Advertisement

Diversity and Phylogeny of Described Aerobic Methanotrophs

  • Svetlana N. Dedysh
  • Claudia Knief
Chapter

Abstract

Aerobic methanotrophs are metabolically unique bacteria that are able to utilize methane as a sole source of energy. They occur in a wide range of habitats where both methane and oxygen are available. Nearly all methanotrophic bacteria that are now isolated in pure cultures belong to the phylum Proteobacteria, while only a limited number of strains represent the Verrucomicrobia. Proteobacterial methanotrophs affiliate with the classes Gammaproteobacteria (type I methanotrophs) and Alphaproteobacteria (type II methanotrophs) and belong to 23 genera and 56 species with validly published names. Several described methanotrophic representatives of the Gammaproteobacteria are not yet obtained in pure cultures and have a “Candidatus” status. Cultivation-independent studies indicate the existence of several further groups of methanotrophic bacteria that have not yet been obtained in culture. However, the currently cultivated strains cover a surprisingly broad range of methanotrophs detected in various environments by molecular approaches. This chapter offers an overview of the currently described methanotroph diversity and the major groups of methanotrophic bacteria that have so far eluded isolation efforts.

Keywords

Methanotrophic bacteria Methane monooxygenase Methylococcaceae Methylothermaceae Methylocystaceae Beijerinckiaceae Methanotrophic Verrucomicrobia 

References

  1. Anvar SY, Frank J, Pol A, Schmitz A, Kraaijeveld K, den Dunnen JT, den Camp HJMO (2014) The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV. BMC Genomics 15:914CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bao Z, Shinoda R, Minamisawa K (2016) Draft genome sequence of Methylosinus sp. strain 3S-1, an isolate from rice root in a low-nitrogen paddy field. Genome Announc 4:e00932–e00916CrossRefPubMedPubMedCentralGoogle Scholar
  3. Belova SE, Kulichevskaya IS, Bodelier PLE, Dedysh SN (2013) Methylocystis bryophila sp. nov., a novel, facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 63:1096–1104CrossRefPubMedGoogle Scholar
  4. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MS, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng JF, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC (2011) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 193:7001–7002CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bowman J (2006) The methanotrophs – the families Methylococcaceae and Methylocystaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, vol 5, 3rd edn. Springer, New York, pp 266–289CrossRefGoogle Scholar
  6. Bowman JP (2011) Approaches for the characterization and description of novel methanotrophic bacteria. In: Rosenzweig AC, Ragsdale SW (eds) Methods in enzymology, vol 495. Academic Press, Burlington, NJ, pp 45–62Google Scholar
  7. Bowman JP (2015a) Methylococcus. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01181
  8. Bowman JP (2015b) Methylosphaera. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01185
  9. Bowman JP (2015c) Methylocystis. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm00832
  10. Bowman JP (2015d) Methylosinus. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm00833
  11. Bowman JP (2016a) Methylococcaceae. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.fbm00225.pub2
  12. Bowman JP (2016b) Methylomonas. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01183.pub2
  13. Chen Y, Crombie A, Rahman MT, Dedysh SN, Liesack W, Stott MB, Alam M, Theisen AR, Murrell JC, Dunfield PF (2010) Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol 192:3840–3841CrossRefPubMedPubMedCentralGoogle Scholar
  14. Dam B, Kube M, Dam S, Reinhardt R, Liesack W (2012) Complete sequence analysis of two methanotroph-specific repABC-containing plasmids from Methylocystis sp. strain SC2. Appl Environ Microbiol 78:4373–4379CrossRefPubMedPubMedCentralGoogle Scholar
  15. Dam B, Dam S, Blom J, Liesack W (2013) Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. PLoS One 8:e74767CrossRefPubMedPubMedCentralGoogle Scholar
  16. Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN (2016) A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME J 10:2734–2743CrossRefPubMedPubMedCentralGoogle Scholar
  17. Dedysh SN, Dunfield PF (2011) Facultative and obligate methanotrophs: how to identify and differentiate them. In: Rosenzweig AC, Ragsdale SW (eds) Methods in enzymology, vol 495. Academic Press, Burlington, NJ, pp 31–44Google Scholar
  18. Dedysh SN, Dunfield PF (2014) Cultivation of methanotrophs. In: McGenity TJ et al (eds) Hydrocarbon and lipid microbiology protocols, Springer protocols handbooks. Springer-Verlag, Berlin Heidelberg.  https://doi.org/10.1007/8623_2014_14CrossRefGoogle Scholar
  19. Dedysh SN, Naumoff DG, Vorobev AV, Kyrpides N, Woyke T, Shapiro N, Crombie AT, Murrell JC, Kalyuzhnaya MG, Smirnova AV, Dunfield PF (2015) Draft genome sequence of Methyloferula stellata AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome announc 3:e01555-01514CrossRefGoogle Scholar
  20. Dedysh SN, Haupt ES, Dunfield PF (2016) Emended description of the family Beijerinckiaceae and transfer of the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov. Int J Syst Evol Microbiol 66:3177–3182CrossRefPubMedGoogle Scholar
  21. Dedysh SN, Dunfield PF (2016a) Beijerinckiaceae. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.fbm00164.pub2
  22. Dedysh SN, Dunfield PF (2016b) Methylocella. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm00797.pub2
  23. Dedysh SN, Dunfield PF (2016c) Methyloferula. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01403
  24. Dedysh SN (2016) Methylocapsa. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01402.
  25. del Cerro C, Garcia JM, Rojas A, Tortajada M, Ramon D, Galan B, Prieto MA, Garcia JL (2012) Genome sequence of the methanotrophic poly-beta-hydroxybutyrate producer Methylocystis parvus OBBP. J Bacteriol 194:5709–5710CrossRefPubMedPubMedCentralGoogle Scholar
  26. Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PL, Liesack W, Feng L, Wang L, Alam M (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879–882CrossRefPubMedGoogle Scholar
  27. Dunfield PF (2007) The soil methane sink. In: Reay DS, Hewitt CN, Smith KA, Grace J (eds) Greenhouse gas sinks. CABI Wallingford, UK, pp 152–170CrossRefGoogle Scholar
  28. Dunfield PF (2016) Methylohalobius. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01418
  29. Erikstad HA, Birkeland NK (2015) Draft genome sequence of “Candidatus Methylacidiphilum kamchatkense” Strain Kam1, a thermoacidophilic methanotrophic Verrucomicrobium. Genome Announc 3:e00065–e00015CrossRefPubMedPubMedCentralGoogle Scholar
  30. Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548CrossRefPubMedGoogle Scholar
  31. Flynn JD, Hirayama H, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Khmelenina VN, Trotsenko YA, Murrell JC, Semrau JD, Svenning MM, Stein LY, Kyrpides N, Shapiro N, Woyke T, Bringel F, Vuilleumier S, DiSpirito AA, Kalyuzhnaya MG (2016) Draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc 4:e01629–e01615CrossRefPubMedPubMedCentralGoogle Scholar
  32. Green PN (1992) Taxonomy of methylotrophic bacteria. In: Murrell JC, Kelly DP (eds) Microbial growth on C1-compounds. Intercept Press, Andover, UK, pp 23–84Google Scholar
  33. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439–471PubMedPubMedCentralGoogle Scholar
  34. Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnaya MG (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3:e00515–e00515CrossRefPubMedPubMedCentralGoogle Scholar
  35. Heylen K, De Vos P, Vekeman B (2016) Draft genome sequences of eight obligate methane oxidizers occupying distinct niches based on their nitrogen metabolism. Genome Announc 4:e00421–e00416CrossRefPubMedPubMedCentralGoogle Scholar
  36. Hirayama H, Abe M, Miyazaki M, Nunoura T, Furushima Y, Yamamoto H et al (2014) Methylomarinovum caldicuralii gen. nov., sp. nov., a moderately thermophilic methanotroph isolated from a shallow submarine hydrothermal system, and proposal of the family Methylothermaceae fam. nov. Int J Syst Evol Microbiol 64:989–999CrossRefPubMedGoogle Scholar
  37. Hirayama H (2016a) Methylomarinum. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01411
  38. Hirayama H (2016b) Methylothermaceae. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.fbm00277
  39. Hirayama H (2016c) Methylothermus. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01420
  40. Hirayama H (2016d) Methylomarinovum. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01419
  41. Hoefman S, van der Ha D, Iguchi H, Yurimoto H, Sakai Y, Boon N, Vandamme P, Heylen K, De Vos P (2014) Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 64:2100–2107CrossRefPubMedGoogle Scholar
  42. Hou SB, Makarova KS, Saw JHW, Senin P, Ly BV, Zhou ZM, Ren Y, Wang JM, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3:26CrossRefPubMedPubMedCentralGoogle Scholar
  43. Iguchi H, Yurimoto H, Sakai Y (2016) Methylovulum. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01416
  44. Islam T, Jensen S, Reigstad LJ, Larsen O, Birkeland NK (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci USA 105:300–304CrossRefPubMedGoogle Scholar
  45. Kalyuzhnaya MG, Lamb AE, McTaggart TL, Oshkin IY, Shapiro N, Woyke T, Chistoserdova L (2015) Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment. Genome Announc 3:e00103–e00115CrossRefPubMedPubMedCentralGoogle Scholar
  46. Kalyuzhnaya M (2016a) Methylomicrobium. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01182.pub2
  47. Kalyuzhnaya M (2016b) Methylosarcina. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01184.pub2
  48. Kalyuzhnaya M (2017) Methylobacter. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2017 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust. (in press).Google Scholar
  49. Khadem AF, Wieczorek AS, Pol A, Vuilleumier S, Harhangi HR, Dunfield PF, Kalyuzhnaya MG, Murrell JC, Francoijs KJ, Stunnenberg HG, Stein LY, DiSpirito AA, Semrau JD, Lajus A, Medigue C, Klotz MG, Jetten MS, Op den Camp HJ (2012) Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph Methylacidiphilum fumariolicum strain SolV. J Bacteriol 194:3729–3730CrossRefPubMedPubMedCentralGoogle Scholar
  50. Khalifa A, Lee CG, Ogiso T, Ueno C, Dianou D, Demachi T, Katayama A, Asakawa S (2015) Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. Int J Syst Evol Microbiol 65:3527–3534CrossRefPubMedGoogle Scholar
  51. Khmelenina VN, Beck DA, Munk C, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Scholz M, Teshima H, Xu Y, Chain P, Bringel F, Vuilleumier S, Dispirito A, Dunfield P, Jetten MS, Klotz MG, Knief C, Murrell JC, Op den Camp HJ, Sakai Y, Semrau J, Svenning M, Stein LY, Trotsenko YA, Kalyuzhnaya MG (2013) Draft genome sequence of Methylomicrobium buryatense strain 5G, a haloalkaline-tolerant methanotrophic bacterium. Genome Announc 1:e00053-00013CrossRefGoogle Scholar
  52. Kleiveland CR, Hult LTO, Kuczkowska K, Jacobsen M, Lea T, Pope PB (2012) Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas). J Bacteriol 194:6626–6626CrossRefPubMedPubMedCentralGoogle Scholar
  53. Kits KD, Klotz MG, Stein LY (2015) Methane oxidation coupled to nitrate reduction under hypoxia by the gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1. Environ Microbiol 17:3219–3232CrossRefPubMedGoogle Scholar
  54. Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Medigue C, Pitluck S, Woyke T, Zeytun A, Stein LY (2013) Genome sequence of the obligate gammaproteobacterial methanotroph Methylomicrobium album strain BG8. Genome Announc 1:e0017013CrossRefPubMedGoogle Scholar
  55. Knief C (2015) Diversity and habitat preferences of cultivated and uncultivated methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 6:1346.  https://doi.org/10.3389/fmicb.2015.01346CrossRefPubMedPubMedCentralGoogle Scholar
  56. Kolb S (2009) The quest for atmospheric methane oxidizers in forest soils. Environ Microbiol Rep 1:336–346CrossRefPubMedGoogle Scholar
  57. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckman N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371CrossRefPubMedPubMedCentralGoogle Scholar
  58. Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol 12:862–872CrossRefPubMedGoogle Scholar
  59. Lüke C, Frenzel P (2011) Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl Environ Microbiol 77:6305–6309CrossRefPubMedPubMedCentralGoogle Scholar
  60. Nazaries L, Murrell JC, Millard P, Baggs L, Singh BK (2013) Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol 15:2395–2417CrossRefPubMedGoogle Scholar
  61. Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland N-K, Pol A, Dunfield PF (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 1:293–306CrossRefGoogle Scholar
  62. Oshkin IY, Belova SE, Danilova OV, Miroshnikov KK, Rijpstra IW, Sinninghe Damsté JS, Liesack W, Dedysh SN (2016) Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum. Int J Syst Evol Microbiol 66:2417–2423CrossRefPubMedGoogle Scholar
  63. Parte AC (2014) LPSN - list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616CrossRefPubMedGoogle Scholar
  64. Poehlein A, Deutzmann JS, Daniel R, Simeonova DD (2013) Draft genome sequence of the methanotrophic Gammaproteobacterium Methyloglobulus morosus DSM 22980 strain KoM1. Genome Announc 1:e01078-01013Google Scholar
  65. Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MSM (2007) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450:874–878CrossRefPubMedGoogle Scholar
  66. Rahalkar M, Pandit PS, Dhakephalkar PK, Pore S, Arora P, Kapse N (2016) Genome characteristics of a novel type I methanotroph (Sn10-6) isolated from a flooded Indian rice field. Microbial Ecol 71:519–523CrossRefGoogle Scholar
  67. Schink B, Deutzmann JS (2016) Methyloglobulus. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01412
  68. Schink B, Rahalkar M (2016) Methylosoma. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01415
  69. Semrau JD, DiSpirito AA, Yoon S (2010) Methanotrophs and copper. FEMS Microbiol Rev 34:496–531CrossRefPubMedGoogle Scholar
  70. Sharp CE, Smirnova AV, Graham JM, Stott MB, Khadka R, Moore TR, Grasby SE, Strack M, Dunfield PF (2014) Distribution and diversity of Verrucomicrobia methanotrophs in geothermal and acidic environments. Environ Microbiol 16:1867–1878CrossRefPubMedGoogle Scholar
  71. Sharp CE, Smirnova AV, Kalyuzhnaya MG, Bringel F, Hirayama H, Jetten MS, Khmelenina VN, Klotz MG, Knief C, Kyrpides N, Op den Camp HJ, Reshetnikov AS, Sakai Y, Shapiro N, Trotsenko YA, Vuilleumier S, Woyke T, Dunfield PF (2015) Draft genome sequence of the moderately halophilic methanotroph Methylohalobius crimeensis Strain 10Ki. Genome Announc 3:e00644-00615CrossRefGoogle Scholar
  72. Shrestha PM, Kammann C, Lenhart K, Dam B, Liesack W (2012) Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil. ISME J 6:1115–1126CrossRefPubMedGoogle Scholar
  73. Skennerton CT, Ward LM, Michel A, Metcalfe K, Valiente C, Mullin S, Chan KY, Gradinaru V, Orphan VJ (2015) Genomic reconstruction of an uncultured hydrothermal vent gammaproteobacterial methanotroph (Family Methylothermaceae) indicates multiple adaptations to oxygen limitation. Front Microbiol 6:1425CrossRefPubMedPubMedCentralGoogle Scholar
  74. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420CrossRefGoogle Scholar
  75. Söhngen NL (1906) Über Bakterien, welche Methan als Kohlenstoffnahrung und Energiequelle gebrauchen. Zentralbl Bakteriol Parasitik Abt. I 15:513–517Google Scholar
  76. Stein LY, Roy R, Dunfield PF (2012) Aerobic methanotrophy and nitrification: Processes and connections. In: Battista J et al (eds) Encyclopedia of life sciences. Wiley, Chichester. www.els.net
  77. Stein LY, Yoon S, Semrau JD, Dispirito AA, Crombie A, Murrell JC, Vuilleumier S, Kalyuzhnaya MG, Op den Camp HJ, Bringel F, Bruce D, Cheng JF, Copeland A, Goodwin L, Han S, Hauser L, Jetten MS, Lajus A, Land ML, Lapidus A, Lucas S, Medigue C, Pitluck S, Woyke T, Zeytun A, Klotz MG (2010) Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b. J Bacteriol 192:6497–6498CrossRefPubMedPubMedCentralGoogle Scholar
  78. Stein LY, Bringel F, DiSpirito AA, Han S, Jetten MS, Kalyuzhnaya MG, Kits KD, Klotz MG, Op den Camp HJ, Semrau JD, Vuilleumier S, Bruce DC, Cheng JF, Davenport KW, Goodwin L, Han S, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Medigue C, Pitluck S, Woyke T (2011) Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242). J Bacteriol 193:2668–2669CrossRefPubMedPubMedCentralGoogle Scholar
  79. Stoecker K, Bendinger B, Schoning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M (2006) Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci USA 103:2363–2367CrossRefPubMedGoogle Scholar
  80. Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG, Spang A, Bringel F, Vuilleumier S, Lajus A, Medigue C, Bruce DC, Cheng JF, Goodwin L, Ivanova N, Han J, Han CS, Hauser L, Held B, Land ML, Lapidus A, Lucas S, Nolan M, Pitluck S, Woyke T (2011) Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol 193:6418–6419CrossRefPubMedPubMedCentralGoogle Scholar
  81. Takeuchi M (2016) Methylocaldum. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01180.pub2
  82. Tamas I, Smirnova AV, He Z, Dunfield PF (2014) The (d)evolution of methanotrophy in the Beijerinckiaceae – a comparative genomics analysis. ISME J 8:369–382CrossRefPubMedGoogle Scholar
  83. Tarlera S (2016) Methylogaea. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01410
  84. Tavormina PL (2016) Methyloprofundus. In: Bergey’s manual of systematics of archaea and bacteria, Online © 2015 Bergey’s Manual Trust. This article is © 2016 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc., in association with Bergey’s Manual Trust.  https://doi.org/10.1002/9781118960608.gbm01414
  85. Trotsenko YA, Murrell JC (2008) Metabolic aspects of aerobic obligate methanotrophy. In: Laskin AI, Sariaslani S, Gadd GM (eds) Advances in applied microbiology, vol 63. Elsevier, Boston, MA, pp 183–229Google Scholar
  86. van Teeseling MCF, Pol A, Harhangi HR, van der Zwart S, Jetten MSM, Op den Camp HJM (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov. Appl Environ Microbiol 80:6782–6791CrossRefPubMedPubMedCentralGoogle Scholar
  87. Vekeman B, Kerckhof FM, Cremers G, de Vos P, Vandamme P, Boon N, Op den Camp HJ, Heylen K (2016) New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ Microbiol 18:4523–4536CrossRefPubMedGoogle Scholar
  88. Vigliotta G, Nutricati E, Carata E, Tredici SM, De Stephano M, Massardo DR, Prati MV, Bellis LD, Alifano P (2007) Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic γ-proteobacterium. Appl Environ Microbiol 73:3556–3565CrossRefPubMedPubMedCentralGoogle Scholar
  89. Vorobev A, Jagadevan S, Jain S, Anantharaman K, Dick GJ, Vuilleumier S, Semrau JD (2014) Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Appl Environ Microbiol 80:3044–3052CrossRefPubMedPubMedCentralGoogle Scholar
  90. Vuilleumier S, Khmelenina VN, Bringel F, Reshetnikov AS, Lajus A, Mangenot S, Rouy Z, Op den Camp HJ, Jetten MS, Dispirito AA, Dunfield P, Klotz MG, Semrau JD, Stein LY, Barbe V, Médigue C, Trotsenko YA, Kalyuzhnaya MG (2012) Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J Bacteriol 194:551–552CrossRefPubMedPubMedCentralGoogle Scholar
  91. Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang LX, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren QH, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (2004) Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol 2:1616–1628Google Scholar
  92. Whittenbury R, Dalton H (1991) The methylotrophic bacteria. In: Starr MP, Stolph H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes. Springer-Verlag KG, Berlin, pp 894–902Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Svetlana N. Dedysh
    • 1
  • Claudia Knief
    • 2
  1. 1.Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscowRussia
  2. 2.Institute of Crop Science and Resource Conservation – Molecular Biology of the RhizosphereUniversity of BonnBonnGermany

Personalised recommendations