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The three-domain system is a biological classification introduced by Carl Woese in 1977 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese argued that, on the basis of differences in 16S rRNA genes, these two groups and the 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. Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings now referred to as "domains," until the latter term was coined in 1990.
The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the 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 their fellow prokaryotic bacteria. The current system has the following kingdoms in the three domains:
Archaea Domain – prokaryotic, no nuclear membrane, distinct biochemistry and RNA markers from eubacteria, possess unique ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth; traditionally classified as archaebacteria; often characterized by living in extreme environments
- Kingdom Archaebacteria
Bacteria Domain – prokaryotic, consists of prokaryotic cells possessing primarily diacyl glycerol diester lipids in their membranes and bacterial rRNA, no nuclear membrane, traditionally classified as bacteria, contain most known pathogenic prokaryotic organisms (see  for exceptions), studied far more extensively than Archaea
- Kingdom Eubacteria
- Kingdom Fungi or fungi
- Kingdom Plantae or plants
- Kingdom Animalia or animals
- Kingdom Protista or protists (recognized to be paraphyletic, and thus subject to dissolution and/or redefinition)
Each of the three cell types tends to fit into recurring specialties 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.
Parts of the three-domain theory have been challenged by some scientists, including Ernst Mayr, Thomas Cavalier-Smith, Radhey Gupta, and Steven Voutier. 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 sequence 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.
- Woese C, Fox G (1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms.". Proc Natl Acad Sci USA 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
- 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): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. Retrieved 11 Feb 2010.
- Paul B. Eckburg, Paul W. Lepp, and David A. Relman (2003) Archaea and Their Potential Role in Human Disease. Infection and Immunity, pp. 591–596, Vol. 71, No. 2 doi:10.1128/IAI.71.2.591-596.2003
- 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. http://dx.doi.org/10.1006/tpbi.1998.1376
- E. Mayr (1998). "Two empires or three?" Proc. Natl. Acad. Sci. USA 95, 9720-9723
- Cavalier-Smith T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification." Int J Syst Evol Microbiol 52(Pt 1):7-76.