Wikipedia

Hadesarchaea

Hadesarchaea, formerly called the South-African Gold Mine Miscellaneous Euryarchaeal Group, are a class of thermophile microorganisms that have been found in deep mines, hot springs, marine sediments, and other subterranean environments.[1][2][3][4][5]

Hadesarchaea
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Hadesarchaeota

McGonigle et al. 2019
Class:
Hadesarchaea

Baker et al. 2016
Order
  • "Hadarchaeales"
Synonyms
  • "Hadarchaeota" Chuvochina et al. 2019
  • "Hadarchaeia" Chuvochina et al. 2019
  • "Stygia" Adam et al. 2017

Nomenclature

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These archaea were initially called South-African Gold Mine Miscellaneous Euryarchaeal Group (SAGMEG), after their initial site of discovery.[6][7] The name Hadesarchaea was proposed by Baker et al. in 2016, a reference to the Greek god of the underworld.[1]

Phylogeny

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Previously, Hadesarchaea (or SAGMEG) were only known to exist through their distinctive phylogenetic position in the tree of life. In 2016, scientists using metagenomic shotgun sequencing were able to assemble several near-full genomes of these archaea.[1] It was shown that the genome of Hadesarchaea is approximately 1.5 Megabase pairs in size,[1] which is about 0.5 Mbp smaller than most archaea.[8] These archaea have not been successfully cultivated in the laboratory, but their metabolic properties have been inferred from the genomic reconstructions.[1] Hadesarchaea may have evolved from a methanogenic ancestor based on the genetic similarity with other methanogenic organisms.[9]

Taxonomy

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  • "Persephonarchaeia" corrig. Mwirichia et al. 2016 (MSBL-1)
  • "Hadarchaeia" Chuvochina et al. 2019 ["Hadesarchaea" Baker et al. 2016] (SAGMEG)[10][11][12][13]
    • "Hadarchaeales" Chuvochina et al. 2019 ["Hadesarchaeales" Hua et al. 2019]
      • "Cerberiarchaeaceae" Benito Merino et al. 2024
        • "Candidatus Cerberiarchaeum" Benito Merino et al. 2024
          • "Ca. C. oleivorans" Benito Merino et al. 2024
        • "Candidatus Melinoarchaeum" Yu et al. 2024
          • "Ca. M. fermentans" Yu et al. 2024
      • "Hadarchaeaceae" Chuvochina et al. 2019
        • "Candidatus Hadarchaeum" Chuvochina et al. 2019
          • "Ca. H. yellowstonense" Chuvochina et al. 2019
        • "Candidatus Hadesarchaeum" Hua et al. 2019
          • "Ca. H. tengchongensis" Hua et al. 2019
        • "Candidatus Methanourarchaeum" Hua et al. 2019
          • "Ca. M. thermotelluricum" Hua et al. 2019

Habitat and metabolism

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These microbes were first discovered in a gold mine in South Africa at a depth of approximately 3 km (2 mi),[6] where they are able to live without oxygen or light.[8][14][15] They were later also found in the White Oak River estuary in North Carolina and in Yellowstone National Park's Lower Culex Basin.[16] These areas are approximately 70 °C (158 °F) and highly alkaline.[16] Based on phylogenetic marker gene survey, Hadesarchaeota might be present in soils in ancient mining areas in East Harz region, Germany.[17]

The microbes have been found in other marine environments as well. Some of these areas include cold seep systems in the South China Sea. Hadesarchaea has been found to be a dominant member of the archaeal community in the area. These cold seeps contain gas hydrate bearing sediments in which microbes play a major role in biogeochemical cycling. It is believed that Hadesarchaea is involved in the reaction of carbon dioxide with water in this environment.[18] Hadesarchaea have also been found in subseafloor habitats located in the Guaymas Basin and Sonora Margin around the Gulf of California.[19]

In addition to being present in marine sediments, mines, and hot springs, Hadesarchaea has been identified in the gut microbiome of certain fish species. The freshwater pufferfish (Tetraodon cutcutia), native to India, Assam, Bihar, and West Bengal, was found to have Hadesarchaea present in their gut microbiome. Hadesarchaea was found to be in the second most abundant in the archaeal community of the freshwater pufferfish. This was found to be similar to community abundance found in the gut of carnivorous Salmon and herbivorous grass carp. While Hadesarchaea are found to be in such high abundance for these environments, it is not completely known how they influence the health and trophic level of these fish.[20]

Hadesarchaea are unique among known archaea in that they can convert carbon monoxide and water to carbon dioxide and oxygen, producing hydrogen as a by-product. From metagenome-assembled genome (MAG) data, Hadesarchaea possess genes associated with Wood-Ljungdahl carbon fixation pathway, methanogenesis and alkane metabolism.[21][22] Hadesarchaeal genomes have also been reported to contain genes that enable them to metabolize sugars and amino acids in a heterotrophic lifestyle, and perform dissimilatory nitrite reduction to ammonium.[1][3] Initial research suggests that these organisms are also involved in significant geochemical processes.[1]

Because of their relatively small genome, it is assumed that the genomes of Hadesarchaea have been subjected to genome streamlining, possibly as a result of nutrient limitation.[1]

See also

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References

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  1. ^ a b c d e f g h Baker, Brett J.; Saw, Jimmy H.; Lind, Anders E.; Lazar, Cassandra Sara; Hinrichs, Kai-Uwe; Teske, Andreas P.; Ettema, Thijs J.G. (February 16, 2016). "Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea". Nature Microbiology. 1 (3): 16002. doi:10.1038/nmicrobiol.2016.2. PMID 27572167.
  2. ^ Parkes, R. John; Webster, Gordon; Cragg, Barry A.; Weightman, Andrew J.; Newberry, Carole J.; Ferdelman, Timothy G.; Kallmeyer, Jens; Jørgensen, Bo B.; Aiello, Ivano W.; Fry, John C. (July 2007). "Deep sub-seafloor prokaryotes stimulated at interfaces over geological time" (PDF). Nature. 436 (7049): 390–394. doi:10.1038/nature03796. ISSN 0028-0836. PMID 16034418. S2CID 4390333.
  3. ^ a b Biddle, J. F.; Lipp, J. S.; Lever, M. A.; Lloyd, K. G.; Sorensen, K. B.; Anderson, R.; Fredricks, H. F.; Elvert, M.; Kelly, T. J.; Schrag, D. P.; Sogin, M. L. (2006-02-27). "Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru". Proceedings of the National Academy of Sciences. 103 (10): 3846–3851. doi:10.1073/pnas.0600035103. ISSN 0027-8424. PMC 1533785. PMID 16505362.
  4. ^ Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka; Salavirta, Heikki; Nyyssönen, Mari; Nuppunen-Puputti, Maija; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja (2016-05-30). "Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids". Biogeosciences. 13 (10): 3091–3108. doi:10.5194/bg-13-3091-2016. hdl:10023/10226. ISSN 1726-4189.
  5. ^ Bomberg, Malin; Nyyssönen, Mari; Pitkänen, Petteri; Lehtinen, Anne; Itävaara, Merja (2015). "Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland". BioMed Research International. 2015: 979530. doi:10.1155/2015/979530. ISSN 2314-6133. PMC 4573625. PMID 26425566.
  6. ^ a b Ettema, Thijs (February 17, 2016). "New paper about the Hadesarchaea published!". Ettema Lab. Archived from the original on March 4, 2016. Retrieved February 25, 2016.
  7. ^ Takai, K.; Moser, D. P.; DeFlaun, M.; Onstott, T. C.; Fredrickson, J. K. (2001-12-01). "Archaeal Diversity in Waters from Deep South African Gold Mines". Applied and Environmental Microbiology. 67 (12): 5750–5760. doi:10.1128/aem.67.21.5750-5760.2001. ISSN 0099-2240. PMC 93369. PMID 11722932.
  8. ^ a b "Hadesarchaea: a New Archaeal Class of Cosmopolitan Deep Microbes". Deep Carbon Observatory. February 18, 2016. Archived from the original on March 4, 2016. Retrieved February 25, 2016.
  9. ^ Evans, Paul N.; Boyd, Joel A.; Leu, Andy O.; Woodcroft, Ben J.; Parks, Donovan H.; Hugenholtz, Philip; Tyson, Gene W. (April 2019). "An evolving view of methane metabolism in the Archaea". Nature Reviews Microbiology. 17 (4): 219–232. doi:10.1038/s41579-018-0136-7. ISSN 1740-1534. PMID 30664670. S2CID 58572324.
  10. ^ "GTDB release 06-RS202". Genome Taxonomy Database.
  11. ^ "ar122_r202.sp_label". Genome Taxonomy Database.
  12. ^ "Taxon History". Genome Taxonomy Database.
  13. ^ Sayers; et al. "Hadesarchaea". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-06-05.
  14. ^ "Scientists discover new microbes that thrive deep in the earth" (Press release). Uppsala University. February 15, 2016. Retrieved February 25, 2016.
  15. ^ "Underworld microbes shock scientists: Mystery of Hadesarchaea". India Today. New Delhi. February 17, 2016. Archived from the original on February 24, 2016. Retrieved February 25, 2016.
  16. ^ a b Atherton, Matt (February 15, 2016). "God of the underworld microbes Hadesarchaea discovered living on toxic gas deep below Yellowstone hot springs". IB Times. Retrieved February 25, 2016.
  17. ^ Köhler, J. Michael; Kalensee, Franziska; Cao, Jialan; Günther, P. Mike (2019-07-09). "Hadesarchaea and other extremophile bacteria from ancient mining areas of the East Harz region (Germany) suggest an ecological long-term memory of soil". SN Applied Sciences. 1 (8): 839. doi:10.1007/s42452-019-0874-9. ISSN 2523-3971.
  18. ^ Cui, Hongpeng; Su, Xin; Chen, Fang; Holland, Melanie; Yang, Shengxiong; Liang, Jinqiang; Su, Pibo; Dong, Hailiang; Hou, Weiguo (February 2019). "Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea". Marine Environmental Research. 144: 230–239. doi:10.1016/j.marenvres.2019.01.009. PMID 30732863. S2CID 73443709.
  19. ^ Deb, Sushanta; Das, Lipika; Das, Subrata K. (December 2020). "Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia)". Archives of Microbiology. 202 (10): 2761–2770. doi:10.1007/s00203-020-01997-7. ISSN 0302-8933. PMID 32737543. S2CID 220888551.
  20. ^ Ramírez, Gustavo A.; McKay, Luke J.; Fields, Matthew W.; Buckley, Andrew; Mortera, Carlos; Hensen, Christian; Ravelo, Ana Christina; Teske, Andreas P. (September 2020). "The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories". iScience. 23 (9): 101459. doi:10.1016/j.isci.2020.101459. PMC 7476861. PMID 32861995.
  21. ^ Hua, Zheng-Shuang; Wang, Yu-Lin; Evans, Paul N.; Qu, Yan-Ni; Goh, Kian Mau; Rao, Yang-Zhi; Qi, Yan-Ling; Li, Yu-Xian; Huang, Min-Jun; Jiao, Jian-Yu; Chen, Ya-Ting (2019-10-08). "Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea". Nature Communications. 10 (1): 4574. doi:10.1038/s41467-019-12574-y. ISSN 2041-1723. PMC 6783470. PMID 31594929.
  22. ^ Wang, Yinzhao; Wegener, Gunter; Hou, Jialin; Wang, Fengping; Xiao, Xiang (2019-03-04). "Expanding anaerobic alkane metabolism in the domain of Archaea" (PDF). Nature Microbiology. 4 (4): 595–602. doi:10.1038/s41564-019-0364-2. ISSN 2058-5276. PMID 30833728. S2CID 71145257.
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