域 (生物)

在生物分类学中，域（英语：domain、empire、拉丁语：regio）或总界（superkingdom）是美国生物学家卡尔·沃斯1990年设计的三域系统中最高的分类单元，该系统中，生命之树（英语：Tree of life (biology)）包含细菌、古菌与真核生物等三个域，其中前两者为原核生物，不具有细胞核；后者则具有细胞核和内膜系统包裹的细胞器^[参1]。

Thumb — 基于16S 核糖体RNA序列的系统发生树，显示了可明显区别的三支：细菌、古菌和真核生物

古菌

古菌属于单细胞原核生物，外形类似细菌，但部分分子序列与代谢途径与真核生物较相近，其细胞膜为醚酯（英语：Ether lipid）所组成，不同于另两域生物细胞膜主要成分为酯类^[参2]。早期发现的古菌多为嗜极生物，后来渐发现古菌普遍存在各种环境中^[参3]。

细菌

细菌也属于单细胞原核生物，其细胞膜为酯类组成，广泛分布于不同环境中，外形、营养方式与生长环境都有很高的多样性。细菌的大小一般为0.5-5微米，少数特例如纳米比亚嗜硫珠菌^[参4]与费氏刺骨鱼菌（英语：Epulopiscium fishelsoni）可大至0.5毫米而能以肉眼观察^[参5]，而小型者如霉浆菌仅有约0.3微米，与大型的病毒大小相仿^[参6]，甚至还有更小的超微细菌（英语：Ultramicrobacteria）^[参7]。

真核生物

真核生物具有细胞核以及多种膜结构组成的内膜系统，包括动物、植物、真菌等^[参8]。2005年，国际原生生物学家协会（英语：International Society of Protistologists）将真核生物分为六个超类群（supergroups），包括后鞭毛生物、古虫界、变形虫界、囊泡藻界、有孔虫界与原始色素体生物^[参9]^[参10]，但随即有学者质疑囊泡藻界并非单系群，并有后续研究将其拆分^[参11]^[参12]。近年来持续有许多真核生物的分类理论被提出^[参13]^[参14]。

2002年，英国生物学家汤玛斯·卡弗利尔-史密斯提出了新壁总域的概念，即古菌与真核生物共同组成一演化支，为细菌中放线菌门的姊妹群^[参15]。后续分子系统发生学的研究亦支持古菌与真核生物的亲缘关系较与细菌的亲缘关系近^[参16]。

除了三域系统外，其他较常用的分类系统还包括：

两域系统（英语：Two-empire system）：将生物分成原核生物与真核生物两群，其中原核生物域有真细菌界和古细菌界，真核生物域有原生生物界、菌物界、植物界和动物界^[参17]^[参18]。
泉古菌假说（英语：Eocyte hypothesis）：将生物分成两域，古菌与真核生物共组成一域，由美国生物学家詹姆斯·A·雷克（英语：James A. Lake）于1984年提出^[参19]^[参20]。
三域系统中并未包含病毒。2011年，有学者认为核质巨DNA病毒可能是生物分类的第四个域，此观点进一步在2012年获得支持^[参21]。同年，塞尔维亚生物学家史蒂芬·卢基塔（Stefan Luketa）提出了五域的分类系统，在三域之外加入病毒（无细胞但有核酸的生命体）与朊蛋白（无细胞与核酸的生命体）两域^[参22]。
在中国大百科全书引用过中国生物学界的另一种三域系统，把病毒等列生物和成立专属的总界，称为无细胞结构总界，与多细胞生物(包括动物、植物、真菌)和单细胞生物（包括原生生物和原核生物），各成为一个总界共有三个总界（域）和六个界别。^[参23]

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参:

[参1]
Woese C, Kandler O, Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.. Proc Natl Acad Sci USA. 1990, 87 (12): 4576–9 [11 February 2010]. Bibcode:1990PNAS...87.4576W. PMC 54159 . PMID 2112744. doi:10.1073/pnas.87.12.4576. （原始内容存档于2008-06-27）.
[参2]
De Rosa M, Gambacorta A, Gliozzi A. Structure, biosynthesis, and physicochemical properties of archaebacterial lipids. Microbiological Reviews. March 1986, 50 (1): 70–80 [2019-07-13]. PMC 373054 . PMID 3083222. （原始内容存档于2019-10-16）.
[参3]
DeLong EF. Everything in moderation: archaea as 'non-extremophiles'. Current Opinion in Genetics & Development. December 1998, 8 (6): 649–54. PMID 9914204. doi:10.1016/S0959-437X(98)80032-4.
[参4]
Schulz HN, Jorgensen BB. Big bacteria. Annual Review of Microbiology. 2001, 55: 105–37. PMID 11544351. doi:10.1146/annurev.micro.55.1.105.
[参5]
Williams C. Who are you calling simple?. New Scientist. 2011, 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0.
[参6]
Robertson J, Gomersall M, Gill P. Mycoplasma hominis: growth, reproduction, and isolation of small viable cells. Journal of Bacteriology. November 1975, 124 (2): 1007–18. PMC 235991 . PMID 1102522.
[参7]
Velimirov B. Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium. Microbes and Environments. 2001, 16 (2): 67–77. doi:10.1264/jsme2.2001.67.
[参8]
Woese C, Kandler O, Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.. Proc Natl Acad Sci USA. 1990, 87 (12): 4576–9 [11 February 2010]. Bibcode:1990PNAS...87.4576W. PMC 54159 . PMID 2112744. doi:10.1073/pnas.87.12.4576. （原始内容存档于2008-06-27）.
[参9]
Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher-level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology. 2005, 52 (5): 399–451. PMID 16248873. doi:10.1111/j.1550-7408.2005.00053.x.
[参10]
Holt, Jack R. and Carlos A. Iudica, (2010) "Taxa of Life." Retrieved 09-03-2011.
[参11]
Harper, J. T.; Waanders, E. & Keeling, P. J. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes (PDF). Nt. J. System. Evol. Microbiol. 2005, 55 (Pt 1): 487–496 [2019-07-13]. PMID 15653923. doi:10.1099/ijs.0.63216-0. （原始内容 (PDF)存档于2011-05-11）.
[参12]
Parfrey, Laura W.; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J. & Katz, Laura A. Evaluating support for the current classification of eukaryotic diversity. PLoS Genetics. 2006, 2 (12): e220. PMC 1713255 . PMID 17194223. doi:10.1371/journal.pgen.0020220.
[参13]
Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne; Skjæveland, Åsmund; Nikolaev, Sergey I.; Jakobsen, Kjetill S. & Pawlowski, Jan. Butler, Geraldine , 编. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2007, 2 (8): e790. Bibcode:2007PLoSO...2..790B. PMC 1949142 . PMID 17726520. doi:10.1371/journal.pone.0000790.
[参14]
Kim, E.; Graham, L. E. & Redfield, Rosemary Jeanne. Redfield, Rosemary Jeanne , 编. EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS ONE. 2008, 3 (7): e2621. Bibcode:2008PLoSO...3.2621K. PMC 2440802 . PMID 18612431. doi:10.1371/journal.pone.0002621.
[参15]
Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. March 2002, 52 (Pt 2): 297–354 [2013-07-13]. PMID 11931142. （原始内容存档于2017-07-29）.
[参16]
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life (PDF). Science. 2006, 311 (5765): 1283–7 [2019-07-13]. Bibcode:2006Sci...311.1283C. PMID 16513982. doi:10.1126/science.1123061. （原始内容 (PDF)存档于2016-03-04）.
[参17]
Mayr, Ernst. Two empires or three?. Proc Natl Acad Sci USA. 1998, 95 (17): 9720–9723 [5 September 2011]. Bibcode:1998PNAS...95.9720 请检查|bibcode=值 (帮助). PMC 33883 . PMID 9707542. doi:10.1073/pnas.95.17.9720. （原始内容存档于2019-06-13）.
[参18]
Cavalier-Smith, T. Only six kingdoms of life (PDF). Proc. R. Soc. Lond. B. 2004, 271 (1545): 1251–62 [2010-04-29]. PMC 1691724 . PMID 15306349. doi:10.1098/rspb.2004.2705. （原始内容存档 (PDF)于2011-01-10）.
[参19]
Archibald, John M. The eocyte hypothesis and the origin of eukaryotic cells. PNAS. 23 December 2008, 105 (51): 20049–20050. Bibcode:2008PNAS..10520049A. PMC 2629348 . PMID 19091952. doi:10.1073/pnas.0811118106.
[参20]
Lake, James A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. PNAS. June 1984, 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. PMC 345305 . PMID 6587394. doi:10.1073/pnas.81.12.3786.
[参21]
Nasir, Arshan; Kim, Kyung Mo; and Caetano-Anolles, Gustavo, "Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya." BMC Evol Biol. 2012; 12: 156. Published online 2012 August 24. doi: 10.1186/1471-2148-12-156
[参22]
Luketa S. New views on the megaclassification of life (PDF). Protistology. 2012, 7 (4): 218–237 [2019-07-13]. （原始内容存档 (PDF)于2015-04-02）.
[参23]
中国大百科全书生物学分册

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[2] [参1]
Woese C, Kandler O, Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.. Proc Natl Acad Sci USA. 1990, 87 (12): 4576–9 [11 February 2010]. Bibcode:1990PNAS...87.4576W. PMC 54159 . PMID 2112744. doi:10.1073/pnas.87.12.4576. （原始内容存档于2008-06-27）.

[4] [参2]
De Rosa M, Gambacorta A, Gliozzi A. Structure, biosynthesis, and physicochemical properties of archaebacterial lipids. Microbiological Reviews. March 1986, 50 (1): 70–80 [2019-07-13]. PMC 373054 . PMID 3083222. （原始内容存档于2019-10-16）.

[DeLong-6] [参3]
DeLong EF. Everything in moderation: archaea as 'non-extremophiles'. Current Opinion in Genetics & Development. December 1998, 8 (6): 649–54. PMID 9914204. doi:10.1016/S0959-437X(98)80032-4.

[8] [参4]
Schulz HN, Jorgensen BB. Big bacteria. Annual Review of Microbiology. 2001, 55: 105–37. PMID 11544351. doi:10.1146/annurev.micro.55.1.105.

[Williams2011-10] [参5]
Williams C. Who are you calling simple?. New Scientist. 2011, 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0.

[12] [参6]
Robertson J, Gomersall M, Gill P. Mycoplasma hominis: growth, reproduction, and isolation of small viable cells. Journal of Bacteriology. November 1975, 124 (2): 1007–18. PMC 235991 . PMID 1102522.

[14] [参7]
Velimirov B. Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium. Microbes and Environments. 2001, 16 (2): 67–77. doi:10.1264/jsme2.2001.67.

[Woese1990-16] [参8]
Woese C, Kandler O, Wheelis M. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.. Proc Natl Acad Sci USA. 1990, 87 (12): 4576–9 [11 February 2010]. Bibcode:1990PNAS...87.4576W. PMC 54159 . PMID 2112744. doi:10.1073/pnas.87.12.4576. （原始内容存档于2008-06-27）.

[18] [参9]
Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher-level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology. 2005, 52 (5): 399–451. PMID 16248873. doi:10.1111/j.1550-7408.2005.00053.x.

[20] [参10]
Holt, Jack R. and Carlos A. Iudica, (2010) "Taxa of Life." Retrieved 09-03-2011.

[22] [参11]
Harper, J. T.; Waanders, E. & Keeling, P. J. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes (PDF). Nt. J. System. Evol. Microbiol. 2005, 55 (Pt 1): 487–496 [2019-07-13]. PMID 15653923. doi:10.1099/ijs.0.63216-0. （原始内容 (PDF)存档于2011-05-11）.

[parfrey-24] [参12]
Parfrey, Laura W.; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J. & Katz, Laura A. Evaluating support for the current classification of eukaryotic diversity. PLoS Genetics. 2006, 2 (12): e220. PMC 1713255 . PMID 17194223. doi:10.1371/journal.pgen.0020220.

[Burki2007-26] [参13]
Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne; Skjæveland, Åsmund; Nikolaev, Sergey I.; Jakobsen, Kjetill S. & Pawlowski, Jan. Butler, Geraldine , 编. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2007, 2 (8): e790. Bibcode:2007PLoSO...2..790B. PMC 1949142 . PMID 17726520. doi:10.1371/journal.pone.0000790.

[28] [参14]
Kim, E.; Graham, L. E. & Redfield, Rosemary Jeanne. Redfield, Rosemary Jeanne , 编. EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS ONE. 2008, 3 (7): e2621. Bibcode:2008PLoSO...3.2621K. PMC 2440802 . PMID 18612431. doi:10.1371/journal.pone.0002621.

[Cavalier-Smith_T-30] [参15]
Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. March 2002, 52 (Pt 2): 297–354 [2013-07-13]. PMID 11931142. （原始内容存档于2017-07-29）.

[32] [参16]
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life (PDF). Science. 2006, 311 (5765): 1283–7 [2019-07-13]. Bibcode:2006Sci...311.1283C. PMID 16513982. doi:10.1126/science.1123061. （原始内容 (PDF)存档于2016-03-04）.

[Mayr1998-34] [参17]
Mayr, Ernst. Two empires or three?. Proc Natl Acad Sci USA. 1998, 95 (17): 9720–9723 [5 September 2011]. Bibcode:1998PNAS...95.9720 请检查|bibcode=值 (帮助). PMC 33883 . PMID 9707542. doi:10.1073/pnas.95.17.9720. （原始内容存档于2019-06-13）.

[36] [参18]
Cavalier-Smith, T. Only six kingdoms of life (PDF). Proc. R. Soc. Lond. B. 2004, 271 (1545): 1251–62 [2010-04-29]. PMC 1691724 . PMID 15306349. doi:10.1098/rspb.2004.2705. （原始内容存档 (PDF)于2011-01-10）.

[Archibald-38] [参19]
Archibald, John M. The eocyte hypothesis and the origin of eukaryotic cells. PNAS. 23 December 2008, 105 (51): 20049–20050. Bibcode:2008PNAS..10520049A. PMC 2629348 . PMID 19091952. doi:10.1073/pnas.0811118106.

[Lake-40] [参20]
Lake, James A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. PNAS. June 1984, 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. PMC 345305 . PMID 6587394. doi:10.1073/pnas.81.12.3786.

[42] [参21]
Nasir, Arshan; Kim, Kyung Mo; and Caetano-Anolles, Gustavo, "Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya." BMC Evol Biol. 2012; 12: 156. Published online 2012 August 24. doi: 10.1186/1471-2148-12-156

[44] [参22]
Luketa S. New views on the megaclassification of life (PDF). Protistology. 2012, 7 (4): 218–237 [2019-07-13]. （原始内容存档 (PDF)于2015-04-02）.

[46] [参23]
中国大百科全书生物学分册

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域 (生物)

古菌

细菌

真核生物

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域 (生物)

古菌

细菌

真核生物

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