Korarchaeota
Korarchaeota | |
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Scanning electron micrograph of the Obsidian Pool enrichment culture, showing Korarchaeota. | |
Scientific classification | |
Domain: | Archaea |
Kingdom: | "Proteoarchaeota" |
Superphylum: | TACK |
Phylum: | "Korarchaeota" Barns et al. 1996 |
Class: | "Korarchaeia" Rinke et al. 2020[1] |
Order: | "Korarchaeales" Petitjean et al. 2015[2] |
Family: | "Korarchaeaceae" Rinke et al. 2020 |
Species | |
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Synonyms | |
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The Korarchaeota is a proposed phylum within the Archaea.[3] 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.[4] They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.[5]
Taxonomy
The Korarchaeota are a proposed phylum in the domain, Archaea.[6] They are thought to have diverged relatively early in the genesis of Archaea and are among the deep-branching lineages.[6] Korarchaeota are also known as Xenarchaeota. Korarchaeaota, along with Thaumarchaeota, Aigarchaeota, Crenarchaeota, belong to the superphylum called TACK.[7] The evolutionary link between Asgard archaea and Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) is yet unknown.[7]
The first member of Korarchaeota to have its genome reconstructed was Korarchaeum crypotfilum, which was found in a hot spring in Yellowstone National Park and described in 2008.[8] Since then only a few Korarchaeal genomes have been described.[9] To check for Korarchaeota, samples from a variety of hot springs in Iceland and Kamchatka were gathered. According to the samples and analysis, the Icelandic samples contained about 87 distinct 16S ribosomal nucleic acid sequences, whereas the Kamchatkan samples contained about 33.[10]
Based on protein sequences and phylogenetic analysis of conserved single genes, the Korarchaeote was identified as a “deep archaeal lineage” with a possible relationship to the Crenarchaeota.[11] Furthermore, given the known genetic makeup of archaea, the Korarchaeota may have preserved a set of biological traits that correspond to the earliest known archaeal form.[11]
Analysis of their 16S rRNA gene sequences suggests that they are a deeply branching lineage that does not belong to the main archaeal groups, Thermoproteota and Euryarchaeota.[12] Analysis of the genome of one korarchaeote that was enriched from a mixed culture revealed a number of both Crenarchaeota- and Euryarchaeota-like features and supports the hypothesis of a deep-branching ancestry.[13]
Species
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI).
Listed below are the known species of Korarcheota[14] Candidatus Korarchaeota
- Genus Candidatus Korarchaeota archaeon[15]
- Genus Candidatus Korarchaeota archaeon NZ13-K[15]
- Genus Candidatus Korarchaeum[6]
- Species Candidatus Korarchaeum cryptofilum[6]
- Candidatus Korarchaeum cryptofilum OPF8[6]
- Species Candidatus Korarchaeum cryptofilum[6]
- Genus Candidatus Methanodesulfokores[16]
- Species Candidatus Methanodesulfokores washburnensis[16]
- Genus Korarchaeote SRI-306 [15]
- Genus environmental samples[15]
- uncultured korarchaeote pBA5[15]
- uncultured korarchaeote pJP27[15]
- uncultured korarchaeote pJP78[15]
Reference species
A strain of Korarchaeum cryptofilum was cultivated from an enrichment culture from a hot spring in Yellowstone National Park, USA and described in 2008.[13] The cells are long and needle-shaped, which gave the species its name, alluding to its "cryptical filaments". This organism lacks the genes for purine nucleotide biosynthesis and thus relies on environmental sources to meet its purine requirements.[17]
Characteristics
Korarchaeota are a proposed phylum within the domain, Archaea, and therefore exhibit characteristics such as having a cell wall without peptidoglycan, as well as lipid membranes that are ether-linked.[18] They have a surface layer of paracrystalline protein.[19] This surface layer, known as the S-layer, is densely packed and consists of 1-2 proteins form various lattice structures and are most likely what maintains the cells’ structural integrity.[18][19] They are typically rod-shaped, however, it has been found that this morphology can change to be thicker-shaped in the presence of higher sodium dodecyl sulfate (SDS) concentrations.[20] Korarchaeota cells have an ultrathin filamentous morphology that may vary in length.[6] They typically average 15 μm in length and 0.16 μm in diameter but can be seen up to 100 μm long.[20] Some Archaea can fix carbon dioxide through the 3-hydroxypropionate/4-hydroxybutyrate pathway into organic compounds[21]
Ecology
Korarcheota have only been found in hydrothermal environments ranging from terrestrial, including hot springs [6][22] to marine, including shallow hydrothermal vents and deep-sea hydrothermal vents.[23] Previous research has shown greater diversity of Korarchaea found in terrestrial hot springs compared to marine environments.[23] Korarchaeota have been found in nature in only low abundances.[24][25][26] Korarcheota likely originated in marine environments and then adapted to terrestrial ones.[27]
Geographically, Korarcheota have been found in a variety of locations around the world including Japan, Yellowstone National Park, the Gulf of California, Iceland and Russia.[18][23]
Korarchaeota are thermophiles, having been found living in conditions of up to 128 degrees Celsius.[23] The lowest temperature they have been found in is 52 degrees Celsius.[18] While they have frequently been observed living in acidic conditions, they have also been found living in conditions up to a pH of 10.[28][23]
Researchers have identified a virus that can potentially infect Korarcheota.[29]
![Each of these six hot springs (from top left, clockwise: Uzon4, Uzon7, Uzon8, Uzon9, Mut11, Mut13) in Kamchatka were found to contain Korarchaeota.](http://upload.wikimedia.org/wikipedia/commons/thumb/a/a4/KamchatkaKorHotSprings.jpg/700px-KamchatkaKorHotSprings.jpg)
See also
References
- ^ Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
- ^ Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota
- ^ See the NCBI webpage on Korarchaeota. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
- ^ Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (23): 8102–8107. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC 2430366. PMID 18535141.
- ^ Boone DR, Brenner DJ, Castenholz RW, De Vos P, Garrity GM, Krieg NR, Goodfellow M (2001). Bergey's manual of systematic bacteriology (2nd ed.). New York: Springer. ISBN 978-0-387-21609-6. OCLC 619443681.
- ^ a b c d e f g Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (23): 8102–8107. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC 2430366. PMID 18535141.
- ^ a b Liu Y, Li M (June 2022). "The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea". mLife. 1 (2): 218–222. doi:10.1002/mlf2.12020. ISSN 2770-100X. PMC 10989867. S2CID 249298036.
- ^ Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, et al. (2012-05-04). "Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning". PLOS ONE. 7 (5): e35964. doi:10.1371/journal.pone.0035964. PMC 3344838. PMID 22574130.
- ^ Barns SM, Delwiche CF, Palmer JD, Pace NR (August 1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America. 93 (17): 9188–9193. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC 38617. PMID 8799176.
- ^ Reigstad LJ, Jorgensen SL, Schleper C (March 2010). "Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka". The ISME Journal. 4 (3): 346–356. doi:10.1038/ismej.2009.126. PMID 19956276. S2CID 6951841.
- ^ a b Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (23): 8102–8107. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC 2430366. PMID 18535141.
- ^ Barns SM, Delwiche CF, Palmer JD, Pace NR (August 1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America. 93 (17): 9188–9193. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC 38617. PMID 8799176.
- ^ a b Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (23): 8102–8107. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC 2430366. PMID 18535141.
- ^ Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. (January 2020). "NCBI Taxonomy: a comprehensive update on curation, resources and tools". Database. 2020: baaa062. doi:10.1093/database/baaa062. PMC 7408187. PMID 32761142.
- ^ a b c d e f g Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. (January 2020). "NCBI Taxonomy: a comprehensive update on curation, resources and tools". Database. 2020: baaa062. doi:10.1093/database/baaa062. PMC 7408187. PMID 32761142.
- ^ a b McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, Jay ZJ, et al. (April 2019). "Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota". Nature Microbiology. 4 (4): 614–622. doi:10.1038/s41564-019-0362-4. OSTI 1779059. PMID 30833730. S2CID 256705892.
- ^ Brown AM, Hoopes SL, White RH, Sarisky CA (December 2011). "Purine biosynthesis in archaea: variations on a theme". Biology Direct. 6: 63. doi:10.1186/1745-6150-6-63. PMC 3261824. PMID 22168471.
- ^ a b c d Miller RL (January 2008). "Diversity, biogeography, and geochemical habitat of Korarchaeota in continental hot springs". UNLV Retrospective Theses & Dissertations. doi:10.25669/6h98-vit6.
- ^ a b Rodrigues-Oliveira T, Belmok A, Vasconcellos D, Schuster B, Kyaw CM (2017). "Archaeal S-Layers: Overview and Current State of the Art". Frontiers in Microbiology. 8: 2597. doi:10.3389/fmicb.2017.02597. PMC 5744192. PMID 29312266.
- ^ a b Elkins JG, Kunin V, Anderson I, Barry K, Goltsman E, Lapidus A, et al. (May 2007). The Korarchaeota: Archaeal orphans representing an ancestral lineage of life (Report). Berkeley, CA (United States): Lawrence Berkeley National Lab. (LBNL). doi:10.2172/960397. OSTI 960397.
- ^ Berg IA, Kockelkorn D, Buckel W, Fuchs G (December 2007). "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea". Science. 318 (5857): 1782–1786. doi:10.1126/science.1149976. PMID 18079405. S2CID 13218676.
- ^ Takai K, Yoshihiko S (1 February 1999). "A molecular view of archaeal diversity in marine and terrestrial hot water environments". Microbiology Ecology. 28 (2): 177–188. doi:10.1111/j.1574-6941.1999.tb00573.x. S2CID 84495991.
- ^ a b c d e Reigstad LJ, Jorgensen SL, Schleper C (March 2010). "Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka". The ISME Journal. 4 (3): 346–356. doi:10.1038/ismej.2009.126. PMID 19956276. S2CID 6951841.
- ^ a b Auchtung TA, Shyndriayeva G, Cavanaugh CM (January 2011). "16S rRNA phylogenetic analysis and quantification of Korarchaeota indigenous to the hot springs of Kamchatka, Russia". Extremophiles. 15 (1): 105–116. doi:10.1007/s00792-010-0340-5. PMID 21153671. S2CID 12091232.
- ^ Reigstad LJ, Jorgensen SL, Schleper C (March 2010). "Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka". The ISME Journal. 4 (3): 346–356. doi:10.1038/ismej.2009.126. PMID 19956276.
- ^ Auchtung TA (2007). Ecology of the hydrothermal candidate archaeal division, Korarchaeota (PhD thesis). Harvard University.
- ^ Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, et al. (2012-05-04). Mormile MR (ed.). "Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning". PLOS ONE. 7 (5): e35964. doi:10.1371/journal.pone.0035964. PMC 3344838. PMID 22574130.
- ^ Marteinsson VT, Kristjánsson JK, Kristmannsdóttir H, Dahlkvist M, Saemundsson K, Hannington M, et al. (February 2001). "Discovery and description of giant submarine smectite cones on the seafloor in Eyjafjordur, northern Iceland, and a novel thermal microbial habitat". Applied and Environmental Microbiology. 67 (2): 827–833. doi:10.1128/AEM.67.2.827-833.2001. PMC 92654. PMID 11157250.
- ^ Liu Y, Brandt D, Ishino S, Ishino Y, Koonin EV, Kalinowski J, et al. (June 2019). "New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures". Environmental Microbiology. 21 (6): 2002–2014. doi:10.1111/1462-2920.14479. PMC 11128462. PMID 30451355. S2CID 53950297.
Further reading
- Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, et al. (May 2002). "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 3): 1043–1047. doi:10.1099/ijs.0.02360-0. PMID 12054223.
- Gürtler V, Mayall BC (January 2001). "Genomic approaches to typing, taxonomy and evolution of bacterial isolates". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 1): 3–16. doi:10.1099/00207713-51-1-3. PMID 11211268.
- Dalevi D, Hugenholtz P, Blackall LL (March 2001). "A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 2): 385–391. doi:10.1099/00207713-51-2-385. PMID 11321083.
- Keswani J, Whitman WB (March 2001). "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 2): 667–678. doi:10.1099/00207713-51-2-667. PMID 11321113.
- Young JM (May 2001). "Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 3): 945–953. doi:10.1099/00207713-51-3-945. PMID 11411719.
- Christensen H, Bisgaard M, Frederiksen W, Mutters R, Kuhnert P, Olsen JE (November 2001). "Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision)". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 6): 2221–2225. doi:10.1099/00207713-51-6-2221. PMID 11760965.
- Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (May 2000). "DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA". International Journal of Systematic and Evolutionary Microbiology. 50 (3): 1095–1102. doi:10.1099/00207713-50-3-1095. PMID 10843050.
- Xu HX, Kawamura Y, Li N, Zhao L, Li TM, Li ZY, et al. (July 2000). "A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube". International Journal of Systematic and Evolutionary Microbiology. 50 (4): 1463–1469. doi:10.1099/00207713-50-4-1463. PMID 10939651.
- Young JM (July 2000). "Suggestions for avoiding on-going confusion from the Bacteriological Code". International Journal of Systematic and Evolutionary Microbiology. 50 (4): 1687–1689. doi:10.1099/00207713-50-4-1687. PMID 10939677.
- Hansmann S, Martin W (July 2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis". International Journal of Systematic and Evolutionary Microbiology. 50 (4): 1655–1663. doi:10.1099/00207713-50-4-1655. PMID 10939673.
- Tindall BJ (July 1999). "Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes". International Journal of Systematic Bacteriology. 49 Pt 3 (3): 1317–1319. doi:10.1099/00207713-49-3-1317. PMID 10490293.
- Tindall BJ (July 1999). "Proposal to change Rule 18a, Rule 18f and Rule 30 to limit the retroactive consequences of changes accepted by the ICSB". International Journal of Systematic Bacteriology. 49 (3): 1321–1322. doi:10.1099/00207713-49-3-1321. PMID 10425797.
- Tindall BJ (July 1999). "Misunderstanding the Bacteriological Code". International Journal of Systematic Bacteriology. 49 (3): 1313–1316. doi:10.1099/00207713-49-3-1313. PMID 10425796.
- Tindall BJ (July 1999). "Proposals to update and make changes to the Bacteriological Code". International Journal of Systematic Bacteriology. 49 Pt 3 (3): 1309–1312. doi:10.1099/00207713-49-3-1309. PMID 10425795.
- Palys T, Nakamura LK, Cohan FM (October 1997). "Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data". International Journal of Systematic Bacteriology. 47 (4): 1145–1156. doi:10.1099/00207713-47-4-1145. PMID 9336922.
- Euzéby JP (April 1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic Bacteriology. 47 (2): 590–592. doi:10.1099/00207713-47-2-590. PMID 9103655.
- Burggraf S, Heyder P, Eis N (February 1997). "A pivotal Archaea group". Nature. 385 (6619): 780. Bibcode:1997Natur.385..780B. doi:10.1038/385780a0. PMID 9039908. S2CID 4357113.
- Barns SM, Delwiche CF, Palmer JD, Pace NR (August 1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America. 93 (17): 9188–9193. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC 38617. PMID 8799176.
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- Barns SM, Fundyga RE, Jeffries MW, Pace NR (March 1994). "Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment". Proceedings of the National Academy of Sciences of the United States of America. 91 (5): 1609–1613. Bibcode:1994PNAS...91.1609B. doi:10.1073/pnas.91.5.1609. PMC 43212. PMID 7510403.
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- Winker S, Woese CR (1991). "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics". Systematic and Applied Microbiology. 14 (4): 305–310. doi:10.1016/s0723-2020(11)80303-6. PMID 11540071.
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- 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): 5088–5090. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
- v
- t
- e
- Domain
- Archaea
- Bacteria
- Eukaryota
- (major groups
- Excavata
- Diaphoretickes
- Hacrobia
- Cryptista
- Rhizaria
- Alveolata
- Stramenopiles
- Plants
- Hacrobia
- Amorphea
- Amoebozoa
- Opisthokonta
- Animals
- Fungi
- Mesomycetozoea)
Hadarchaeota |
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"Hydrothermarchaeota" |
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"Methanobacteriota" |
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"Halobacteriota" |
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"Thermoplasmatota" |
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- "Aenigmatarchaeota"
- "Aenigmatarchaeia"
- "Altarchaeota"
- "Altarchaeia"
- "Iainarchaeota"
- "Iainarchaeia"
- "Huberarchaeota"
- "Huberarchaeia"
- "Micrarchaeota"
- "Micrarchaeia"
- "Nanohalarchaeota"
- "Nanohalarchaeia"
- "Nanoarchaeota"
- "Nanoarchaeia"
- "Nanohalobiia"
- "Undinarchaeota"
- "Undinarchaeia"
TACK |
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Asgard |
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- Source:
- Alternative views: Wikispecies