Editing Three-domain system

{{short description|Hypothesis for classification of life}}
[[File:Phylogenetic tree of life 1990 LUCA.svg|thumb|upright=1.75|A [[phylogenetic tree]] based on [[Ribosomal RNA|rRNA]] data, emphasizing the separation of bacteria, archaea, and eukarya  as proposed by [[Carl Woese]] et al. in 1990,<ref name="w1990" /> with the hypothetical [[last universal common ancestor]]]]<!--Please note that the tree in PhylomapB is NOT the one that Woese et al actually proposed in 1990, see the image in their paper for yourself: someone has "improved" it with later accretions, making the caption false-->
The '''three-domain system''' is a [[taxonomy (biology)|taxonomic]] [[classification system]] that groups all [[cell (biology)|cell]]ular [[life]] into three [[domain (biology)|domain]]s, namely [[Archaea]], [[Bacteria]] and [[Eukarya]], introduced by [[Carl Woese]], [[Otto Kandler]] and [[Mark Wheelis]] in 1990.<ref name="w1990">{{cite journal | vauthors = Woese CR, Kandler O, Wheelis ML | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 87 | issue = 12 | pages = 4576–9 | date = June 1990 | pmid = 2112744 | pmc = 54159 | doi = 10.1073/pnas.87.12.4576 | bibcode=1990PNAS...87.4576W| doi-access = free }}</ref> The key difference from earlier classifications such as the [[two-empire system]] and the five-kingdom classification is the splitting of Archaea (previously named "archaebacteria") from Bacteria as completely different organisms. 

The three domain hypothesis is considered obsolete by some since it is thought that eukaryotes do not form a separate domain of life; instead, they arose from a fusion between two different species, one from within Archaea and one from within Bacteria.<ref name="Gabaldón"/><ref name=":02">{{Cite journal |last1=Nobs |first1=Stephanie-Jane |last2=MacLeod |first2=Fraser I. |last3=Wong |first3=Hon Lun |last4=Burns |first4=Brendan P. |date=2022 |title=Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life? |url=https://linkinghub.elsevier.com/retrieve/pii/S0966842X21002699 |journal=Trends in Microbiology |volume=30 |issue=5 |pages=421–431 |doi=10.1016/j.tim.2021.11.003|pmid=34863611 |s2cid=244823103 |url-access=subscription }}</ref><ref name=":3">{{Cite journal |last=Doolittle |first=W. Ford |date=2020 |title=Evolution: Two Domains of Life or Three? |journal=Current Biology |volume=30 |issue=4 |pages=R177–R179 |doi=10.1016/j.cub.2020.01.010 |pmid=32097647 |doi-access=free |bibcode=2020CBio...30.R177D }}</ref> (see  [[Two-domain system]])

==Background==
Woese argued, on the basis of differences in [[16S ribosomal RNA|16S rRNA]] [[gene]]s, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed [[genetics|genetic]] machinery, often called a [[progenote]]. To reflect these primary lines of descent, he treated each as a domain, divided into several different [[kingdom (biology)|kingdoms]]. Originally his split of the prokaryotes was into ''Eubacteria'' (now ''Bacteria'') and ''Archaebacteria'' (now ''Archaea'').<ref name="pmid270744">{{cite journal |vauthors=Woese CR, Fox GE |date=November 1977 |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=74 |issue=11 |pages=5088–90 |bibcode=1977PNAS...74.5088W |doi=10.1073/pnas.74.11.5088 |pmc=432104 |pmid=270744 |doi-access=free}}</ref> Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990.<ref name=w1990/>

Acceptance of the validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including [[Salvador Luria]] and [[Ernst Mayr]] objected to his division of the prokaryotes.<ref>{{Cite journal | title = Two empires or three?| doi = 10.1073/pnas.95.17.9720| volume = 95
| issue = 17| pages = 9720–9723| last = Mayr| first = Ernst| author-link = Ernst Mayr| journal = Proceedings of the National Academy of Sciences |year = 1998| bibcode=1998PNAS...95.9720M| pmid=9707542| pmc=33883| doi-access = free}}</ref><ref name="sapp2007">{{Cite journal| title = The structure of microbial evolutionary theory| doi = 10.1016/j.shpsc.2007.09.011| pmid = 18053933|  volume = 38| issue = 4| pages = 780–95 | last = Sapp| first = Jan A.| author-link = Jan Sapp| journal = Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences |date=December 2007}}</ref> Not all criticism of him was restricted to the scientific level. A decade of labor-intensive [[oligonucleotide]] cataloging left him with a reputation as "a crank", and Woese would go on to be dubbed "Microbiology's Scarred Revolutionary" by a news article printed in the journal ''[[science (journal)|Science]]'' in 1997.<ref name="morell1997">{{Cite journal| title = Microbiology's scarred revolutionary| doi = 10.1126/science.276.5313.699| issn = 0036-8075| volume = 276| issue = 5313| pages = 699–702| last = Morell| first = V.| journal = Science| date = 1997-05-02| pmid = 9157549| s2cid = 84866217}}</ref> The growing amount of supporting data led the [[scientific community]] to accept the Archaea by the mid-1980s.<ref name="sapp2009">{{Cite book
| publisher = Oxford University Press
| isbn = 978-0-199-73438-2
| last = Sapp
| first = Jan A.
| title = The new foundations of evolution: on the tree of life
| location = New York
| year = 2009
}}</ref> Today, very few scientists still accept the concept of a unified Prokarya.<ref>{{cite journal |last1=Koonin |first1=Eugene |title=Carl Woese's vision of cellular evolution and the domains of life |journal=RNA Biology |year=2014 |volume=11 |issue=3 |pages=197–204 |publisher=RNA Biol. |doi=10.4161/rna.27673 |pmid=24572480 |pmc=4008548 }}</ref>

== Classification ==
{{multiple images
| width1            = 154
| image1            = RT8-4 scale.jpg
| alt1              = Electron micrograph of Sulfolobus infected with Sulfolobus virus STSV1.
| width2            = 205
| image2            = Staphylococcus aureus VISA 2.jpg
| alt2              = Scanning electron micrograph of S. aureus; false-color added
| width3            = 240
| image3            = Australia green tree frog (Litoria caerulea) crop.jpg
| alt3              = Australian green tree frog (Litoria caerulea)
| footer            = The three-domain system includes the [[Archaea]] (represented by ''[[Sulfolobus]]'', left), [[Bacteria]] (represented by ''[[Staphylococcus aureus]]'', middle) and [[eukaryote]]s (represented by the [[Australian green tree frog]], right).
}}
The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or [[six-kingdom system]]s. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to eukaryotes than they are to other [[prokaryotes]] – bacteria-like organisms with no [[cell nucleus]]. The three-domain system sorts the previously known kingdoms into these three domains: [[Archaea]], [[Bacteria]], and [[Eukaryote|Eukarya]].<ref name="Gabaldón"/>

===Domain Archaea===
The [[Archaea]] are [[prokaryotic]], with no nuclear membrane, but with biochemistry and RNA markers that are distinct from bacteria. The archaeans possess unique, ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth, most notably their diverse, exotic metabolisms.

Some examples of archaeal organisms are:
* [[methanogen]]s – which produce the gas [[methane]]
* [[halophile]]s – which live in very salty water
* [[thermoacidophile]]s – which thrive in acidic high-temperature water

===Domain Bacteria===
The [[Bacteria]] are also [[prokaryotic]]; their domain consists of cells with bacterial rRNA, no nuclear membrane, and whose membranes possess primarily ''diacyl glycerol diester lipids''. Traditionally classified as bacteria, many thrive in the same environments favored by humans, and were the first prokaryotes discovered; they were briefly called the '''Eubacteria''' or "true" bacteria when the Archaea were first recognized as a distinct [[clade]].

Most known pathogenic prokaryotic organisms belong to bacteria (see<ref name="Eckburg">{{cite journal |last1=Eckburg |first1=Paul B. |last2=Lepp |first2=Paul W. |last3=Relman |first3=David A. |year=2003 |title=Archaea and their potential role in human disease |journal=Infection and Immunity |volume=71 |issue=2 |pages=591–596 |doi=10.1128/IAI.71.2.591-596.2003 |pmid=12540534 |pmc=145348}}</ref> for exceptions). For that reason, and because the Archaea are typically difficult to grow in laboratories, Bacteria are currently studied more extensively than Archaea.

Some examples of bacteria include:
* "[[Cyanobacteria]]" – photosynthesizing bacteria that are related to the chloroplasts of eukaryotic plants and algae
* [[Spirochaetota]] – [[Gram-negative]] bacteria that include those causing syphilis and Lyme disease
* [[Actinomycetota]] – [[Gram-positive]] bacteria including ''[[Bifidobacterium animalis]]'' which is present in the human large intestine

===Domain Eukarya===
[[Eukaryota]] are organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-[[microscopic organism]]s. The domain contains, for example:

* [[Holomycota]] – mushrooms and allies
* [[Viridiplantae]] – green plants
* [[Holozoa]] – animals and allies
* [[Stramenopile]]s – includes brown algae
* [[Amoebozoa]] – solitary and social amoebae
* [[Discoba]] – includes euglenoids

==Niches==
Each of the three cell types tends to fit into recurring specialities or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a eukaryote is likely to have derived from a joining of different cell types, forming [[organelle]]s.

''[[Parakaryon myojinensis]]'' (''[[incertae sedis]]'') is a single-celled organism known to be a unique example. "This organism appears to be a life form distinct from [[prokaryotes]] and [[eukaryotes]]",<ref name=yamaguchi>{{cite journal | vauthors = Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K | title = Prokaryote or eukaryote? A unique microorganism from the deep sea | journal = Journal of Electron Microscopy | volume = 61 | issue = 6 | pages = 423–31 | date = 2012 | pmid = 23024290 | doi = 10.1093/jmicro/dfs062 }}</ref> with features of both.

==Alternatives==
[[File:3 domains.png|thumb|330px|Alternative versions of the three domains of life's phylogeny]]
Parts of the three-domain theory have been challenged by scientists including [[Ernst Mayr]], [[Thomas Cavalier-Smith]], and [[Radhey S. Gupta]].<ref name=Gupta1998>{{cite journal | last1=Gupta | first1=Radhey S. | year=1998 | title=Life's Third Domain (''Archaea''): An Established Fact or an Endangered Paradigm?: A New Proposal for Classification of Organisms Based on Protein Sequences and Cell Structure.| journal=Theoretical Population Biology | volume=54 | issue=2| pages=91–104 | doi=10.1006/tpbi.1998.1376 | pmid=9733652| bibcode=1998TPBio..54...91G }}</ref><ref>{{cite journal | last1=Mayr | first1=E. | year=1998 | title=Two empires or three? | journal=Proc. Natl. Acad. Sci. USA | volume=95 | issue=17| pages=9720–9723 | doi=10.1073/pnas.95.17.9720 | pmid=9707542 | pmc=33883| bibcode=1998PNAS...95.9720M | doi-access=free }}</ref><ref>{{cite journal | last1=Cavalier-Smith | first1=Thomas |author-link=Thomas Cavalier-Smith | year=2002 | title=The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | pmid=11837318| journal=Int J Syst Evol Microbiol | volume=52 | issue=1| pages=7–76 | doi=10.1099/00207713-52-1-7| doi-access=free }}</ref>

Recent work has proposed that Eukaryota may have actually branched off from the domain Archaea. According to Spang ''et al.'', [[Lokiarchaeota]] forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.<ref>{{cite journal | last1=Spang | first1=Anja | year=2015 |  title=Complex archaea that bridge the gap between prokaryotes and eukaryotes | journal=Nature | volume=521 | issue=7551 | pages=173–179 | doi=10.1038/nature14447 | pmid=25945739 | pmc=4444528| bibcode=2015Natur.521..173S }}</ref> This work suggests a [[two-domain system]] as opposed to the three-domain system.<ref name=":02" /><ref name=":3" /><ref name="Gabaldón">{{cite journal |last1=Gabaldón |first1=Toni |title=Origin and Early Evolution of the Eukaryotic Cell |journal=Annual Review of Microbiology |date=8 October 2021 |volume=75 |issue=1 |pages=631–647 |doi=10.1146/annurev-micro-090817-062213 |pmid=34343017 |s2cid=236916203 |url=https://doi.org/10.1146/annurev-micro-090817-062213 |access-date=11 August 2022 |language=en |issn=0066-4227 |quote="A rooted version of this three-domain tree placed Archaea and Eukarya as sister clades, suggesting that eukaryotes were very distantly related to archaea and not more related to any specific group. More recently, phylogenetic analyses using more sophisticated models and expanded gene data sets have provided increasing support for an alternative tree topology in which the eukaryotic clade branches within Archaea, rather than next to it." |url-access=subscription }}</ref> Exactly how and when Archaea, Bacteria, and Eucarya developed and how they are related continues to be debated.<ref name="Callier">{{cite journal |last1=Callier |first1=Viviane |title=Mitochondria and the origin of eukaryotes |journal=Knowable Magazine |date=8 June 2022 |doi=10.1146/knowable-060822-2 |doi-access=free |url=https://knowablemagazine.org/article/living-world/2022/mitochondria-origin-eukaryotes |access-date=18 August 2022}}</ref><ref name="Gabaldón"/><ref name="McCutcheon">{{cite journal |last1=McCutcheon |first1=John P. |title=The Genomics and Cell Biology of Host-Beneficial Intracellular Infections |journal=Annual Review of Cell and Developmental Biology |date=6 October 2021 |volume=37 |issue=1 |pages=115–142 |doi=10.1146/annurev-cellbio-120219-024122 |pmid=34242059 |s2cid=235786110 |language=en |issn=1081-0706|doi-access=free }}</ref>

== See also ==
{{div col}}
* [[Two-domain system]]
* [[Neomura]]
* [[Bacterial phyla]]
* [[Eocyte hypothesis]]
* [[Taxonomy (biology)|Taxonomy]]
* [[Two-empire system]]
{{div col end}}

== References ==
{{Reflist|30em}}

[[Category:Biological classification]]
[[Category:High-level systems of taxonomy]]
[[Category:Biology controversies]]

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