Related Research Articles
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 Urbana–Champaign.
In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.
In biological taxonomy, a domain, also dominion, superkingdom, realm, or empire, 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.
The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. 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 a clade of Archaea.
The Thermoproteota are prokaryotes that have been classified as a phylum of the domain Archaea. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota 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 2005 all cultured Thermoproteota 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. Recent evidence shows that some members of the Thermoproteota are methanogens.
Euryarchaeota is a kingdom of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines; halobacteria, which survive extreme concentrations of salt; and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.
In taxonomy, the Methanopyri are a class of the Euryarchaeota.
The two-empire system was the top-level biological classification system in general use from the early 20th century until 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.
Gracilicutes is a clade in bacterial phylogeny.
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.
In the taxonomy of microorganisms, the Methanomicrobia are a class of the Euryarchaeota.
Methanococci is a class of methanogenic archaea in the phylum Euryarchaeota. They can be mesophilic, thermophilic or hyperthermophilic.
A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. However 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.
Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
Bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks.
There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure, and not based on the molecular evidence.
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: prokaryotes, which 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.
The initial version of a classification system of life by British zoologist Thomas Cavalier-Smith appeared in 1978. This initial system continued to be modified in subsequent versions that were published until he died in 2021. As with classifications of others, such as Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy., Cavalier-Smith used his classifications to convey his opinions about the evolutionary relationships among various organisms, principally microbial. His classifications complemented his ideas communicated in scientific publications, talks, and diagrams. Different iterations might have a wider or narrow scope, include different groupings, provide greater or lesser detail, and place groups in different arrangements as his thinking changed. His classifications has been a major influence in the modern taxonomy, particularly of protists.
The two-domain system is a biological classification by which all organisms in the tree of life are classified into two domains, Bacteria and Archaea. It emerged from development of knowledge of archaea diversity and challenges the widely accepted three-domain system that classifies life into Bacteria, Archaea, and Eukarya. It was preceded by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system, due to evidence at the time. Better understanding of archaea, especially of their roles in the origin of eukaryotes through symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became more widely accepted after the discovery of a large group (superphylum) of archaea called Asgard in 2017, which evidence suggests to be the evolutionary root of eukaryotes, thereby making eukaryotes members of the domain Archaea.
References
- 1 2 Cavalier-Smith T (March 2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". Int. J. Syst. Evol. Microbiol. 52 (Pt 2): 297–354. doi:10.1099/00207713-52-2-297. PMID 11931142.
- 1 2 3 Devos, Damien P (2021), "Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life", Molecular Biology and Evolution, 38 (9): 3531–3542, doi:10.1093/molbev/msab186, PMC 8382908 , PMID 34229349
- ↑ 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.
- ↑ 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.
- 1 2 Gribaldo, Simonetta; Poole, Anthony M.; Daubin, Vincent; Forterre, Patrick & Brochier-Armanet, Céline (2010-10-01). "The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?". Nature Reviews Microbiology. 8 (10): 743–752. doi:10.1038/nrmicro2426. PMID 20844558. S2CID 12111029.
- ↑ López-García, Purificación & Moreira, David (2015). "Open Questions on the Origin of Eukaryotes". Trends in Ecology and Evolution. 30 (11): 697–708. Bibcode:2015TEcoE..30..697L. doi:10.1016/j.tree.2015.09.005. PMC 4640172 . PMID 26455774.
- ↑ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C. & Banfield, Jillian F. (2016-04-11). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi: 10.1038/nmicrobiol.2016.48 . PMID 27572647.
- ↑ Cavalier-Smith, Thomas & Chao, Ema E-Yung (2020). "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)". Protoplasma. 257 (3): 621–753. doi:10.1007/s00709-019-01442-7. PMC 7203096 . PMID 31900730.
