon!Examples| Phototrophs  Sunlight  Organic compounds | Halobacterium | Lithotrophs Inorganic compounds Organic compounds or carbon fixationFerroglobus, Methanobacteria or Pyrolobus | Organotrophs Organic compounds  Organic compounds or carbon fixation | Pyrococcus, Sulfolobus or Methanosarcinales Some Euryarchaeota are methanogens (archaea that produce methane as a result of metabolism) living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen.JOURNAL, Koch AL, How did bacteria come to be?, Advances in Microbial Physiology, 40, 353–99, 1998, 9889982, 10.1016/S0065-2911(08)60135-6, 978-0-12-027740-7, Advances in Microbial Physiology, A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran.JOURNAL, DiMarco AA, Bobik TA, Wolfe RS, Unusual coenzymes of methanogenesis, Annual Review of Biochemistry, 59, 355–94, 1990, 2115763, 10.1146/annurev.bi.59.070190.002035, Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors 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.JOURNAL, Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B, Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass, Systematic and Applied Microbiology, 31, 3, 190–205, August 2008, 18501543, 10.1016/j.syapm.2008.02.003, etal, File:Bacteriorhodopsin.png|thumb|right|Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in proton transfer are shown as (ball-and-stick model]]s.Based on PDB 1FBB. Data published in JOURNAL, Subramaniam S, Henderson R, Molecular mechanism of vectorial proton translocation by bacteriorhodopsin, Nature, 406, 6796, 653–57, August 2000, 10949309, 10.1038/35020614, )Other archaea use {{chem|CO|2}} in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycleJOURNAL, Mueller-Cajar O, Badger MR, New roads lead to Rubisco in archaebacteria, BioEssays, 29, 8, 722–24, August 2007, 17621634, 10.1002/bies.20616, or another metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle.JOURNAL, Berg IA, Kockelkorn D, Buckel W, Fuchs G, A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea, Science, 318, 5857, 1782–86, December 2007, 18079405, 10.1126/science.1149976, 2007Sci...318.1782B, The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway.JOURNAL, Thauer RK, Microbiology. A fifth pathway of carbon fixation, Science, 318, 5857, 1732–33, December 2007, 18079388, 10.1126/science.1152209, Carbon–fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis.JOURNAL, Bryant DA, Frigaard NU, Prokaryotic photosynthesis and phototrophy illuminated, Trends in Microbiology, 14, 11, 488–96, November 2006, 16997562, 10.1016/j.tim.2006.09.001, Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the NitrosopumilalesJOURNAL, Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA, Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, 437, 7058, 543–46, September 2005, 16177789, 10.1038/nature03911, 2005Natur.437..543K, JOURNAL, Francis CA, Beman JM, Kuypers MM, New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation, The ISME Journal, 1, 1, 19–27, May 2007, 18043610, 10.1038/ismej.2007.8, to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of and into the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.JOURNAL, Lanyi JK, Bacteriorhodopsin, Annual Review of Physiology, 66, 665–88, 2004, 14977418, 10.1146/annurev.physiol.66.032102.150049,

Genetics

{{further|Plasmid|Genome}}Archaea usually have a single circular chromosome, with as many as 5,751,492 base pairs in Methanosarcina acetivorans,JOURNAL, Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B, 6, The genome of M. acetivorans reveals extensive metabolic and physiological diversity, Genome Research, 12, 4, 532–42, April 2002, 11932238, 187521, 10.1101/gr.223902, the largest known archaeal genome. The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes.JOURNAL, Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M, The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism, Proceedings of the National Academy of Sciences of the United States of America, 100, 22, 12984–88, October 2003, 14566062, 240731, 10.1073/pnas.1735403100,weblink 6, 2003PNAS..10012984W, Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.JOURNAL, Schleper C, Holz I, Janekovic D, Murphy J, Zillig W, A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating, Journal of Bacteriology, 177, 15, 4417–26, August 1995, 7635827, 177192,weblink BOOK,weblink Sota M, Top EM, 2008, Horizontal Gene Transfer Mediated by Plasmids, Plasmids: Current Research and Future Trends, Caister Academic Press, 978-1-904455-35-6, File:RT8-4.jpg|thumb|200px|left|Sulfolobus infected with the DNA virus STSV1.JOURNAL, Xiang X, Chen L, Huang X, Luo Y, She Q, Huang L, Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features, Journal of Virology, 79, 14, 8677–86, July 2005, 15994761, 1168784, 10.1128/JVI.79.14.8677-8686.2005,weblink Bar is 1 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, including bottles, hooked rods, or teardrops.JOURNAL, Prangishvili D, Forterre P, Garrett RA, Viruses of the Archaea: a unifying view, Nature Reviews. Microbiology, 4, 11, 837–48, November 2006, 17041631, 10.1038/nrmicro1527, These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales.JOURNAL, Prangishvili D, Garrett RA, Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses, Biochemical Society Transactions, 32, Pt 2, 204–08, April 2004, 15046572, 10.1042/BST0320204,weblink Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 ("Pleolipoviridae") infecting halophilic archaeaJOURNAL, Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH, An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope, Molecular Microbiology, 72, 2, 307–19, April 2009, 19298373, 10.1111/j.1365-2958.2009.06642.x, and the other one by the Aeropyrum coil-shaped virus ("Spiraviridae") infecting a hyperthermophilic (optimal growth at 90–95 Â°C) host.JOURNAL, Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D, Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome, Proceedings of the National Academy of Sciences of the United States of America, 109, 33, 13386–91, August 2012, 22826255, 3421227, 10.1073/pnas.1203668109, 2012PNAS..10913386M, Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.JOURNAL, Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, Journal of Molecular Evolution, 60, 2, 174–82, February 2005, 15791728, 10.1007/s00239-004-0046-3, 2005JMolE..60..174M, JOURNAL, Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV, 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, Biology Direct, 1, 7, March 2006, 16545108, 1462988, 10.1186/1745-6150-1-7, Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function.JOURNAL, Graham DE, Overbeek R, Olsen GJ, Woese CR, An archaeal genomic signature, Proceedings of the National Academy of Sciences of the United States of America, 97, 7, 3304–08, March 2000, 10716711, 16234, 10.1073/pnas.050564797,weblink 2000PNAS...97.3304G, Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.JOURNAL, Gaasterland T, Archaeal genomics, Current Opinion in Microbiology, 2, 5, 542–47, October 1999, 10508726, 10.1016/S1369-5274(99)00014-4, Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes;JOURNAL, Allers T, Mevarech M, Archaeal genetics – the third way, Nature Reviews. Genetics, 6, 1, 58–73, January 2005, 15630422, 10.1038/nrg1504, while archaeal translation shows signs of both bacterial and eukaryal equivalents.JOURNAL, Dennis PP, Ancient ciphers: translation in Archaea, Cell, 89, 7, 1007–10, June 1997, 9215623, 10.1016/S0092-8674(00)80288-3, 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 protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter,JOURNAL, Werner F, Structure and function of archaeal RNA polymerases, Molecular Microbiology, 65, 6, 1395–404, September 2007, 17697097, 10.1111/j.1365-2958.2007.05876.x, but other archaeal transcription factors are closer to those found in bacteria.JOURNAL, Aravind L, Koonin EV, DNA-binding proteins and evolution of transcription regulation in the archaea, Nucleic Acids Research, 27, 23, 4658–70, December 1999, 10556324, 148756, 10.1093/nar/27.23.4658,weblink Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes,JOURNAL, Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA, Archaeal introns: splicing, intercellular mobility and evolution, Trends in Biochemical Sciences, 22, 9, 326–31, September 1997, 9301331, 10.1016/S0968-0004(97)01113-4, and introns may occur in a few protein-encoding genes.JOURNAL, Watanabe Y, Yokobori S, Inaba T, Yamagishi A, Oshima T, Kawarabayasi Y, Kikuchi H, Kita K, Introns in protein-coding genes in Archaea, FEBS Letters, 510, 1-2, 27–30, January 2002, 11755525, 10.1016/S0014-5793(01)03219-7, etal, JOURNAL, Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, Oshima T, Kita K, Watanabe Y, Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease, Biochemical and Biophysical Research Communications, 346, 3, 1024–32, August 2006, 16781672, 10.1016/j.bbrc.2006.06.011, etal,

Gene transfer and genetic exchange

Halobacterium volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.JOURNAL, Rosenshine I, Tchelet R, Mevarech M, The mechanism of DNA transfer in the mating system of an archaebacterium, Science, 245, 4924, 1387–89, September 1989, 2818746, 10.1126/science.2818746, 1989Sci...245.1387R, When the hyperthermophilic archaea Sulfolobus solfataricusJOURNAL, Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV, UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation, Molecular Microbiology, 70, 4, 938–52, November 2008, 18990182, 10.1111/j.1365-2958.2008.06459.x, etal, and Sulfolobus acidocaldariusJOURNAL, Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C, UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili, Molecular Microbiology, 82, 4, 807–17, November 2011, 21999488, 10.1111/j.1365-2958.2011.07861.x, etal, are exposed to DNA-damaging UV irradiation or to the agents bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in S. solfataricus could not be induced by other physical stressors, such as pH or temperature shift, suggesting that aggregation is induced specifically by DNA damage. Ajon et al. showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in S. acidocaldarius. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al.JOURNAL, Fröls S, White MF, Schleper C, Reactions to UV damage in the model archaeon Sulfolobus solfataricus, Biochemical Society Transactions, 37, Pt 1, 36–41, February 2009, 19143598, 10.1042/BST0370036, and Ajon et al. hypothesized that cellular aggregation enhances species-specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.BOOK, Bernstein H, Bernstein C, 2013, Evolutionary Origin and Adaptive Function of Meiosis, Meiosis, Carol, Bernstein, 978-953-51-1197-9, InTech,weblink

Reproduction

{{further|Asexual reproduction}}Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; mitosis and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material.BOOK, Bergey's Manual of Systematic Bacteriology, Krieg, Noel, 2005, Springer, US, 978-0-387-24143-2, 21–26, Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides.JOURNAL, Bernander R, Archaea and the cell cycle, Molecular Microbiology, 29, 4, 955–61, August 1998, 9767564, 10.1046/j.1365-2958.1998.00956.x, In the genus Sulfolobus, the cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting-points (origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes.JOURNAL, Kelman LM, Kelman Z, Multiple origins of replication in archaea, Trends in Microbiology, 12, 9, 399–401, September 2004, 15337158, 10.1016/j.tim.2004.07.001, In euryarchaea the cell division protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents. In cren-JOURNAL, Lindås AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R, A unique cell division machinery in the Archaea, Proceedings of the National Academy of Sciences of the United States of America, 105, 48, 18942–46, December 2008, 18987308, 2596248, 10.1073/pnas.0809467105, 2008PNAS..10518942L, JOURNAL, Samson RY, Obita T, Freund SM, Williams RL, Bell SD, A role for the ESCRT system in cell division in archaea, Science, 322, 5908, 1710–13, December 2008, 19008417, 4121953, 10.1126/science.1165322, 2008Sci...322.1710S, and thaumarchaea,JOURNAL, Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R, Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus, Molecular Microbiology, 82, 3, 555–66, November 2011, 21923770, 10.1111/j.1365-2958.2011.07834.x, but the cell division machinery Cdv fulfills a similar role. This machinery is related to the eukaryotic ESCRT-III machinery which, while best known for its role in cell sorting, also has been seen to fulfill a role in separation between divided cell, suggesting an ancestral role in cell division.Both bacteria and eukaryotes, but not archaea, make spores.JOURNAL, Onyenwoke RU, Brill JA, Farahi K, Wiegel J, Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes), Archives of Microbiology, 182, 2-3, 182–92, October 2004, 15340788, 10.1007/s00203-004-0696-y, Some species of Haloarchaea undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.JOURNAL, Kostrikina NA, Zvyagintseva IS, Duda VI, Cytological peculiarities of some extremely halophilic soil archaeobacteria, Arch. Microbiol., 156, 5, 344–49, 1991, 10.1007/BF00248708,

Ecology

Habitats

File:Morning-Glory Hotspring.jpg|300px|thumb|Archaea that grow in the hot water of the Morning Glory Hot Spring in Yellowstone National ParkYellowstone National ParkArchaea exist in a broad range of habitats, and as a major part of global ecosystems, may represent about 20% of microbial cells in the oceans.JOURNAL, DeLong EF, Pace NR, Environmental diversity of bacteria and archaea, Systematic Biology, 50, 4, 470–78, August 2001, 12116647, 10.1080/106351501750435040, The first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above {{convert|100|C|F}}, as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils.Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above {{convert|45|C|F}}, in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than {{convert|80|C}}.BOOK, Brock Biology of Microorganisms, 2006, Madigan MT, Martino JM, 11th, 136, Pearson, 0-13-196893-9, The archaeal Methanopyrus kandleri Strain 116 can even reproduce at {{convert|122|C}}, the highest recorded temperature of any organism.JOURNAL, Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K, Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation, Proceedings of the National Academy of Sciences of the United States of America, 105, 31, 10949–54, August 2008, 18664583, 2490668, 10.1073/pnas.0712334105, 2008PNAS..10510949T, Other archaea exist in very acidic or alkaline conditions.JOURNAL, Pikuta EV, Hoover RB, Tang J, Microbial extremophiles at the limits of life, Critical Reviews in Microbiology, 33, 3, 183–209, 2007, 17653987, 10.1080/10408410701451948, 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 sulfuric acid.JOURNAL, Ciaramella M, Napoli A, Rossi M, Another extreme genome: how to live at pH 0, Trends in Microbiology, 13, 2, 49–51, February 2005, 15680761, 10.1016/j.tim.2004.12.001, This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life.JOURNAL, Javaux EJ, Extreme life on Earth--past, present and possibly beyond, Research in Microbiology, 157, 1, 37–48, 2006, 16376523, 10.1016/j.resmic.2005.07.008, Some extremophile habitats are not dissimilar to those on Mars,JOURNAL, Nealson KH, Post-Viking microbiology: new approaches, new data, new insights, Origins of Life and Evolution of the Biosphere, 29, 1, 73–93, January 1999, 11536899, 10.1023/A:1006515817767,weblink leading to the suggestion that viable microbes could be transferred between planets in meteorites.JOURNAL, Davies PC, The transfer of viable microorganisms between planets, Ciba Foundation Symposium, 202, 304–14; discussion 314–17, 1996, 9243022, 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.JOURNAL, López-García P, López-López A, Moreira D, Rodríguez-Valera F, Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front, FEMS Microbiology Ecology, 36, 2-3, 193–202, July 2001, 11451524, 10.1016/s0168-6496(01)00133-7, Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the plankton community (as part of the picoplankton).JOURNAL, Karner MB, DeLong EF, Karl DM, Archaeal dominance in the mesopelagic zone of the Pacific Ocean, Nature, 409, 6819, 507–10, January 2001, 11206545, 10.1038/35054051, 2001Natur.409..507K, 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.JOURNAL, Giovannoni SJ, Stingl U, Molecular diversity and ecology of microbial plankton, Nature, 437, 7057, 343–48, September 2005, 16163344, 10.1038/nature04158, 2005Natur.437..343G, Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored.JOURNAL, DeLong EF, Karl DM, Genomic perspectives in microbial oceanography, Nature, 437, 7057, 336–42, September 2005, 16163343, 10.1038/nature04157, 2005Natur.437..336D, Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy.JOURNAL, Agogué H, Brink M, Dinasquet J, Herndl GJ, Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic, Nature, 456, 7223, 788–91, December 2008, 19037244, 10.1038/nature07535, 2008Natur.456..788A, Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.JOURNAL, Teske A, Sørensen KB, Uncultured archaea in deep marine subsurface sediments: have we caught them all?, The ISME Journal, 2, 1, 3–18, January 2008, 18180743, 10.1038/ismej.2007.90, JOURNAL, Lipp JS, Morono Y, Inagaki F, Hinrichs KU, Significant contribution of Archaea to extant biomass in marine subsurface sediments, Nature, 454, 7207, 991–94, August 2008, 18641632, 10.1038/nature07174, 2008Natur.454..991L, It has been demonstrated that in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally.JOURNAL, Danovaro R, Dell'Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D, Virus-mediated archaeal hecatomb in the deep seafloor, Science Advances, 2, 10, e1600492, October 2016, 27757416, 5061471, 10.1126/sciadv.1600492, 2016SciA....2E0492D,

Role in chemical cycling

{{further|Biogeochemical cycle}}Archaea recycle elements such as carbon, nitrogen and sulfur through their various habitats. Although these activities are vital for normal ecosystem function, archaea can also contribute to human-made changes, and even cause pollution.Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation).JOURNAL, Cabello P, Roldán MD, Moreno-Vivián C, Nitrate reduction and the nitrogen cycle in archaea, Microbiology, 150, Pt 11, 3527–46, November 2004, 15528644, 10.1099/mic.0.27303-0,weblink JOURNAL, Mehta MP, Baross JA, Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon, Science, 314, 5806, 1783–86, December 2006, 17170307, 10.1126/science.1134772, 2006Sci...314.1783M, Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans.JOURNAL, Coolen MJ, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MM, Wakeham SG, Sinninghe Damsté JS, 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, Environmental Microbiology, 9, 4, 1001–16, April 2007, 17359272, 10.1111/j.1462-2920.2006.01227.x, etal, The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.JOURNAL, Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C, Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, 442, 7104, 806–09, August 2006, 16915287, 10.1038/nature04983, 2006Natur.442..806L, James I. Prosser, In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage.JOURNAL, Baker BJ, Banfield JF, Microbial communities in acid mine drainage, FEMS Microbiology Ecology, 44, 2, 139–52, May 2003, 19719632, 10.1016/S0168-6496(03)00028-X, In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes and sewage-treatment works.JOURNAL, Schimel J, Playing scales in the methane cycle: from microbial ecology to the globe, Proceedings of the National Academy of Sciences of the United States of America, 101, 34, 12400–01, August 2004, 15314221, 515073, 10.1073/pnas.0405075101,weblink 2004PNAS..10112400S,

Interactions with other organisms

{{further|Biological interaction}}File:Coptotermes formosanus shiraki USGov k8204-7.jpg|thumb|right|Methanogenic archaea form a symbiosis with termitetermiteThe well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or parasites,JOURNAL, Eckburg PB, Lepp PW, Relman DA, Archaea and their potential role in human disease, Infection and Immunity, 71, 2, 591–96, February 2003, 12540534, 145348, 10.1128/IAI.71.2.591-596.2003, JOURNAL, Cavicchioli R, Curmi PM, Saunders N, Thomas T, Pathogenic archaea: do they exist?, BioEssays, 25, 11, 1119–28, November 2003, 14579252, 10.1002/bies.10354, but some species of methanogens have been suggested to be involved in infections in the mouth,JOURNAL, Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA, Methanogenic Archaea and human periodontal disease, Proceedings of the National Academy of Sciences of the United States of America, 101, 16, 6176–81, April 2004, 15067114, 395942, 10.1073/pnas.0308766101, 2004PNAS..101.6176L, JOURNAL, Vianna ME, Conrads G, Gomes BP, Horz HP, Identification and quantification of archaea involved in primary endodontic infections, Journal of Clinical Microbiology, 44, 4, 1274–82, April 2006, 16597851, 1448633, 10.1128/JCM.44.4.1274-1282.2006,weblink 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 hospitalis, and appears to offer no benefit to its host.JOURNAL, Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stetter KO, Rachel R, Huber H, Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea, Journal of Bacteriology, 190, 5, 1743–50, March 2008, 18165302, 2258681, 10.1128/JB.01731-07,weblink etal, Connections between archaeal cells can also be found between the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) and another species of archaea called Thermoplasmatales, within acid mine drainage biofilms.JOURNAL, Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF, Enigmatic, ultrasmall, uncultivated Archaea, Proceedings of the National Academy of Sciences of the United States of America, 107, 19, 8806–11, May 2010, 20421484, 2889320, 10.1073/pnas.0914470107,weblink 2010PNAS..107.8806B, Although the nature of this relationship is unknown, it is distinct from that of Nanarchaeaum–Ignicoccus in that the ultrasmall ARMAN cells are usually independent of the Thermoplasmatales cells.

Mutualism

One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites.JOURNAL, Chaban B, Ng SY, Jarrell KF, Archaeal habitats--from the extreme to the ordinary, Canadian Journal of Microbiology, 52, 2, 73–116, February 2006, 16541146, 10.1139/w05-147, In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy.JOURNAL, Schink B, Energetics of syntrophic cooperation in methanogenic degradation, Microbiology and Molecular Biology Reviews, 61, 2, 262–80, June 1997, 9184013, 232610, In anaerobic protozoa, such as Plagiopyla frontata, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes.JOURNAL, Lange M, Westermann P, Ahring BK, Archaea in protozoa and metazoa, Applied Microbiology and Biotechnology, 66, 5, 465–74, February 2005, 15630514, 10.1007/s00253-004-1790-4, JOURNAL, van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, Hackstein JH, Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates, Molecular Biology and Evolution, 17, 2, 251–58, February 2000, 10677847, 10.1093/oxfordjournals.molbev.a026304,weblink etal, Archaea also associate with larger organisms. For example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) the sponge Axinella mexicana.JOURNAL, Preston CM, Wu KY, Molinski TF, DeLong EF, A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov, Proceedings of the National Academy of Sciences of the United States of America, 93, 13, 6241–46, June 1996, 8692799, 39006, 10.1073/pnas.93.13.6241, 1996PNAS...93.6241P,

Commensalism

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, making up about one in ten of all the prokaryotes in the human gut.JOURNAL, Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA, Diversity of the human intestinal microbial flora, Science, 308, 5728, 1635–38, June 2005, 15831718, 1395357, 10.1126/science.1110591, 2005Sci...308.1635E, 1, In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion.JOURNAL, Samuel BS, Gordon JI, A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism, Proceedings of the National Academy of Sciences of the United States of America, 103, 26, 10011–16, June 2006, 16782812, 1479766, 10.1073/pnas.0602187103, 2006PNAS..10310011S, Archaean communities also associate with a range of other organisms, such as on the surface of corals,JOURNAL, 2004, Coral-associated Archaea, Marine Ecology Progress Series, 273, 89–96,weblink 10.3354/meps273089, PDF, Mya Breitbart, Wegley L, Yu Y, Breitbart M, Casas V, Kline DI, Rohwer F, yes,weblink" title="web.archive.org/web/20080911074810weblink">weblink 11 September 2008, 2004MEPS..273...89W, and in the region of soil that surrounds plant roots (the rhizosphere).JOURNAL, Chelius MK, Triplett EW, The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L, Microbial Ecology, 41, 3, 252–263, April 2001, 11391463, 10.1007/s002480000087, 4251818, JOURNAL, Simon HM, Dodsworth JA, Goodman RM, Crenarchaeota colonize terrestrial plant roots, Environmental Microbiology, 2, 5, 495–505, October 2000, 11233158, 10.1046/j.1462-2920.2000.00131.x,

Significance in technology and industry

{{further|Biotechnology}}Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions.JOURNAL, Breithaupt H, The hunt for living gold. The search for organisms in extreme environments yields useful enzymes for industry, EMBO Reports, 2, 11, 968–71, November 2001, 11713183, 1084137, 10.1093/embo-reports/kve238, JOURNAL, Egorova K, Antranikian G, Industrial relevance of thermophilic Archaea, Current Opinion in Microbiology, 8, 6, 649–55, December 2005, 16257257, 10.1016/j.mib.2005.10.015, These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over {{convert|100|C|F}} allow food processing at high temperatures, such as the production of low lactose milk and whey.JOURNAL, Synowiecki J, Grzybowska B, Zdziebło A, Sources, properties and suitability of new thermostable enzymes in food processing, Critical Reviews in Food Science and Nutrition, 46, 3, 197–205, 2006, 16527752, 10.1080/10408690590957296, Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds. This stability makes them easier to use in structural biology. Consequently, the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.JOURNAL, Jenney FE, Adams MW, The impact of extremophiles on structural genomics (and vice versa), Extremophiles, 12, 1, 39–50, January 2008, 17563834, 10.1007/s00792-007-0087-9, In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas.JOURNAL, Schiraldi C, Giuliano M, De Rosa M, Perspectives on biotechnological applications of archaea, Archaea, 1, 2, 75–86, September 2002, 15803645, 2685559, 10.1155/2002/436561, In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.JOURNAL, Norris PR, Burton NP, Foulis NA, Acidophiles in bioreactor mineral processing, Extremophiles, 4, 2, 71–76, April 2000, 10805560, 10.1007/s007920050139, Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.BOOK, Shand RF, Leyva KJ, Archaeal Antimicrobials: An Undiscovered Country, Blum P, Archaea: New Models for Prokaryotic Biology, Caister Academic Press, 2008, 978-1-904455-27-1,

See also

{{Div col|colwidth=30em}} {{div col end}}

References

{{Reflist}}

Further reading

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

External links

General Classification Genomics {{microorganisms}}{{Archaea classification}}{{Extremophile}}{{Taxonbar|from=Q10872}}{{Authority control}}{{featured article}}

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