Domain (biology)

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The hierarchy of biological classification's eight major taxonomic ranks. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown. Biological classification L Pengo vflip.svg DomainKingdomClassOrderFamily
The hierarchy of biological classification's eight major taxonomic ranks. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown.

In biological taxonomy, a domain ( /dəˈmn/ or /dˈmn/ ) (Latin: regio [1] ), also dominion, [2] superkingdom, realm, or empire, [3] is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990. [1]


According to the domain system, the tree of life consists of either three domains such as Archaea, Bacteria, and Eukarya, [1] or two domains consisting of Archaea and Bacteria, with Eukarya included in Archaea. [4] [5] The first two are all prokaryotes, single-celled microorganisms without a membrane-bound nucleus. All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and are called eukaryotes.

Non-cellular life is not included in this system. Alternatives to the three-domain system include the earlier two-empire system (with the empires Prokaryota and Eukaryota), and the eocyte hypothesis (with two domains of Bacteria and Archaea, with Eukarya included as a branch of Archaea).


The term domain was proposed by Carl Woese, Otto Kandler, and Mark Wheelis (1990) in a three-domain system. This term represents a synonym for the category of dominion (Lat. dominium), introduced by Moore in 1974. [2]

Development of the Domain System

Carolus Linnaeus made the classification of domain popular in the famous taxonomy system he created in the middle of the eighteenth century. This system was further improved by the studies of Charles Darwin later on but failed to properly classify the domain, Bacteria, due to it having very few observable features to compare to the other domains. [6]

Carl Woese made a revolutionary breakthrough when, in 1977, he compared the nucleotide sequences of the 16s ribosomal RNA and discovered that the rank, domain, contained three branches, not two like scientists had previously thought. Initially, due to their physical similarities, Archaea and Bacteria were classified together and called "archaebacteria". However, scientists now know that these two domains are hardly similar and are internally wildly different. [7]

Characteristics of the three domains

A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota Phylogenetic tree.svgAquifexThermotogaBacteroides–CytophagaPlanctomyces"Cyanobacteria"ProteobacteriaSpirochetesGram-positivesChloroflexiThermoproteus–PyrodictiumHaloarchaeaSlime moldsAnimalsFungiPlantsCiliatesFlagellatesTrichomonadsDiplomonads
A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota
The three-domains tree and the Eocyte hypothesis (Two domains tree), 2008. Two domain tree.png
The three-domains tree and the Eocyte hypothesis (Two domains tree), 2008.
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006 Eukaryotes are colored red, archaea green, and bacteria blue. Collapsed tree labels simplified.png
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006 Eukaryotes are colored red, archaea green, and bacteria blue.

Each of these three domains contains unique ribosomal RNA. This forms the basis of the three-domain system. While the presence of a nuclear membrane differentiates the Eukarya from the Archaea and Bacteria, both of which lack a nuclear envelope, the Archaea and Bacteria are distinct from each other due to differences in the biochemistry of their cell membranes and RNA markers. [1]


Archaea are prokaryotic cells, typically characterized by membrane lipids that are branched hydrocarbon chains attached to glycerol by ether linkages. The presence of these ether linkages in Archaea adds to their ability to withstand extreme temperatures and highly acidic conditions, but many archaea live in mild environments. Halophiles, organisms that thrive in highly salty environments, and hyperthermophiles, organisms that thrive in extremely hot environments, are examples of Archaea. [1]

Archaea evolved many cell sizes, but all are relatively small. Their size ranges from 0.1 μm to 15 μm diameter and up to 200 μm long. They are about the size of bacteria, or similar in size to the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest of the Archaea. [1]


Cyanobacteria and mycoplasmas are two examples of bacteria. Even though bacteria are prokaryotic cells just like Archaea, their cell membranes are instead made of phospholipid bilayers. Bacteria cell membranes are distinct from Archean membranes: They characteristically have none of the ether linkages that Archaea have. Internally, bacteria have different RNA structures in their ribosomes, hence they are grouped into a different category. In the two- and three-domain systems, this puts them into a separate domain.

There is a great deal of diversity in the domain Bacteria. That diversity is further confounded by exchange of genes between different bacterial lineages. The occurrence of duplicate genes between otherwise distantly-related bacteria makes it nearly impossible to distinguish bacterial species, or count the bacterial species on the Earth, or to organize them into a tree-like structure (unless the structure includes cross-connections between branches, making it a "network" instead of a "tree"). [1]


Members of the domain Eukarya – called eukaryotes – have membrane-bound organelles (including a nucleus containing genetic material) and are represented by five kingdoms: Plantae, Protozoa, Animalia, Chromista, and Fungi. [1]

Exclusion of viruses and prions

The three-domain system does not include any form of non-cellular life. Stefan Luketa proposed a five-domain system in 2012, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains. [10]

Alternative classifications

Taxonomical root nodeTwo superdomains (controversial) Two empires Three domains Five Dominiums [11] Five kingdoms Six kingdoms Eocyte hypothesis
Biota / Vitae / Life Acytota / Aphanobionta - Non-cellular life Virusobiota (Viruses, Viroids)
Prionobiota (Prions)
cellular life
Prokaryota / Procarya
Bacteria Bacteria Monera Eubacteria Bacteria
Archaea Archaea Archaebacteria Archaea including eukaryotes
Eukaryota / Eukarya Protista

Alternative classifications of life include:

See also

Related Research Articles

<span class="mw-page-title-main">Carl Woese</span> American microbiologist (1928–2012)

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois at Urbana-Champaign.

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

<span class="mw-page-title-main">Three-domain system</span> Hypothesis for classification of life

The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea from bacteria as completely different organisms. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as Eukaryotes are considered as one group of Archaea.

The Thermoprotei is a class of the Thermoproteota.

In taxonomy, the Methanopyri are a class of the Euryarchaeota.

<span class="mw-page-title-main">Two-empire system</span> Biological classification system

The two-empire system was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

The term cellularization (cellularisation) has been used in theories to explain the evolution of cells, for instance in the pre-cell theory, dealing with the evolution of the first cells on this planet, and in the syncytial theory attempting to explain the origin of Metazoa from unicellular organisms.

<span class="mw-page-title-main">Neomura</span>

Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan cell walls with other glycoproteins. As of August 2017, the neomuran hypothesis is not accepted by most workers; molecular phylogenies suggest that eukaryotes are most closely related to one group of archaeans and evolved from them, rather than forming a clade with all archaeans, and that Archaea and Bacteria are sister groups.

<span class="mw-page-title-main">Thermococci</span> Class of archaea

In taxonomy, the Thermococci are a class of microbes within the Euryarchaeota.

<span class="mw-page-title-main">Methanomicrobia</span> Class of archaea

In the taxonomy of microorganisms, the Methanomicrobia are a class of the Euryarchaeota.

<span class="mw-page-title-main">Methanococci</span> Class of archaea

Methanococci is a class of methanogenic archaea in the phylum Euryarchaeota. They can be mesophilic, thermophilic or hyperthermophilic.

<span class="mw-page-title-main">Pre-cell</span>

The terms pre-cell (precell), proto-cell (protocell), progenote, etc. are frequently used to designate the hypothetical ancestral entities of first life on earth precursing complete cells. The meanings of these terms as well as the concepts of this ancestral entities, vary with the different hypotheses dealing with this subject and, accordingly, with the corresponding publications.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<span class="mw-page-title-main">Eukaryote</span> Domain of life whose cells have nuclei

Eukaryota, whose members are known as eukaryotes, is a diverse domain of organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms are eukaryotes. They constitute a major group of living things, along with the two groups of prokaryotes, the Bacteria and the Archaea.

<span class="mw-page-title-main">Eocyte hypothesis</span> Hypothesis in evolutionary biology

The eocyte hypothesis in evolutionary biology proposes that the eukaryotes originated from a group of prokaryotes called eocytes. After his team at the University of California, Los Angeles discovered eocytes in 1984, James A. Lake formulated the hypothesis as "eocyte tree" that proposed eukaryotes as part of archaea. Lake hypothesised the tree of life as having only two primary branches: Parkaryoates that include Bacteria and Archaea, and karyotes that comprise Eukaryotes and eocytes. Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.

<span class="mw-page-title-main">Otto Kandler</span>

Otto Kandler was a German botanist and microbiologist. Until his retirement in 1986 he was professor of botany at the Ludwig Maximilian University of Munich.

The Woeseian revolution was the progression of the phylogenetic tree of life concept from two main divisions, known as the Prokarya and Eukarya, into three domains now classified as Bacteria, Archaea, and Eukaryotes. The discovery of the new domain stemmed from the work of biophysicist Carl Woese in 1977 from a principle of evolutionary biology designated as Woese's dogma. It states that the evolution of ribosomal RNA (rRNA) was a necessary precursor to the evolution of modern life forms. Although the three-domain system has been widely accepted, the initial introduction of Woese’s discovery received criticism from the scientific community.

<span class="mw-page-title-main">Eukaryogenesis</span> Process of forming the first eukaryotic cell

Eukaryogenesis, the process which created the eukaryotic cell and lineage, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The process is widely agreed to have involved symbiogenesis, in which archaea and bacteria came together to create the first eukaryotic common ancestor (FECA). This cell had a new level of complexity and capability, with a nucleus, at least one centriole and cilium, facultatively aerobic mitochondria, sex, a dormant cyst with a cell wall of chitin and/or cellulose and peroxisomes. It evolved into a population of single-celled organisms that included the last eukaryotic common ancestor (LECA), gaining capabilities along the way, though the sequence of the steps involved has been disputed, and may not have started with symbiogenesis. In turn, the LECA gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms.

Small subunit ribosomal ribonucleic acid is the smaller of the two major RNA components of the ribosome. Associated with a number of ribosomal proteins, the SSU rRNA forms the small subunit of the ribosome. It is encoded by SSU-rDNA.

<span class="mw-page-title-main">Two-domain system</span> Biological classification system

The two-domain system is a biological classification by which all organisms in the tree of life are classified into two big domains, Bacteria and Archaea. It emerged from development in the knowledge of archaea diversity and challenge over the widely accepted three-domain system that defines life into Bacteria, Archaea, and Eukarya. It was predicted by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system due to better compelling evidences at the time. Better understanding of archaea, especially in their roles in the origin of eukaryotes by symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became widely appreciated after the discovery of a large group (superphylum) of archaea called Asgard in 2017, evidences of which suggest to be the evolutionary root of eukaryotes – implying that eukaryotes are members of the domain Archaea.


  1. 1 2 3 4 5 6 7 8 Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya". Proc Natl Acad Sci USA . 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi: 10.1073/pnas.87.12.4576 . PMC   54159 . PMID   2112744.
  2. 1 2 Moore R.T. (1974). "Proposal for the recognition of super ranks" (PDF). Taxon. 23 (4): 650–652. doi:10.2307/1218807. JSTOR   1218807.
  3. "The scientific taxonomy and classification of all creatures". Flash cards. Retrieved 19 October 2015.
  4. Nobs, Stephanie-Jane; MacLeod, Fraser I.; Wong, Hon Lun; Burns, Brendan P. (2022). "Eukarya the chimera: Eukaryotes, a secondary innovation of the two domains of life?". Trends in Microbiology. 30 (5): 421–431. doi:10.1016/j.tim.2021.11.003. PMID   34863611. S2CID   244823103.
  5. Doolittle, W. Ford (2020). "Evolution: Two domains of life or three?". Current Biology. 30 (4): R177–R179. doi: 10.1016/j.cub.2020.01.010 . PMID   32097647.
  6. "Domains of Life, Genomics | Learn Science at Scitable". Retrieved 1 December 2022.
  7. "Taxonomy I | Biology". Visionlearning. Retrieved 1 December 2022.
  8. Cox, C.J.; Foster, P.G.; Hirt, R.P.; Harris, S.R.; Embley, T.M. (2008). "The archaebacterial origin of eukaryotes". Proc Natl Acad Sci USA . 105 (51): 20356–61. Bibcode:2008PNAS..10520356C. doi: 10.1073/pnas.0810647105 . PMC   2629343 . PMID   19073919.
  9. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006). "Toward automatic reconstruction of a highly resolved tree of life" (PDF). Science. 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C. CiteSeerX . doi:10.1126/science.1123061. PMID   16513982. S2CID   1615592.
  10. Luketa S. (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.
  11. Luketa, Stefan (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.
  12. Mayr, E. (1998). "Two empires or three?". PNAS. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi: 10.1073/pnas.95.17.9720 . PMC   33883 . PMID   9707542.
  13. Cavalier-Smith, T. (2004). "Only six kingdoms of life" (PDF). Proc. R. Soc. Lond. B. 271 (1545): 1251–1262. doi:10.1098/rspb.2004.2705. PMC   1691724 . PMID   15306349 . Retrieved 29 April 2010.
  14. 1 2 Lake, J.A.; Henderson, Eric; Oakes, Melanie; Clark, Michael W. (June 1984). "Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes". PNAS. 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. doi: 10.1073/pnas.81.12.3786 . PMC   345305 . PMID   6587394.
  15. Archibald, John M. (23 December 2008). "The eocyte hypothesis and the origin of eukaryotic cells". PNAS. 105 (51): 20049–20050. Bibcode:2008PNAS..10520049A. doi: 10.1073/pnas.0811118106 . PMC   2629348 . PMID   19091952.
  16. Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.; Embley, T. Martin (December 2013). "An archaeal origin of eukaryotes supports only two primary domains of life". Nature. 504 (7479): 231–236. Bibcode:2013Natur.504..231W. doi:10.1038/nature12779. PMID   24336283. S2CID   4461775.