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Nitrososphaerota

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Nitrososphaerota
Nitrosopumilus maritimus, partially with virions of Nitrosopumilus spindle-shaped virus 1 (Thaspiviridae) attached.
Scientific classification
Domain:
Archaea
Superphylum:
"Proteoarchaeota"
Phylum:
Nitrososphaerota

Brochier-Armanet et al. 2021[1]
Class:
Nitrososphaeria
Order
Synonyms
  • "Nitrososphaerota" Whitman et al. 2018
  • "Nitrososphaeraeota" Oren et al. 2015
  • "Thaumarchaeota" Brochier-Armanet et al. 2008[2]

The Nitrososphaerota (syn. Thaumarchaeota) are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota (formerly Crenarchaeota).[3][2][4] Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis.[2] The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes.[2][5] This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum.[6] The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum.[7][8] Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.[9]

Nitrososphaerota-derived membrane-spanning tetraether lipids (glycerol dialkyl glycerol tetraethers; GDGTs) from marine sediments can be used to reconstruct past temperatures via the TEX86 paleotemperature proxy, as these lipids vary in structure according to temperature.[10] Because most Nitrososphaerota seem to be autotrophs that fix CO2, their GDGTs can act as a record for past Carbon-13 ratios in the dissolved inorganic carbon pool, and thus have the potential to be used for reconstructions of the carbon cycle in the past.[7]

Taxonomy

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Phylogeny of Nitrososphaerota[11][12][13]
Phylogeny of Nitrososphaerota[14][15][16]
Nitrososphaeria

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[17] and National Center for Biotechnology Information (NCBI)[18]

Metabolism

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Nitrososphaerota are important ammonia oxidizers in aquatic and terrestrial environments, and are the first archaea identified as being involved in nitrification.[32] They are capable of oxidizing ammonia at much lower substrate concentrations than ammonia-oxidizing bacteria, and so probably dominate in oligotrophic conditions.[8][33] Their ammonia oxidation pathway requires less oxygen than that of ammonia-oxidizing bacteria, so they do better in environments with low oxygen concentrations like sediments and hot springs. Ammonia-oxidizing Nitrososphaerota can be identified metagenomically by the presence of archaeal ammonia monooxygenase (amoA) genes, which indicate that they are overall more dominant than ammonia oxidizing bacteria.[8] In addition to ammonia, at least one Nitrososphaerota strain has been shown to be able to use urea as a substrate for nitrification. This would allow for competition with phytoplankton that also grow on urea.[34] One study of microbes from wastewater treatment plants found that not all Nitrososphaerota that express amoA genes are active ammonia oxidizers. These Nitrososphaerota may be capable of oxidizing methane instead of ammonia, or they may be heterotrophic, indicating a potential for a diversity of metabolic lifestyles within the phylum.[35] Marine Nitrososphaerota have also been shown to produce nitrous oxide, which as a greenhouse gas has implications for climate change. Isotopic analysis indicates that most nitrous oxide flux to the atmosphere from the ocean, which provides around 30% of the natural flux, may be due to the metabolic activities of archaea.[36]

Many members of the phylum assimilate carbon by fixing HCO3−.[9] This is done using a hydroxypropionate/hydroxybutyrate cycle similar to the Thermoproteota but which appears to have evolved independently. All Nitrososphaerota that have been identified by metagenomics thus far encode this pathway. Notably, the Nitrososphaerota CO2-fixation pathway is more efficient than any known aerobic autotrophic pathway. This efficiency helps explain their ability to thrive in low-nutrient environments.[33] Some Nitrososphaerota such as Nitrosopumilus maritimus are able to incorporate organic carbon as well as inorganic, indicating a capacity for mixotrophy.[9] At least two isolated strains have been identified as obligate mixotrophs, meaning they require a source of organic carbon in order to grow.[34]

A study has revealed that Nitrososphaerota are most likely the dominant producers of the critical vitamin B12. This finding has important implications for eukaryotic phytoplankton, many of which are auxotrophic and must acquire vitamin B12 from the environment; thus the Nitrososphaerota could play a role in algal blooms and by extension global levels of atmospheric carbon dioxide. Because of the importance of vitamin B12 in biological processes such as the citric acid cycle and DNA synthesis, production of it by the Nitrososphaerota may be important for a large number of aquatic organisms.[37]

Environment

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Many Nitrososphaerota, such as Nitrosopumilus maritimus, are marine and live in the open ocean.[9] Most of these planktonic Nitrososphaerota, which compose the Marine Group I.1a, are distributed in the subphotic zone, between 100m and 350m.[7] Other marine Nitrososphaerota live in shallower waters. One study has identified two novel Nitrososphaerota species living in the sulfidic environment of a tropical mangrove swamp. Of these two species, Candidatus Giganthauma insulaporcus and Candidatus Giganthauma karukerense, the latter is associated with Gammaproteobacteria with which it may have a symbiotic relationship, though the nature of this relationship is unknown. The two species are very large, forming filaments larger than ever before observed in archaea. As with many Nitrososphaerota, they are mesophilic.[38] Genetic analysis and the observation that the most basal identified Nitrososphaerota genomes are from hot environments suggests that the ancestor of Nitrososphaerota was thermophilic, and mesophily evolved later.[32]

See also

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References

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  1. ^ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987.
  2. ^ a b c d Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (March 2008). "Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota". Nature Reviews Microbiology. 6 (3): 245–52. doi:10.1038/nrmicro1852. PMID 18274537. S2CID 8030169.
  3. ^ Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (May 2011). "Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil". Proceedings of the National Academy of Sciences of the United States of America. 108 (20): 8420–5. Bibcode:2011PNAS..108.8420T. doi:10.1073/pnas.1013488108. PMC 3100973. PMID 21525411.
  4. ^ DeLong EF (1992-06-15). "Archaea in coastal marine environments". Proceedings of the National Academy of Sciences. 89 (12): 5685–5689. Bibcode:1992PNAS...89.5685D. doi:10.1073/pnas.89.12.5685. ISSN 0027-8424. PMC 49357. PMID 1608980.
  5. ^ Brochier-Armanet C, Gribaldo S, Forterre P (December 2008). "A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya". Biology Direct. 3: 54. doi:10.1186/1745-6150-3-54. PMC 2621148. PMID 19105819.
  6. ^ Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C (August 2010). "Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota". Trends in Microbiology. 18 (8): 331–40. doi:10.1016/j.tim.2010.06.003. PMID 20598889.
  7. ^ a b c Pearson A, Hurley SJ, Walter SR, Kusch S, Lichtin S, Zhang YG (2016). "Stable carbon isotope ratios of intact GDGTs indicate heterogeneous sources to marine sediments". Geochimica et Cosmochimica Acta. 181: 18–35. Bibcode:2016GeCoA.181...18P. doi:10.1016/j.gca.2016.02.034.
  8. ^ a b c Pester M, Schleper C, Wagner M (June 2011). "The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology". Current Opinion in Microbiology. 14 (3): 300–6. doi:10.1016/j.mib.2011.04.007. PMC 3126993. PMID 21546306.
  9. ^ a b c d Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA (May 2010). "Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea". Proceedings of the National Academy of Sciences of the United States of America. 107 (19): 8818–23. Bibcode:2010PNAS..107.8818W. doi:10.1073/pnas.0913533107. PMC 2889351. PMID 20421470.
  10. ^ Schouten S, Hopmans EC, Schefuß E, Damste JS (2002). "Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures?". Earth and Planetary Science Letters. 204 (1–2): 265–274. Bibcode:2002E&PSL.204..265S. doi:10.1016/S0012-821X(02)00979-2. S2CID 54198843.
  11. ^ "The LTP". Retrieved 10 May 2023.
  12. ^ "LTP_all tree in newick format". Retrieved 10 May 2023.
  13. ^ "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
  14. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  15. ^ "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  16. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  17. ^ J.P. Euzéby. "Thaumarchaeota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-03-20.
  18. ^ Sayers, et al. "Thaumarchaeota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  19. ^ Stieglmeier M, Klingl A, Alves RJ, Rittmann SK, Melcher M, Leisch N, et al. (August 2014). "Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota". International Journal of Systematic and Evolutionary Microbiology. 64 (Pt 8): 2738–52. doi:10.1099/ijs.0.063172-0. PMC 4129164. PMID 24907263.
  20. ^ Muller F, Brissac T, Le Bris N, Felbeck H, Gros O (August 2010). "First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat". Environmental Microbiology. 12 (8): 2371–83. Bibcode:2010EnvMi..12.2371M. doi:10.1111/j.1462-2920.2010.02309.x. PMID 21966926.
  21. ^ Zhalnina KV, Dias R, Leonard MT, Dorr de Quadros P, Camargo FA, Drew JC, et al. (7 July 2014). "Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea". PLOS ONE. 9 (7): e101648. Bibcode:2014PLoSO...9j1648Z. doi:10.1371/journal.pone.0101648. PMC 4084955. PMID 24999826.
  22. ^ Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (September 2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–6. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID 16177789. S2CID 4340386.
  23. ^ Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (September 2011). "Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil". Proceedings of the National Academy of Sciences of the United States of America. 108 (38): 15892–7. Bibcode:2011PNAS..10815892L. doi:10.1073/pnas.1107196108. PMC 3179093. PMID 21896746.
  24. ^ Lebedeva EV, Hatzenpichler R, Pelletier E, Schuster N, Hauzmayer S, Bulaev A, Grigor'eva NV, Galushko A, Schmid M, Palatinszky M, Le Paslier D, Daims H, Wagner M (2013). "Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats". PLOS ONE. 8 (11): e80835. Bibcode:2013PLoSO...880835L. doi:10.1371/journal.pone.0080835. PMC 3835317. PMID 24278328.
  25. ^ Li Y, Ding K, Wen X, Zhang B, Shen B, Yang Y (March 2016). "A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics". Scientific Reports. 6: 23747. Bibcode:2016NatSR...623747L. doi:10.1038/srep23747. PMC 4814877. PMID 27030530.
  26. ^ Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, et al. (January 2015). "Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean". Proceedings of the National Academy of Sciences of the United States of America. 112 (4): 1173–8. Bibcode:2015PNAS..112.1173S. doi:10.1073/pnas.1416223112. PMC 4313803. PMID 25587132.
  27. ^ Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (February 2011). "Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis". PLOS ONE. 6 (2): e16626. Bibcode:2011PLoSO...616626B. doi:10.1371/journal.pone.0016626. PMC 3043068. PMID 21364937.
  28. ^ Kim BK, Jung MY, Yu DS, Park SJ, Oh TK, Rhee SK, Kim JF (October 2011). "Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1". Journal of Bacteriology. 193 (19): 5539–40. doi:10.1128/JB.05717-11. PMC 3187385. PMID 21914867.
  29. ^ Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, Kwon K, Lee JH, Rhee SK (December 2012). "Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment". Journal of Bacteriology. 194 (24): 6940–1. doi:10.1128/JB.01857-12. PMC 3510587. PMID 23209206.
  30. ^ Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA (April 2012). "Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary". Journal of Bacteriology. 194 (8): 2121–2. doi:10.1128/JB.00013-12. PMC 3318490. PMID 22461555.
  31. ^ Bayer B, Vojvoda J, Offre P, Alves RJ, Elisabeth NH, Garcia JA, Volland JM, Srivastava A, Schleper C, Herndl GJ (May 2016). "Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation". The ISME Journal. 10 (5): 1051–63. Bibcode:2016ISMEJ..10.1051B. doi:10.1038/ismej.2015.200. PMC 4839502. PMID 26528837.
  32. ^ a b Brochier-Armanet C, Gribaldo S, Forterre P (February 2012). "Spotlight on the Thaumarchaeota". The ISME Journal. 6 (2): 227–30. Bibcode:2012ISMEJ...6..227B. doi:10.1038/ismej.2011.145. PMC 3260508. PMID 22071344.
  33. ^ a b Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA (June 2014). "Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation". Proceedings of the National Academy of Sciences of the United States of America. 111 (22): 8239–44. Bibcode:2014PNAS..111.8239K. doi:10.1073/pnas.1402028111. PMC 4050595. PMID 24843170.
  34. ^ a b Qin W, Amin SA, Martens-Habbena W, Walker CB, Urakawa H, Devol AH, Ingalls AE, Moffett JW, Armbrust EV (2014). "Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation". Proceedings of the National Academy of Sciences. 111 (34): 12504–12509. Bibcode:2014PNAS..11112504Q. doi:10.1073/PNAS.1324115111. ISSN 0027-8424. PMC 4151751. PMID 25114236.
  35. ^ Mussmann M, Brito I, Pitcher A, Sinninghe Damsté JS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen PH, Müller A, Daims H, Wagner M, Head IM (October 2011). "Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers". Proceedings of the National Academy of Sciences of the United States of America. 108 (40): 16771–6. Bibcode:2011PNAS..10816771M. doi:10.1073/pnas.1106427108. PMC 3189051. PMID 21930919.
  36. ^ Santoro AE, Buchwald C, McIlvin MR, Casciotti KL (2011-09-02). "Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea". Science. 333 (6047): 1282–1285. Bibcode:2011Sci...333.1282S. doi:10.1126/science.1208239. ISSN 0036-8075. PMID 21798895. S2CID 36668258.
  37. ^ Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD (February 2015). "Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production". The ISME Journal. 9 (2): 461–71. Bibcode:2015ISMEJ...9..461D. doi:10.1038/ismej.2014.142. PMC 4303638. PMID 25126756.
  38. ^ Muller F, Brissac T, Le Bris N, Felbeck H, Gros O (August 2010). "First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat". Environmental Microbiology. 12 (8): 2371–83. Bibcode:2010EnvMi..12.2371M. doi:10.1111/j.1462-2920.2010.02309.x. PMID 21966926.

Further reading

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