Korarchaeota

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Korarchaeota
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
Synonyms
  • "Xenarchaea"
  • "Xenarchaeota"

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]
  • 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.
Each of these six hot springs (clockwise from top left: Uzon4, Uzon7, Uzon8, Uzon9, Mut11, Mut13) in Kamchatka was found to contain Korarchaeota.[24]







See also

References

  1. ^ Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
  2. ^ Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota
  3. ^ See the NCBI webpage on Korarchaeota. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
  18. ^ 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.
  19. ^ 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.
  20. ^ 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.
  21. ^ 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.
  22. ^ 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.
  23. ^ 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.
  24. ^ 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.
  25. ^ 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.
  26. ^ Auchtung TA (2007). Ecology of the hydrothermal candidate archaeal division, Korarchaeota (PhD thesis). Harvard University.
  27. ^ 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.
  28. ^ 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.
  29. ^ 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

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