Myhre GSD, Bréon FM, Collins W, Fuglestvedt J, Huang J, KochD LJF, Lee D, Mendoza B, Nakajima T, Robock A, Stephens G, Takemura T, Zhang H. Climate change 2013—the physical science basis; working group 1 contribution to the fifth assessment report. Intergovernmental Panel on Climate Change. Cambridge: Cambridge University Press; 2014.
EPA. Methane and nitrous oxide emissions from natural sources. vol. EPA 430-R-10-001. US Environmental Protection Agency; 2010.
Etiope G, Feyzullayev A, Baciu CL. Terrestrial methane seeps and mud volcanoes: a global perspective of gas origin. Mar Pet Geol. 2009;26:333–44.
Article
CAS
Google Scholar
Etiope G, Ciccioli P. Earth’s degassing: a missing ethane and propane source. Science. 2009;323:478.
Article
PubMed
CAS
Google Scholar
Baciu C, Caracausi A, Etiope G, Italiano F. Mud volcanoes and methane seeps in Romania: main features and gas flux. Ann Geophyiology. 2007;50:501–11.
Google Scholar
Baciu C, Ionescu A, Etiope G. Hydrocarbon seeps in Romania: gas origin and release to the atmosphere. Mar Pet Geol. 2018;89:130–43.
Article
CAS
Google Scholar
Kroeger KF, di Primio R, Horsfield B. Atmospheric methane from organic carbon mobilization in sedimentary basins—the sleeping giant? Earth Sci Rev. 2011;107:423–42.
Article
CAS
Google Scholar
Etiope G, Klusman RW. Microseepage in drylands: flux and implications in the global atmospheric source/sink budget of methane. Glob Planet Chang. 2010;72:265–74.
Article
Google Scholar
Anthony KMW, Anthony P, Grosse G, Chanton J. Geologic methane seeps along boundaries of Arctic permafrost thaw and melting glaciers. Nat Geosci. 2012;5:419–26.
Article
CAS
Google Scholar
Tassi F, Fiebig J, Vaselli O, Nocentini M. Origins of methane discharging from volcanic-hydrothermal, geothermal and cold emissions in Italy. Chem Geol. 2012;310-311:36–48.
Article
CAS
Google Scholar
Oremland RS, Miller LG, Whiticar MJ. Sources and flux of natural gases from Mono Lake, California. Geochim Cosmochim Acta. 1987;51:2915–29.
Article
CAS
Google Scholar
Etiope G, Drobniak A, Schimmelmann A. Natural seepage of shale gas and the origin of “eternal flames” in the Northern Appalachian Basin, USA. Mar Pet Geol. 2013;43:178–86.
Article
CAS
Google Scholar
Reddy CM, Arey JS, Seewald JS, Sylva SP, Lemkau KL, Nelson RK, Carmichael CA, McIntyre CP, Fenwick J, Ventura GT, et al. Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A. 2012;109:20229–34.
Article
PubMed
Google Scholar
Osborn SG, Vengosh A, Warner NR, Jackson RB. Methane contamination of drinking water accompanying gas-well drilling and hydraulic fracturing. Proc Natl Acad Sci U S A. 2011;108:8172–6.
Article
PubMed
PubMed Central
Google Scholar
Howarth RW, Santoro R, Ingraffea A. Methane and the greenhouse-gas footprint of natural gas from shale formations. Clim Chang. 2011;106:679–90.
Article
CAS
Google Scholar
Jackson RB, Vengosh A, Darrah TH, Warner NR, Down A, Poreda RJ, Osborn SG, Zhao K, Karr JD. Increased stray gas abundance in a subset of drinking water wells near Marcellus shale gas extraction. Proc Natl Acad Sci U S A. 2013;110:11250–5.
Article
PubMed
PubMed Central
Google Scholar
Wang Q, Chen X, Jha AN, Rogers H. Natural gas from shale formation—the evolution, evidences and challenges of shale gas revolution in United States. Renew Sust Energ Rev. 2014;30:1–28.
Article
Google Scholar
Kolb S. The quest for atmospheric methane oxidizers in forest soils. Environ Microbiol Rep. 2009;1:336–46.
Article
PubMed
CAS
Google Scholar
Dunfield PF. The soil methane sink. In: Greenhouse gas sinks. Wallingford: CABI; 2007.
Google Scholar
Dalal RC, Allen DE. Greenhouse gas fluxes from natural ecosystems. Aust J Bot. 2008;56:369–407.
Article
CAS
Google Scholar
Semrau JD, DiSpirito AA, Vuilleumier S. Facultative methanotrophy: false leads, true results, and suggestions for future research. FEMS Microbiol Lett. 2011;323:1–12.
Article
PubMed
CAS
Google Scholar
Vorobev A, Jagadevan S, Jain S, Anantharaman K, Dick GJ, Vuilleumier S, Semrau JD. Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Appl Environ Microbiol. 2014;80:3044–52.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem. 2017;22:307–19.
Article
PubMed
CAS
Google Scholar
Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. In: Advances in Applied Microbiology. Washington, DC: vol. 63: Academic Press; 2008. p. 183–229.
Chistoserdova L. Modularity of methylotrophy, revisited. Environ Microbiol. 2011;13:2603–22.
Article
PubMed
CAS
Google Scholar
Chistoserdova L, Lidstrom ME. Aerobic methylotrophic prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The prokaryotes: prokaryotic physiology and biochemistry. Berlin: Springer Berlin Heidelberg; 2013. p. 267–85.
Chapter
Google Scholar
Knief C. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol. 2015;6:1346.
Article
PubMed
PubMed Central
Google Scholar
Ghashghavi M, Jetten MSM, Luke C. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers. AMB Express. 2017;7:162.
Article
PubMed
PubMed Central
CAS
Google Scholar
Semrau JD, DiSpirito AA, Murrell JC. Life in the extreme: thermoacidophilic methanotrophy. Trends Microbiol. 2008;16:190–3.
Article
PubMed
CAS
Google Scholar
Stein LY, Yoon S, Semrau JD, Dispirito AA, Crombie A, Murrell JC, Vuilleumier S, Kalyuzhnaya MG, Op den Camp HJ, Bringel F, et al. Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b. J Bacteriol. 2010;192:6497–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ashraf W, Mihdhir A, Murrell JC. Bacterial oxidation of propane. FEMS Microbiol Lett. 1994;122:1–6.
Article
PubMed
CAS
Google Scholar
Tetsuya K, Yui K, Hiroya Y, Nobuo K, Yasuyoshi S. Gene structure and regulation of alkane monooxygenases in propane-utilizing Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7. J Biosci Bioeng. 2016;102(3):184–192.
Nicholas VC, Sheree Y, Neil LW, Laura MN, Margaret DM, Mai-anh L, Ben C, Andrew JH. Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. Environ Microbiol Rep. 2011;3(3):297–307.
Johnson EL, Hyman MR. Propane and n-butane oxidation by Pseudomonas putida GPo1. Appl Environ Microbiol. 2006;72:950–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dubbels BL, Sayavedra-Soto LA, Arp DJ. Butane monooxygenase of Pseudomonas butanovora: purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase. Microbiology. 2007;153:1808–16.
Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ. Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as Pseudomonas butanovora. Int J Syst Evol Microbiol. 2009;59:1576–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shennan JL. Utilisation of C2–C4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol. 2006;81:237–56.
Article
CAS
Google Scholar
Cappelletti M, Presentato A, Milazzo G, Turner RJ, Fedi S, Frascari D, Zannoni D. Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes. Front Microbiol. 2015;6:393.
Article
PubMed
PubMed Central
Google Scholar
Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol. 2000;50(Pt 3):955–69.
Article
PubMed
CAS
Google Scholar
Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN. Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int J Syst Evol Microbiol. 2003;53:1231–9.
Article
PubMed
CAS
Google Scholar
Dedysh SN, Berestovskaya YY, Vasylieva LV, Belova SE, Khmelenina VN, Suzina NE, Trotsenko YA, Liesack W, Zavarzin GA. Methylocella tundrae sp. nov., a novel methanotrophic bacterium from acidic tundra peatlands. Int J Syst Evol Microbiol. 2004;54:151–6.
Article
PubMed
CAS
Google Scholar
Dedysh SN, Knief C, Dunfield PF. Methylocella species are facultatively methanotrophic. J Bacteriol. 2005;187:4665–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Theisen AR, Ali MH, Radajewski S, Dumont MG, Dunfield PF, McDonald IR, Dedysh SN, Miguez CB, Murrell JC. Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Mol Microbiol. 2005;58:682–92.
Article
PubMed
CAS
Google Scholar
Tamas I, Smirnova AV, He Z, Dunfield PF. The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis. ISME J. 2014;8:369–82.
Article
PubMed
CAS
Google Scholar
Chen Y, Crombie A, Rahman MT, Dedysh SN, Liesack W, Stott MB, Alam M, Theisen AR, Murrell JC, Dunfield PF. Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol. 2010;192:3840–1.
Article
PubMed
PubMed Central
CAS
Google Scholar
Crombie AT, Murrell JC. Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature. 2014;510:148–51.
Article
PubMed
CAS
Google Scholar
Hall J. Geology of New York: survey of the fourth geological district. Albany: Carol and Cook; 1843.
Google Scholar
Lyell C. Lyell’s travels in North America in the years 1841–1842. NY: C. E. Merrill; 1909.
Google Scholar
Macauley J. The natural, statistical and civil history of New York. Albany: Gould and Banks; 1829.
Google Scholar
Alain K, Holler T, Musat F, Elvert M, Treude T, Kruger M. Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environ Microbiol. 2006;8:574–90.
Article
PubMed
CAS
Google Scholar
Chen Y, Wu L, Boden R, Hillebrand A, Kumaresan D, Moussard H, Baciu M, Lu Y, Colin Murrell J. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. ISME J. 2009;3:1093.
Article
PubMed
CAS
Google Scholar
Kumaresan D, Wischer D, Stephenson J, Hillebrand-Voiculescu A, Murrell JC. Microbiology of Movile Cave—a chemolithoautotrophic ecosystem. Geomicrobiol J. 2014;31:186–93.
Article
CAS
Google Scholar
Sarbu SM, Kane TC, Kinkle BK. A chemoautotrophically based cave ecosystem. Science. 1996;272:1953–5.
Article
PubMed
CAS
Google Scholar
McDonald IR, Bodrossy L, Chen Y, Murrell JC. Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol. 2008;74:1305–15.
Article
PubMed
CAS
Google Scholar
Wang J, Geng K, Farhan Ul Haque M, Crombie A, Street L, Wookey P, Ma K, Murrell JC, Pratscher J. Draft genome sequence of Methylocella silvestris TVC, a facultative methanotroph isolated from permafrost. Genome Announc. 2018;6:e00040–18.
PubMed
PubMed Central
Google Scholar
Rahman MT, Crombie A, Chen Y, Stralis-Pavese N, Bodrossy L, Meir P, McNamara NP, Murrell JC. Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J. 2011;5:1061–6.
Article
PubMed
CAS
Google Scholar
Kumaresan D, Stephenson J, Doxey AC, Bandukwala H, Brooks E, Hillebrand-Voiculescu A, Whiteley AS, Murrell JC. Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses. Microbiome. 2018;6:1.
Article
PubMed
PubMed Central
Google Scholar
Kolb S, Knief C, Dunfield PF, Conrad R. Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ Microbiol. 2005;7:1150–61.
Article
PubMed
CAS
Google Scholar
Kallistova A, Montonen L, Jurgens G, Munster U, Kevbrina MV, Nozhevnikova AN. Culturable psychrotolerant methanotrophic bacteria in landfill cover soil. Mikrobiologia. 2014;83:109–18.
Google Scholar
Miller DN, Yavitt JB, Madsen EL, Ghiorse WC. Methanotrophic activity, abundance, and diversity in forested swamp pools: spatiotemporal dynamics and influences on methane fluxes. Geomicrobiol J. 2004;21:257–71.
Article
CAS
Google Scholar
Dedysh SN, Panikov NS, Liesack W, Großkopf R, Zhou J, Tiedje JM. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science. 1998;282:281–4.
Article
PubMed
CAS
Google Scholar
Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology. 2002;148:2331–42.
Article
PubMed
CAS
Google Scholar
Chen Y, Dumont MG, McNamara NP, Chamberlain PM, Bodrossy L, Stralis-Pavese N, Murrell JC. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ Microbiol. 2008;10:446–59.
Article
PubMed
CAS
Google Scholar
Putkinen A, Larmola T, Tuomivirta T, Siljanen HMP, Bodrossy L, Tuittila E-S, Fritze H. Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs. FEMS Microbiol Ecol. 2014;88:596–611.
Meyer KM, Klein AM, Rodrigues JLM, Nüsslein K, Tringe SG, Mirza BS, Tiedje JM, Bohannan BJM. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Mol Ecol. 2017;26:1547–56.
Article
PubMed
CAS
Google Scholar
Morris SA, Radajewski S, Willison TW, Murrell JC. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol. 2002;68:1446–53.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liebner S, Svenning MM. Environmental transcription of mmoX by methane-oxidizing proteobacteria in a subarctic palsa peatland. Appl Environ Microbiol. 2013;79:701–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dedysh SN, Derakshani M, Liesack W. Detection and enumeration of methanotrophs in acidic sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris. Appl Environ Microbiol. 2001;67:4850–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Duddleston KN, Kinney MA, Kiene RP, Hines ME: Anaerobic microbial biogeochemistry in a northern bog: acetate as a dominant metabolic end product. Glob Biogeochem Cycles 2002;16:11-11-11-19.
Vekeman B, Kerckhof FM, Cremers G, de Vos P, Vandamme P, Boon N, Op den Camp HJ, Heylen K. New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ Microbiol. 2016;18:4523–36.
Article
PubMed
CAS
Google Scholar
Dedysh SN, Naumoff DG, Vorobev AV, Kyrpides N, Woyke T, Shapiro N, Crombie AT, Murrell JC, Kalyuzhnaya MG, Smirnova AV, Dunfield PF. Draft genome sequence of Methyloferula stellata AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome Announc. 2015;3:e01555–14.
Article
PubMed
PubMed Central
Google Scholar
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. 2015;3:e1420.
Article
PubMed
PubMed Central
Google Scholar
Crombie A, Murrell JC. Development of a system for genetic manipulation of the facultative methanotroph Methylocella silvestris BL2. In: Rosenzweig AC, Ragsdale SW, editors. Methods in Enzymology, vol. 495. Burlington: Academic Press; 2011. p. 119–33.
Google Scholar
Whittenbury R, Phillips KC, Wilkinson JF. Enrichment, isolation and some properties of methane-utilizing bacteria. Microbiology. 1970;61:205–18.
CAS
Google Scholar
Lane DJ. 16S/23S rRNA sequencing. New York: John Wiley & Sons; 1991.
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Article
PubMed
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
PubMed
CAS
Google Scholar
Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis. 2008;5:459–72.
Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008;8:125.
Article
PubMed
PubMed Central
CAS
Google Scholar
Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ. Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. PLoS One. 2011;6:e26732.
Article
PubMed
PubMed Central
CAS
Google Scholar
Capone KA, Dowd SE, Stamatas GN, Nikolovski J. Diversity of the human skin microbiome early in life. J Investig Dermatol. 2011;131:2026–32.
Article
PubMed
PubMed Central
CAS
Google Scholar
Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, et al. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J. 2011;5:639–49.
Article
PubMed
CAS
Google Scholar
T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbio. 2006;72(7):5069–5072.
Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Article
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Article
Google Scholar
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ. 2014;2:e593.
Article
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Article
PubMed
CAS
Google Scholar