fbpx
Wikipedia

Nitrososphaerota

January 01, 1970

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
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]

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 edit

Phylogeny of Nitrososphaerota[11][12][13]
Conexivisphaeria
Conexivisphaerales
Conexivisphaeraceae

Conexivisphaera

Nitrososphaeria
Phylogeny of Nitrososphaerota[14][15][16]
Nitrososphaeria
"Geothermarchaeales"

"Geothermarchaeaceae"

Conexivisphaerales
Conexivisphaeraceae

Conexivisphaera

Nitrososphaerales
"Nitrosocaldaceae"

"Ca. Nitrosothermus"

"Ca. Nitrosocaldus"

Nitrososphaeraceae

"Ca. Nitrosocosmicus"

"Ca. Nitrosopolaris"

Nitrososphaera

Nitrosopumilaceae

"Ca. Nitrosotalea"

"Ca. Nitrosotenuis"

"Ca. Nitrosopelagicus"

"Cenarchaeum"

Nitrosarchaeum

Nitrosopumilus

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]

  • Class Nitrososphaeria Stieglmeier et al. 2014[19] [Conexivisphaeria Kato et al. 2020]
    • ?"Cenoporarchaeum" corrig. Zhang et al. 2019
    • ?"Candidatus Giganthauma" Muller et al. 2010[20]
    • ?"Candidatus Nitrosodeserticola" Hwang et al. 2021
    • Order "Geothermarchaeales" Adam et al. 2022
      • Family Geothermarchaeaceae Adam et al. 2022
        • ?"Geothermarchaeum" Adam et al. 2022
        • ?"Scotarchaeum" Adam et al. 2022
    • Order Conexivisphaerales Kato et al. 2020
      • Family Conexivisphaeraceae Kato et al. 2020
        • Conexivisphaera Kato et al. 2020
    • Order "Nitrosocaldales" de la Torre et al. 2008
      • Family "Nitrosocaldaceae" Qin et al. 2016
        • "Candidatus Nitrosothermus" Luo et al. 2021
        • "Candidatus Nitrosocaldus" de la Torre et al. 2008
    • Order Nitrososphaerales Stieglmeier et al. 2014
      • Family Methylarchaeaceae Hua et al. 2019
        • ?"Candidatus Methylarchaeum" Hua et al. 2019
        • ?"Candidatus Methanotowutia" Ou et al. 2022
      • Family Nitrososphaeraceae Stieglmeier et al. 2014
        • "Candidatus Nitrosocosmicus" Lehtovirta-Morley et al. 2016
        • Nitrososphaera Stieglmeier et al. 2014[21]
    • Order Nitrosopumilales Qin et al. 2017[22]

Metabolism edit

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 edit

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 edit

References edit

  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 edit

  • Breuker A, Schippers A, Nishizawa M, Takaki Y, Sunamura M, Urabe T, Nunoura T, Takai K (October 2014). "Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)". Applied and Environmental Microbiology. 80 (19): 6126–35. Bibcode:2014ApEnM..80.6126Y. doi:10.1128/AEM.01741-14. PMC 4178666. PMID 25063666.
  • Wu Y, Conrad R (July 2014). "Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms". FEMS Microbiology Ecology. 89 (1): 127–34. Bibcode:2014FEMME..89..127W. doi:10.1111/1574-6941.12340. PMID 24724989.
  • Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P (June 2014). "Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota". Genome Biology and Evolution. 6 (7): 1549–63. doi:10.1093/gbe/evu127. PMC 4122925. PMID 24923324.

January 01, 1970
nitrososphaerota, thaumarchaeota, phylum, archaea, proposed, 2008, after, genome, cenarchaeum, symbiosum, sequenced, found, differ, significantly, from, other, members, hyperthermophilic, phylum, thermoproteota, formerly, crenarchaeota, three, described, speci. 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 Nitrosopumilus maritimus partially with virions of Nitrosopumilus spindle shaped virus 1 Thaspiviridae attached Scientific classification Domain Archaea Superphylum Proteoarchaeota Phylum NitrososphaerotaBrochier Armanet et al 2021 1 Class Nitrososphaeria Order Conexivisphaerales Geothermarchaeales Nitrososphaerales Synonyms Nitrososphaerota Whitman et al 2018 Nitrososphaeraeota Oren et al 2015 Thaumarchaeota Brochier Armanet et al 2008 2 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 Contents 1 Taxonomy 2 Metabolism 3 Environment 4 See also 5 References 6 Further readingTaxonomy editPhylogeny of Nitrososphaerota 11 12 13 Conexivisphaeria Conexivisphaerales Conexivisphaeraceae Conexivisphaera Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Nitrososphaera Nitrosopumilales Nitrosopumilaceae Nitrosarchaeum Nitrosopumilus Phylogeny of Nitrososphaerota 14 15 16 Nitrososphaeria Geothermarchaeales Geothermarchaeaceae Conexivisphaerales Conexivisphaeraceae Conexivisphaera Nitrososphaerales Nitrosocaldaceae Ca Nitrosothermus Ca Nitrosocaldus Nitrososphaeraceae Ca Nitrosocosmicus Ca Nitrosopolaris Nitrososphaera Nitrosopumilaceae Ca Nitrosotalea Ca Nitrosotenuis Ca Nitrosopelagicus Cenarchaeum Nitrosarchaeum Nitrosopumilus 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 Class Nitrososphaeria Stieglmeier et al 2014 19 Conexivisphaeria Kato et al 2020 Cenoporarchaeum corrig Zhang et al 2019 Candidatus Giganthauma Muller et al 2010 20 Candidatus Nitrosodeserticola Hwang et al 2021 Order Geothermarchaeales Adam et al 2022 Family Geothermarchaeaceae Adam et al 2022 Geothermarchaeum Adam et al 2022 Scotarchaeum Adam et al 2022 Order Conexivisphaerales Kato et al 2020 Family Conexivisphaeraceae Kato et al 2020 Conexivisphaera Kato et al 2020 Order Nitrosocaldales de la Torre et al 2008 Family Nitrosocaldaceae Qin et al 2016 Candidatus Nitrosothermus Luo et al 2021 Candidatus Nitrosocaldus de la Torre et al 2008 Order Nitrososphaerales Stieglmeier et al 2014 Family Methylarchaeaceae Hua et al 2019 Candidatus Methylarchaeum Hua et al 2019 Candidatus Methanotowutia Ou et al 2022 Family Nitrososphaeraceae Stieglmeier et al 2014 Candidatus Nitrosocosmicus Lehtovirta Morley et al 2016 Nitrososphaera Stieglmeier et al 2014 21 Order Nitrosopumilales Qin et al 2017 22 Family Nitrosopumilaceae Qin et al 2017 Candidatus Nitrosospongia Moeller et al 2019 Candidatus Nitrosotalea Lehtovirta 2011 23 Candidatus Nitrosotenuis Li et al 2016 24 25 Candidatus Nitrosopelagicus Santoro et al 2015 26 Cenarchaeum DeLong amp Preston 1996 Nitrosarchaeum corrig Jung et al 2018 27 28 Nitrosopumilus Qin et al 2017 29 30 31 Metabolism editNitrososphaerota 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 editMany 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 editEocyte hypothesis List of Archaea generaReferences edit 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 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 Tourna M Stieglmeier M Spang A Konneke 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 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 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 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 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 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 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 Hugler M Karr EA Konneke 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 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 amp PSL 204 265S doi 10 1016 S0012 821X 02 00979 2 S2CID 54198843 The LTP Retrieved 10 May 2023 LTP all tree in newick format Retrieved 10 May 2023 LTP 06 2022 Release Notes PDF Retrieved 10 May 2023 GTDB release 08 RS214 Genome Taxonomy Database Retrieved 10 May 2023 ar53 r214 sp label Genome Taxonomy Database Retrieved 10 May 2023 Taxon History Genome Taxonomy Database Retrieved 10 May 2023 J P Euzeby Thaumarchaeota List of Prokaryotic names with Standing in Nomenclature LPSN Retrieved 2021 03 20 Sayers et al Thaumarchaeota National Center for Biotechnology Information NCBI taxonomy database Retrieved 2021 03 20 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 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 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 Konneke 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 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 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 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 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 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 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 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 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 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 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 a b Konneke M Schubert DM Brown PC Hugler 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 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 Mussmann M Brito I Pitcher A Sinninghe Damste JS Hatzenpichler R Richter A Nielsen JL Nielsen PH Muller 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 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 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 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 editBreuker A Schippers A Nishizawa M Takaki Y Sunamura M Urabe T Nunoura T Takai K October 2014 Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid Okinawa Trough Integrated Ocean Drilling Program Expedition 331 Applied and Environmental Microbiology 80 19 6126 35 Bibcode 2014ApEnM 80 6126Y doi 10 1128 AEM 01741 14 PMC 4178666 PMID 25063666 Wu Y Conrad R July 2014 Ammonia oxidation dependent growth of group I 1b Thaumarchaeota in acidic red soil microcosms FEMS Microbiology Ecology 89 1 127 34 Bibcode 2014FEMME 89 127W doi 10 1111 1574 6941 12340 PMID 24724989 Deschamps P Zivanovic Y Moreira D Rodriguez Valera F Lopez Garcia P June 2014 Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota Genome Biology and Evolution 6 7 1549 63 doi 10 1093 gbe evu127 PMC 4122925 PMID 24923324 Retrieved from https en wikipedia org w index php title Nitrososphaerota amp oldid 1198971889, wikipedia, wiki, book, books, library,

article

, read, download, free, free download, mp3, video, mp4, 3gp, jpg, jpeg, gif, png, picture, music, song, movie, book, game, games.