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{{Automatic Taxobox | fossil_range = {{long fossil range|3500|0|3.5–0 Ga|earliest=3800}}[[太古代]]－現今 | image = Halobacteria.jpg | image_caption = NRC-1系[[盐杆菌纲]]，每一細胞長度大約5μm | taxon = Archaea | authority = [[卡爾·沃斯|Woese]], [[Otto Kandler|Kandler]] & [[Mark Wheelis|Wheelis]], 1990<ref name="Woese"/> | subdivision_ranks = 界<ref>{{Cite journal |last=Petitjean |first=Céline |last2=Deschamps |first2=Philippe |last3=López-García |first3=Purificación |last4=Moreira |first4=David |date=2015-01 |title=Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota |url=https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evu274 |journal=Genome Biology and Evolution |language=en |volume=7 |issue=1 |doi=10.1093/gbe/evu274 |issn=1759-6653 |pmc=4316627 |pmid=25527841 |access-date=2022-10-13 |archive-date=2022-10-13 |archive-url=https://web.archive.org/web/20221013155713/https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evu274 |dead-url=no }}</ref>与門<ref name="NCBI taxonomy page on Archaea">{{cite journal |title=NCBI taxonomy page on Archaea |url=http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2157&lvl=5&lin=f&keep=1&srchmode=1&unlock |journal= |access-date=2017-04-27 |archive-date=2020-12-01 |archive-url=https://web.archive.org/web/20201201004224/https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2157&lvl=5&lin=f&keep=1&srchmode=1&unlock |dead-url=no }}</ref> | subdivision ranks = 界 | subdivision = * [[Methanobacteriati]] | subdivision ranks = 門 | subdivision = * [[甲烷桿菌界]] Methanobacteriati * [[納蛭古菌界]] Nanobdellati * [[普羅米修斯古菌界]] (包括[[真核生物]]) Promethearchaeati * [[熱變形菌界]] Thermoproteati <hr> * {{le|迷古菌門|Aenigmatarchaeota}} Aenigmatarchaeota * {{le|深古菌門|Altiarchaeota}} Altiarchaeota * [[阿斯加德古菌門]] Asgardarchaeota * {{le|哈德古菌門|Hadarchaeota}} Hadarchaeota * {{le|鹽桿菌門|Halobacteriota}} Halobacteriota * {{le|胡伯古菌門|Huberarchaeota}} Huberarchaeota * {{le|熱泉古菌門|Hydrothermarchaeota}} Hydrothermarchaeota * {{le|伊恩古菌門|Iainarchaeota}} Iainarchaeota * {{le|初古菌門|Korarchaeota}} Korarchaeota * [[甲烷桿菌門]] Methanobacteriota * {{le|微古菌門|Micrarchaeota}} Micrarchaeota * [[納蛭古菌門]] Nanobdellota * {{le|納鹽古菌門|Nanohalarchaeota}} Nanohalarchaeota * [[熱原體門]] Thermoplasmatota * [[熱變形菌門]] Thermoproteota * {{le|溫蒂古菌門|Undinarchaeota}} Undinarchaeota | diversity = 約10,000種<ref>{{Cite web |title=GTDB - R232 Statistics |url=https://gtdb.ecogenomic.org/stats/r232 |website=gtdb.ecogenomic.org |language=en |access-date=2026-05-17}}</ref> }} {{bio-taxonomy}} '''古菌'''（{{langx|la|Archaea}}，来自{{langx|grc|ἀρχαῖα}}<span>，意为“古代的东西”</span>）又稱'''古核生物'''<ref>{{Cite web |url=https://www.termonline.cn/word/213570/1#s1 |title=存档副本 |access-date=2023-07-24 |archive-date=2023-07-24 |archive-url=https://web.archive.org/web/20230724151236/https://www.termonline.cn/word/213570/1#s1 |dead-url=no }}</ref>，旧称'''古細菌'''<ref>{{Cite web |url=https://www.termonline.cn/word/99712/1#s1 |title=存档副本 |access-date=2023-07-24 |archive-date=2023-07-24 |archive-url=https://web.archive.org/web/20230724151234/https://www.termonline.cn/word/99712/1#s1 |dead-url=no }}</ref>（Archaebacteria）、'''古生菌'''、'''太古生物'''，是[[单细胞生物|单细胞]][[微生物]]，构成生物分类的一个[[域 (生物)|域]]，或一个[[界 (生物)|界]]。这些微生物1970年前的分類属于[[原核生物]]，它們與[[细菌]]有很多相似之處，即它们没有[[细胞核]]与任何其他膜狀胞器，同時另一些特徵相似於[[真核生物]]，比如存在重复序列与[[核小体]]。 过去曾经将古菌和细菌一同归为[[原核生物]]，并将其命名为“古细菌”，但这种分类方式已过时<ref>{{Cite journal |last=Pace |first=Norman R. |date=2006-05 |title=Time for a change |url=http://www.nature.com/articles/441289a |journal=Nature |language=en |volume=441 |issue=7091 |bibcode=2006Natur.441..289P |doi=10.1038/441289a |issn=0028-0836 |pmid=16710401 |access-date=2022-10-13 |archive-date=2019-04-11 |archive-url=https://web.archive.org/web/20190411201104/https://www.nature.com/articles/441289a |dead-url=no }}</ref>。事实上古菌有其独特的进化历程，并与其它生命形式有显著的[[生化]]差异，所以现在将其列为[[三域系统]]中的一个域。在这个系统中，古菌、细菌与真核生物各为一个域，并进一步划分为[[界 (生物)|界]]与[[门 (生物)|门]]。到目前为止，古菌已被划分为公认的四个门，随着进一步研究，还可能建立更多的门类。在这些类群中，研究最深入的是[[泉古菌门]]与[[广古菌门]]。但对古菌进行分类仍然是困难的，因为绝大多数的古菌都无法在实验室中纯化培养，只能通过环境宏基因组检测来分析。 古菌和细菌的大小和形状非常相似，但少数古菌有不寻常的形状，如嗜鹽古菌{{le|窩氏鹽方扁平古菌|Haloquadratum walsbyi}}拥有平面正方形的细胞。<ref>{{Cite web |title=鹽方扁平古菌：生活在鹽田裡的天然小方塊光電板 |url=https://pansci.asia/archives/90541 |website=PanSci 泛科學 |language=zh-TW |access-date=2022-10-13 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017214344/https://pansci.asia/archives/90541 |dead-url=no }}</ref><ref>{{Cite journal |last=Stoeckenius |first=W |date=1981-10 |title=Walsby's square bacterium: fine structure of an orthogonal procaryote |url=https://journals.asm.org/doi/10.1128/jb.148.1.352-360.1981 |journal=Journal of Bacteriology |language=en |volume=148 |issue=1 |doi=10.1128/jb.148.1.352-360.1981 |issn=0021-9193 |pmc=216199 |pmid=7287626 |access-date=2022-10-13 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017045215/https://journals.asm.org/doi/10.1128/jb.148.1.352-360.1981 |dead-url=no }}</ref>尽管看起来与细菌更相似，但古菌与真核生物的亲缘关系更为密切，特别是在一些[[代谢途径]]（如[[转录]]和[[翻译 (遗传学)|转译]]）有关[[酶]]的相似性上。古菌还有一些性状是独一无二的，比如由依赖醚键构成的[[细胞膜]]。与真核生物相比，古菌有更多的能量来源，从熟悉的有机物[[糖类]]到[[氨]]到[[离子|金属离子]]直到[[氢气]]。{{le|嗜盐菌|Halophile}}，如{{le|嗜滷鹽菌|Haloarchaea}}可以以太阳光为能源，其它一些种类的古菌能进行[[固碳反應]]；没有一种古菌能像[[蓝藻]]与[[植物]]进行[[光合作用]]。古菌通过[[分裂生殖|分裂]]、[[出芽生殖|出芽]]、[[断裂生殖|断裂]]来进行[[无性生殖]]，但没有发现能产生[[孢子]]的种类。 一开始，古菌被认为都是一些生活在[[温泉]]、[[咸水湖|盐湖]]之类极端环境的[[嗜极生物]]，但近来发现它们的[[栖息地]]其实十分广泛，从[[土壤]]、[[海洋]]、到[[河流湿地]]。它们也被发现在人类的[[大肠]]、口腔、与[[皮肤]]<ref name="Bang2015">{{Cite journal |last=Bang |first=Corinna |last2=Schmitz |first2=Ruth A. |date=2015-09 |editor-last=Narberhaus |editor-first=Franz |title=Archaea associated with human surfaces: not to be underestimated |url=https://academic.oup.com/femsre/article-lookup/doi/10.1093/femsre/fuv010 |journal=FEMS Microbiology Reviews |language=en |volume=39 |issue=5 |doi=10.1093/femsre/fuv010 |issn=1574-6976 |pmid=2590711 |access-date=2022-10-13 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123111216/https://academic.oup.com/femsre/article-lookup/doi/10.1093/femsre/fuv010 |dead-url=no }}</ref>。尤其是在海洋中古菌特别多，一些[[浮游生物]]中的古菌可能是这个星球上数量最大的生物群体。现在，古菌被认为是地球生命的一个重要组成部分，在[[碳循环]]和[[氮循环]]中可能扮演重要的角色。目前没有已知的作为[[病原体]]或[[寄生虫]]的古菌，他们往往是[[偏利共生]]或[[互利共生]]。一个例子是[[产甲烷菌]]，生活在人和[[反刍]]动物的肠道中帮助消化，[[产甲烷菌]]还被用于[[沼气]]生产和[[污水处理]]。嗜极生物古菌中的酶能承受高温和[[有机溶剂]]，常被[[生物技术]]所利用。 == 歷史 == === 新域的诞生 === [[File:Aerial image of Grand Prismatic Spring (view from the south).jpg|thumb|right|250px|古菌最早是在一些极端环境，如火山[[温泉]]中发现的。图为[[黄石国家公园]]的[[大棱镜温泉]]。]] 在20世纪的大部分时间里，原核生物因其[[生物化学|生化]]、[[生物形態學|形态]]和[[代谢]]上的一致性被视为分类上的单组生物。在这一时期，微生物学家试图根据其形状、[[细胞壁]]结构以及所消耗的物质来对微生物进行分类<ref>{{Cite journal |last=Staley |first=James T |date=2006-11-29 |title=The bacterial species dilemma and the genomic–phylogenetic species concept |url=https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1914 |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |language=en |volume=361 |issue=1475 |doi=10.1098/rstb.2006.1914 |issn=0962-8436 |pmc=1857736 |pmid=17062409 |access-date=2022-10-13 |archive-date=2022-09-30 |archive-url=https://web.archive.org/web/20220930201102/https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1914 |dead-url=no }}</ref>。然而，在1965年有一种新方法被提出<ref>{{Cite journal |last=Zuckerkandl |first=Emile |last2=Pauling |first2=Linus |date=1965-03-01 |title=Molecules as documents of evolutionary history |url=https://www.sciencedirect.com/science/article/pii/0022519365900834 |journal=Journal of Theoretical Biology |language=en |volume=8 |issue=2 |doi=10.1016/0022-5193(65)90083-4 |issn=0022-5193 |pmid=5876245 |access-date=2022-10-13 |archive-date=2018-12-08 |archive-url=https://web.archive.org/web/20181208131131/https://www.sciencedirect.com/science/article/pii/0022519365900834 |dead-url=no }}</ref>，即使用生物体的[[基因]]序列来搞清这些生物是如何相关联的。这种方法称为[[系统发生学]]（phylogenetics），是今天生物分类所使用的主要方法。 [[Image:Morning-Glory Hotspring.jpg|thumb|left|250px|古菌賦予溫泉（例如牽牛花溫泉）顏色。]] 「古细菌」这个概念第一次出现是在1977年，由[[卡尔·乌斯]]和[[乔治·福克斯 (生物学家)|乔治·福克斯]]提出的，原因是它們在[[16S 核糖体RNA]]的[[系統發生樹]]上和其牠原核生物的區別<ref>{{Cite journal |last=Woese |first=Carl R. |last2=Fox |first2=George E. |date=1977-11 |title=Phylogenetic structure of the prokaryotic domain: The primary kingdoms |url=https://pnas.org/doi/full/10.1073/pnas.74.11.5088 |journal=Proceedings of the National Academy of Sciences |language=en |volume=74 |issue=11 |bibcode=1977PNAS...74.5088W |doi=10.1073/pnas.74.11.5088 |issn=0027-8424 |access-date=2022-10-13 |archive-date=2022-10-13 |archive-url=https://web.archive.org/web/20221013155155/https://www.pnas.org/doi/full/10.1073/pnas.74.11.5088 |dead-url=no }}</ref>。這兩組原核生物起初被定為古細菌和真細菌兩個[[界 (生物)|界]]或[[亞界]]（当时乌斯与福克斯更倾向于用「总界」一词）。后来[[卡尔·乌斯|乌斯]]認為它們是兩支根本不同的生物，於是在1990年重新命名其為古菌和細菌<ref name="Woese">{{Cite journal |last=Woese |first=C R |last2=Kandler |first2=O |last3=Wheelis |first3=M L |date=1990-06 |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. |url=https://pnas.org/doi/full/10.1073/pnas.87.12.4576 |journal=Proceedings of the National Academy of Sciences |language=en |volume=87 |issue=12 |bibcode=1990PNAS...87.4576W |doi=10.1073/pnas.87.12.4576 |issn=0027-8424 |pmc=54159 |pmid=2112744 |access-date=2022-10-13 |archive-date=2023-09-16 |archive-url=https://web.archive.org/web/20230916192227/https://www.pnas.org/doi/abs/10.1073/pnas.87.12.4576 |dead-url=no }}</ref>，并将這兩支和真核生物划为[[域 (生物)|域]]这一新建立的[[分類階級|分类阶元]]，一起構成了生物的[[三域系統]]。 起初只有一些[[产甲烷菌]]属于这个新域，这些古菌以一些极端环境为栖息地，比如[[温泉]]和[[咸水湖|盐湖]]。到20世纪末，微生物学家意识到古菌是一个庞大而多元化的群体，不只局限于极端环境，而是广泛存在于自然界中，如土壤和海洋里<ref name="DeLong">{{Cite journal |last=DeLong |first=Edward F |date=1998-12-01 |title=Everything in moderation: Archaea as ‘non-extremophiles’ |url=https://www.sciencedirect.com/science/article/pii/S0959437X98800324 |journal=Current Opinion in Genetics & Development |language=en |volume=8 |issue=6 |doi=10.1016/S0959-437X(98)80032-4 |issn=0959-437X |pmid=9914204}}</ref>。由于[[聚合酶链式反应]]（PCR）被大量用于探测采样土壤或水中的[[原核生物]]的[[核酸]]，古菌的重要性和独特性得到新的重视。PCR方法可以不经{{Link-en|细菌培养|microbiological culture}}而直接探测和鉴别微生物<ref>{{Cite journal |last=Theron |first=J. |last2=Cloete |first2=T. E. |date=2000-01 |title=Molecular Techniques for Determining Microbial Diversity and Community Structure in Natural Environments |url=http://www.tandfonline.com/doi/full/10.1080/10408410091154174 |journal=Critical Reviews in Microbiology |language=en |volume=26 |issue=1 |doi=10.1080/10408410091154174 |issn=1040-841X |pmid=10782339}}</ref><ref>{{Cite journal |last=Schmidt |first=Thomas M. |date=2006-09 |title=The maturing of microbial ecology |url=https://pubmed.ncbi.nlm.nih.gov/17061212/ |journal=International Microbiology: The Official Journal of the Spanish Society for Microbiology |volume=9 |issue=3 |issn=1139-6709 |pmid=17061212 |access-date=2022-10-13 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014180727/https://pubmed.ncbi.nlm.nih.gov/17061212/ |dead-url=no }}</ref>。 === 现行分类 === {{See also|生物分類法|系統分類學}} [[File:Rio tinto river CarolStoker NASA Ames Research Center.jpg|thumb|200px|left|{{tsl|en|archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}：2006年在西班牙[[廷托河]]的{{le|矿渣酸性废水|acid mine drainage}}中发现的古菌新类群]] 古菌和原核生物的分类一般是一个快速发展并充满争议的领域。现行的分类体系旨在将古菌组织成具有共同结构特征和共同祖先的生物群<ref name="Gevers">{{Cite journal |last=Gevers |first=Dirk |last2=Dawyndt |first2=Peter |last3=Vandamme |first3=Peter |last4=Willems |first4=Anne |last5=Vancanneyt |first5=Marc |last6=Swings |first6=Jean |last7=De Vos |first7=Paul |date=2006-11-29 |title=Stepping stones towards a new prokaryotic taxonomy |url=https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1915 |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=361 |issue=1475 |doi=10.1098/rstb.2006.1915 |issn=0962-8436 |pmc=1764938 |pmid=17062410 |access-date=2022-10-13 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017010347/https://royalsocietypublishing.org/doi/10.1098/rstb.2006.1915 |dead-url=no }}</ref>。这些分类很大程度上依赖于使用[[核糖体RNA]]基因序列来揭示生物之间的关系（[[分子系统发生学]]）<ref name="Robertson">{{Cite journal |last=Robertson |first=Charles E |last2=Harris |first2=J Kirk |last3=Spear |first3=John R |last4=Pace |first4=Norman R |date=2005-12-01 |title=Phylogenetic diversity and ecology of environmental Archaea |url=https://www.sciencedirect.com/science/article/pii/S1369527405001591 |journal=Current Opinion in Microbiology |series=Growth development / edited by John N Reeve and Ruth A Schmitz |language=en |volume=8 |issue=6 |doi=10.1016/j.mib.2005.10.003 |issn=1369-5274 |pmid=16236543}}</ref>。目前大部分可纯化培养的并研究清楚的古菌都可以划为两个主要的[[门 (生物)|门]]：[[泉古菌门]]和[[廣古菌门]]。其它的门类还在初步创立阶段，比如2002年由[[卡尔·施泰特尔]]發現的奇特的物種{{tsl|en|Nanoarchaeum equitans|骑行纳古菌}}而建立的[[納古菌门]]<ref>{{Cite journal |last=Huber |first=Harald |last2=Hohn |first2=Michael J. |last3=Rachel |first3=Reinhard |last4=Fuchs |first4=Tanja |last5=Wimmer |first5=Verena C. |last6=Stetter |first6=Karl O. |date=2002-05-02 |title=A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont |url=https://www.nature.com/articles/417063a |journal=Nature |language=en |volume=417 |issue=6884 |bibcode=2002Natur.417...63H |doi=10.1038/417063a |issn=0028-0836 |pmid=11986665 |access-date=2022-10-13 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018043353/https://www.nature.com/articles/417063a |dead-url=no }}</ref>。还有1994年Barns等建议建立的一个新门[[初古菌门]]包括一小群不寻常的嗜热品种，但这个门与泉古菌门演化关系密切<ref>{{Cite journal |last=Barns |first=S M |last2=Delwiche |first2=C F |last3=Palmer |first3=J D |last4=Pace |first4=N R |date=1996-08-20 |title=Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. |url=https://pnas.org/doi/full/10.1073/pnas.93.17.9188 |journal=Proceedings of the National Academy of Sciences |language=en |volume=93 |issue=17 |bibcode=1996PNAS...93.9188B |doi=10.1073/pnas.93.17.9188 |issn=0027-8424 |pmc=38617 |pmid=8799176}}</ref><ref>{{Cite journal |last=Elkins |first=James G. |last2=Podar |first2=Mircea |last3=Graham |first3=David E. |last4=Makarova |first4=Kira S. |last5=Wolf |first5=Yuri |last6=Randau |first6=Lennart |last7=Hedlund |first7=Brian P. |last8=Brochier-Armanet |first8=Céline |last9=Kunin |first9=Victor |last10=Anderson |first10=Iain |last11=Lapidus |first11=Alla |date=2008-06-10 |title=A korarchaeal genome reveals insights into the evolution of the Archaea |url=https://pnas.org/doi/full/10.1073/pnas.0801980105 |journal=Proceedings of the National Academy of Sciences |language=en |volume=105 |issue=23 |bibcode=2008PNAS..105.8102E |doi=10.1073/pnas.0801980105 |issn=0027-8424 |pmc=2430366 |pmid=18535141 |access-date=2022-10-13 |archive-date=2022-11-08 |archive-url=https://web.archive.org/web/20221108154907/https://www.pnas.org/doi/full/10.1073/pnas.0801980105 |dead-url=no }}</ref>。其它最近探别出来的古菌与已知古菌门类关系较远，如2006年发现的環境樣品{{tsl|en|Archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}<ref>{{Cite journal |last=Baker |first=Brett J. |last2=Tyson |first2=Gene W. |last3=Webb |first3=Richard I. |last4=Flanagan |first4=Judith |last5=Hugenholtz |first5=Philip |last6=Allen |first6=Eric E. |last7=Banfield |first7=Jillian F. |date=2006-12-22 |title=Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis |url=https://www.science.org/doi/10.1126/science.1132690 |journal=Science |language=en |volume=314 |issue=5807 |bibcode=2006Sci...314.1933B |doi=10.1126/science.1132690 |issn=0036-8075 |pmid=17185602 |access-date=2022-10-13 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014171212/https://www.science.org/doi/10.1126/science.1132690 |dead-url=no }}</ref><ref name="Baker BJ, Comolli LR, Dick GJ, et al. 8806–11">{{cite journal |author=Baker BJ |author2=Comolli LR |author3=Dick GJ |display-authors=etal|date=May 2010 |title=Enigmatic, ultrasmall, uncultivated Archaea |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=107 |issue=19 |pages=8806–11 |bibcode=2010PNAS..107.8806B |doi=10.1073/pnas.0914470107 |pmc=2889320 |pmid=20421484}}</ref>。{{tsl|en|Archaeal Richmond Mine Acidophilic Nanoorganisms|ARMAN}}是已知的生命體中最小的生命體<ref name="Baker BJ, Comolli LR, Dick GJ, et al. 8806–11" />。 一个超门（superphylum）分类-TACK（又稱[[變形古菌界]]），已经被提出，包括{{le|奇古菌门|Thaumarchaeota}}，{{le|曙古菌門|Aigarchaeota}}，[[泉古菌門]]和[[初古菌門]]<ref name="Guy2011">{{Cite journal |last=Guy |first=Lionel |last2=Ettema |first2=Thijs J. G. |date=2011-12-01 |title=The archaeal ‘TACK’ superphylum and the origin of eukaryotes |url=https://www.cell.com/trends/microbiology/abstract/S0966-842X(11)00174-0 |journal=Trends in Microbiology |language=en |volume=19 |issue=12 |doi=10.1016/j.tim.2011.09.002 |issn=0966-842X |pmid=22018741 |access-date=2022-10-13 |archive-date=2013-10-16 |archive-url=https://web.archive.org/web/20131016220820/http://www.cell.com/trends/microbiology/abstract/S0966-842X(11)00174-0 |dead-url=no }}</ref>。这个超门可能与真核生物的起源有关。最近，[[阿斯加德古菌超门]]被命名，并被提议与真核生物的起源和一个TACK姊妹组织更紧密相关<ref>{{Cite journal |last=Zaremba-Niedzwiedzka |first=Katarzyna |last2=Caceres |first2=Eva F. |last3=Saw |first3=Jimmy H. |last4=Bäckström |first4=Disa |last5=Juzokaite |first5=Lina |last6=Vancaester |first6=Emmelien |last7=Seitz |first7=Kiley W. |last8=Anantharaman |first8=Karthik |last9=Starnawski |first9=Piotr |last10=Kjeldsen |first10=Kasper U. |last11=Stott |first11=Matthew B. |date=2017-01-19 |title=Asgard archaea illuminate the origin of eukaryotic cellular complexity |url=https://www.nature.com/articles/nature21031 |journal=Nature |language=en |volume=541 |issue=7637 |doi=10.1038/nature21031 |issn=0028-0836 |access-date=2022-10-13 |archive-date=2022-12-03 |archive-url=https://web.archive.org/web/20221203044937/https://www.nature.com/articles/nature21031 |dead-url=no }}</ref>。 == 細菌、古菌和真核生物的比较 == 在[[細胞]]結構和[[代謝]]上，古菌在很多方面接近其它原核生物。然而在基因[[轉錄]]和[[翻译 (遗传学)|轉译]]這兩個[[分子生物學]]的中心過程上，它們並不明顯表現出細菌的特徵，反而非常接近[[真核生物]]。比如，古菌的[[翻译 (遗传学)|轉译]]使用[[真核生物]]的啓動和延伸因子，且轉譯過程需要真核生物中的TATA框結合蛋白和TFIIB。许多这些特征也被讨论如下。 古菌還具有一些其它特徵。與大多數細菌不同，它們只有一層[[細胞膜]]而缺少[[肽聚糖]]細胞壁。而且，絕大多數細菌和真核生物的細胞膜中的[[脂類]]主要由甘油[[酯]]組成，而古菌的膜脂由甘油[[醚]]構成。這些區別也許是對[[超高溫環境]]的適應。古菌[[鞭毛]]的成分和形成過程也與細菌不同。 {{生命系统发生树|align=right|size=320px|caption=基於[[rRNA]]序列的[[系統發生樹]]，顯示了可明顯區別的三支：細菌、古菌和真核生物}} {| class="wikitable" |- ! 与细菌相同 ! 与真核生物相同 ! 古菌独有 |- | 没有细胞核和膜结合细胞器 | 没有[[肽聚糖]] | 独特的细胞壁结构 |- | 环状基因组 | DNA与[[组蛋白]]结合<ref>{{Cite journal |last=Talbert |first=Paul B. |last2=Henikoff |first2=Steven |date=2010-04 |title=Histone variants — ancient wrap artists of the epigenome |url=https://www.nature.com/articles/nrm2861 |journal=Nature Reviews Molecular Cell Biology |language=en |volume=11 |issue=4 |doi=10.1038/nrm2861 |issn=1471-0080 |access-date=2022-10-13 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017074204/https://www.nature.com/articles/nrm2861 |dead-url=no }}</ref><ref>{{Cite journal |last=Sandman |first=Kathleen |last2=Reeve |first2=John N |date=2006-10-01 |title=Archaeal histones and the origin of the histone fold |url=https://www.sciencedirect.com/science/article/pii/S1369527406001251 |journal=Current Opinion in Microbiology |series=Antimicrobials/Genomics |language=en |volume=9 |issue=5 |doi=10.1016/j.mib.2006.08.003 |issn=1369-5274}}</ref> | 细胞膜由醚键构成 |- | 基因组成[[操纵子]] | 翻译从[[甲硫氨酸]]起始 | [[鞭毛]]蛋白结构<ref name="Zillig">{{Cite journal |last=Zillig |first=Wolfram |date=1991-12-01 |title=Comparative biochemistry of Archaea and Bacteria |url=https://www.sciencedirect.com/science/article/pii/S0959437X05802060 |journal=Current Opinion in Genetics & Development |language=en |volume=1 |issue=4 |doi=10.1016/S0959-437X(05)80206-0 |issn=0959-437X |access-date=2022-10-13 |archive-date=2020-07-01 |archive-url=https://web.archive.org/web/20200701075749/https://www.sciencedirect.com/science/article/pii/S0959437X05802060 |dead-url=no }}</ref> |- | 没有像真核生物一样复杂的[[转录后修饰]] | 相似的[[RNA聚合酶]]、[[启动子]]以及其它转录机制<ref name="Zillig" /><ref>{{Cite journal |last=Bell |first=Stephen D |last2=Jackson |first2=Stephen P |date=2001-04-01 |title=Mechanism and regulation of transcription in archaea |url=https://www.sciencedirect.com/science/article/pii/S1369527400001909 |journal=Current Opinion in Microbiology |language=en |volume=4 |issue=2 |doi=10.1016/S1369-5274(00)00190-9 |issn=1369-5274 |pmid=11282478}}</ref><ref>{{Cite journal |last=Reeve |first=John N. |date=2003-05 |title=Archaeal chromatin and transcription |url=https://pubmed.ncbi.nlm.nih.gov/12694606 |journal=Molecular Microbiology |volume=48 |issue=3 |doi=10.1046/j.1365-2958.2003.03439.x |issn=0950-382X |pmid=12694606 |access-date=2022-10-13 |archive-date=2022-10-01 |archive-url=https://web.archive.org/web/20221001130819/https://pubmed.ncbi.nlm.nih.gov/12694606/ |dead-url=no }}</ref> | 核糖体结构 |- | 多顺反子mRNA | 相似的DNA复制与修复<ref>{{Cite journal |last=Kelman |first=Lori M. |last2=Kelman |first2=Zvi |date=2003-05 |title=Archaea: an archetype for replication initiation studies? |url=https://pubmed.ncbi.nlm.nih.gov/12694608/ |journal=Molecular Microbiology |volume=48 |issue=3 |doi=10.1046/j.1365-2958.2003.03369.x |issn=0950-382X |pmid=12694608 |access-date=2022-10-13 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018052113/https://pubmed.ncbi.nlm.nih.gov/12694608/ |dead-url=no }}</ref> | tRNA的序列和代谢<ref name="Zillig" /><ref>{{Cite journal |last=Phillips |first=Gabriela |last2=Chikwana |first2=Vimbai M. |last3=Maxwell |first3=Adrienne |last4=El-Yacoubi |first4=Basma |last5=Swairjo |first5=Manal A. |last6=Iwata-Reuyl |first6=Dirk |last7=Crécy-Lagard |first7=Valérie de |date=2010-04-23 |title=Discovery and Characterization of an Amidinotransferase Involved in the Modification of Archaeal tRNA *♦ |url=https://www.jbc.org/article/S0021-9258(20)55051-5/abstract |journal=Journal of Biological Chemistry |language=en |volume=285 |issue=17 |doi=10.1074/jbc.M110.102236 |issn=0021-9258 |pmc=2857094 |pmid=20129918}}</ref> |- | 细胞大小（远小于真核生物） | 相似的[[ATP酶]] | 独有的紫膜光合系统 |} 古菌和真核生物的關係仍然是個重要問題。除掉上面所提到的相似性，很多其他遺傳樹也將二者併在一起。在一些樹中真核生物離廣古菌比離泉古菌更近，但生物膜化學的結論相反。然而，在一些細菌，（如[[棲熱袍菌]]）中發現了和古菌類似的基因，使這些關係變得複雜起來。一些人認爲真核生物起源於一個古菌和細菌的融合，二者分別成爲細胞核和細胞質。這解釋了很多基因上的相似性，但在解釋細胞結構上存在困難。 == 形态 == [[Image:Relative scale.svg|thumb|250px|left|原核细胞的大小，相对于其他细胞和生物分子（[[對數尺度|对数刻度]]）]] 單個古菌細胞直徑在0.1到15微米之間，有一些種類形成細胞團簇或者纖維，長度可達200微米。它們可有各種形狀，一般是球形、桿形、螺旋形、葉狀或方形。这些不寻常的形状可能是由它们的细胞壁和原核生物[[细胞骨架]]两者维持的。其他生物的细胞骨架成分蛋白在古菌内存在<ref>{{Cite journal |last=Hara |first=Futoshi |last2=Yamashiro |first2=Kan |last3=Nemoto |first3=Naoki |last4=Ohta |first4=Yoshinori |last5=Yokobori |first5=Shin-ichi |last6=Yasunaga |first6=Takuo |last7=Hisanaga |first7=Shin-ichi |last8=Yamagishi |first8=Akihiko |date=2007-03 |title=An Actin Homolog of the Archaeon Thermoplasma acidophilum That Retains the Ancient Characteristics of Eukaryotic Actin |url=https://journals.asm.org/doi/10.1128/JB.01454-06 |journal=Journal of Bacteriology |language=en |volume=189 |issue=5 |doi=10.1128/JB.01454-06 |issn=0021-9193 |pmc=1855749 |pmid=17189356 |access-date=2022-10-13 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123111009/https://journals.asm.org/doi/10.1128/jb.01454-06 |dead-url=no }}</ref>，长丝在其细胞内形成<ref>{{Cite journal |last=Trent |first=Jonathan D. |last2=Kagawa |first2=Hiromi K. |last3=Yaoi |first3=Takuro |last4=Olle |first4=Eric |last5=Zaluzec |first5=Nestor J. |date=1997-05-13 |title=Chaperonin filaments: The archaeal cytoskeleton? |url=https://pnas.org/doi/full/10.1073/pnas.94.10.5383 |journal=Proceedings of the National Academy of Sciences |language=en |volume=94 |issue=10 |bibcode=1997PNAS...94.5383T |doi=10.1073/pnas.94.10.5383 |issn=0027-8424 |pmc=24687 |pmid=9144246 |access-date=2022-10-13 |archive-date=2022-10-16 |archive-url=https://web.archive.org/web/20221016093107/https://www.pnas.org/doi/full/10.1073/pnas.94.10.5383 |dead-url=no }}</ref>，但与其他生物体不同的是，这些细胞结构被理解的很少<ref>{{Cite journal |last=Hixon |first=William G. |last2=Searcy |first2=Dennis G. |date=1993-01-01 |title=Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts |url=https://www.sciencedirect.com/science/article/pii/030326479390091P |journal=Biosystems |language=en |volume=29 |issue=2 |doi=10.1016/0303-2647(93)90091-P |issn=0303-2647 |pmid=8374067}}</ref>。 == 细胞结构、组成和运行 == 古菌和细菌的细胞结构大体类似。古菌和细菌一样没有内膜系统和细胞器<ref name="PMID8177167">{{Cite journal |last=Woese |first=C R |date=1994-03 |title=There must be a prokaryote somewhere: microbiology's search for itself |url=https://journals.asm.org/doi/10.1128/mr.58.1.1-9.1994 |journal=Microbiological Reviews |language=en |volume=58 |issue=1 |doi=10.1128/mr.58.1.1-9.1994 |issn=0146-0749 |pmc=372949 |pmid=8177167 |access-date=2022-10-13 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018141026/https://journals.asm.org/doi/10.1128/mr.58.1.1-9.1994 |dead-url=no }}</ref>。古菌也和细菌一样在细胞膜之外还有一层细胞壁，它们同样也具有一个或多个[[鞭毛]]结构<ref name="Thomas">{{Cite journal |last=Thomas |first=Nikhil A. |last2=Bardy |first2=Sonia L. |last3=Jarrell |first3=Ken F. |date=2001-04 |title=The archaeal flagellum: a different kind of prokaryotic motility structure |url=https://academic.oup.com/femsre/article-lookup/doi/10.1111/j.1574-6976.2001.tb00575.x |journal=FEMS Microbiology Reviews |language=en |volume=25 |issue=2 |doi=10.1111/j.1574-6976.2001.tb00575.x |issn=1574-6976 |pmid=11250034 |access-date=2022-10-13 |archive-date=2022-11-21 |archive-url=https://web.archive.org/web/20221121083000/https://academic.oup.com/femsre/article-lookup/doi/10.1111/j.1574-6976.2001.tb00575.x |dead-url=no }}</ref>。 === 膜 === 古菌膜由从那些在其它生命形式的强烈不同的分子组成，显示出古菌与细菌和真核生物关系都比较遥远。 === 细胞壁和鞭毛 === 大部分古菌种类（非Thermoplasma属和Ferroplasma属）都有细胞壁。<ref name="Golyshina">{{Cite journal |last=Golyshina |first=O V |last2=Pivovarova |first2=T A |last3=Karavaiko |first3=G I |last4=Kondratéva |first4=T F |last5=Moore |first5=E R |last6=Abraham |first6=W R |last7=Lünsdorf |first7=H |last8=Timmis |first8=K N |last9=Yakimov |first9=M M |last10=Golyshin |first10=P N |date=2000-05-01 |title=Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-50-3-997 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=50 |issue=3 |doi=10.1099/00207713-50-3-997 |issn=1466-5026 |pmid=10843038 |access-date=2022-10-13 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123112225/https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-50-3-997 |dead-url=no }}</ref>，多由表面层蛋白质组成，形成一个[[S层]]。一个[[S层]]是蛋白质分子的刚性阵列覆盖了细胞的外侧（如同[[鎖子甲]]）。<ref>{{Cite journal |last=Engelhardt |first=Harald |last2=Peters |first2=Jürgen |date=1998-12-15 |title=Structural Research on Surface Layers: A Focus on Stability, Surface Layer Homology Domains, and Surface Layer–Cell Wall Interactions |url=https://www.sciencedirect.com/science/article/pii/S1047847798940709 |journal=Journal of Structural Biology |language=en |volume=124 |issue=2 |doi=10.1006/jsbi.1998.4070 |issn=1047-8477 |pmid=10049812 |access-date=2022-10-13 |archive-date=2020-10-02 |archive-url=https://web.archive.org/web/20201002021003/https://www.sciencedirect.com/science/article/pii/S1047847798940709 |dead-url=no }}</ref>该层提供化学和物理保护，并能防止[[高分子|大分子]]接触细胞膜。<ref name="Kandler1998">{{Cite journal |last=Kandler |first=O. |last2=König |first2=H. |date=1998-04 |title=Cell wall polymers in Archaea (Archaebacteria) |url=http://link.springer.com/10.1007/s000180050156 |journal=Cellular and Molecular Life Sciences CMLS |language=en |volume=54 |issue=4 |doi=10.1007/s000180050156 |issn=1420-682X}}</ref>与細菌不同，古菌的細胞壁缺少[[肽聚糖]]。<ref name="Howland">{{cite book|last=Howland|first=John L.|year=2000|title=The Surprising Archaea: Discovering Another Domain of Life|url=https://archive.org/details/surprisingarchae0000howl|page=[https://archive.org/details/surprisingarchae0000howl/page/32 32]|location=Oxford|publisher=Oxford University Press|isbn=0-19-511183-4}}</ref> 古菌鞭毛操作类似细菌鞭毛，它们的长梗是由在座部的旋转马达驱动。然而，古菌鞭毛在组成和发育上有着明显的不同。<ref name="Thomas" />这两种类型的鞭毛是从不同的祖先进化而来的。细菌鞭毛与[[III型分泌系统]]共享一个共同的祖先，<ref>{{Cite journal |last=Gophna |first=Uri |last2=Ron |first2=Eliora Z. |last3=Graur |first3=Dan |date=2003-07-17 |title=Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events |url=https://www.sciencedirect.com/science/article/pii/S0378111903006127 |journal=Gene |language=en |volume=312 |doi=10.1016/S0378-1119(03)00612-7 |issn=0378-1119 |pmid=12909351 |access-date=2022-10-13 |archive-date=2018-11-06 |archive-url=https://web.archive.org/web/20181106212919/https://www.sciencedirect.com/science/article/pii/S0378111903006127 |dead-url=no }}</ref><ref>{{cite journal |author=Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH |date=April 2000 |title=Phylogenetic analyses of the constituents of Type III protein secretion systems |journal=J. Mol. Microbiol. Biotechnol. |volume=2 |issue=2 |pages=125–44 |pmid=10939240}}</ref>但是，古菌鞭毛似乎已经从细菌IV型菌的[[性菌毛]]进化而来。<ref>{{Cite journal |last=Ng |first=Sandy Y.M. |last2=Chaban |first2=Bonnie |last3=Jarrell |first3=Ken F. |date=2006 |title=Archaeal Flagella, Bacterial Flagella and Type IV Pili: A Comparison of Genes and Posttranslational Modifications |url=https://www.karger.com/Article/FullText/94053 |journal=Microbial Physiology |language=en |volume=11 |issue=3-5 |doi=10.1159/000094053 |issn=2673-1665 |pmid=16983194 |access-date=2022-10-13 |archive-date=2014-04-21 |archive-url=https://web.archive.org/web/20140421050838/http://www.karger.com/Article/FullText/94053 |dead-url=no }}</ref>对比，细菌鞭毛是空心的，并且是由其子单元从中心孔向上移动到鞭毛的末端装配，但是，古菌鞭毛是由在基座中添加子单元合成。<ref>{{Cite journal |last=Bardy |first=Sonia L. |last2=Ng |first2=Sandy Y. M. |last3=Jarrell |first3=Ken F. |date=2003-02-01 |title=Prokaryotic motility structures |url=https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.25948-0 |journal=Microbiology |language=en |volume=149 |issue=2 |doi=10.1099/mic.0.25948-0 |issn=1350-0872 |pmid=12624192 |access-date=2022-10-13 |archive-date=2022-10-15 |archive-url=https://web.archive.org/web/20221015111309/https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.25948-0 |dead-url=no }}</ref> ==遗传学== {{further2|[[质粒]]、[[基因組]]}} 古菌通常拥有单个环状的[[染色体]]<ref name="Allers">{{Cite journal |last=Allers |first=Thorsten |last2=Mevarech |first2=Moshe |date=2005-01 |title=Archaeal genetics — the third way |url=http://www.nature.com/articles/nrg1504 |journal=Nature Reviews Genetics |language=en |volume=6 |issue=1 |doi=10.1038/nrg1504 |issn=1471-0056 |pmid=15630422 |access-date=2022-10-14 |archive-date=2022-10-16 |archive-url=https://web.archive.org/web/20221016082900/https://www.nature.com/articles/nrg1504 |dead-url=no }}</ref>，其大小差异悬殊。目前已知最大的是''{{tsl|en|Methanosarcina acetivorans}}''的基因组，达5,751,492个[[碱基对]]<ref>{{Cite journal |last=Galagan |first=James E. |last2=Nusbaum |first2=Chad |last3=Roy |first3=Alice |last4=Endrizzi |first4=Matthew G. |last5=Macdonald |first5=Pendexter |last6=FitzHugh |first6=Will |last7=Calvo |first7=Sarah |last8=Engels |first8=Reinhard |last9=Smirnov |first9=Serge |last10=Atnoor |first10=Deven |last11=Brown |first11=Adam |date=2002-04-01 |title=The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity |url=http://genome.cshlp.org/lookup/doi/10.1101/gr.223902 |journal=Genome Research |language=en |volume=12 |issue=4 |doi=10.1101/gr.223902 |issn=1088-9051 |pmc=187521 |pmid=11932238}}</ref>，而除{{link-en|里奇蒙德矿井嗜酸纳米古生物|Archaeal Richmond Mine Acidophilic Nanoorganisms}}（ARMAN）外最小的{{tsl|en|Nanoarchaeum equitans|骑行纳古菌}}只有490,885个碱基对，不到前者的十分之一，据估只能编码537种蛋白质<ref>{{Cite journal |last=Waters |first=Elizabeth |last2=Hohn |first2=Michael J. |last3=Ahel |first3=Ivan |last4=Graham |first4=David E. |last5=Adams |first5=Mark D. |last6=Barnstead |first6=Mary |last7=Beeson |first7=Karen Y. |last8=Bibbs |first8=Lisa |last9=Bolanos |first9=Randall |last10=Keller |first10=Martin |last11=Kretz |first11=Keith |date=2003-10-28 |title=The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism |url=https://pnas.org/doi/full/10.1073/pnas.1735403100 |journal=Proceedings of the National Academy of Sciences |language=en |volume=100 |issue=22 |bibcode=2003PNAS..10012984W |doi=10.1073/pnas.1735403100 |issn=0027-8424 |pmc=240731 |pmid=14566062 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018220110/https://www.pnas.org/doi/full/10.1073/pnas.1735403100 |dead-url=no }}</ref>。一些小型的独立DNA片段[[质粒]]也存在于古菌中，可能通过细胞之间的直接接触传递，其过程可能与[[接合|细菌之间的接合]]类似<ref>{{Cite journal |last=Schleper |first=C |last2=Holz |first2=I |last3=Janekovic |first3=D |last4=Murphy |first4=J |last5=Zillig |first5=W |date=1995-08 |title=A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating |url=https://journals.asm.org/doi/10.1128/jb.177.15.4417-4426.1995 |journal=Journal of Bacteriology |language=en |volume=177 |issue=15 |doi=10.1128/jb.177.15.4417-4426.1995 |issn=0021-9193 |pmc=177192 |pmid=7635827 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018203403/https://journals.asm.org/doi/10.1128/jb.177.15.4417-4426.1995 |dead-url=no }}</ref><ref name="SotaTop">{{cite book|chapterurl=http://www.horizonpress.com/pla|author=Sota M; Top EM|year=2008|chapter=Horizontal Gene Transfer Mediated by Plasmids|title=Plasmids: Current Research and Future Trends|publisher=Caister Academic Press|isbn=978-1-904455-35-6|access-date=2014-01-15|archive-date=2008-04-11|archive-url=https://web.archive.org/web/20080411053922/http://www.horizonpress.com/pla|dead-url=no}}</ref>。 [[File:RT8-4.jpg|thumb|200px|left|DNA病毒STSV1感染的[[硫化叶菌属|硫化叶菌]]<ref>{{Cite journal |last=Xiang |first=Xiaoyu |last2=Chen |first2=Lanming |last3=Huang |first3=Xiaoxing |last4=Luo |first4=Yuanmin |last5=She |first5=Qunxin |last6=Huang |first6=Li |date=2005-07 |title=Sulfolobus tengchongensis Spindle-Shaped Virus STSV1: Virus-Host Interactions and Genomic Features |url=https://journals.asm.org/doi/10.1128/JVI.79.14.8677-8686.2005 |journal=Journal of Virology |language=en |volume=79 |issue=14 |doi=10.1128/JVI.79.14.8677-8686.2005 |issn=0022-538X |pmc=1168784 |pmid=15994761}}</ref>，图片下方尺标为1[[微米]]]] 古菌可被双链[[DNA病毒]]感染，这些双链DNA病毒形态各异，包括瓶状、杆状、雨滴状等<ref>{{Cite journal |last=Prangishvili |first=David |last2=Forterre |first2=Patrick |last3=Garrett |first3=Roger A. |date=2006-11-01 |title=Viruses of the Archaea: a unifying view |url=https://www.nature.com/articles/nrmicro1527 |journal=Nature Reviews Microbiology |language=en |volume=4 |issue=11 |doi=10.1038/nrmicro1527 |issn=1740-1526 |pmid=17041631 |access-date=2022-10-14 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017024127/https://www.nature.com/articles/nrmicro1527 |dead-url=no }}</ref>。这些病毒在一些嗜热菌中研究得最为详致，特别是{{le|硫化叶菌目|Sulfolobales}}和[[热变形菌目]]的古菌中<ref>{{Cite journal |last=Prangishvili |first=D. |last2=Garrett |first2=R.A. |date=2004-04-01 |title=Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses |url=https://portlandpress.com/biochemsoctrans/article/32/2/204/63961/Exceptionally-diverse-morphotypes-and-genomes-of |journal=Biochemical Society Transactions |language=en |volume=32 |issue=2 |doi=10.1042/bst0320204 |issn=0300-5127 |pmid=15046572 |access-date=2022-10-14 |archive-date=2023-01-19 |archive-url=https://web.archive.org/web/20230119101838/https://portlandpress.com/biochemsoctrans/article/32/2/204/63961/Exceptionally-diverse-morphotypes-and-genomes-of |dead-url=no }}</ref>。最近发现了两类可感染古菌的单链DNA病毒：一种是典型的{{Link-en|嗜盐菌多形病毒|Pleolipoviridae}}，这病毒感染嗜盐菌<ref>{{cite journal |author=Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH |date=March 2009 |title=An ssDNA virus infecting archaea; A new lineage of viruses with a membrane envelope |journal=Mol. Microbiol. |volume=72 |issue=2 |pages=307–19 |doi=10.1111/j.1365-2958.2009.06642.x |pmid=19298373}}</ref>另外一种嗜热的{{Link-en|圈形病毒|Spiraviridae}}感染[[嗜极生物|嗜超热菌]]（这些古菌生长在90到95°C的温度下）<ref>{{Cite journal |last=Mochizuki |first=Tomohiro |last2=Krupovic |first2=Mart |last3=Pehau-Arnaudet |first3=Gérard |last4=Sako |first4=Yoshihiko |last5=Forterre |first5=Patrick |last6=Prangishvili |first6=David |date=2012-08-14 |title=Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome |url=https://pnas.org/doi/full/10.1073/pnas.1203668109 |journal=Proceedings of the National Academy of Sciences |language=en |volume=109 |issue=33 |bibcode=2012PNAS..10913386M |doi=10.1073/pnas.1203668109 |issn=0027-8424 |pmc=3421227 |pmid=22826255 |access-date=2022-10-14 |archive-date=2022-10-21 |archive-url=https://web.archive.org/web/20221021205924/https://www.pnas.org/doi/full/10.1073/pnas.1203668109 |dead-url=no }}</ref>其中后者有已知最大的单链[[脱氧核糖核酸|DNA]]基因组。古菌可以利用针对病毒基因的[[RNA干扰]]和[[重复序列|DNA重复]]影响病毒在寄主内的繁殖。<ref>{{Cite journal |last=Mojica |first=Francisco J.M. |last2=Díez-Villaseñor |first2=Chc)sar |last3=García-Martínez |first3=Jesús |last4=Soria |first4=Elena |date=2005-02 |title=Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements |url=http://link.springer.com/10.1007/s00239-004-0046-3 |journal=Journal of Molecular Evolution |language=en |volume=60 |issue=2 |doi=10.1007/s00239-004-0046-3 |issn=0022-2844 |pmid=15791728}}</ref><ref>{{Cite journal |last=Makarova |first=Kira S |last2=Grishin |first2=Nick V |last3=Shabalina |first3=Svetlana A |last4=Wolf |first4=Yuri I |last5=Koonin |first5=Eugene V |date=2006-12 |title=A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action |url=https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-7 |journal=Biology Direct |language=en |volume=1 |issue=1 |doi=10.1186/1745-6150-1-7 |issn=1745-6150 |pmc=1462988 |pmid=16545108 |access-date=2022-10-14 |archive-date=2022-11-09 |archive-url=https://web.archive.org/web/20221109055840/https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-7 |dead-url=no }}</ref> 古菌在基因上与细菌真核生物有许多不同，大约有15%古菌基因是古菌中独有的。这些古菌独有蛋白质的功能大部分还未知<ref>{{Cite journal |last=Graham |first=David E. |last2=Overbeek |first2=Ross |last3=Olsen |first3=Gary J. |last4=Woese |first4=Carl R. |date=2000-03-28 |title=An archaeal genomic signature |url=https://pnas.org/doi/full/10.1073/pnas.97.7.3304 |journal=Proceedings of the National Academy of Sciences |language=en |volume=97 |issue=7 |bibcode=2000PNAS...97.3304G |doi=10.1073/pnas.97.7.3304 |issn=0027-8424 |pmc=16234 |pmid=10716711 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014011303/https://www.pnas.org/doi/full/10.1073/pnas.97.7.3304 |dead-url=no }}</ref>，其余已知功能的独有蛋白质大部分属于广古菌门中的产甲烷菌。古菌、细菌、真核生物共有的蛋白质都涉及细胞的核心功能，如[[转录]]、[[翻译 (遗传学)|翻译]]和[[核苷酸|核苷酸代谢]]。古菌基因组别的特点还有基因的组织常与功能相关（如催化相同[[代谢途径]]的酶会组成一个独有的[[操纵子]]），以及不同的[[tRNA]]基因之间差异很大，其[[氨酰-tRNA合成酶]]之间也是如此<ref name="Gaasterland">{{Cite journal |last=Gaasterland |first=Terry |date=1999-10-01 |title=Archaeal genomics |url=https://www.sciencedirect.com/science/article/pii/S1369527499000144 |journal=Current Opinion in Microbiology |language=en |volume=2 |issue=5 |doi=10.1016/S1369-5274(99)00014-4 |issn=1369-5274 |pmid=10508726 |access-date=2022-10-14 |archive-date=2019-03-22 |archive-url=https://web.archive.org/web/20190322153855/https://www.sciencedirect.com/science/article/pii/S1369527499000144 |dead-url=no }}</ref>。 较之细菌的转录与翻译，古菌中的这些过程更接近于真核生物，特别是古菌中的[[RNA聚合酶]]与[[核糖体]]，可以说非常接近于真核生物中的对应物<ref name="Allers" />。尽管古菌中只有一种RNA聚合酶，但其结构与功能与真核生物中最主要的[[RNA聚合酶Ⅱ]]非常相似，且其结合到基因[[启动子]]上所需的蛋白质组件（[[通用转录因子]]）也非常相似<ref>{{Cite journal |last=Werner |first=Finn |date=2007-09 |title=Structure and function of archaeal RNA polymerases |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05876.x |journal=Molecular Microbiology |language=en |volume=65 |issue=6 |doi=10.1111/j.1365-2958.2007.05876.x |issn=0950-382X |pmid=17697097 |access-date=2022-10-14 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017051540/https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05876.x |dead-url=no }}</ref>。但是，其它的古菌[[转录因子]]却与细菌中的相似<ref>{{Cite journal |last=Aravind |first=L |date=1999-12-01 |title=DNA-binding proteins and evolution of transcription regulation in the archaea |url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/27.23.4658 |journal=Nucleic Acids Research |volume=27 |issue=23 |doi=10.1093/nar/27.23.4658 |pmc=148756 |pmid=10556324 |access-date=2022-10-14 |archive-date=2022-08-08 |archive-url=https://web.archive.org/web/20220808180204/https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/27.23.4658 |dead-url=no }}</ref>，[[转录后修饰]]也比真核生物中的简单（大部分古菌基因缺少[[内含子]]，其内含子主要集中在[[tRNA]]和[[rRNA]]基因中<ref>{{cite journal |author=Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA |date=September 1997 |title=Archaeal introns: splicing, intercellular mobility and evolution |journal=Trends Biochem. Sci. |volume=22 |issue=9 |pages=326–31 |doi=10.1016/S0968-0004(97)01113-4 |pmid=9301331}}</ref>，少数出现在编码蛋白质的基因中<ref>{{Cite journal |last=Watanabe |first=Yoh-ichi |last2=Yokobori |first2=Shin-ichi |last3=Inaba |first3=Toshiro |last4=Yamagishi |first4=Akihiko |last5=Oshima |first5=Tairo |last6=Kawarabayasi |first6=Yutaka |last7=Kikuchi |first7=Hisasi |last8=Kita |first8=Kiyoshi |date=2002-01-02 |title=Introns in protein-coding genes in Archaea |url=http://doi.wiley.com/10.1016/S0014-5793%2801%2903219-7 |journal=FEBS Letters |language=en |volume=510 |issue=1-2 |doi=10.1016/S0014-5793(01)03219-7 |pmid=11755525}}</ref><ref>{{Cite journal |last=Yoshinari |first=Shigeo |last2=Itoh |first2=Takashi |last3=Hallam |first3=Steven J. |last4=DeLong |first4=Edward F. |last5=Yokobori |first5=Shin-ichi |last6=Yamagishi |first6=Akihiko |last7=Oshima |first7=Tairo |last8=Kita |first8=Kiyoshi |last9=Watanabe |first9=Yoh-ichi |date=2006-08-04 |title=Archaeal pre-mRNA splicing: A connection to hetero-oligomeric splicing endonuclease |url=https://www.sciencedirect.com/science/article/pii/S0006291X06013003 |journal=Biochemical and Biophysical Research Communications |language=en |volume=346 |issue=3 |doi=10.1016/j.bbrc.2006.06.011 |issn=0006-291X |pmid=16781672 |access-date=2022-10-14 |archive-date=2019-03-22 |archive-url=https://web.archive.org/web/20190322153324/https://www.sciencedirect.com/science/article/pii/S0006291X06013003 |dead-url=no }}</ref>）。 目前已有一百五十余个[[已测序古菌基因组列表|古菌基因組已經完成了測序]]，另外许多測序工作正在進行中。<ref>{{Cite web |title=Genome List - Genome |url=http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi |website=NCBI |archive-url=https://web.archive.org/web/20210210112843/https://www.ncbi.nlm.nih.gov/genomes/lproks.cgi |archive-date=2021-02-10 |access-date=2005-07-13 |dead-url=no}}</ref> ===基因的转移与交换=== ''沃氏富盐菌''一种极端嗜盐古菌，可在两个细胞的细胞质之间形成桥梁，可能用于DNA的任意方向的转移<ref>{{Cite journal |last=Rosenshine |first=Ilan |last2=Tchelet |first2=Ronen |last3=Mevarech |first3=Moshe |date=1989-09-22 |title=The Mechanism of DNA Transfer in the Mating System of an Archaebacterium |url=https://www.science.org/doi/10.1126/science.2818746 |journal=Science |language=en |volume=245 |issue=4924 |doi=10.1126/science.2818746 |issn=0036-8075 |pmid=2818746 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014111815/https://www.science.org/doi/10.1126/science.2818746 |dead-url=no }}</ref>。 当嗜热的古菌{{Link-en|硫化叶菌|Sulfolobus solfataricus}}<ref name="Frols2008">{{Cite journal |last=Fröls |first=Sabrina |last2=Ajon |first2=Malgorzata |last3=Wagner |first3=Michaela |last4=Teichmann |first4=Daniela |last5=Zolghadr |first5=Behnam |last6=Folea |first6=Mihaela |last7=Boekema |first7=Egbert J. |last8=Driessen |first8=Arnold J. M. |last9=Schleper |first9=Christa |last10=Albers |first10=Sonja-Verena |date=2008-10-09 |title=UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation: UV-inducible cellular aggregation |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2008.06459.x |journal=Molecular Microbiology |language=en |volume=70 |issue=4 |doi=10.1111/j.1365-2958.2008.06459.x |pmid=2818746 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014012806/https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2008.06459.x |dead-url=no }}</ref>和{{Link-en|嗜酸热硫化叶菌|Sulfolobus acidocaldarius}}<ref name="Ajon">{{Cite journal |last=Ajon |first=Małgorzata |last2=Fröls |first2=Sabrina |last3=van Wolferen |first3=Marleen |last4=Stoecker |first4=Kilian |last5=Teichmann |first5=Daniela |last6=Driessen |first6=Arnold J. M. |last7=Grogan |first7=Dennis W. |last8=Albers |first8=Sonja-Verena |last9=Schleper |first9=Christa |date=2011-11 |title=UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili: UV-inducible DNA exchange in hyperthermophilic archaea |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2011.07861.x |journal=Molecular Microbiology |language=en |volume=82 |issue=4 |doi=10.1111/j.1365-2958.2011.07861.x |pmid=21999488 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014012805/https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2011.07861.x |dead-url=no }}</ref>在DNA突变源，例如[[紫外线]]、[[博来霉素]]和[[丝裂霉素]]的暴露下，不同种类的古菌会出现不同的变化。硫化叶菌的[[基因突变|基因变化]]不会因为其他物理突变源，如[[酸碱值]]和[[温度]]，<ref name="Frols2008" />这说明了古菌的进化是来自于DNA的损伤，<ref name="Ajon" />这也说明了紫外线导致的细胞进化促使[[染色体]]在硫化叶菌之间交换。重组的几率级别比没有经过紫外线照射的古菌多出三级。<ref name="Frols2008" /><ref name="Ajon" /><ref>{{Cite journal |last=Fröls |first=Sabrina |last2=White |first2=Malcolm F. |last3=Schleper |first3=Christa |date=2009-02-01 |title=Reactions to UV damage in the model archaeon Sulfolobus solfataricus |url=https://portlandpress.com/biochemsoctrans/article/37/1/36/65598/Reactions-to-UV-damage-in-the-model-archaeon |journal=Biochemical Society Transactions |language=en |volume=37 |issue=1 |doi=10.1042/BST0370036 |issn=0300-5127 |pmid=19143598 |access-date=2022-10-14 |archive-date=2022-10-17 |archive-url=https://web.archive.org/web/20221017081407/https://portlandpress.com/biochemsoctrans/article/37/1/36/65598/Reactions-to-UV-damage-in-the-model-archaeon |dead-url=no }}</ref>这使科学家猜测可能[[硫化叶菌]]为了维修它们自己损坏的DNA而与有类似基因的硫化叶菌交换质粒。这反应可能是原始的性交流，这与被经常研究的[[细菌]]固定的DNA交换以维修受损DNA类似。<ref>{{Cite book|title=Evolutionary Origin and Adaptive Function of Meiosis|url=https://www.intechopen.com/state.item.id|publisher=IntechOpen|date=2013-09-11|isbn=978-953-51-1197-9|language=en|first=Harris|last=Bernstein|first2=Carol|last2=Bernstein}}{{Dead link}}</ref> ==繁殖== {{See also|无性繁殖}} 古菌利用[[二分裂]]、[[分裂生殖|分裂]]和[[出芽生殖|出芽]]进行无性繁殖；古菌不会进行[[减数分裂]]，所以拥有同样的[[基因]]的一个[[物种|种]]的古菌可能拥有不同的形态<ref name="Bergey">{{cite book|title=Bergey's Manual of Systematic Bacteriology|last=Krieg|first=Noel|year=2005|publisher=Springer|location=US|isbn=978-0-387-24143-2|pages=21–6}}</ref>。古菌的[[细胞分裂]]被它们的[[细胞周期]]所控制；在细胞的[[染色体]]复制并分离后，细胞开始一分为二<ref name="Bernander">{{Cite journal |last=Bernander |first=Rolf |date=1998-08 |title=Archaea and the cell cycle |url=http://doi.wiley.com/10.1046/j.1365-2958.1998.00956.x |journal=Molecular Microbiology |language=en |volume=29 |issue=4 |doi=10.1046/j.1365-2958.1998.00956.x |pmid=9767564}}</ref>。虽说目前古菌中只有[[硫化叶菌]]的复制周期被阐明，但是这样的细胞周期大体上类似于在[[细菌]]和[[真核生物]]的周期。和真核生物一样，古菌的染色体也可以在多个位点（[[复制起点]]）开始用[[DNA聚合酶]]复制<ref>{{Cite journal |last=Kelman |first=Lori M. |last2=Kelman |first2=Zvi |date=2004-09-01 |title=Multiple origins of replication in archaea |url=https://www.cell.com/trends/microbiology/abstract/S0966-842X(04)00143-X |journal=Trends in Microbiology |language=En |volume=12 |issue=9 |doi=10.1016/j.tim.2004.07.001 |issn=0966-842X |pmid=15337158 |access-date=2022-10-14 |archive-date=2013-10-16 |archive-url=https://web.archive.org/web/20131016215914/http://www.cell.com/trends/microbiology/abstract/S0966-842X(04)00143-X |dead-url=no }}</ref>。然而古菌用于控制细胞分裂的蛋白（例如[[FtsZ]]，制造逐渐缩小的“Z环”以帮助[[细胞质]]分裂）和分离两个子细胞的[[隔膜]]部分，这些与细菌的二分裂相似<ref name="Bernander" />。 但与细菌、真核生物不同，目前未发现有古菌进行[[孢子]]生殖<ref>{{Cite journal |last=Onyenwoke |first=RobU. |last2=Brill |first2=JuliaA. |last3=Farahi |first3=Kamyar |last4=Wiegel |first4=Juergen |date=2004-10 |title=Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch (Firmicutes) |url=http://link.springer.com/10.1007/s00203-004-0696-y |journal=Archives of Microbiology |language=en |volume=182 |issue=2-3 |doi=10.1007/s00203-004-0696-y |issn=0302-8933 |pmid=15340788}}</ref>。一些[[盐杆菌纲]]的种类可以进行{{link-en|表型转换|Phenotypic switching}}并生长成为不同的形态。这些形态包括拥有可以防止{{link-en|渗透压休克|Osmotic shock}}出现的厚[[细胞壁]]，这使嗜卤盐菌可以在盐度低的水中存活。这些古菌特征不是生殖结构，但是它们可以帮助古菌在新的环境下生存<ref>{{Cite journal |last=Kostrikina |first=N. A. |last2=Zvyagintseva |first2=I. S. |last3=Duda |first3=V. I. |date=1991-10 |title=Cytological peculiarities of some extremely halophilic soil archaeobacteria |url=http://link.springer.com/10.1007/BF00248708 |journal=Archives of Microbiology |language=en |volume=156 |issue=5 |doi=10.1007/BF00248708 |issn=0302-8933}}</ref>。 ==生态学== ===生活环境=== 古菌可以在各种各样的[[動物棲地|栖息地]]中出现并且是全球[[生态系统|生态]]重要的一部分<ref name="DeLong" />，古菌占有地球上20%的[[生物量]]。<ref>{{Cite journal |last=DeLong |first=Edward F. |last2=Pace |first2=Norman R. |date=2001-08-01 |title=Environmental Diversity of Bacteria and Archaea |url=http://www.catchword.com/cgi-bin/cgi?body=linker&ini=xref&reqdoi=10.1080/106351501750435040 |journal=Systematic Biology |volume=50 |issue=4 |doi=10.1080/106351501750435040 |pmid=12116647 }}{{Dead link}}</ref>很多古菌是生存在{{le|極端環境|extreme environment}}中的，包括最早发现的古菌也是[[嗜极生物]]。<ref name="valentine">{{cite journal |author=Valentine DL |year=2007 |title=Adaptations to energy stress dictate the ecology and evolution of the Archaea |journal=Nature Reviews Microbiology |volume=5 |issue=4 |pages=316–23 |doi=10.1038/nrmicro1619 |pmid=17334387}}</ref>一些生存在極高的溫度（經常100 °C以上）下，比如[[間歇泉]]、石油井或者海底[[深海熱泉]]中。還有的生存在很冷的環境或者高鹽、強酸或強鹼性的水中。然而也有些古菌是[[嗜中性]]的，能夠在[[沼澤]]、[[廢水]]、[[海洋]]和[[土壤]]中被發現。<ref name="DeLong" />很多產[[甲烷]]的古菌生存在動物的消化道中，如[[反芻動物]]、[[白蟻]]或者人類。古菌通常對其它生物無害，且未知有致病古菌。 [[File:Plankton satellite image.jpg|thumb|left|300px|海洋中[[浮游生物]]（淺綠色）的圖，古菌是海洋浮游生物中重要的一部份]] 極端環境下的古菌主要可以分為四種[[生理學|生理]]群：{{link-en|嗜鹽生物|halophile}}、[[嗜熱生物]]、{{link-en|嗜鹼生物|alkaliphile}}及[[嗜酸性 (生物)|嗜酸生物]]<ref name="Pikuta">{{Cite journal |last=Pikuta |first=Elena V. |last2=Hoover |first2=Richard B. |last3=Tang |first3=Jane |date=2007-01 |title=Microbial Extremophiles at the Limits of Life |url=http://www.tandfonline.com/doi/full/10.1080/10408410701451948 |journal=Critical Reviews in Microbiology |language=en |volume=33 |issue=3 |doi=10.1080/10408410701451948 |issn=1040-841X |pmid=17653987 |access-date=2022-10-14 |archive-date=2022-06-19 |archive-url=https://web.archive.org/web/20220619234916/https://www.tandfonline.com/doi/full/10.1080/10408410701451948 |dead-url=no }}</ref>。這些不是具體的分類，這些分類也不是互斥的，因此有些古菌有時屬於其中的幾類中，不過這仍然可以做為分類的起點。 嗜鹽類的古菌，生活在高含鹽量的環境中，例如[[鹹水湖|鹽湖]]，鹽度比嗜鹽細菌可以生活的20-25%要高<ref name="valentine" />。嗜熱古菌適合生長在超過{{convert|45|C|F}}的溫度，例如熱泉中，[[超嗜熱生物|超嗜熱古菌]]在溫度超過{{convert|80|C}}時生長的最好<ref>{{cite book|title=Brock Biology of Microorganisms|year=2006|author=Madigan MT, Martino JM|edition=11th|page=136|publisher=Pearson|isbn=0-13-196893-9}}</ref>。古菌Methanopyrus kandleri的116菌種甚至{{convert|122|C}}繁殖，是生物中最高的記錄<ref>{{Cite journal |last=Takai |first=Ken |last2=Nakamura |first2=Kentaro |last3=Toki |first3=Tomohiro |last4=Tsunogai |first4=Urumu |last5=Miyazaki |first5=Masayuki |last6=Miyazaki |first6=Junichi |last7=Hirayama |first7=Hisako |last8=Nakagawa |first8=Satoshi |last9=Nunoura |first9=Takuro |last10=Horikoshi |first10=Koki |date=2008-08-05 |title=Cell proliferation at 122°C and isotopically heavy CH 4 production by a hyperthermophilic methanogen under high-pressure cultivation |url=https://pnas.org/doi/full/10.1073/pnas.0712334105 |journal=Proceedings of the National Academy of Sciences |language=en |volume=105 |issue=31 |bibcode=2008PNAS..10510949T |doi=10.1073/pnas.0712334105 |issn=0027-8424 |pmc=2490668 |pmid=18664583 |access-date=2022-10-14 |archive-date=2022-10-21 |archive-url=https://web.archive.org/web/20221021164941/https://www.pnas.org/doi/full/10.1073/pnas.0712334105 |dead-url=no }}</ref>。 有些古菌可以生長在極酸性或極鹼性的環境中<ref name="Pikuta" />，例如嗜酸古菌中的Picrophilus torridus可以生長在pH值為0的環境下，相當於1.2 [[體積莫耳濃度|M]][[硫酸]]<ref>{{Cite journal |last=Ciaramella |first=Maria |last2=Napoli |first2=Alessandra |last3=Rossi |first3=Mosè |date=2005-02-01 |title=Another extreme genome: how to live at pH 0 |url=https://www.cell.com/trends/microbiology/abstract/S0966-842X(04)00267-7 |journal=Trends in Microbiology |language=En |volume=13 |issue=2 |doi=10.1016/j.tim.2004.12.001 |issn=0966-842X |pmid=15680761}}</ref>。 古菌可以抵抗極端環境的能力也讓科學家推測[[外星生命]]具有的可能的特質<ref>{{Cite journal |last=Javaux |first=Emmanuelle J. |date=2006-01-01 |title=Extreme life on Earth—past, present and possibly beyond |url=https://www.sciencedirect.com/science/article/pii/S0923250805002597 |journal=Research in Microbiology |series=Space Microbiology |language=en |volume=157 |issue=1 |doi=10.1016/j.resmic.2005.07.008 |issn=0923-2508 |pmid=16376523 |access-date=2022-10-14 |archive-date=2020-10-31 |archive-url=https://web.archive.org/web/20201031095320/https://www.sciencedirect.com/science/article/pii/S0923250805002597 |dead-url=no }}</ref>，有些極端的環境和[[火星]]的環境有些相近。<ref>{{Cite journal |last=Nealson |first=K. H. |date=1999-01 |title=Post-Viking microbiology: new approaches, new data, new insights |url=https://pubmed.ncbi.nlm.nih.gov/11536899 |journal=Origins of Life and Evolution of the Biosphere: The Journal of the International Society for the Study of the Origin of Life |volume=29 |issue=1 |doi=10.1023/a:1006515817767 |issn=0169-6149 |pmid=11536899 |access-date=2022-10-14 |archive-date=2022-10-05 |archive-url=https://web.archive.org/web/20221005063901/https://pubmed.ncbi.nlm.nih.gov/11536899/ |dead-url=no }}</ref>，因此推測這些古菌有可能在[[隕石]]上，在各[[行星]]之間移動<ref>{{Cite book|chapter=The Transfer of Viable Microorganisms Between Planets|title=Novartis Foundation Symposia|url=https://onlinelibrary.wiley.com/doi/10.1002/9780470514986.ch16|publisher=John Wiley & Sons, Ltd.|date=2007-09-28|location=Chichester, UK|isbn=978-0-470-51498-6|pages=304–317|doi=10.1002/9780470514986.ch16|first=P. C. W.|last=Davies|editor-first=Gregoy R.|editor-last=Bock|pmid=9243022|access-date=2022-10-14|archive-date=2022-10-16|archive-url=https://web.archive.org/web/20221016092010/https://onlinelibrary.wiley.com/doi/10.1002/9780470514986.ch16|dead-url=no}}</ref>。 近來許多研究發現古菌不只可在高溫及中溫的環境下生存，也可以在極低溫的環境下生存，例如在極地的海洋中就有許多的古菌<ref>{{Cite journal |last=López-García |first=P |date=2001-07 |title=Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front |url=http://doi.wiley.com/10.1016/S0168-6496(01)00133-7 |journal=FEMS Microbiology Ecology |volume=36 |issue=2-3 |doi=10.1016/S0168-6496(01)00133-7 |pmid=11451524}}</ref>，不過數量更多的是在海洋非極端環境中的古菌，是[[浮游生物]]中的微微型浮游生物<ref name="Karner">{{Cite journal |last=Karner |first=Markus B. |last2=DeLong |first2=Edward F. |last3=Karl |first3=David M. |date=2001-01 |title=Archaeal dominance in the mesopelagic zone of the Pacific Ocean |url=http://www.nature.com/articles/35054051 |journal=Nature |language=en |volume=409 |issue=6819 |doi=10.1038/35054051 |issn=0028-0836 |pmid=11206545 |access-date=2022-10-14 |archive-date=2022-12-09 |archive-url=https://web.archive.org/web/20221209041331/https://www.nature.com/articles/35054051 |dead-url=no }}</ref>。雖然這種古菌數量很多（佔純生物生物量的40%），但其中幾乎都無法在實驗室隔離的進行{{link-en|純培養|pure culture}}<ref>{{Cite journal |last=Giovannoni |first=Stephen J. |last2=Stingl |first2=Ulrich |date=2005-09 |title=Molecular diversity and ecology of microbial plankton |url=http://www.nature.com/articles/nature04158 |journal=Nature |language=en |volume=437 |issue=7057 |bibcode=2005Natur.437..343G |doi=10.1038/nature04158 |issn=0028-0836 |pmid=16163344 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123105713/https://www.nature.com/articles/nature04158 |dead-url=no }}</ref>。因此古菌在海洋生態中的角色是基礎的，古菌對整體[[生物地球化学]]循環的影響大部份都還不清楚。<ref>{{Cite journal |last=DeLong |first=Edward F. |last2=Karl |first2=David M. |date=2005-09-15 |title=Genomic perspectives in microbial oceanography |url=http://www.nature.com/articles/nature04157 |journal=Nature |language=en |volume=437 |issue=7057 |bibcode=2005Natur.437..336D |doi=10.1038/nature04157 |issn=0028-0836 |pmid=16163343 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123105708/https://www.nature.com/articles/nature04157 |dead-url=no }}</ref>有些海洋的奇古菌可以產生[[硝化作用]]，因此推測對海洋的[[氮循环]]應該有影響<ref>{{Cite journal |last=Könneke |first=Martin |last2=Bernhard |first2=Anne E. |last3=de la Torre |first3=José R. |last4=Walker |first4=Christopher B. |last5=Waterbury |first5=John B. |last6=Stahl |first6=David A. |date=2005-09 |title=Isolation of an autotrophic ammonia-oxidizing marine archaeon |url=http://www.nature.com/articles/nature03911 |journal=Nature |language=en |volume=437 |issue=7058 |bibcode=2005Natur.437..543K |doi=10.1038/nature03911 |issn=0028-0836 |pmid=16177789 |access-date=2022-10-14 |archive-date=2022-10-20 |archive-url=https://web.archive.org/web/20221020100528/https://www.nature.com/articles/nature03911 |dead-url=no }}</ref>，不過這些泉古菌也會使用其他的能量來源<ref>{{Cite journal |last=Agogué |first=Hélène |last2=Brink |first2=Maaike |last3=Dinasquet |first3=Julie |last4=Herndl |first4=Gerhard J. |date=2008-12-11 |title=Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic |url=http://www.nature.com/articles/nature07535 |journal=Nature |language=en |volume=456 |issue=7223 |bibcode=2008Natur.456..788A |doi=10.1038/nature07535 |issn=0028-0836 |pmid=19037244 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018205502/https://www.nature.com/articles/nature07535 |dead-url=no }}</ref>。在[[海床]]上的[[沉積物]]中可以找到大量的古菌，這也是在海底深度超過一米的區域中，在數量上佔大多數的生物體<ref>{{Cite journal |last=Lipp |first=Julius S. |last2=Morono |first2=Yuki |last3=Inagaki |first3=Fumio |last4=Hinrichs |first4=Kai-Uwe |date=2008-08 |title=Significant contribution of Archaea to extant biomass in marine subsurface sediments |url=http://www.nature.com/articles/nature07174 |journal=Nature |language=en |volume=454 |issue=7207 |bibcode=2008Natur.454..991L |doi=10.1038/nature07174 |issn=0028-0836 |pmid=18641632 |access-date=2022-10-14 |archive-date=2022-11-02 |archive-url=https://web.archive.org/web/20221102201215/https://www.nature.com/articles/nature07174 |dead-url=no }}</ref>。 ===在地球的化学循环中的作用=== {{See also|生物地質化學循環}} 古菌参与了地球上[[碳]]、[[氮]]、[[硫]]的循环。虽说这些细胞活动对[[生态系统]]来说是十分重要的，但是古菌也可能制造与人为变化类似的环境影响，甚至可能造成[[环境污染]]。 古菌也可以进行大部分[[氮循环]]中的化学反应。有一些古菌可以从一个[[生态系统]]中移除有机氮，这些[[化学反应]]包括一些硝酸盐代谢和[[反硝化反应]]；其它古菌可以把[[氮气]]加入生态形成有机氮，这些反应包括氮吸收和[[固氮作用]]。<ref>{{Cite journal |last=Cabello |first=Purificación |last2=Roldán |first2=M. Dolores |last3=Moreno-Vivián |first3=Conrado |date=2004-11-01 |title=Nitrate reduction and the nitrogen cycle in archaea |url=https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.27303-0 |journal=Microbiology |language=en |volume=150 |issue=11 |doi=10.1099/mic.0.27303-0 |issn=1350-0872 |pmid=15528644 |access-date=2022-10-14 |archive-date=2022-10-15 |archive-url=https://web.archive.org/web/20221015214035/https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.27303-0 |dead-url=no }}</ref><ref>{{cite journal |author=Mehta MP, Baross JA |date=December 2006 |title=Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon |url=https://archive.org/details/sim_science_2006-12-15_314_5806/page/1782 |journal=Science |volume=314 |issue=5806 |pages=1783–6 |bibcode=2006Sci...314.1783M |doi=10.1126/science.1134772 |pmid=17170307}}</ref>最近，科学家发现古菌也参与[[氨]]的氧化。这些反应在[[海洋]]里是特别重要的。<ref>{{cite journal |author=Francis CA, Beman JM, Kuypers MM |date=May 2007 |title=New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation |journal=ISME J |volume=1 |issue=1 |pages=19–27 |doi=10.1038/ismej.2007.8 |pmid=18043610}}</ref><ref>{{Cite journal |last=Coolen |first=Marco J. L. |last2=Abbas |first2=Ben |last3=van Bleijswijk |first3=Judith |last4=Hopmans |first4=Ellen C. |last5=Kuypers |first5=Marcel M. M. |last6=Wakeham |first6=Stuart G. |last7=Sinninghe Damsté |first7=Jaap S. |date=2007-04 |title=Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01227.x |journal=Environmental Microbiology |language=en |volume=9 |issue=4 |doi=10.1111/j.1462-2920.2006.01227.x |issn=1462-2912 |pmid=17359272}}</ref>一些古菌也参与[[土壤]]里面的氨氧化。这些古菌会制造[[硝酸盐]]，而其它[[微生物]]则进一步氧化硝酸盐。最后，植物和其它生物会吸收并利用氧化的硝酸盐。<ref>{{Cite journal |last=Leininger |first=S. |last2=Urich |first2=T. |last3=Schloter |first3=M. |last4=Schwark |first4=L. |last5=Qi |first5=J. |last6=Nicol |first6=G. W. |last7=Prosser |first7=J. I. |last8=Schuster |first8=S. C. |last9=Schleper |first9=C. |date=2006-08 |title=Archaea predominate among ammonia-oxidizing prokaryotes in soils |url=http://www.nature.com/articles/nature04983 |journal=Nature |language=en |volume=442 |issue=7104 |bibcode=2006Natur.442..806L |doi=10.1038/nature04983 |issn=0028-0836 |pmid=16915287 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018205921/https://www.nature.com/articles/nature04983 |dead-url=no }}</ref> 在[[硫循环]]中，利用[[硫化物]]氧化代谢的古菌可以把[[硫]]从岩石中释放出来，并提供给其它生物。但是这些古菌，例如[[硫化叶菌]]，会利用硫代谢并最终产出[[硫酸]]，所以这种古菌在废弃的[[矿场]]中的生长会导致{{le|矿渣酸性废水|acid mine drainage}}的出现以及其它环境污染。<ref name="Baker2003">{{Cite journal |last=Baker |first=Brett J. |last2=Banfield |first2=Jillian F. |date=2003-05-01 |title=Microbial communities in acid mine drainage |url=https://pubmed.ncbi.nlm.nih.gov/19719632 |journal=FEMS microbiology ecology |volume=44 |issue=2 |doi=10.1016/S0168-6496(03)00028-X |issn=1574-6941 |pmid=19719632 |access-date=2022-10-14 |archive-date=2022-10-16 |archive-url=https://web.archive.org/web/20221016095725/https://pubmed.ncbi.nlm.nih.gov/19719632/ |dead-url=no }}</ref> 在[[碳循环]]中，制造甲烷的古菌可以移除多余的[[氢]]并且在[[有机化合物]]的缺氧分解中扮演着[[分解者]]的角色。这些古菌可以在[[沉积物]]和[[沼泽]]等缺氧环境中生活，它们也可以被用于[[污水处理]]<ref>{{Cite journal |last=Schimel |first=Joshua |date=2004-08-24 |title=Playing scales in the methane cycle: From microbial ecology to the globe |url=https://pnas.org/doi/full/10.1073/pnas.0405075101 |journal=Proceedings of the National Academy of Sciences |language=en |volume=101 |issue=34 |bibcode=2004PNAS..10112400S |doi=10.1073/pnas.0405075101 |issn=0027-8424 |pmc=515073 |pmid=15314221 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018195301/https://www.pnas.org/doi/full/10.1073/pnas.0405075101 |dead-url=no }}</ref> 产甲烷菌是[[大气甲烷]]的主要来源，它们每年释放的甲烷占了世界上大部分的甲烷排放。<ref name="Trace Gases">{{cite web |title=Trace Gases: Current Observations, Trends, and Budgets |url=http://www.grida.no/climate/ipcc_tar/wg1/134.htm#4211 |work=Climate Change 2001 |publisher=United Nations Environment Programme |accessdate=2014-09-08 |deadurl=yes |archiveurl=https://web.archive.org/web/20111210035926/http://www.grida.no/climate/ipcc_tar/wg1/134.htm#4211 |archivedate=2011-12-10}}</ref>产甲烷菌排放的甲烷加速了全球的[[温室气体]]排放和[[全球变暖]]。 全球甲烷数值于前工业化时期的722PPB（10亿吨大气内有722吨甲烷）增加到2011年的1800PPB，这期间甲烷数值上升到了之前的2.5倍，2011年是在80万年内全球甲烷数值最高的一年。<ref>{{Cite web |author=IPCC AR5 WG1 |year=2013 |title=Climate Change 2013: The Physical Science Basis - Summary for Policymakers |url=http://www.climatechange2013.org/images/report/WG1AR5_SPM_FINAL.pdf |publisher=Cambridge University Press |archive-url=https://web.archive.org/web/20140226155600/http://www.climatechange2013.org/images/report/WG1AR5_SPM_FINAL.pdf |archive-date=2014-02-26 |accessdate=2014-09-08 |authorlink=政府間氣候變化專門委員會 |dead-url=no}}</ref>甲烷的[[全球变暖潜能值]]是29，这说明了甲烷可以在100年内吸收比[[二氧化碳]]多29倍的热量。<ref>{{Cite web |author=IPCC AR5 WG1 |year=2013 |title=Climate Change 2013: The Physical Science Basis - Anthropogenic and Natural Radiative Forcing Supplementary Material |url=http://www.climatechange2013.org/images/report/WG1AR5_Ch08SM_FINAL.pdf |publisher=Cambridge University Press |archive-url=https://web.archive.org/web/20160304040017/http://www.climatechange2013.org/images/report/WG1AR5_Ch08SM_FINAL.pdf |archive-date=2016-03-04 |accessdate=2014-09-08 |authorlink=政府間氣候變化專門委員會 |dead-url=no}}</ref> ===与其它生物的关系=== {{See also|种间关系}} [[File:Coptotermes formosanus shiraki USGov k8204-7.jpg|thumb|right|制造[[甲烷]]的古菌与[[白蚁]]拥有[[互利共生]]关系]] 古菌与其它生物之间的关系主要都是[[互利共生]]或者[[偏利共生]]。至今还没有发现古菌是任何其它生物的[[病原体]]或[[寄生虫]]。<ref>{{Cite journal |last=Eckburg |first=Paul B. |last2=Lepp |first2=Paul W. |last3=Relman |first3=David A. |date=2003-02 |title=Archaea and Their Potential Role in Human Disease |url=https://journals.asm.org/doi/10.1128/IAI.71.2.591-596.2003 |journal=Infection and Immunity |language=en |volume=71 |issue=2 |doi=10.1128/IAI.71.2.591-596.2003 |issn=0019-9567 |pmc=145348 |pmid=12540534 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123112417/https://journals.asm.org/doi/10.1128/iai.71.2.591-596.2003 |dead-url=no }}</ref><ref>{{cite journal |author=Cavicchioli R, Curmi P, Saunders N, Thomas T |year=2003 |title=Pathogenic archaea: do they exist? |journal=BioEssays |volume=25 |issue=11 |pages=1119–28 |doi=10.1002/bies.10354 |pmid=14579252}}</ref>虽说至今没有发现并确定古菌病原体，但是研究证明一些产甲烷菌的种类可能与[[牙周疾病]]有关。<ref>{{Cite journal |last=Lepp |first=Paul W. |last2=Brinig |first2=Mary M. |last3=Ouverney |first3=Cleber C. |last4=Palm |first4=Katherine |last5=Armitage |first5=Gary C. |last6=Relman |first6=David A. |date=2004-04-20 |title=Methanogenic Archaea and human periodontal disease |url=https://pnas.org/doi/full/10.1073/pnas.0308766101 |journal=Proceedings of the National Academy of Sciences |language=en |volume=101 |issue=16 |bibcode=2004PNAS..101.6176L |doi=10.1073/pnas.0308766101 |issn=0027-8424 |pmc=395942 |pmid=15067114 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014021220/https://www.pnas.org/doi/full/10.1073/pnas.0308766101 |dead-url=no }}</ref><ref>{{Cite journal |last=Vianna |first=M. E. |last2=Conrads |first2=G. |last3=Gomes |first3=B. P. F. A. |last4=Horz |first4=H. P. |date=2006-04 |title=Identification and Quantification of Archaea Involved in Primary Endodontic Infections |url=https://journals.asm.org/doi/10.1128/JCM.44.4.1274-1282.2006 |journal=Journal of Clinical Microbiology |language=en |volume=44 |issue=4 |doi=10.1128/JCM.44.4.1274-1282.2006 |issn=0095-1137 |pmc=1448633 |pmid=16597851 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123110705/https://journals.asm.org/doi/10.1128/jcm.44.4.1274-1282.2006 |dead-url=no }}</ref>另外，一种{{Link-en|骑行纳古菌|Nanoarchaeum equitans}}''Nanoarchaeum equitans''可能是[[泉古菌门|泉古菌]]{{link-en|適宜火球古菌|Ignicoccus hospitalis}}的寄生物，必须在宿主细胞内生活并繁殖，<ref>{{Cite journal |last=Waters |first=Elizabeth |last2=Hohn |first2=Michael J. |last3=Ahel |first3=Ivan |last4=Graham |first4=David E. |last5=Adams |first5=Mark D. |last6=Barnstead |first6=Mary |last7=Beeson |first7=Karen Y. |last8=Bibbs |first8=Lisa |last9=Bolanos |first9=Randall |last10=Keller |first10=Martin |last11=Kretz |first11=Keith |date=2003-10-28 |title=The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism |url=https://pnas.org/doi/full/10.1073/pnas.1735403100 |journal=Proceedings of the National Academy of Sciences |language=en |volume=100 |issue=22 |doi=10.1073/pnas.1735403100 |issn=0027-8424 |pmc=240731 |pmid=14566062 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018220110/https://www.pnas.org/doi/full/10.1073/pnas.1735403100 |dead-url=no }}</ref>但是对[[寄主]]没有任何好处。<ref>{{Cite journal |last=Jahn |first=Ulrike |last2=Gallenberger |first2=Martin |last3=Paper |first3=Walter |last4=Junglas |first4=Benjamin |last5=Eisenreich |first5=Wolfgang |last6=Stetter |first6=Karl O. |last7=Rachel |first7=Reinhard |last8=Huber |first8=Harald |date=2008-03 |title=Nanoarchaeum equitans and Ignicoccus hospitalis : New Insights into a Unique, Intimate Association of Two Archaea |url=https://journals.asm.org/doi/10.1128/JB.01731-07 |journal=Journal of Bacteriology |language=en |volume=190 |issue=5 |doi=10.1128/JB.01731-07 |issn=0021-9193 |pmc=2258681 |pmid=18165302 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123113528/https://journals.asm.org/doi/10.1128/jb.01731-07 |dead-url=no }}</ref>相反的，{{link-en|里奇蒙德矿井嗜酸纳米古生物|Archaeal Richmond Mine Acidophilic Nanoorganisms}}（ARMAN）只是与酸性矿井内[[生物薄膜]]的其它古菌偶尔接触。<ref>{{Cite journal |last=Baker |first=Brett J. |last2=Comolli |first2=Luis R. |last3=Dick |first3=Gregory J. |last4=Hauser |first4=Loren J. |last5=Hyatt |first5=Doug |last6=Dill |first6=Brian D. |last7=Land |first7=Miriam L. |last8=VerBerkmoes |first8=Nathan C. |last9=Hettich |first9=Robert L. |last10=Banfield |first10=Jillian F. |date=2010-05-11 |title=Enigmatic, ultrasmall, uncultivated Archaea |url=https://pnas.org/doi/full/10.1073/pnas.0914470107 |journal=Proceedings of the National Academy of Sciences |language=en |volume=107 |issue=19 |bibcode=2010PNAS..107.8806B |doi=10.1073/pnas.0914470107 |issn=0027-8424 |pmc=2889320 |pmid=20421484 |access-date=2022-10-14 |archive-date=2022-10-21 |archive-url=https://web.archive.org/web/20221021170422/https://www.pnas.org/doi/full/10.1073/pnas.0914470107 |dead-url=no }}</ref>这种关系的性质至今仍然是未知的。但是科学家知道{{link-en|纳古菌门|Nanarchaeaum}}和{{link-en|燃球菌属|Ignicoccus}}之间的关系与微小的ARMAN古菌不同，ARMAN古菌一般与{{link-en|嗜酸热菌|Thermoplasmatales}}细胞不会相互影响。 ====互利共生==== 所有[[反刍动物]]和[[白蚁]]的[[消化道]]中有其中一种在[[产甲烷菌]]和[[原生动物]]之间的[[互利共生]]，它们帮助[[寄主]]消化[[纤维素]]。<ref name="Chaban">{{Cite journal |last=Chaban |first=Bonnie |last2=Ng |first2=Sandy Y.M |last3=Jarrell |first3=Ken F |date=2006-02-01 |title=Archaeal habitats — from the extreme to the ordinary |url=http://www.nrcresearchpress.com/doi/10.1139/w05-147 |journal=Canadian Journal of Microbiology |language=en |volume=52 |issue=2 |doi=10.1139/w05-147 |issn=0008-4166 |pmid=16541146 |access-date=2022-10-14 |archive-date=2019-05-18 |archive-url=https://web.archive.org/web/20190518054654/https://www.nrcresearchpress.com/doi/10.1139/w05-147 |dead-url=no }}</ref>在这缺氧的环境中，原生动物利用纤维素获得能量并同时释放产物[[氢气]]。大量的氢气会影响原生动物获得能量的效率。当产甲烷菌把氢气经过[[化学反应]]变成甲烷后，原生动物会因为能获得更多能量而获益。<ref>{{Cite journal |last=Schink |first=B |date=1997-06 |title=Energetics of syntrophic cooperation in methanogenic degradation |url=https://journals.asm.org/doi/10.1128/mmbr.61.2.262-280.1997 |journal=Microbiology and Molecular Biology Reviews |language=en |volume=61 |issue=2 |doi=10.1128/mmbr.61.2.262-280.1997 |issn=1092-2172 |pmc=232610 |pmid=9184013 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014120813/https://journals.asm.org/doi/10.1128/mmbr.61.2.262-280.1997 |dead-url=no }}</ref> 一些古菌生活在[[厭氧生物|厌氧]]原生动物里面并利用寄主{{link-en|造氢体|hydrogenosome}}制造的氢气，这些原生动物包括[[纤毛虫]]{{link-en|Plagiopyla frontata|Plagiopyla frontata}}。<ref name="Lange2005">{{Cite journal |last=Lange |first=Marianne |last2=Westermann |first2=Peter |last3=Ahring |first3=Birgitte Kiær |date=2005-02 |title=Archaea in protozoa and metazoa |url=http://link.springer.com/10.1007/s00253-004-1790-4 |journal=Applied Microbiology and Biotechnology |language=en |volume=66 |issue=5 |doi=10.1007/s00253-004-1790-4 |issn=0175-7598 |pmid=15630514}}</ref><ref>{{Cite journal |last=van Hoek |first=Angela H. A. M. |last2=van Alen |first2=Theo A. |last3=Sprakel |first3=Vera S. I. |last4=Leunissen |first4=Jack A. M. |last5=Brigge |first5=Theo |last6=Vogels |first6=Godfried D. |last7=Hackstein |first7=Johannes H. P. |date=2000-02-01 |title=Multiple Acquisition of Methanogenic Archaeal Symbionts by Anaerobic Ciliates |url=http://academic.oup.com/mbe/article/17/2/251/1001839 |journal=Molecular Biology and Evolution |language=en |volume=17 |issue=2 |doi=10.1093/oxfordjournals.molbev.a026304 |issn=0737-4038 |pmid=10677847 |access-date=2022-10-14 |archive-date=2023-01-23 |archive-url=https://web.archive.org/web/20230123105713/https://academic.oup.com/mbe/article/17/2/251/1001839 |dead-url=no }}</ref>古菌也与更大的生物有共生关系。例如海里的古菌{{link-en|Cenarchaeum symbiosum|Cenarchaeum symbiosum}}生活在[[海绵]]{{link-en|Axinella mexicana|Axinella mexicana}}的里并与海绵拥有共生关系。<ref name="Preston1996">{{Cite journal |last=Preston |first=C M |last2=Wu |first2=K Y |last3=Molinski |first3=T F |last4=DeLong |first4=E F |date=1996-06-25 |title=A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. |url=https://pnas.org/doi/full/10.1073/pnas.93.13.6241 |journal=Proceedings of the National Academy of Sciences |language=en |volume=93 |issue=13 |bibcode=1996PNAS...93.6241P|doi=10.1073/pnas.93.13.6241 |issn=0027-8424 |pmc=39006 |pmid=8692799}}</ref> ====偏利共生==== 古菌也可以是[[偏利共生]]中的获益者，同时寄主既没有获益也没有受害。例如{{le|史密斯甲烷菌|Methanobrevibacter smithii}}就是在的[[正常菌群|人体正常肠道菌群]]中最常见的古菌，这种古菌占了[[腸臟|肠道]]中[[原核生物]]的十分之一<ref>{{Cite journal |last=Eckburg |first=Paul B. |last2=Bik |first2=Elisabeth M. |last3=Bernstein |first3=Charles N. |last4=Purdom |first4=Elizabeth |last5=Dethlefsen |first5=Les |last6=Sargent |first6=Michael |last7=Gill |first7=Steven R. |last8=Nelson |first8=Karen E. |last9=Relman |first9=David A. |date=2005-06-10 |title=Diversity of the Human Intestinal Microbial Flora |url=https://www.science.org/doi/10.1126/science.1110591 |journal=Science |language=en |volume=308 |issue=5728 |bibcode=2005Sci...308.1635E |doi=10.1126/science.1110591 |issn=0036-8075 |pmc=1395357 |pmid=15831718 |access-date=2022-10-14 |archive-date=2023-03-11 |archive-url=https://web.archive.org/web/20230311230702/https://www.science.org/doi/10.1126/science.1110591 |dead-url=no }}</ref>。在[[白蚁]]和[[人体]]内，这些产甲烷菌甚至可能是有益的，这些古菌会与其它菌群互相影响并协助消化<ref>{{Cite journal |last=Samuel |first=Buck S. |last2=Gordon |first2=Jeffrey I. |date=2006-06-27 |title=A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism |url=https://pnas.org/doi/full/10.1073/pnas.0602187103 |journal=Proceedings of the National Academy of Sciences |language=en |volume=103 |issue=26 |bibcode=2006PNAS..10310011S |doi=10.1073/pnas.0602187103 |issn=0027-8424 |pmc=1479766 |pmid=16782812 |access-date=2022-10-14 |archive-date=2022-10-20 |archive-url=https://web.archive.org/web/20221020181527/https://www.pnas.org/doi/full/10.1073/pnas.0602187103 |dead-url=no }}</ref>。古菌的菌落也与不少其它[[生物]]表面或附近生活，例如在[[珊瑚]]的表面<ref>{{Cite journal |last=Wegley |first=L |last2=Yu |first2=Y |last3=Breitbart |first3=M |last4=Casas |first4=V |last5=Kline |first5=Di |last6=Rohwer |first6=F |date=2004 |title=Coral-associated Archaea |url=http://www.int-res.com/abstracts/meps/v273/p89-96/ |journal=Marine Ecology Progress Series |language=en |volume=273 |doi=10.3354/meps273089 |issn=0171-8630 |access-date=2022-10-14 |archive-date=2022-10-18 |archive-url=https://web.archive.org/web/20221018210721/https://www.int-res.com/abstracts/meps/v273/p89-96/ |dead-url=no }}</ref>和环绕植物[[根冠]]的[[根际]]。<ref>{{Cite journal |last=Chelius |first=M.K. |last2=Triplett |first2=E.W. |date=2001-04 |title=The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L. |url=http://link.springer.com/10.1007/s002480000087 |journal=Microbial Ecology |language=en |volume=41 |issue=3 |doi=10.1007/s002480000087 |issn=0095-3628 |pmid=11391463}}</ref><ref>{{Cite journal |last=Simon |first=Holly M. |last2=Dodsworth |first2=Jeremy A. |last3=Goodman |first3=Robert M. |date=2000-10 |title=Crenarchaeota colonize terrestrial plant roots |url=http://doi.wiley.com/10.1046/j.1462-2920.2000.00131.x |journal=Environmental Microbiology |language=en |volume=2 |issue=5 |doi=10.1046/j.1462-2920.2000.00131.x |pmid=11233158}}</ref> ==在技术与工业中的作用== {{further|生物技术}} 一些耐热或耐酸碱的[[嗜极生物|嗜极古菌]]可以作为一些在极端环境下活跃的[[酶]]的来源。<ref>{{Cite journal |last=Breithaupt |first=Holger |date=2001-11 |title=The hunt for living gold: The search for organisms in extreme environments yields useful enzymes for industry |url=https://onlinelibrary.wiley.com/doi/10.1093/embo-reports/kve238 |journal=EMBO reports |language=en |volume=2 |issue=11 |doi=10.1093/embo-reports/kve238 |issn=1469-221X |pmc=1084137 |pmid=11713183}}</ref><ref name="Egorova">{{Cite journal |last=Egorova |first=Ksenia |last2=Antranikian |first2=Garabed |date=2005-12-01 |title=Industrial relevance of thermophilic Archaea |url=https://www.sciencedirect.com/science/article/pii/S1369527405001712 |journal=Current Opinion in Microbiology |series=Growth development / edited by John N Reeve and Ruth A Schmitz |language=en |volume=8 |issue=6 |doi=10.1016/j.mib.2005.10.015 |issn=1369-5274 |pmid=16257257 |access-date=2022-10-14 |archive-date=2011-12-16 |archive-url=https://web.archive.org/web/20111216173935/http://www.sciencedirect.com/science/article/pii/S1369527405001712 |dead-url=no }}</ref>这些来自古菌的酶拥有很多用途。其中耐高温的[[DNA聚合酶]]，例如从{{link-en|焦酚火球菌|Pyrococcus furiosus}}中提取的{{link-en|火球菌DNA聚合酶|Pfu DNA polymerase}}可以在需要进行[[聚合酶链式反应]]时简单并快速地复制DNA，这彻底改变了对[[分子生物学]]地研究。在工业中，来自其它{{link-en|焦酚菌|Pyrococcus}}的[[淀粉酶]]、{{link-en|半乳糖苷酶|galactosidases}}和{{link-en|普鲁兰酶|pullulanase}}可以在高达{{convert|100|°C|°F}}的环境下仍然活跃，这使[[食品加工]]可以在高温下进行，这些酶可以被用来加工低[[乳糖]]牛奶和[[乳清]]。<ref>{{Cite journal |last=Synowiecki |first=Józef |last2=Grzybowska |first2=Beata |last3=Zdziebło |first3=Anna |date=2006-04 |title=Sources, Properties and Suitability of New Thermostable Enzymes in Food Processing |url=http://www.tandfonline.com/doi/abs/10.1080/10408690590957296 |journal=Critical Reviews in Food Science and Nutrition |language=en |volume=46 |issue=3 |doi=10.1080/10408690590957296 |issn=1040-8398 |pmid=16527752 |access-date=2022-10-14 |archive-date=2022-08-08 |archive-url=https://web.archive.org/web/20220808071027/https://www.tandfonline.com/doi/abs/10.1080/10408690590957296 |dead-url=no }}</ref>嗜热古菌生产的酶可以在[[有机溶剂]]内仍然保持稳定，这些酶可以在保持环保的前提下用来合成有机化合物。<ref name="Egorova" />这种稳定性使它们更容易在[[结构生物学]]中研究。这就是为什么与细菌和真核生物对应的嗜极古菌生产的酶经常被用于分子结构的研究。<ref>{{Cite journal |last=Jenney Jr |first=Francis E. |last2=Adams |first2=Michael W. W. |date=2008-01 |title=The impact of extremophiles on structural genomics (and vice versa) |url=http://link.springer.com/10.1007/s00792-007-0087-9 |journal=Extremophiles |language=en |volume=12 |issue=1 |doi=10.1007/s00792-007-0087-9 |issn=1431-0651 |pmid=17563834}}</ref> 相較於酵素領域的應用，古菌本身在生物科技上的應用就比較少了。產甲烷的古菌是進行[[厭氧消化]]，產生[[生物氣體]]的[[微生物]]群體的一部份，是[[污水處理]]中重要的一環<ref>{{Cite journal |last=Schiraldi |first=Chiara |last2=Giuliano |first2=Mariateresa |last3=De Rosa |first3=Mario |date=2002 |title=Perspectives on biotechnological applications of archaea |url=http://www.hindawi.com/journals/archaea/2002/436561/abs/ |journal=Archaea |language=en |volume=1 |issue=2 |doi=10.1155/2002/436561 |issn=1472-3646 |pmc=2685559 |pmid=15803645 |access-date=2022-10-14 |archive-date=2019-05-18 |archive-url=https://web.archive.org/web/20190518104439/https://www.hindawi.com/journals/archaea/2002/436561/abs/ |dead-url=no }}</ref>。在[[礦石處理]]中，嗜酸古菌可以用來從[[礦物]]中萃取包括[[金]]、[[鈷]]及[[銅]]等金屬<ref>{{Cite journal |last=Norris |first=P. R. |last2=Burton |first2=N. P. |last3=Foulis |first3=N. A. |date=2000-04 |title=Acidophiles in bioreactor mineral processing |url=https://pubmed.ncbi.nlm.nih.gov/10805560 |journal=Extremophiles: Life Under Extreme Conditions |volume=4 |issue=2 |doi=10.1007/s007920050139 |issn=1431-0651 |pmid=10805560 |access-date=2022-10-14 |archive-date=2022-10-14 |archive-url=https://web.archive.org/web/20221014121344/https://pubmed.ncbi.nlm.nih.gov/10805560/ |dead-url=no }}</ref>。 古菌也是一些潛在有效[[抗細菌藥]]的來源，已經分析了其中幾種的[[古菌素]]，一般認為有幾百種，特別是由[[盐杆菌纲|嗜鹽细菌]]及[[硫化叶菌属|硫化葉菌]]所產生的。這些古菌素的結構和從細菌產生的抗細菌藥不同，所以可能有新的作用方式。此外它們可以創建新的{{link-en|选择标记|selectable marker}}，可以用在古菌分子生物學中<ref>{{cite book|author=Shand RF; Leyva KJ|chapter=Archaeal Antimicrobials: An Undiscovered Country|editor=Blum P (ed.)|title=Archaea: New Models for Prokaryotic Biology|publisher=Caister Academic Press|year=2008|isbn=978-1-904455-27-1}}</ref>。 ==新分類== “Miscellaneous Crenarchaeota Group” (MCG)古菌是迄今为止发现分布最为广泛的一类未培养古菌，不仅分布广泛，而且数量庞大，被认为是[[海]]底深部[[生物圈]]中最丰富，并且最活跃的类群之一，很可能在全球[[物质]]和[[能量]]循环过程中发挥了重要的作用。然而到目前为止，尚未获得此类古菌的纯培养，其生理和功能特征以及在环境中发挥的作用都不得而知，并且其分类地位也不明确，暂时归类于[[泉古菌门]]。研究者们发现[[MCG古菌]]在深部生物圈沉积物中广泛并大量存在，代表了一类自然界较古老的古菌，在系统发育上处于一个深的分支，显著不同于目前分类已确定的所有古菌[[門 (生物)|门]]类，包括新近确立的[[奇古菌门]]和[[曙古菌门]]。因此，提议将MCG古菌归类于一个全新的门类，命名为深古菌門（Bathyarchaeota）。是古菌和[[生命起源]]和[[演化]]研究的重要进展之一，也将为本领域的[[科学]]研究起到积极推动作用。 本域包括以下门：<ref>{{cite web |title=Domain Archaea |url=https://lpsn.dsmz.de/domain/archaea |website=LPSN |accessdate=2024-05-17 |archive-date=2020-04-20 |archive-url=https://web.archive.org/web/20200420171557/https://lpsn.dsmz.de/domain/archaea |dead-url=no }}</ref> {{common taxon list|italic=no ||Methanobacteriota |Garrity and Holt 2023 ||Microcaldota |Sakai et al. 2023 ||Nanobdellota |Huber et al. 2023 * Nanobdellia Kato et al. 2022 ** Nanobdellales Kato et al. 2022 *** Nanobdellaceae Kato et al. 2022 **** ''Nanobdella'' Kato et al. 2022 ***** ''Nanobdella aerobiophila'' Kato et al. 2022<ref>Kato S, Ogasawara A, Itoh T, Sakai HD, Shimizu M, Yuki M, Kaneko M, Takashina T, Ohkuma M. Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. Int J Syst Evol Microbiol 2022; 72:5489.</ref> ||Thermoproteota |Garrity and Holt 2021 }} == 參見 == {{Portal box|生物学|分子与细胞生物学}} * [[古菌分類表]] * [[已测序古菌基因组列表]] == 参考文献 == {{Reflist|30em}} {{-}} {{古菌域}} {{Taxonbar|from=Q10872}} [[Category:古菌| ]] [[Category:嗜极生物]] [[Category:域 (生物學)]]
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