Skip to main content

Methanotroph Ecology, Environmental Distribution and Functioning

  • Chapter
  • First Online:
Methanotrophs

Part of the book series: Microbiology Monographs ((MICROMONO,volume 32))

Abstract

The dynamics of methane concentrations in the atmosphere in recent decades has demonstrated many anomalies which are poorly understood. The only biological way of degrading this potent greenhouse gas is by microbial oxidation. Aerobic methanotrophic bacteria (MB) play an important role in many ecosystems worldwide degrading methane before it can escape to the atmosphere. This group of bacteria has intensively been studied as a model microbial functional guild because there is a strong link between the consumption of methane and the composition of MB communities, facilitating the study of microbial “behavior” in the environment. These studies have revealed a strong biogeography of MB which is displayed in their phylogeny not only on the basis of single functional marker genes but also on genome sequence basis. Novel environmental controlling factors have been revealed (e.g. rare earth metals) as well as novel organisms with as yet unknown traits for MB. The resistance and resilience of methane consumption and methane consuming communities have been shown to depend on specific community members. The current knowledge on environmental distribution and of MB has led to propose a life-history scheme, classifying MB communities on their collective traits rather than singly on their capacity the oxidise methane alone.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Arp J, Gotze S, Mukherji R, Mattern DJ, Garcia-Altares M, Klapper M, Brock DA, Brakhage AA, Strassmann JE, Queller DC, Bardl B, Willing K, Peschel G, Stallforth P (2018) Synergistic activity of cosecreted natural products from amoebae-associated bacteria. Proc Natl Acad Sci USA 115:3758–3763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bao ZH, Okubo T, Kubota K, Kasahara Y, Tsurumaru H, Anda M, Ikeda S, Minamisawa K (2014) Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl Environ Microbiol 80:5043–5052

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bastviken D, Cole J, Pace M, Tranvik L (2004) Methane emissions from lakes: dependence of lake characteristics, two regional assessments, and a global estimate. Global Biogeochem Cycles 18. https://doi.org/10.1029/2004GB002238

    Article  CAS  Google Scholar 

  • Bastviken D, Tranvik LJ, Downing JA, Crill PM, Enrich-Prast A (2011) Freshwater methane emissions offset the continental carbon sink. Science 331:50

    Article  CAS  PubMed  Google Scholar 

  • Beck DAC, Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L (2013) A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 1:e23-e23

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bessette S, Moalic Y, Gautey S, Lesongeur F, Godfroy A, Toffin L (2017) Relative abundance and diversity of bacterial methanotrophs at the oxic-anoxic interface of the Congo deep-sea fan. Front Microbiol 8:715

    Article  PubMed  PubMed Central  Google Scholar 

  • Biderre-Petit C, Jezequel D, Dugat-Bony E, Lopes F, Kuever J, Borrel G, Viollier E, Fonty G, Peyret P (2011) Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol Ecol 77:533–545

    Article  CAS  PubMed  Google Scholar 

  • Blees J, Niemann H, Wenk CB, Zopfi J, Schubert CJ, Kirf MK, Veronesi ML, Hitz C, Lehmann MF (2014) Micro-aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south-Alpine Lake Lugano (Switzerland). Limnol Oceanogr 59:311–324

    Article  CAS  Google Scholar 

  • Bodelier PLE (2011) Interactions between nitrogenous fertilizers and methane cycling in wetland and upland soils. Curr Opin Environ Sustain 3:379–388

    Article  Google Scholar 

  • Bodelier PLE, Frenzel P (1999) Contribution of methanotrophic and nitrifying bacteria to CH4 and NH4 + oxidation in the rhizosphere of rice plants as determined by new methods of discrimination. Appl Environ Microbiol 65:1826–1833

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bodelier PLE, Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47:265–277

    Article  CAS  PubMed  Google Scholar 

  • Bodelier PLE, Steenbergh AK (2014a) Interactions between methane and the nitrogen cycle in light of climate change. Curr Opin Environ Sustain 9–10:26–36

    Article  Google Scholar 

  • Bodelier PLE, Steenbergh AK (2014b) Interactions between methane and nitrogen cycling; current metagenomic studies and future trends. In: Marco D (ed) Metagenomics of the microbial nitrogen cycle: theory, methods and applications. Caister Academic Press, Norfolk, pp 33–63

    Google Scholar 

  • Bodelier PLE, Roslev P, Henckel T, Frenzel P (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403:421–424

    Article  CAS  PubMed  Google Scholar 

  • Bodelier PLE, Gillisen MJB, Hordijk K, Damste JSS, Rijpstra WIC, Geenevasen JA, Dunfield PF (2009) A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME J 3:606–617

    Article  CAS  PubMed  Google Scholar 

  • Bodelier PLE, Meima-Franke M, Hordijk CA, Steenbergh AK, Hefting MM, Bodrossy L, von Bergen M, Seifert J (2013) Microbial minorities modulate methane consumption through niche partitioning. ISME J 7:2214–2228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers. Nature 392:801–805

    Article  CAS  Google Scholar 

  • Bowman JP, Sly LI, Nichols PD, Hayward AC (1993) Revised taxonomy of the methanotrophs – description of methylobacter gen-nov, emendation of methylococcus, validation of methylosinus and methylocystis species, and a proposal that the family methylococcaceae includes only the group-i methanotrophs. Int J Syst Bacteriol 43:735–753

    Article  Google Scholar 

  • Bridgham SD, Cadillo-Quiroz H, Keller JK, Zhuang QL (2013) Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales. Glob Change Biol 19:1325–1346

    Article  Google Scholar 

  • Bussmann I (2005) Methane release through resuspension of littoral sediment. Biogeochemistry 74:283–302

    Article  CAS  Google Scholar 

  • Cai YF, Zheng Y, Bodelier PLE, Conrad R, Jia ZJ (2016) Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat Commun 7:11728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cappenberg TE (1974) Interrelations between sulfate-reducing and methane-producing bacteria in bottom deposits of a fresh-water lake. II. Inhibition experiments. Antonie van Leeuwenhoek 40:297–306

    Article  CAS  PubMed  Google Scholar 

  • Carini S, Bano N, LeCleir G, Joye SB (2005) Aerobic methane oxidation and methanotroph community composition during seasonal stratification in Mono Lake, California (USA). Environ Microbiol 7:1127–1138

    Article  CAS  PubMed  Google Scholar 

  • Chang J, Gu WY, Park D, Semrau JD, DiSpirito AA, Yoon S (2018) Methanobactin from methylosinus trichosporium OB3b inhibits N2O reduction in denitrifiers. ISME J 12:2086–2089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chistoserdova L (2016) Lanthanides: new life metals? World J Microbiol Biotechnol 32:138

    Article  PubMed  CAS  Google Scholar 

  • Chistoserdova L, Kalyuzhnaya MG (2018) Current trends in methylotrophy. Trends Microbiol 26:703–714

    Article  CAS  PubMed  Google Scholar 

  • Chowdhury TR, Dick RP (2013) Ecology of aerobic methanotrophs in controlling methane fluxes from wetlands. Appl Soil Ecol 65:8–22

    Article  Google Scholar 

  • Chronopoulou PM, Shelley F, Pritchard WJ, Maanoja ST, Trimmer M (2017) Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone. ISME J 11:1386–1399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609

    CAS  PubMed  PubMed Central  Google Scholar 

  • Conrad R (2007) Microbial ecology of methanogens and methanotrophs. Adv Agron 96:1–63

    Article  CAS  Google Scholar 

  • Crevecoeur SVW, Comte J, Matveev A, Lovejoy C (2017) Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds. PLoS One 12:e0188223

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Crombie AT, Murrell JC (2014) Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 510:148

    Article  CAS  PubMed  Google Scholar 

  • Daebeler A, Bodelier PLE, Yan Z, Hefting MM, Jia ZJ, Laanbroek HJ (2014) Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME J 8:2397–2410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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:e74767

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 10:2734–2743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dean JF, Middelburg JJ, Rockmann T, Aerts R, Blauw LG, Egger M, Jetten MS, Jong AE, Meisel OH, Rasigraf O (2018) Methane feedbacks to the global climate system in a warmer world. Rev Geophys 56:207–250

    Article  Google Scholar 

  • Dedysh SN (2009) Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivation-based studies. Microbiology 78:655–669

    Article  CAS  Google Scholar 

  • Dedysh SN, Knief C (2018) Diversity and phylogeny of described aerobic methanotrophs. In: Kalyuzhnaya MG, Xing XH (eds) Methane biocatalysis: paving the way to sustainability. Springer, Cham, pp 17–42

    Chapter  Google Scholar 

  • Dedysh SN, Belova SE, Bodelier PLE, Smirnova KV, Khmelenina VN, Chidthaisong A, Trotsenko YA, Liesack W, Dunfield PF (2007) Methylocystis heyeri sp nov., a novel type II methanotrophic bacterium possessing ‘signature’ fatty acids of type I methanotrophs. Int J Syst Evol Microbiol 57:472–479

    Article  CAS  PubMed  Google Scholar 

  • DelSontro T, del Giorgio PA, Prairie YT (2017) No longer a paradox: the interaction between physical transport and biological processes explains the spatial distribution of surface water methane within and across lakes. Ecosystems 21:1073–1087

    Article  CAS  Google Scholar 

  • DiSpirito AA, Semrau JD, Murrell JC, Gallagher WH, Dennison C, Vuilleumier S (2016) Methanobactin and the link between copper and bacterial methane oxidation. Microbiol Mol Biol Rev 80:387–409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dunfield PF (2007) The soil methane sink. In: Reay DS, Hewitt CN, Smith KA, Grace J (eds) Greenhouse gas sinks. CABI, Wallingford, pp 152–170

    Chapter  Google Scholar 

  • Dunfield PF, Dedysh SN (2014) Methylocella: a gourmand among methanotrophs. Trends Microbiol 22:368–369

    Article  CAS  PubMed  Google Scholar 

  • Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879-U18

    Article  CAS  PubMed  Google Scholar 

  • Durisch-Kaiser E, Klauser L, Wehrli B, Schubert C (2005) Evidence of intense archaeal and bacterial methanotrophic activity in the Black Sea water column. Appl Environ Microbiol 71:8099–8106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ebrahimi A, Or D (2018) On upscaling of soil microbial processes and biogeochemical fluxes from aggregates to landscapes. J Geophys Res Biogeosci 123:1526–1547

    Article  Google Scholar 

  • Edwards CROT, Miller JM, Wiggins JB, Wang W, Lee CK, Cary SC, Pointing SB, Lau MCY (2017) Draft genome sequence of uncultured upland soil cluster Gammaproteobacteria gives molecular insights into high-affinity methanotrophy. Genome Announc 5:e00047-17

    Google Scholar 

  • Eller G, Känel L, Krüger M (2005) Cooccurrence of aerobic and anaerobic methane oxidation in the water column of lake Plußsee. Appl Environ Microbiol 71:8925–8928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 464:543–548

    Article  CAS  PubMed  Google Scholar 

  • Farhan Ul Haque M, Crombie AT, Ensminger SA, Baciu C, Murrell JC (2018) Facultative methanotrophs are abundant at terrestrial natural gas seeps. Microbiome 6:118

    Article  PubMed  PubMed Central  Google Scholar 

  • Fest B, Hinko-Najera N, von Fischer JC, Livesley SJ, Arndt SK (2017) Soil methane uptake increases under continuous throughfall reduction in a temperate evergreen, Broadleaved Eucalypt Forest. Ecosystems 20:368–379

    Article  CAS  Google Scholar 

  • Graf JS, Mayr MJ, Marchant HK, Tienken D, Hach PF, Brand A, Schubert CJ, Kuypers MMM, Milucka J (2018) Bloom of a denitrifying methanotroph, ‘Candidatus Methylomirabilis limnetica’, in a deep stratified lake. Environ Microbiol 20:2598–2614

    Article  CAS  PubMed  Google Scholar 

  • Gray ND, McCann CM, Christgen B, Ahammad SZ, Roberts JA, Graham DW (2014) Soil geochemistry confines microbial abundances across an arctic landscape; implications for net carbon exchange with the atmosphere. Biogeochemistry 120:307–317

    Article  CAS  Google Scholar 

  • Grossart HP, Frindte K, Dziallas C, Eckert W, Tang KW (2011) Microbial methane production in oxygenated water column of an oligotrophic lake. Proc Natl Acad Sci USA 108:19657–19661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guerrero-Cruz S, Cremers G, van Alen TA, den Camp H, Jetten MSM, Rasigraf O, Vaksmaa A (2018) Response of the anaerobic methanotroph “Candidatus Methanoperedens nitroreducens” to oxygen stress. Appl Environ Microbiol 84:17

    Article  Google Scholar 

  • Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev 60:439

    CAS  PubMed  PubMed Central  Google Scholar 

  • Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567

    Article  CAS  PubMed  Google Scholar 

  • He D, Ren L, Wu Q (2012) Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity. Chin J Oceanol Limnol 30:237–247

    Article  Google Scholar 

  • He ZF, Wang JQ, Hu JJ, Yu HG, Jetten MSM, Liu H, Ren H, Zhang X, Hua M, Xu X, Zheng P, Hu B (2019) Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers. Environ Pollut 244:228–237

    Article  CAS  PubMed  Google Scholar 

  • Hernandez ME, Beck DAC, Lidstrom ME, Chistoserdova L (2015) Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation. PeerJ 3:13

    Article  CAS  Google Scholar 

  • Heyer J, Galchenko VF, Dunfield PF (2002) Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology 148:2831–2846

    Article  CAS  PubMed  Google Scholar 

  • Ho A, Bodelier PLE (2015) Diazotrophic methanotrophs in peatlands: the missing link? Plant Soil 389:419–423

    Article  CAS  Google Scholar 

  • Ho A, Erens H, Mujinya BB, Boeckx P, Baert G, Schneider B, Frenzel P, Boon N, Van Ranst E (2013a) Termites facilitate methane oxidation and shape the methanotrophic community. Appl Environ Microbiol 79:7234–7240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PL (2013b) Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. Environ Microbiol Rep 5:335–345

    Article  CAS  PubMed  Google Scholar 

  • Ho ADRK, Thas O, De Neve J, Hoefman S, Vandamme P, Heylen K, Boon N (2014) The more, the merrier: heterotroph richness stimulates methanotrophic activity. ISME J 8:1945–1948

    Article  PubMed  PubMed Central  Google Scholar 

  • Ho A, Reim A, Kim SY, Meima-Franke M, Termorshuizen A, De Boer W, van der Putten WH, Bodelier PL (2015) Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application. Glob Change Biol 21:3864–3879

    Article  Google Scholar 

  • Ho A, Angel R, Veraart AJ, Daebeler A, Jia ZJ, Kim SY, Kerckhof FM, Boon N, Bodelier PL (2016a) Biotic interactions in microbial communities as modulators of biogeochemical processes: methanotrophy as a model system. Front Microbiol 7:1285

    Article  PubMed  PubMed Central  Google Scholar 

  • Ho A, van den Brink E, Reim A, Krause SMB, Bodelier PLE (2016b) Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure. Front Microbiol 6:1493

    PubMed  PubMed Central  Google Scholar 

  • Ho A, Di Lonardo DP, Bodelier PLE (2017a) Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol 93. https://doi.org/10.1093/femsec/fix006

  • Ho A, Ijaz UZ, Janssens TKS, Ruijs R, Kim SY, de Boer W, Termorshuizen A, Putten WH, Bodelier PL (2017b) Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition. Glob Change Biol Bioenergy 9:1707–1720

    Article  CAS  Google Scholar 

  • Ho A, Lee HJ, Reumer M, Meima-Franke M, Raaijmakers C, Zweers H, de Boer W, Van der Putten WH, Bodelier PLE (2019) Unexpected role of canonical aerobic methanotrophs in upland agricultural soils. Soil Biol Biochem 131:1–8

    Article  CAS  Google Scholar 

  • Iguchi H, Yurimoto H, Sakai Y (2011) Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl Environ Microbiol 77:8509–8515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ikeda S, Sasaki K, Okubo T, Yamashita A, Terasawa K, Bao Z, Liu D, Watanabe T, Murase J, Asakawa S, Eda S, Mitsui H, Sato T, Minamisawa K (2014) Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions. Microbes Environ 29:50–59

    Article  PubMed  PubMed Central  Google Scholar 

  • in ‘t Zandt MH, de Jong AEE, Slomp CP, Jetten MSM (2018) The hunt for the most-wanted chemolithoautotrophic spookmicrobes. FEMS Microbiol Ecol 94. https://doi.org/10.1093/femsec/fiy064

  • IPCC (2014) Climate change 2013: the physical science basis: Working Group I contribution to the Fifth assessment report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge

    Google Scholar 

  • Jeong SY, Kim TG (2019) Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3. J Appl Microbiol 126:534–544

    Article  CAS  PubMed  Google Scholar 

  • Kalyuzhnaya MG, Yang S, Rozova ON, Smalley NE, Clubb J, Lamb A, Gowda GA, Raftery D, Fu Y, Bringel F, Vuilleumier S, Beck DA, Trotsenko YA, Khmelenina VN, Lidstrom ME (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun 4:2785

    Article  CAS  PubMed  Google Scholar 

  • Karl DM, Beversdorf L, Björkman KM, Church MJ, Martinez A, Delong EF (2008) Aerobic production of methane in the sea. Nat Geosci 1:473–478

    Article  CAS  Google Scholar 

  • Keltjens JT, Pol A, Reimann J, Op den Camp HJM (2014) PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl Microbiol Biotechnol 98:6163–6183

    Article  CAS  PubMed  Google Scholar 

  • Khadem AF, Pol A, Wieczorek A, Mohammadi SS, Francoijs KJ, Stunnenberg HG, Jetten MS, Op den Camp HJ (2011) Autotrophic methanotrophy in verrucomicrobia: methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J Bacteriol 193:4438–4446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khadka R, Clothier L, Wang L, Lim CK, Klotz MG, Dunfield PF (2018) Evolutionary history of copper membrane monooxygenases. Front Microbiol 9:2493

    Article  PubMed  PubMed Central  Google Scholar 

  • Kip N, van Winden JF, Pan Y, Bodrossy L, Reichart G-J, Smolders AJP, Jetten MSM, Damsté JSS, Op den Camp HJM (2010) Global prevalence of methane oxidation by symbiotic bacteria in peat-moss ecosystems. Nat Geosci 3:617–621

    Article  CAS  Google Scholar 

  • Kirschke S, Bousquet P, Ciais P, Saunois M, Canadell JG, Dlugokencky EJ, Bergamaschi P, Bergmann D, Blake DR, Bruhwiler L, Cameron-Smith P, Castaldi S, Chevallier F, Feng L, Fraser A, Heimann M, Hodson EL, Houweling S, Josse B, Fraser PJ, Krummel PB, Lamarque J-F, Langenfelds RL, Le Quéré C, Naik V, O’Doherty S, Palmer PI, Pison I, Plummer D, Poulter B, Prinn RG, Rigby M, Ringeval B, Santini M, Schmidt M, Shindell DT, Simpson IJ, Spahni R, Steele LP, Strode SA, Sudo K, Szopa S, van der Werf GR, Voulgarakis A, van Weele M, Weiss RF, Williams JE, Zeng G (2013) Three decades of global methane sources and sinks. Nat Geosci 6:813–823

    Article  CAS  Google Scholar 

  • 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 17:3219–3232

    Article  CAS  PubMed  Google Scholar 

  • Kits KDSC, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549:269–272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knief C (2015) Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 6:1346

    Article  PubMed  PubMed Central  Google Scholar 

  • Knief C, Dunfield PF (2005) Response and adaptation of different methanotrophic bacteria to low methane mixing ratios. Environ Microbiol 7:1307–1317

    Article  CAS  PubMed  Google Scholar 

  • Kojima H, Iwata T, Fukui M (2009) DNA-based analysis of planktonic methanotrophs in a stratified lake. Freshwater Biol 54:1501–1509

    Article  CAS  Google Scholar 

  • Kojima H, Tokizawa R, Kogure K, Kobayashi Y, Itoh M, Shiah FK, Okuda N, Fukui M (2014) Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer. Sci Rep 4:5728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kolb S (2009) The quest for atmospheric methane oxidizers in forest soils. Environ Microbiol Rep 1:336–346

    Article  CAS  PubMed  Google Scholar 

  • Kolb S, Horn MA (2012) Microbial CH4 and N2O consumption in acidic wetlands. Front Microbiol 3:78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kox MAR, Aalto SL, Penttila T, Ettwig KF, Jetten MSM, van Kessel M (2018) The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses. AMB Exp 8:76

    Article  CAS  Google Scholar 

  • Krause S, Meima-Franke M, Hefting MM, Bodelier PLE (2013) Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland. FEMS Microbiol Ecol 86:59–70

    Article  CAS  PubMed  Google Scholar 

  • Krause S, Le Roux X, Niklaus PA, Van Bodegom PM, Lennon JT, Bertilsson S, Grossart H-P, Philippot L, Bodelier PLE (2014) Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Front Microbiol 5:10

    Article  Google Scholar 

  • Krause SMB, Johnson T, Karunaratne YS, Fu YF, Beck DAC, Chistoserdova L, Lidstrom ME (2017) Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions. Proce Natl Acad Sci USA 114:358–363

    Article  CAS  Google Scholar 

  • Krause SMB, Meima-Franke M, Veraart AJ, Ren GD, Ho A, Bodelier PLE (2018) Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system. Sci Rep 8:8862

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kruger M, Eller G, Conrad R, Frenzel P (2002) Seasonal variation in pathways of CH4 production and in CH4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors. Glob Change Biol 8:265–280

    Article  Google Scholar 

  • Krukenberg V, Riedel D, Gruber-Vodicka HR, Buttigieg PL, Tegetmeyer HE, Boetius A, Wegener G (2018) Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. Environ Microbiol 20:1651–1666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16:263–276

    Article  CAS  PubMed  Google Scholar 

  • Larmola T, Tuittila E-S, Tiirola M, Nykänen H, Martikainen PJ, Yrjälä K, Tuomivirta T, Fritze H (2010) The role of Sphagnum mosses in the methane cycling of a boreal mire. Ecology 91:2356–2365

    Article  PubMed  Google Scholar 

  • Larmola T, Leppanen SM, Tuittila ES, Aarva M, Merila P, Fritze H, Tiirola M (2014) Methanotrophy induces nitrogen fixation during peatland development. Proc Natl Acad Sci USA 111:734–739

    Article  CAS  PubMed  Google Scholar 

  • Lau MCY, Stackhouse BT, Layton AC, Chauhan A, Vishnivetskaya TA, Chourey K, Ronholm J, Mykytczuk NC, Bennett PC, Lamarche-Gagnon G, Burton N, Pollard WH, Omelon CR, Medvigy DM, Hettich RL, Pfiffner SM, Whyte LG, Onstott TC (2015) An active atmospheric methane sink in high Arctic mineral cryosols. ISME J 9:1880–1891

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lenhart K, Bunge M, Ratering S, Neu TR, Schuttmann I, Greule M, Kammann C, Schnell S, Müller C, Zorn H, Keppler F (2012) Evidence for methane production by saprotrophic fungi. Nat Commun 3:1046

    Article  PubMed  CAS  Google Scholar 

  • Levine UY, Teal TK, Robertson GP, Schmidt TM (2011) Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. ISME J 5:1683–1691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Makipaa R, Leppanen SM, Munoz SS, Smolander A, Tiirola M, Tuomivirta T, Fritze H (2018) Methanotrophs are core members of the community in decayingdiazotroph Norway spruce logs. Soil Biol Biochem 120:230–232

    Article  CAS  Google Scholar 

  • Maurer D, Kolb S, Haumaier L, Borken W (2008) Inhibition of atmospheric methane oxidation by monoterpenes in Norway spruce and European beech soils. Soil Biol Biochem 40:3014–3020

    Article  CAS  Google Scholar 

  • McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74:1305–1315

    Article  CAS  PubMed  Google Scholar 

  • McGinnis DF, Flury S, Tang KW, Grossart HP (2017) Porewater methane transport within the gas vesicles of diurnally migrating Chaoborus spp.: an energetic advantage. Sci Rep 7:44478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGlynn SE, Chadwick GL, O’Neill A, Mackey M, Thor A, Deerinck TJ, Ellisman MH, Orphan VJ (2018) Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners as revealed by integrated multimodal analytical microscopy. Appl Environ Microbiol 84:e00399-18

    Google Scholar 

  • Menyailo OV, Abraham W-R, Conrad R (2010) Tree species affect atmospheric CH4 oxidation without altering community composition of soil methanotrophs. Soil Biol Biochem 42:101–107

    Article  CAS  Google Scholar 

  • Michaud AB, Dore JE, Achberger AM, Christner BC, Mitchell AC, Skidmore ML, Vick-Majors TJ, Priscu JC (2017) Microbial oxidation as a methane sink beneath the West Antarctic Ice Sheet. Nat Geosci 10:582

    Article  CAS  Google Scholar 

  • Milucka J, Kirf M, Lu L, Krupke A, Lam P, Littmann S, Kuypers MM, Schubert CJ (2015) Methane oxidation coupled to oxygenic photosynthesis in anoxic waters. ISME J 9:1991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Naguib M, Overbeck J (1970) On methane oxidizing bacteria in fresh waters. I. Introduction to the problem and investigations on the presence of obligate methane oxidizers. Zeitschrift für allgemeine Mikrobiologie 10:17–36

    Article  CAS  PubMed  Google Scholar 

  • Naqvi SWA, Lam P, Narvenkar G, Sarkar A, Naik H, Pratihary A, Shenoy DM, Gauns M, Kurian S, Damare S, Duret M, Lavik G, Kuypers MMM (2018) Methane stimulates massive nitrogen loss from freshwater reservoirs in India. Nat Commun 9:1265

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nauer PA, Dam B, Liesack W, Zeyer J, Schroth MH (2012) Activity and diversity of methane-oxidizing bacteria in glacier forefields on siliceous and calcareous bedrock. Biogeosciences 9:2259–2274

    Article  CAS  Google Scholar 

  • Nauer PA, Hutley LB, Arndt SK (2018) Termite mounds mitigate half of termite methane emissions. Proc Natl Acad Sci USA 115:13306–13311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nazaries L, Tate KR, Ross DJ, Singh J, Dando J, Saggar S, Baggs EM, Millard P, Murrell JC, Singh BK (2011) Response of methanotrophic communities to afforestation and reforestation in New Zealand. ISME J 5:1832–1836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nazaries L, Karunaratne SB, Delgado-Baquerizo M, Campbell CD, Singh BK (2018) Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey. Soil Biol Biochem 127:264–279

    Article  CAS  Google Scholar 

  • Nguyen AD, Hwang IY, Lee OK, Hur DH, Jeon YC, Hadiyati S, Kim MS, Yoon SH, Jeong H, Lee EY (2018) Functional analysis of methylomonas sp. DH-1 genome as a promising biocatalyst for bioconversion of methane to valuable chemicals. Catalysts 8:117

    Article  CAS  Google Scholar 

  • Nisbet EG, Dlugokencky EJ, Bousquet P (2014) Methane on the rise-again. Science 343:493–495

    Article  CAS  PubMed  Google Scholar 

  • Oliveira Junior ES, Temmink RJM, Buhler BF, Souza RM, Resende N, Spanings T, Muniz CC, Lamers LPM, Kosten S (2019) Benthivorous fish bioturbation reduces methane emissions, but increases total greenhouse gas emissions. Freshw Biol 64:197–207

    Article  CAS  Google Scholar 

  • Orata FD, Kits KD, Stein LY (2018) Complete genome sequence of methylomonas denitrificans strain FJG1, an obligate aerobic methanotroph that can couple methane oxidation with denitrification. Microbiol Resour Announ 6. https://doi.org/10.1128/genomeA.00276-18

  • Orellana LH, Chee-Sanford JC, Sanford RA, Loffler FE, Konstantinidis KT (2018) Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization. Appl Environ Microbiol 84. https://doi.org/10.1128/AEM.01646-17

  • Osborne CD, Haritos VS (2018) Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the proteobacteria. Mol Phylogenet Evol 129:171–181

    Article  CAS  PubMed  Google Scholar 

  • Oshkin IY, Beck DAC, Lamb AE, Tchesnokova V, Benuska G, McTaggart TL, Kalyuzhnaya MG, Dedysh SN, Lidstrom ME, Chistoserdova L (2015) Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response. ISME J 9:1119–1129

    Article  CAS  PubMed  Google Scholar 

  • Oswald K, Milucka J, Brand A, Littmann S, Wehrli B, Kuypers MM, Schubert CJ (2015) Light-dependent aerobic methane oxidation reduces methane emissions from seasonally stratified lakes. PLoS One 10:e0132574

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Oswald K, Milucka J, Brand A, Hach P, Littmann S, Wehrli B, Kuypers MMM, Schubert CJ (2016) Aerobic gammaproteobacterial methanotrophs mitigate methane emissions from oxic and anoxic lake waters. Limnol Oceanogr 61:S101–SS18

    Article  CAS  Google Scholar 

  • Oswald K, Graf JS, Littmann S, Tienken D, Brand A, Wehrli B, Albertsen M, Daims H, Wagner M, Kuypers MM, Schubert CJ, Milucka J (2017) Crenothrix are major methane consumers in stratified lakes. ISME J 11:2124–2140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996

    Article  CAS  PubMed  Google Scholar 

  • Pieja AJ, Morse MC, Cal AJ (2017) Methane to bioproducts: the future of the bioeconomy? Curr Opin Chem Biol 41:123–131

    Article  CAS  PubMed  Google Scholar 

  • Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MSM, den Camp H (2007) Methanotrophy below pH1 by a new Verrucomicrobia species. Nature 450:874–U17

    Article  CAS  PubMed  Google Scholar 

  • Pol A, Barends TRM, Dietl A, Khadem AF, Eygensteyn J, Jetten MS, Op den Camp HJ (2014) Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ Microbiol 16:255–264

    Article  CAS  PubMed  Google Scholar 

  • Ponnudurai R, Kleiner M, Sayavedra L, Petersen JM, Moche M, Otto A, Becher D, Takeuchi T, Satoh N, Dubilier N, Schweder T, Markert S (2017) Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. ISME J 11:463–477

    Article  CAS  PubMed  Google Scholar 

  • Pratscher J, Dumont MG, Conrad R (2011) Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USC alpha clade. Environ Microbiol 13:2692–2701

    Article  CAS  PubMed  Google Scholar 

  • Pratscher J, Vollmers J, Wiegand S, Dumont MG, Kaster AK (2018) Unravelling the identity, metabolic potential and global biogeography of the atmospheric methane-oxidizing upland soil cluster alpha. Environ Microbiol 20:1016–1029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Puri AW, LiuD SAL, Yu Z, Pesesky MW, Greenberg PE, Lidstrom ME (2019) Interspecies chemical signaling in a methane-oxidizing bacterial community. Appl Environ Microbiol 85(7):e02702-18

    Google Scholar 

  • R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN: 3-900051-07-0, http://www.R-project.org

  • Raghoebarsing AA, Smolders AJP, Schmid MC, Rijpstra WIC, Wolters-Arts M, Derksen J, Jetten MS, Schouten S, Sinninghe Damsté JS, Lamers LP, Roelofs JG, Op den Camp HJ, Strous M (2005) Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436:1153–1156

    Article  CAS  PubMed  Google Scholar 

  • Rahman MT, Crombie A, Chen Y, Stralis-Pavese N, Bodrossy L, Meir P, McNamara NP, Murrell JC (2010) Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J 5(6):1061

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reay DS, Smith P, Christensen TR, James RH, Clark H (2018) Methane and global environmental change. Annu Rev Environ Resour 43:165–192

    Article  Google Scholar 

  • Reeburgh WS, Heggie DT (1977) Microbial methane consumption reactions and their effect on methane distributions in freshwater and marine environments. Limnol Oceanogr 22:1–9

    Article  CAS  Google Scholar 

  • Reim A, Luke C, Krause S, Pratscher J, Frenzel P (2012) One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME J 6:2128–2139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reumer M, Harnisz M, Lee HJ, Reim A, Grunert O, Putkinen A, Fritze H, Bodelier PLE, Ho A (2018) Impact of peat mining and restoration on methane turnover potential and methane-cycling microorganisms in a Northern bog. Appl Environ Microbiol 84:e02218-17

    Google Scholar 

  • Rissanen AJ, Saarenheimo J, Tiirola M, Peura S, Aalto SL, Karvinen A, Nykänen H (2018) Gammaproteobacterial methanotrophs dominate methanotrophy in aerobic and anaerobic layers of boreal lake waters. Aquat Microb Ecol 81:257–276

    Article  Google Scholar 

  • Roland FAE, Darchambeau F, Morana C, Bouillon S, Borges AV (2017) Emission and oxidation of methane in a meromictic, eutrophic and temperate lake (Dendre, Belgium). Chemosphere 168:756–764

    Article  CAS  PubMed  Google Scholar 

  • Rubin-Blum M, Antony CP, Borowski C, Sayavedra L, Pape T, Sahling H, Bohrmann G, Kleiner M, Redmond MC, Valentine DL, Dubilier N (2017) Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps. Nat Microbiol 2:17093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruff SE, Arnds J, Knittel K, Amann R, Wegener G, Ramette A, Boetius A (2013) Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand). PLoS One 8:e72627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruff SE, Felden J, Gruber-Vodicka HR, Marcon Y, Knittel K, Ramette A, Boetius A (2019) In situ development of a methanotrophic microbiome in deep-sea sediments. ISME J 13:197–213

    Article  CAS  PubMed  Google Scholar 

  • Saunois M, Bousquet P, Poulter B, Peregon A, Ciais P, Canadell JG, Dlugokencky EJ, Etiope G, Bastviken D, Houweling S, Janssens-Maenhout G, Tubiello FN, Castaldi S, Jackson RB, Alexe M, Arora VK, Beerling DJ, Bergamaschi P, Blake DR, Brailsford G, Brovkin V, Bruhwiler L, Crevoisier C, Crill P, Covey K, Curry C, Frankenberg C, Gedney N, Höglund-Isaksson L, Ishizawa M, Ito A, Joos F, Kim HS, Kleinen T, Krummel P, Lamarque JF, Langenfelds R, Locatelli R, Machida T, Maksyutov S, McDonald KC, Marshall J, Melton JR, Morino I, Naik V, O'Doherty S, Parmentier FJW, Patra PK, Peng C, Peng S et al (2016) The global methane budget 2000–2012. Earth Syst Sci Data 8:697–751

    Article  Google Scholar 

  • Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA (2018) Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology 99:714–723

    Article  PubMed  Google Scholar 

  • Schubert CJ, Vazquez F, Losekann-Behrens T, Knittel K, Tonolla M, Boetius A (2011) Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno). FEMS Microbiol Ecol 76:26–38

    Article  CAS  PubMed  Google Scholar 

  • Schulz-Bohm K, Martin-Sanchez L, Garbeva P (2017) Microbial volatiles: small molecules with an important role in infra- and inter-kingdom interactions. Front Microbiol 8:2484

    Article  PubMed  PubMed Central  Google Scholar 

  • Segers R (1998) Methane production and methane consumption: a review of processes underlying wetland methane fluxes. Biogeochemistry 41:23–51

    Article  CAS  Google Scholar 

  • Semrau JD (2018) Metals and methanotrophy. Appl Environ Microbiol 84:e02289-17

    Google Scholar 

  • Semrau JD, DiSpirito AA, Yoon S (2010) Methanotrophs and copper. FEMS Microbiol Rev 34:496–531

    Article  CAS  PubMed  Google Scholar 

  • 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 16:1867–1878

    Article  CAS  PubMed  Google Scholar 

  • Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, Chanton JP, Frolking S, Crill PM, Saleska SR, Rich VI, Tyson GW (2018) Methanotrophy across a natural permafrost thaw environment. ISME J 12:2544–2558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC (2018) Members of the genus methylobacter are inferred to account for the majority of aerobic methane oxidation in oxic soils from a freshwater wetland. Mbio 9. https://doi.org/10.1128/mBio.00815-18

  • Söhngen NL (1906) Ueber Bakterien, welche Methan als Kohlenstoffnahrung und Energiequelle gebrauchen. Centralbl Bakteriol Parasitenk Infektionskr Hyg Abt II 15:513–517

    Google Scholar 

  • Stock M, Hoefman S, Kerckhof FM, Boon N, De Vos P, De Baets B, Heylen K, Waegeman W (2013) Exploration and prediction of interactions between methanotrophs and heterotrophs. Res Microbiol 164:1045–1054

    Article  PubMed  Google Scholar 

  • 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 103:2363–2367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang KW, McGinnis DF, Ionescu D, Grossart H-P (2016) Methane production in oxic lake waters potentially increases aquatic methane flux to air. Environ Sci Technol Lett 3:227–233

    Article  CAS  Google Scholar 

  • Tate KR (2015) Soil methane oxidation and land-use change – from process to mitigation. Soil Biol Biochem 80:260–272

    Article  CAS  Google Scholar 

  • Tavormina PL, Ussler W 3rd, Orphan VJ (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol 74:3985–3995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tays C, Guarnieri MT, Sauvageau D, Stein LY (2018) Combined effects of carbon and nitrogen source to optimize growth of proteobacterial methanotrophs. Front Microbiol 9:2239

    Article  PubMed  PubMed Central  Google Scholar 

  • Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R (2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551:457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tveit A, Schwacke R, Svenning MM, Urich T (2013) Organic carbon transformations in high-Arctic peat soils: key transformations and microorganisms. ISME J 7:299–311

    Article  CAS  PubMed  Google Scholar 

  • Tveit AT, Urich T, Svenning MM (2014) Metatranscriptomic analysis of Arctic peat soil microbiota. Appl Environ Microbiol 80:5761–5772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tveit AT, Urich T, Frenzel P, Svenning MM (2015) Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proc Natl Acad Sci USA 112:E2507–E2E16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vaksmaa A, Guerrero-Cruz S, van Alen TA, Cremers G, Ettwig KF, Lüke C, Jetten MSM (2017a) Enrichment of anaerobic nitrate-dependent methanotrophic ‘Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil. Appl Microbiol Biotechnol 101:7075–7084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Vale G, Jetten MSM, Luke C (2017b) Stratification of diversity and activity of methanogenic and methanotrophic microorganisms in a nitrogen-fertilized Italian paddy soil. Front Microbiol 8:15

    Article  Google Scholar 

  • van der Wal A, Geydan TD, Kuyper TW, de Boer W (2013) A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 37:477–494

    Article  PubMed  CAS  Google Scholar 

  • van der Wal A, Ottosson E, de Boer W (2015) Neglected role of fungal community composition in explaining variation in wood decay rates. Ecology 96:124–133

    Article  PubMed  Google Scholar 

  • van Kessel M, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MS, Lucker S (2015) Complete nitrification by a single microorganism. Nature 528:555

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • van Kruistum H, Bodelier PLE, Ho A, Meima-Franke M, Veraart AJ (2018) Resistance and recovery of methane-oxidizing communities depends on stress regime and history; a microcosm study. Front Microbiol 9:1714

    Article  PubMed  PubMed Central  Google Scholar 

  • van Teeseling MCF, Pol A, Harhangi HR, van der Zwart S, Jetten MSM, den Camp H (2014) Expanding the verrucomicrobial methanotrophic world: description of three novel species of methylacidimicrobium gen. nov. Appl Environ Microbiol 80:6782–6791

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Veraart AJ, Steenbergh AK, Ho A, Kim SY, Bodelier PLE (2015) Beyond nitrogen: the importance of phosphorus for CH4 oxidation in soils and sediments. Geoderma 259:337–346

    Article  CAS  Google Scholar 

  • Veraart AJ, Garbeva P, van Beersum F, Ho A, Hordijk CA, Meima-Franke M, Zweers AJ, Bodelier PLE (2018) Living apart together-bacterial volatiles influence methanotrophic growth and activity. ISME J 12:1163–1166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Verbeke TJ, Dedysh SN, Dunfield PF (2018) Methanotrophy in acidic soils, including Northern Peatlands. In: McGenity TJ (ed) Microbial communities utilizing hydrocarbons and lipids: members, metagenomics and ecophysiology. Springer, Cham, pp 1–25

    Google Scholar 

  • Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, van Alen T, Jetten MSM, Kartal B, Op den Camp HJM, Reimann J (2018) Comparative genomics of candidatus methylomirabilis species and description of Ca. methylomirabilis lanthanidiphila. Front Microbiol 9:1672

    Article  PubMed  PubMed Central  Google Scholar 

  • Vigliotta G, Nutricati E, Carata E, Tredici SM, De Stefano M, Pontieri P, Massardo DR, Prati MV, De Bellis L, Alifano P (2007) Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. Appl Environ Microbiol 73:3556–3565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vollmer D, Regan HM, Andelman SJ (2016) Assessing the sustainability of freshwater systems: a critical review of composite indicators. Ambio 45:765–780

    Article  PubMed  PubMed Central  Google Scholar 

  • Vorob’ev AV, de Boer W, Folman LB, Bodelier PLE, Doronina NV, Suzina NE, Trotsenko YA, Dedysh SN (2009) Methylovirgula ligni gen. nov., sp nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene. Int J Syst Evol Microbiol 59:2538–2545

    Article  PubMed  CAS  Google Scholar 

  • Vorobev AV, Baani M, Doronina NV, Brady AL, Liesack W, Dunfield PF, Dedysh SN (2011) Methyloferula stellata gen. nov., sp nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int J Syst Evol Microbiol 61:2456–2463

    Article  CAS  PubMed  Google Scholar 

  • Walter KM, Smith LC, Chapin FS 3rd (2007) Methane bubbling from northern lakes: present and future contributions to the global methane budget. Philos Trans A Math Phys Eng Sci 365:1657–1676

    Article  CAS  PubMed  Google Scholar 

  • Wang JJ, Krause S, Muyzer G, Meima-Franke M, Laanbroek HJ, Bodelier PLE (2012) Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland. Front Microbiol 3:13

    Google Scholar 

  • Waring CL, Hankin SI, Griffith DWT, Kertesz MA, Kobylski V, Wilson NL, Coleman NV, Kettlewell G, Zlot R, Bosse M, Bell G (2017) Seasonal total methane depletion in limestone caves. Sci Rep 7:8314

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Watsuji TO, Yamamoto A, Takaki Y, Ueda K, Kawagucci S, Takai K (2014) Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri. ISME J 8:1020–1031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJ, Jetten MS, Luke C, Reimann J (2016) Nitrate- and nitrite-dependent anaerobic oxidation of methane. Environ Microbiol Rep 8:941–955

    Article  CAS  PubMed  Google Scholar 

  • Whittenbury R, Philips KC, Wilkinson JF (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61:205–218

    Article  CAS  PubMed  Google Scholar 

  • Wieczorek AS, Drake HL, Kolb S (2011) Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs. FEMS Microbiol Ecol 77:28–39

    Article  CAS  PubMed  Google Scholar 

  • Wieder WR, Allison SD, Davidson EA, Georgiou K, Hararuk O, He Y, Hopkins F, Luo Y, Smith MJ, Sulman B, Todd-Brown K, Wang Y-P, Xia J, Xu X (2015) Explicitly representing soil microbial processes in Earth system models. Glob Biogeochem Cycles 29:1782–1800

    Article  CAS  Google Scholar 

  • Yan X, Xu X, Ji M, Zhang Z, Wang M, Wu S, Wang G, Zhang C, Liu H (2019) Cyanobacteria blooms: a neglected facilitator of CH4 production in eutrophic lakes. Sci Total Environ 651:466–474

    Article  CAS  PubMed  Google Scholar 

  • Yu ZCL (2017) Communal metabolism of methane and the rare earth element switch. J Bacteriol 199:e00328-17

    Google Scholar 

  • Yvon-Durocher G, Montoya J, Woodward G, Jones J, Trimmer M (2011) Warming increases the proportion of primary production emitted as methane from freshwater mesocosms. Glob Change Biol 17:1225–1234

    Article  Google Scholar 

  • Zhao R, Wang HM, Cheng XY, Yun Y, Qiu X (2018) Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave. FEMS Microbiol Ecol 94. https://doi.org/10.1093/femsec/fiy192

  • Zheng Y, Huang R, Wang BZ, Bodelier PLE, Jia ZJ (2014) Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil. Biogeosciences 11:3353–3368

    Article  CAS  Google Scholar 

  • Zhou X, Jin F, Lu C, Baoyin T, Jia Z (2018) Shifts in the community composition of methane-cycling microorganisms during lake shrinkage. Geoderma 311:9–14

    Article  Google Scholar 

  • Zigah PK, Oswald K, Brand A, Dinkel C, Wehrli B, Schubert CJ (2015) Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake. Limnol Oceanogr 60:553–572

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This publication is publication number 6717 of the Netherlands Institute of Ecology (NIOO-KNAW). This publication was supported by a grant of the Applied and Engineering Science division of the Netherlands Organization of Scientific Research (NWO-TTW) grant number 16475.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Paul L. E. Bodelier .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bodelier, P.L.E., Pérez, G., Veraart, A.J., Krause, S.M.B. (2019). Methanotroph Ecology, Environmental Distribution and Functioning. In: Lee, E. (eds) Methanotrophs. Microbiology Monographs, vol 32. Springer, Cham. https://doi.org/10.1007/978-3-030-23261-0_1

Download citation

Publish with us

Policies and ethics