The three domain Hypothesis is no longer valid since it is now widely recognized that eukaryotes do not form a separate domain of life. They originated from a fusion of two lineages; one from within Archaea and one from within Bacteria.[2][3][4]
Background
Woese argued, on the basis of differences in 16S rRNAgenes, 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).[5] 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.[1]
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.[6][7] 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 in 1997.[8] The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s.[9] Today, very few scientists still accept the concept of a unified Prokarya.[10]
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 three-domain system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya.[2]
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.
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[11] 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
Eukaryota are organisms whose cells contain a membrane-bound nucleus. They include many large single-celled organisms and all known non-microscopic organisms. The domain contains, for example:
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.
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.[16] This work suggests a two-domain system as opposed to the three-domain system.[3][4][2] Exactly how and when Archaea, Bacteria, and Eucarya developed and how they are related continues to be debated.[17][2][18]
^ abcdGabaldón, Toni (8 October 2021). "Origin and Early Evolution of the Eukaryotic Cell". Annual Review of Microbiology. 75 (1): 631–647. doi:10.1146/annurev-micro-090817-062213. ISSN0066-4227. PMID34343017. S2CID236916203. Retrieved 11 August 2022. 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.
^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. PMID18053933.
^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. PMID23024290.
^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. Bibcode:1998TPBio..54...91G. doi:10.1006/tpbi.1998.1376. PMID9733652.
