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NC10 phylum

Summary

NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.[1][2][3][4]

NC10 phylum
CLSM image of a microcolony of NC10 bacteria (Ca. Methylomirabilis sinica)[1]
Scientific classification
Domain:
Bacteria
Phylum:
"Methylomirabilota"
Class:
"Methylomirabilia"
Orders
  • "Rokubacteriales"
  • "Methylomirabilales"
Synonyms
  • "Rokubacteria" Hug et al. 2016

Methylomirabilis oxyfera, a member of the NC10 phylum, is the first organism discovered to couple methane oxidation to the reduction of nitrite to dinitrogen (N2).[5] This is significant for several reasons. First, there are only three other biological pathways known to produce oxygen (photosynthesis, chlorate respiration, and the detoxification of reactive oxygen species). Second, anaerobic methane oxidation (AMO) coupled to nitrite reduction links the global carbon and nitrogen cycles, and thus denitrifying methanotrophs in the NC10 phylum may influence methane content in the atmosphere.[1] Third, this finding opens the possibility that oxygen was available in the atmosphere prior to the evolution of oxygenic photosynthesis and the Great Oxidation Event,[5] which challenges certain aspects of modern theories regarding the evolution of early life on Earth.

The NC10 phylum was first proposed in 2003 on the basis of highly divergent 16S rRNA gene sequences from aquatic microbial formations in flooded caves (Nullarbor caves, Australia).[6] The first genome insights for the phylum were published in 2010.[5] Members of the NC10 phylum have been detected in environments including the Brunssummerheide peatlands (Limburg, Netherlands),[7] the deep stratified Lake Zug (Central Switzerland),[8] and a paddy field with long-term fertilization (Hangzhou, China)[9]

NC10 species proposed to date include Methylomirabilis oxyfera[5] and Methylomirabilis lanthanidiphila[10]

Taxonomy edit

120 marker proteins based GTDB 07-RS207[11][12][13]

"Rokubacteriales"

"Ca. Methylomirabilis"

"Ca. M. limnetica"

"Ca. M. lanthanidiphila"

"Ca. M. oxygeniifera"

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[14] and National Center for Biotechnology Information (NCBI).[15] However many taxonomic names are taken from the Genome Taxonomy Database release 06-RS202.[16][17][18][19]

  • Class "Methylomirabilia"
    • Order "Rokubacteriales" (CSP1-6)
    • Order "Methylomirabilales" Cabrol et al. 2020 (NC10)

See also edit

References edit

  1. ^ a b c He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S. M.; Hu, Baolan (2016-09-01). "A novel denitrifying methanotroph of the NC10 phylum and its microcolony". Scientific Reports. 6 (1): 32241. Bibcode:2016NatSR...632241H. doi:10.1038/srep32241. ISSN 2045-2322. PMC 5007514. PMID 27582299.
  2. ^ Raghoebarsing, Ashna A.; Pol, Arjan; van de Pas-Schoonen, Katinka T.; Smolders, Alfons J. P.; Ettwig, Katharina F.; Rijpstra, W. Irene C.; Schouten, Stefan; Damsté, Jaap S. Sinninghe; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Strous, Marc (April 2006). "A microbial consortium couples anaerobic methane oxidation to denitrification". Nature. 440 (7086): 918–921. Bibcode:2006Natur.440..918R. doi:10.1038/nature04617. hdl:1874/22552. ISSN 1476-4687. PMID 16612380. S2CID 4413069.
  3. ^ Ettwig, Katharina F.; Shima, Seigo; Pas‐Schoonen, Katinka T. Van De; Kahnt, Jörg; Medema, Marnix H.; Camp, Huub J. M. Op Den; Jetten, Mike S. M.; Strous, Marc (2008). "Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea". Environmental Microbiology. 10 (11): 3164–3173. doi:10.1111/j.1462-2920.2008.01724.x. hdl:2066/72144. ISSN 1462-2920. PMID 18721142.
  4. ^ Wu, Ming L.; Ettwig, Katharina F.; Jetten, Mike S. M.; Strous, Marc; Keltjens, Jan T.; Niftrik, Laura van (2011-02-01). "A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera'". Biochemical Society Transactions. 39 (1): 243–248. doi:10.1042/BST0390243. hdl:2066/91512. ISSN 0300-5127. PMID 21265781.
  5. ^ a b c d Ettwig, Katharina F.; Butler, Margaret K.; Le Paslier, Denis; Pelletier, Eric; Mangenot, Sophie; Kuypers, Marcel M. M.; Schreiber, Frank; Dutilh, Bas E.; Zedelius, Johannes; de Beer, Dirk; Gloerich, Jolein (March 2010). "Nitrite-driven anaerobic methane oxidation by oxygenic bacteria". Nature. 464 (7288): 543–548. Bibcode:2010Natur.464..543E. doi:10.1038/nature08883. hdl:2066/84284. ISSN 1476-4687. PMID 20336137. S2CID 205220000.
  6. ^ Rappé, Michael S.; Giovannoni, Stephen J. (October 2003). "The Uncultured Microbial Majority". Annual Review of Microbiology. 57 (1): 369–394. doi:10.1146/annurev.micro.57.030502.090759. ISSN 0066-4227. PMID 14527284.
  7. ^ Zhu, Baoli; van Dijk, Gijs; Fritz, Christian; Smolders, Alfons J. P.; Pol, Arjan; Jetten, Mike S. M.; Ettwig, Katharina F. (2012-10-05). "Anaerobic Oxidization of Methane in a Minerotrophic Peatland: Enrichment of Nitrite-Dependent Methane-Oxidizing Bacteria". Applied and Environmental Microbiology. 78 (24): 8657–8665. Bibcode:2012ApEnM..78.8657Z. doi:10.1128/aem.02102-12. ISSN 0099-2240. PMC 3502929. PMID 23042166.
  8. ^ Graf, Jon S.; Mayr, Magdalena J.; Marchant, Hannah K.; Tienken, Daniela; Hach, Philipp F.; Brand, Andreas; Schubert, Carsten J.; Kuypers, Marcel M. M.; Milucka, Jana (2018). "Bloom of a denitrifying methanotroph, 'Candidatus Methylomirabilis limnetica', in a deep stratified lake". Environmental Microbiology. 20 (7): 2598–2614. doi:10.1111/1462-2920.14285. hdl:21.11116/0000-0003-B834-3. ISSN 1462-2920. PMID 29806730.
  9. ^ He, Zhanfei; Cai, Chen; Shen, Lidong; Lou, Liping; Zheng, Ping; Xu, Xinhua; Hu, Baolan (2015-01-01). "Effect of inoculum sources on the enrichment of nitrite-dependent anaerobic methane-oxidizing bacteria". Applied Microbiology and Biotechnology. 99 (2): 939–946. doi:10.1007/s00253-014-6033-8. ISSN 1432-0614. PMID 25186148. S2CID 33695086.
  10. ^ Versantvoort, Wouter; Guerrero-Cruz, Simon; Speth, Daan R.; Frank, Jeroen; Gambelli, Lavinia; Cremers, Geert; van Alen, Theo; Jetten, Mike S. M.; Kartal, Boran; Op den Camp, Huub J. M.; Reimann, Joachim (2018). "Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila". Frontiers in Microbiology. 9: 1672. doi:10.3389/fmicb.2018.01672. ISSN 1664-302X. PMC 6094997. PMID 30140258.
  11. ^ "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  12. ^ "bac120_r207.sp_labels". Genome Taxonomy Database. Retrieved 20 June 2022.
  13. ^ "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  14. ^ J.P. Euzéby. "Bacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  15. ^ Sayers; et al. "Bacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  16. ^ "GTDB release 06-RS202". Genome Taxonomy Database.
  17. ^ Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
  18. ^ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
  19. ^ Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.

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