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Thaumarchaeota
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{{Taxobox| domain = Archaea| regnum = "Proteoarchaeota"| phylum = "Thaumarchaeota"| phylum_authority = | subdivision_ranks = Class| subdivision =Nitrososphaeria JOURNAL, Stieglmeier M, Klingl A, Alves RJ, Rittmann SK, Melcher M, Leisch N, Schleper C, 6, 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, August 2014, 24907263, 4129164, 10.1099/ijs.0.063172-0,
  • "Candidatus Caldiarchaeum" JOURNAL, Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, Takai K, Takami H, 6, Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group, Nucleic Acids Research, 39, 8, 3204–23, April 2011, 21169198, 3082918, 10.1093/nar/gkq1228,
  • "Candidatus Giganthauma" JOURNAL, Muller F, Brissac T, Le Bris N, Felbeck H, Gros O, First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat., Environmental microbiology, August 2010, 12, 8, 2371–83,
  • "Candidatus Nitrosopelagicus" JOURNAL, Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, Yang Y, Orsi WD, Moran DM, Saito MA, 6, 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, January 2015, 25587132, 4313803, 10.1073/pnas.1416223112,
  • "Candidatus Nitrosotalea" JOURNAL, Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW, 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, September 2011, 21896746, 3179093, 10.1073/pnas.1107196108,
  • Cenarchaeales JOURNAL, Cavalier-Smith T, The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, International Journal of Systematic and Evolutionary Microbiology, 52, Pt 1, 7–76, January 2002, 11837318, 10.1099/00207713-52-1-7,
    • "Cenarchaeaceae" JOURNAL, Preston CM, Wu KY, Molinski TF, DeLong EF, A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov, Proceedings of the National Academy of Sciences of the United States of America, 93, 13, 6241–6, June 1996, 8692799, 39006, 10.1073/pnas.93.13.6241,
Cenarchaeum symbiosum â™  "Candidatus Nitrososphaera evergladensis" JOURNAL, Zhalnina KV, Dias R, Leonard MT, Dorr de Quadros P, Camargo FA, Drew JC, Farmerie WG, Daroub SH, Triplett EW, 6, 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, 7 July 2014, 24999826, 4084955, 10.1371/journal.pone.0101648, 2014PLoSO...9j1648Z, "Candidatus Nitrososphaera gargensis" Hatzenpichler et al. 2008 Nitrososphaera viennensis
  • "Candidatus Nitrosopumilales" JOURNAL, Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA, Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, 437, 7058, 543–6, September 2005, 16177789, 10.1038/nature03911,
    • "Candidatus Nitrosopumilaceae"
      • "Candidatus Nitrosoarchaeum" JOURNAL, Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR, Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis, Plos One, 6, 2, e16626, February 2011, 21364937, 3043068, 10.1371/journal.pone.0016626,
"Candidatus Nitrosoarchaeum koreensis" JOURNAL, Kim BK, Jung MY, Yu DS, Park SJ, Oh TK, Rhee SK, Kim JF, Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1, Journal of Bacteriology, 193, 19, 5539–40, October 2011, 21914867, 3187385, 10.1128/JB.05717-11, "Candidatus Nitrosoarchaeum limnia"
      • "Candidatus Nitrosotenuis" JOURNAL, 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, 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, 2013, 24278328, 3835317, 10.1371/journal.pone.0080835,
"Candidatus Nitrosotenuis uzonensis" "Candidatus Nitrosotenuis cloacae" JOURNAL, Li Y, Ding K, Wen X, Zhang B, Shen B, Yang Y, A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics, Scientific Reports, 6, 23747, March 2016, 27030530, 4814877, 10.1038/srep23747, "Candidatus Nitrosopumilus koreensis" JOURNAL, Park SJ, Kim JG, Jung MY, Kim SJ, Cha IT, Kwon K, Lee JH, Rhee SK, Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment, Journal of Bacteriology, 194, 24, 6940–1, December 2012, 23209206, 3510587, 10.1128/JB.01857-12, "Candidatus Nitrosopumilus salaria" JOURNAL, Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA, Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary, Journal of Bacteriology, 194, 8, 2121–2, April 2012, 22461555, 3318490, 10.1128/JB.00013-12, "Candidatus Nitrosopumilus maritimus" "Candidatus Nitrosopumilus adriaticus" JOURNAL, Bayer B, Vojvoda J, Offre P, Alves RJ, Elisabeth NH, Garcia JA, Volland JM, Srivastava A, Schleper C, Herndl GJ, Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation, The ISME Journal, 10, 5, 1051–63, May 2016, 26528837, 4839502, 10.1038/ismej.2015.200, "Candidatus Nitrosopumilus piranensis" }}The Thaumarchaeota or Thaumarchaea (from the ) 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 Crenarchaeota.JOURNAL, Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C, 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, May 2011, 21525411, 3100973, 10.1073/pnas.1013488108, 2011PNAS..108.8420T, JOURNAL, Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P, Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota, Nature Reviews. Microbiology, 6, 3, 245–52, March 2008, 18274537, 10.1038/nrmicro1852, Three described species in addition to C. symbosium are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. 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.JOURNAL, Brochier-Armanet C, Gribaldo S, Forterre P, 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, December 2008, 19105819, 2621148, 10.1186/1745-6150-3-54, 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.JOURNAL, Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C, Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota, Trends in Microbiology, 18, 8, 331–40, August 2010, 20598889, 10.1016/j.tim.2010.06.003, The lipid crenarchaeol has been found only in Thaumarchaea, making it a potential biomarker for the phylum.JOURNAL, 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, en, 181, 18–35, 10.1016/j.gca.2016.02.034, 2016GeCoA.181...18P, JOURNAL, Pester M, Schleper C, Wagner M, The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology, Current Opinion in Microbiology, 14, 3, 300–6, June 2011, 21546306, 3126993, 10.1016/j.mib.2011.04.007, 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.JOURNAL, 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, 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, May 2010, 20421470, 2889351, 10.1073/pnas.0913533107, 2010PNAS..107.8818W, Thaumarchaeota-derived GDGT lipids from marine sediments can be used to reconstruct past temperatures via the TEX86 paleotemperature proxy, as these lipids vary in structure according to temperature.JOURNAL, 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, en, 204, 1–2, 265–274, 10.1016/S0012-821X(02)00979-2, 2002E&PSL.204..265S, Because most Thaumarchaea 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.

Metabolism

Thaumarchaea are important ammonia oxidizers in aquatic and terrestrial environments, and are the first archaea identified as being involved in nitrification.JOURNAL, Brochier-Armanet C, Gribaldo S, Forterre P, Spotlight on the Thaumarchaeota, The ISME Journal, 6, 2, 227–30, February 2012, 22071344, 3260508, 10.1038/ismej.2011.145, They are capable of oxidizing ammonia at much lower substrate concentrations than ammonia-oxidizing bacteria, and so probably dominate in oligotrophic conditions.JOURNAL, Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA, 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, June 2014, 24843170, 4050595, 10.1073/pnas.1402028111, 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 Thaumarchaea 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. It has been suggested that some Thaumarchaea may use substrates other than ammonia for energy or may even be heterotrophs. One study of microbes from wastewater treatment plants found that not all Thaumarchaea that express amoA genes are active ammonia oxidizers. These Thaumarchaea may be oxidizing methane instead of ammonia or may in fact be heterotrophic, indicating a potential for a diversity of metabolic lifestyles within the phylum.JOURNAL, 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, 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, October 2011, 21930919, 3189051, 10.1073/pnas.1106427108, 2011PNAS..10816771M, Many members of the phylum assimilate carbon by CO2 fixation, using dissolved inorganic carbon as a pool. This is done using a hydroxypropionate/hydroxybutyrate cycle similar to the Crenarchaea but which appears to have evolved independently. All Thaumarchaea that have been identified by metagenomics thus far encode this pathway. Notably, the Thaumarchaeal CO2-fixation pathway is more efficient than any known aerobic autotrophic pathway. This efficiency helps explain their ability to thrive in low-nutrient environments. Some Thaumarchaea such as Nitrosopumilus maritimus may be able to incorporate organic carbon to an extent, indicating a capacity for mixotrophy. Others may be entirely heterotrophic and assimilate organic carbon compounds.A study has revealed that Thaumarchaeota 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 Thaumarchaea 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 Thaumarchaea may be important for a large number of aquatic organisms.JOURNAL, Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD, Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production, The ISME Journal, 9, 2, 461–71, February 2015, 25126756, 4303638, 10.1038/ismej.2014.142,

Environment

Many Thaumarchaea, such as Nitrosopumilus maritimus, are marine and live in the open ocean. Most of these planktonic Thaumarchaea are distributed in the subphotic zone, between 100m and 350m. Other marine Thaumarchaea live in shallower waters. One study has identified two novel Thaumarchaeota 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 Thaumarchaea, they are mesophilic.JOURNAL, Muller F, Brissac T, Le Bris N, Felbeck H, Gros O, First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat, Environmental Microbiology, 12, 8, 2371–83, August 2010, 21966926, 10.1111/j.1462-2920.2010.02309.x, Genetic analysis and the observation that the most basal identified Thaumarchaeal genomes are from hot environments suggests that the ancestor of Thaumarchaeota was thermophilic, and mesophily evolved later.JOURNAL, Brochier-Armanet C, Gribaldo S, Forterre P, Spotlight on the Thaumarchaeota, The ISME Journal, 6, 2, 227–30, February 2012, 22071344, 3260508, 10.1038/ismej.2011.145,

See also

References

{{Reflist}}

Further reading

  • JOURNAL, Yanagawa K, Breuker A, Schippers A, Nishizawa M, Ijiri A, Hirai M, Takaki Y, Sunamura M, Urabe T, Nunoura T, Takai K, 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, October 2014, 25063666, 4178666, 10.1128/AEM.01741-14,
  • JOURNAL, Wu Y, Conrad R, Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms, FEMS Microbiology Ecology, 89, 1, 127–34, July 2014, 24724989, 10.1111/1574-6941.12340,
  • JOURNAL, Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P, 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, June 2014, 24923324, 4122925, 10.1093/gbe/evu127,
{{Archaea classification}}{{Taxonbar|from=Q1186957}}{{archaea-stub}}

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