From Wikipedia, the free encyclopedia

NC10 phylum
CLSM image of a microcolony of NC10 bacteria (Ca. Methylomirabilis sinica) [1]
Scientific classification
Domain:
Bacteria
Phylum:
" Methylomirabilota"
Class:
" Methylomirabilia"
Orders
Synonyms

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]

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

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]

See also

References

  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.
Retrieved from " https://en.wikipedia.org/?title=NC10_phylum&oldid=1208835774"