Three-domain system

Last updated
A phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese et al. in 1990 Phylogenetic tree.svgAquifexThermotogaPlanctomycesGreen filantous bacteriaPyrodicticumThermococcus celerMethanobacteriumHalophiles
A phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese et al. in 1990

The three-domain system is a biological classification introduced by Carl Woese et al. in 1990 [1] [2] that divides cellular life forms into archaea , bacteria , and eukaryote domains. The key difference from earlier classifications is the splitting of archaea from bacteria.



Woese argued, on the basis of differences in 16S rRNA genes, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Originally his split of the prokaryotes was into Eubacteria (now Bacteria) and Archaebacteria (now Archaea). 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. [2]

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. [3] [4] 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 . [5] The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s. [6] Today, few scientists cling to the idea of a unified Prokarya. [7]


RT8-4 scale.jpg
Staphylococcus aureus VISA 2.jpg
Australia green tree frog (Litoria caerulea) crop.jpg
The three-domain system includes the Archaea (represented by Sulfolobus , left), Bacteria (represented by S. aureus , middle) and Eukarya (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 systems. 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 current system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya.

Domain Archaea

The Archaea are prokaryotic, with no nuclear membrane, but distinct biochemistry and RNA markers 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, which allow them to feed on inorganic matter. Originally classified as exotic bacteria, and then reclassified as archaebacteria, the only easy way to distinguish them on sight from "true" bacteria is by the extreme, harsh environments in which they notoriously thrive.

Some examples of archaeal organisms are:

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 [8] 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:

Domain Eukarya

Eukarya are uniquely organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-microscopic organisms. A partial list of eukaryotic organisms includes:

Kingdom Fungi or fungi
Kingdom Plantae or plants
Kingdom Animalia or animals


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 organelles.

Parakaryon myojinensis ( incertae sedis ) is a single-celled organism known by a unique example. "This organism appears to be a life form distinct from prokaryotes and eukaryotes", [9] with features of both.


Parts of the three-domain theory have been challenged by scientists including Ernst Mayr, Thomas Cavalier-Smith, and Radhey S. Gupta. [10] [11] [12] In particular, Gupta argues that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria. He claims that sequences of features and phylogenies from some highly conserved proteins are inconsistent with the three-domain theory, and that it should be abandoned despite its widespread acceptance.

Recent work has proposed that Eukarya 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. [13] This work suggests a two-domain system as opposed to the near universally adopted three-domain system.

See also

Related Research Articles

Carl Woese

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique he pioneered that 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, kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

Domain (biology) Taxonomic rank

In biological taxonomy, a domain, also superkingdom, realm, or empire, is the highest taxonomic rank of organisms in the three-domain system of taxonomy devised by Carl Woese et al. in 1990.


Nanoarchaeota are a phylum of the Archaea. This phylum currently has only one representative, Nanoarchaeum equitans.


The Crenarchaeota are archaea that have been classified as a phylum of the Archaea domain. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells.


In taxonomy, the Korarchaeota are a phylum of the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota.

Last universal common ancestor Last recent common ancestor of all current life

The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent population of organisms from which all organisms now living on Earth have a common descent—the most recent common ancestor of all current life on Earth. A related concept is that of progenote. LUCA is not thought to be the first life on Earth, but rather the only type of organism of its time to still have living descendants.

Two-empire 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.


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


Monera is a kingdom that contains unicellular organisms with a prokaryotic cell organization, such as bacteria. They are single-celled organisms with no true nuclear membrane.

Prokaryote Unicellular organism that lacks a membrane-bound nucleus

A prokaryote is a cellular organism that lacks an envelope-enclosed nucleus. The word prokaryote comes from the Greek πρό and κάρυον. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota. In the study of the origins of life, prokaryotes are thought to have arisen before eukaryotes.

Archaea A domain of single-celled prokaryotic microorganisms

Archaea constitute 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 classification is obsolete.

Horizontal gene transfer in evolution The evolutionary consequences of transfer of genetic material between organisms of different taxa

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

Eukaryote Taxonomic domain

Eukaryotes are organisms whose cells have a nucleus enclosed within a nuclear envelope. Eukaryotes belong to the domain Eukaryota or Eukarya; their name comes from the Greek εὖ and κάρυον. The domain Eukaryota makes up one of the domains of life in the now obsolete three-domain system; the two other domains are Bacteria and Archaea, and the Eukaryote are usually now regarded as having emerged in the Archaea in or as sister of the now cultivated Asgard Archaea. Eukaryotes represent a tiny minority of the number of living organisms; however, due to their generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.1-1.6 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs.

Eocyte hypothesis

The Eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota, a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major phylum of archaea, the Euryarchaeota.

Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.

Otto Kandler

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 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 1997 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.

The biological classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorganisations of kingdoms and phyla.

Darwinian threshold

Darwinian threshold or Darwinian transition is a term introduced by Carl Woese to describe a transition period during the evolution of the first cells when genetic transmission moves from a predominantly horizontal mode to a vertical mode. The process starts when the ancestors of the Last Universal Common Ancestor become refractory to horizontal gene transfer (HGT) and become individual entities with vertical heredity upon which natural selection is effective. After this transition, life is characterized by genealogies that have a modern tree-like phylogeny.


  1. Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC   432104 . PMID   270744.
  2. 1 2 Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC   54159 . PMID   2112744.
  3. Mayr, Ernst (1998). "Two empires or three?". Proceedings of the National Academy of Sciences. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi:10.1073/pnas.95.17.9720. PMC   33883 . PMID   9707542.
  4. Sapp, Jan A. (December 2007). "The structure of microbial evolutionary theory". Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. 38 (4): 780–95. doi:10.1016/j.shpsc.2007.09.011. PMID   18053933.
  5. Morell, V. (1997-05-02). "Microbiology's scarred revolutionary". Science. 276 (5313): 699–702. doi:10.1126/science.276.5313.699. ISSN   0036-8075. PMID   9157549.
  6. Sapp, Jan A. (2009). The new foundations of evolution: on the tree of life. New York: Oxford University Press. ISBN   978-0-199-73438-2.
  7. Koonin, Eugene (2014). "Carl Woese's vision of cellular evolution and the domains of life". RNA Biology. RNA Biol. 11 (3): 197–204. doi:10.4161/rna.27673. PMC   4008548 . PMID   24572480.
  8. Eckburg, Paul B.; Lepp, Paul W.; Relman, David A. (2003). "Archaea and their potential role in human disease". Infection and Immunity. 71 (2): 591–596. doi:10.1128/IAI.71.2.591-596.2003. PMC   145348 . PMID   12540534.
  9. Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K (2012). "Prokaryote or eukaryote? A unique microorganism from the deep sea". Journal of Electron Microscopy. 61 (6): 423–31. doi:10.1093/jmicro/dfs062. PMID   23024290.
  10. Gupta, Radhey S. (1998). "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". Theoretical Population Biology. 54 (2): 91–104. doi:10.1006/tpbi.1998.1376. PMID   9733652.
  11. Mayr, E. (1998). "Two empires or three?". Proc. Natl. Acad. Sci. USA. 95 (17): 9720–9723. Bibcode:1998PNAS...95.9720M. doi:10.1073/pnas.95.17.9720. PMC   33883 . PMID   9707542.
  12. Cavalier-Smith, Thomas (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol. 52 (1): 7–76. doi: 10.1099/00207713-52-1-7 . PMID   11837318.
  13. Spang, Anja (2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521 (7551): 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC   4444528 . PMID   25945739.