Candidatus Korarchaeia

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"Candidatus Korarchaeia"
Korarchaeota.jpg
Scanning electron micrograph of the Obsidian Pool enrichment culture, showing Korarchaeia.
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Archaea
Clade: Proteoarchaeota
Kingdom: Thermoproteati
Phylum: Thermoproteota
Class: "Candidatus Korarchaeia"
Rinke et al. 2021 [1]
Orders
  • Korarchaeales
  • Panguiarchaeales
Synonyms
  • Crenarchaeida
  • Korarchaea
  • Korarchaeota
  • Proteoarchaeota

" Candidatus Korarchaeia" is a proposed class of Archaea under the phylum Thermoproteota. 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". [2] It was previously designated as phylum Korarchaeota and as kingdom with various names like Crenarchaeida or Proteoarchaeota. [3]

Contents

Taxonomy

"Candidatus Korarchaeia" had been designated as Korarchaeota in the domain, Archaea. They are thought to have diverged relatively early in the genesis of Archaea and are among the deep-branching lineages. [4] They have been classified as phylum (and sometimes as kingdom [5] ) Korarchaeota, along with Thaumarchaeota, Aigarchaeota, Crenarchaeota, under the kingdom Thermoproteati. The evolutionary link between Promethearchaeati and Thermoproteati. [6]

The first member of "Candidatus Korarchaeia" to have its genome reconstructed was Korarchaeum cryptofilum, which was found in a hot spring, Obsidian Pool, in Yellowstone National Park and described in 2008. [4] [7] Since then only a few Korarchaeal genomes have been described. [8] To check for "Candidatus Korarchaeia", 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. [5]

Based on protein sequences and phylogenetic analysis of conserved single genes, the "Candidatus Korarchaeia" was identified as a "deep archaeal lineage" with a possible relationship to the Crenarchaeota. Furthermore, given the known genetic makeup of archaea, the "Candidatus Korarchaeia" may have preserved a set of biological traits that correspond to the earliest known archaeal form. [4]

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. [9] Analysis of the genome of one "Candidatus Korarchaeia" 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. [4]

Revision

In 2001, George M. Garrity and John G. Holt described the phylum Crenarchaeota to include a single class Thermoprotei. [10] With the growing number of prokaryotic taxa and the inconsistent nomenclature and classification, there was a need to revise the overall classification of archaea. In 2014, French taxonomists led by David Moreira designated "TACK", generally considered as a superphylum, into a single kingdom named Proteoarchaeota. [11] However, such revision was not valid under the rules of the International Committee on Systematics of Prokaryotes (ICSP). [12] In 2021, a team of Australian scientists led by Christian Rinke and Philip Hugenholtz published a new classification on archaea in which their genetic evidence indicated Thermoproteati archaea belong to a unified phylum Thermoproteota, which could be divided into the classes "Candidatus Korarchaeia", Thermoprotei, Methanomethylicia (former phylum Ca. Verstraetearchaeota), Bathyarchaeia and Nitrososphaeria (former phylum Ca. Thaumachaeota). [1] The List of Prokaryotic names with Standing in Nomenclature (LPSN), an authority on maintenance and cataloguing prokaryotic taxons, upheld this classification of "Candidatus Korarchaeia" as a "preferred name" as a class. [13]

In 2022, the ICSP revised its International Code of Nomenclature of Prokaryotes (ICNP, Prokaryotic Code). [14] Following the revised code, Markus Göker and Aharon Oren (leaders of the ICSP), revised the domain and kingdom classifications 2024 in which the traditionally named "TACK" group was renamed to kingdom Thermoproteati. [3] In this way, previous designations such as phylum Korarchaeota or kingdom Proteoarchaeota are invalidated. [15]

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).

Phylogeny of "Candidatus Korarchaeia" [16] [17] [18]
"Ca. Korarchaeia"
"Panguiarchaeales"
"Panguiarchaeaceae"

"Panguiarchaeum symbiosum"

"Korarchaeales"
"Korarchaeaceae"

"Ca. Korarchaeum cryptofilum"

"Ca. Methanodesulfokores washburnensis"

Listed below are the known species of "Candidatus Korarchaeia": [19]

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. [4] 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. [22]

Characteristics

"Candidatus Korarchaeia" exhibit characteristics such as having a cell wall without peptidoglycan, as well as lipid membranes that are ether-linked. [23] They have a surface layer of paracrystalline protein. [24] 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. [23] [24] 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. [25] The cells have an ultrathin filamentous morphology that may vary in length. [4] They typically average 15 μm in length and 0.16 μm in diameter but can be seen up to 100 μm long. [25] Some Archaea can fix carbon dioxide through the 3-hydroxypropionate/4-hydroxybutyrate pathway into organic compounds [26]

Ecology

"Candidatus Korarchaeia" have only been found in hydrothermal environments ranging from terrestrial, including hot springs [4] [27] to marine, including shallow hydrothermal vents and deep-sea hydrothermal vents. Previous research has shown greater diversity of "Candidatus Korarchaeia" found in terrestrial hot springs compared to marine environments. [5] "Candidatus Korarchaeia" have been found in nature in only low abundances. [28] [29] Korarcheota likely originated in marine environments and then adapted to terrestrial ones. [30]

Geographically, "Candidatus Korarchaeia" have been found in a variety of locations around the world including Japan, Yellowstone National Park, the Gulf of California, Iceland and Russia. [5] [23]

"Candidatus Korarchaeia" are thermophiles, having been found living in conditions of up to 128 degrees Celsius. [5] The lowest temperature they have been found in is 52 degrees Celsius. [23] While they have frequently been observed living in acidic conditions, they have also been found living in conditions up to a pH of 10. [31]

Researchers have identified a virus that can potentially infect "Candidatus Korarchaeia". [32]

Each of these six hot springs (clockwise from top left: Uzon4, Uzon7, Uzon8, Uzon9, Mut11, Mut13) in Kamchatka was found to contain "Candidatus Korarchaeia". KamchatkaKorHotSprings.jpg
Each of these six hot springs (clockwise from top left: Uzon4, Uzon7, Uzon8, Uzon9, Mut11, Mut13) in Kamchatka was found to contain "Candidatus Korarchaeia".

See also

References

  1. 1 2 Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database". Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN   2058-5276. PMID   34155373.
  2. ↑ 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.
  3. 1 2 Göker, Markus; Oren, Aharon (2024). "Valid publication of names of two domains and seven kingdoms of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 74 (1): 006242. doi: 10.1099/ijsem.0.006242 . ISSN   1466-5034. PMID   38252124.
  4. 1 2 3 4 5 6 7 8 9 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. 1 2 3 4 5 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  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. ↑ Garrity, George M.; Holt, John G.; Reysenbach, Anna-Louise; Huber, Harald; Stetter, Karl O.; Zillig, Wolfram; Itoh, Takashi; Suzuki, Ken-Ichiro; Sanchez, Priscilla C. (2001), Boone, David R.; Castenholz, Richard W.; Garrity, George M. (eds.), "Phylum Al. Crenarchaeota phy. nov.", Bergey’s Manual® of Systematic Bacteriology: Volume One : The Archaea and the Deeply Branching and Phototrophic Bacteria, New York, NY: Springer, pp. 169–210, doi:10.1007/978-0-387-21609-6_16, ISBN   978-0-387-21609-6 , retrieved 2025-06-25
  11. ↑ Petitjean, Céline; Deschamps, Philippe; López-García, Purificación; Moreira, David (2015-01-01). "Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota". Genome Biology and Evolution. 7 (1): 191–204. doi:10.1093/gbe/evu274. ISSN   1759-6653. PMC   4316627 . PMID   25527841.
  12. ↑ Chuvochina, Maria; Rinke, Christian; Parks, Donovan H.; Rappé, Michael S.; Tyson, Gene W.; Yilmaz, Pelin; Whitman, William B.; Hugenholtz, Philip (2019-01-01). "The importance of designating type material for uncultured taxa". Systematic and Applied Microbiology. Taxonomy of uncultivated Bacteria and Archaea. 42 (1): 15–21. doi: 10.1016/j.syapm.2018.07.003 . ISSN   0723-2020. PMID   30098831.
  13. ↑ "Class: Korarchaeia". lpsn.dsmz.de. Retrieved 2025-06-25.
  14. ↑ Oren, Aharon; Arahal, David R.; Göker, Markus; Moore, Edward R. B.; Rossello-Mora, Ramon; Sutcliffe, Iain C. (2023). "International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision)". International Journal of Systematic and Evolutionary Microbiology. 73 (5a): 005585. doi: 10.1099/ijsem.0.005585 . ISSN   1466-5034. PMID   37219928.
  15. ↑ "Phylum: Thermoproteota". lpsn.dsmz.de. Retrieved 2025-06-25.
  16. ↑ "GTDB release 09-RS220". Genome Taxonomy Database . Retrieved 10 May 2024.
  17. ↑ "ar53_r220.sp_label". Genome Taxonomy Database . Retrieved 10 May 2024.
  18. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2024.
  19. 1 2 3 4 5 6 7 8 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.
  20. ↑ Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota
  21. 1 2 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.
  22. ↑ 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.
  23. 1 2 3 4 Miller RL (January 2008). "Diversity, biogeography, and geochemical habitat of Korarchaeota in continental hot springs". UNLV Retrospective Theses & Dissertations. doi:10.25669/6h98-vit6.
  24. 1 2 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.
  25. 1 2 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.
  26. ↑ 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.
  27. ↑ 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.
  28. 1 2 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.
  29. ↑ Auchtung TA (2007). Ecology of the hydrothermal candidate archaeal division, Korarchaeota (PhD thesis). Harvard University.
  30. ↑ 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.
  31. ↑ 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.
  32. ↑ 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.

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