Brune A. Methanogenesis in the digestive tracts of insects. In: Timmis KN (ed). Handbook of hydrocarbon and lipid microbiology. Berlin, Heidelberg: Springer-Verlag; 2010. pp. 707–728.
Zimmerman PR, Greenberg JP, Wandiga SO, Crutzen PJ. Termites: a potentially large source of atmospheric methane, carbon dioxide, and molecular hydrogen. Science. 1982;218:563–5.
Rasmussen RA, Khalil MAK. Global production of methane by termites. Nature. 1983;301:700.
Sugimoto A, Inoue T, Tayasu I, Miller L, Takeichi S, Abe T. Methane and hydrogen production in a termite-symbiont system. Ecol Res. 1998;13:241–57.
Brauman A, Kane MD, Labat M, Breznak JA. Genesis of acetate and methane by gut bacteria of nutritionally diverse termites. Science. 1992;257:1384–7.
Kirschke S, Bousquet P, Ciais P, Saunois M, Canadell JG, Dlugokencky EJ, et al. Three decades of global methane sources and sinks. Nat Geosci. 2013;6:813–23.
Nauer PA, Hutley LB, Arndt SK. Termite mounds mitigate half of termite methane emissions. Proc Natl Acad Sci USA. 2018;115:13306–11.
Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev. 1996;60:439–71.
Reuß J, Rachel R, Kämpfer P, Rabenstein A, Küver J, Dröge S, et al. Isolation of methanotrophic bacteria from termite gut. Microbiol Res. 2015;179:29–37.
Pester M, Tholen A, Friedrich MW, Brune A. Methane oxidation in termite hindguts: absence of evidence and evidence of absence. Appl Environ Microbiol. 2007;73:2024–8.
Dunfield PF. The soil methane sink. In: Reay D, Hewitt K, Smith K, Grace J, editors. Greenhouse gas sinks. Wallingford: CABI; 2007. pp. 152–70.
Bignell DE, Eggleton P, Nunes L, Thomas KL. Termites as mediators of forest carbon fluxes in tropical forests: budgets for carbon dioxide and methane emissions. In: Watt AD, Stork NE, Hunter MD (eds). Forests and insects. London: Chapman & Hall; 1997. pp. 109–134.
Jamali H, Livesley SJ, Grover SP, Dawes TZ, Hutley LB, Cook GD, et al. The importance of termites to the CH4 balance of a tropical savanna woodland of northern Australia. Ecosystems. 2011;14:698–709.
Ho A, Erens H, Mujinya BB, Boeckx P, Baert G, Schneider B, et al. Termites facilitate methane oxidation and shape the methanotrophic community. Appl Environ Microbiol. 2013;79:7234–40.
Noirot C, Darlington JPEC. Termite nests: architecture, regulation and defence. In: Abe T, Bignell DE, Higashi M (eds). Termites: Evolution, Sociality Symbioses, Ecology. Dordrecht: Springer; 2000. pp. 121–139.
Korb J. Termite mound architecture, from function to construction. In: Bignell DE, Roisin Y, Lo N (eds). Biology of termites: a modern synthesis. Dordrecht: Springer Netherlands; 2010. pp. 349–373.
Jones DT, Eggleton P. Global biogeography of termites: a compilation of sources. In: Bignell DE, Roisin Y, Lo N, editors. Biology of termites: a modern synthesis. Dordrecht: Springer; 2011. pp. 1–576.
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.
Nauer PA, Chiri E, Souza D, de, Hutley LB, Arndt SK. Rapid image-based field methods improve the quantification of termite mound structures and greenhouse-gas fluxes. Biogeosciences. 2018;15:3731–42.
Holmes AJ, Costello A, Lidstrom ME, Murrell JC. Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett. 1995;132:203–8.
Costello AM, Lidstrom ME. Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol. 1999;65:5066–74.
Henneberger R, Chiri E, Bodelier PEL, Frenzel P, Lüke C, Schroth MH. Field‐scale tracking of active methane‐oxidizing communities in a landfill cover soil reveals spatial and seasonal variability. Environ Microbiol. 2015;17:1721–37.
Ji R, Brune A. Nitrogen mineralization, ammonia accumulation, and emission of gaseous NH3 by soil-feeding termites. Biogeochemistry. 2006;78:267–83.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.
Apprill A, McNally S, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Micro Ecol. 2015;75:129–37.
Heil JR, Lynch MDJ, Cheng J, Matysiakiewicz O, D’Alessio M, Charles TC. The completed PacBio single-molecule real-time sequence of Methylosinus trichosporium strain OB3b reveals the presence of a third large plasmid. Genome Announc. 2017;5:e01349–17.
Kolb S, Knief C, Stubner S, Conrad R. Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol. 2003;69:2423–9.
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.
Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE. 2013;8:e57923.
Chiri E, Nauer PA, Rainer E-M, Zeyer J, Schroth MH. High temporal and spatial variability of atmospheric-methane oxidation in Alpine glacier-forefield soils. Appl Environ Microbiol. 2017;83:e01139–17.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Wen X, Yang S, Liebner S. Evaluation and update of cutoff values for methanotrophic pmoA gene sequences. Arch Microbiol. 2016;198:629–36.
Dumont MG, Lüke C, Deng Y, Frenzel P. Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN. Front Microbiol. 2014;5:34.
Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27:221–4.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:2584.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011;5:169.
Andrews S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Cambridge, UK: The Babraham Institute; 2010.
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047–8.
Bushnell B. BBMap: A fast, accurate, splice-aware aligner. Berkeley, CA, US: Lawrence Berkeley National Lab (LBNL); 2015.
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Kang D, Li F, Kirton ES, Thomas A, Egan RS, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26.
Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144.
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43.
Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, et al. VizBin—an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome. 2015;3:1–7.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864.
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
Rusley C, Onstott TC, Vishnivetskaya TA, Layton A, Chauhan A, Pfiffner SM, et al. Metagenome-assembled genome of USCα AHI, a potential high-affinity methanotroph from Axel Heiberg Island, Canadian High Arctic. Microbiol Resour Announc. 2019;8:1–4.
Ricke P, Kube M, Nakagawa S, Erkel C, Reinhardt R, Liesack W. First genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to Methylocapsa acidiphila. Appl Environ Microbiol. 2005;71:7472–82.
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014;32:268–74.
Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25:1307–20.
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256–9.
Dong X, Strous M. An integrated pipeline for annotation and visualization of metagenomic contigs. Front Genet. 2019;10:1–10.
Zhou Z, Tran P, Liu Y, Kieft K, Anantharaman K. METABOLIC: a scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes. bioRxiv. 2019:761643.
Urmann K, Gonzalez-Gil G, Schroth MH, Hofer M, Zeyer J. New field method: gas push–pull test for the in-situ quantification of microbial activities in the vadose zone. Environ Sci Technol. 2005;39:304–10.
Reim A, Lüke C, Krause S, Pratscher J, Frenzel P. 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. 2012;6:2128.
Raj SS, Sumangala RK, Lal KB, Panicker PK. Gas chromatographic analysis of oxygen and argon at room temperature. J Chromatogr Sci. 1996;34:465–7.
Schroth MH, Istok JD. Models to determine first‐order rate coefficients from single‐well push‐pull tests. Groundwater. 2006;44:275–83.
Urmann K, Schroth MH, Noll M, Gonzalez‐Gil G, Zeyer J. Assessment of microbial methane oxidation above a petroleum‐contaminated aquifer using a combination of in situ techniques. J Geophys Res Biogeosciences. 2008;113:G02006.
R Development Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2017.
Holt JA. Microbial activity in the mounds of some Australian termites. Appl Soil Ecol. 1998;9:183–7.
Knief C, Lipski A, Dunfield PF. Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol. 2003;69:6703–14.
King H, Ocko S, Mahadevan L. Termite mounds harness diurnal temperature oscillations for ventilation. Proc Natl Acad Sci USA. 2015;112:11589–93.
Bristow KL, Holt JA. Can termites create local energy sinks to regulate mound temperature? J Therm Biol. 1987;12:19–21.
Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, et al. Widespread soil bacterium that oxidizes atmospheric methane. Proc Natl Acad Sci USA. 2019;116:8515–24.
Pratscher J, Vollmers J, Wiegand S, Dumont MG, Kaster A-K. Unravelling the identity, metabolic potential and global biogeography of the atmospheric methane-oxidizing upland soil cluster α. Environ Microbiol. 2018;20:1016–29.
Bender M, Conrad R. Kinetics of CH4 oxidation in oxic soils exposed to ambient air or high CH4 mixing ratios. FEMS Microbiol Lett. 1992;101:261–70.
Nauer PA, Schroth MH. In situ quantification of atmospheric methane oxidation in near-surface soils. Vadose Zo J. 2010;9:1052–62.
Judd CR, Koyama A, Simmons MP, Brewer P, von Fischer JC. Co-variation in methanotroph community composition and activity in three temperate grassland soils. Soil Biol Biochem. 2016;95:78–86.
Schroth MH, Eugster W, Gómez KE, Gonzalez-Gil G, Niklaus PA, Oester P. Above-and below-ground methane fluxes and methanotrophic activity in a landfill-cover soil. Waste Manag. 2012;32:879–89.
Baani M, Liesack W. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci USA. 2008;105:10203–8.
Gebert J, Stralis‐Pavese N, Alawi M, Bodrossy L. Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray. Environ Microbiol. 2008;10:1175–88.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK, Steen JA, et al. Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature. 2017;552:400–3.
Pratscher J, Dumont MG, Conrad R. Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade. Environ Microbiol. 2011;13:2692–701.
Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10:761–77.
Cordero PRF, Bayly K, Leung PM, Huang C, Islam ZF, Schittenhelm RB, et al. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J. 2019;13:2868–81.
Carere CR, Hards K, Houghton KM, Power JF, McDonald B, Collet C, et al. Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. ISME J. 2017;11:2599–610.
Schmitz RA, Pol A, Mohammadi SS, Hogendoorn C, van Gelder AH, Jetten MSM, et al. The thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV oxidizes subatmospheric H2 with a high-affinity, membrane-associated [NiFe] hydrogenase. ISME J. 2020;14:1223.
Mohammadi SS, Pol A, van Alen T, Jetten MSM, Op, den Camp HJM. Ammonia oxidation and nitrite reduction in the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV. Front Microbiol. 2017;8:1901.
Jamali H, Livesley SJ, Hutley LB, Fest B, Arndt SK. The relationships between termite mound CH4/CO2 emissions and internal concentration ratios are species specific. Biogeosciences. 2013;10:2229–40.
Schnell S, King GM. Mechanistic analysis of ammonium inhibition of atmospheric methane consumption in forest soils. Appl Environ Microbiol. 1994;60:3514–21.
Carlsen HN, Joergensen L, Degn H. Inhibition by ammonia of methane utilization in Methylococcus capsulatus (Bath). Appl Microbiol Biotechnol. 1991;35:124–7.
Bodelier PLE, Laanbroek HJ. Nitrogen as a regulatory factor of methane oxidation in soils and sediments. Fems Microbiol Ecol. 2004;47:265–77.
Veraart AJ, Steenbergh AK, Ho A, Kim SY, Bodelier PLE. Beyond nitrogen: the importance of phosphorus for CH4 oxidation in soils and sediments. Geoderma. 2015:259–60.
Chiri E, Nauer PA, Henneberger R, Zeyer J, Schroth MH. Soil–methane sink increases with soil age in forefields of Alpine glaciers. Soil Biol Biochem. 2015;84:83–95.
Angel R, Conrad R. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environ Microbiol. 2009;11:2598–610.
de Caritat P, Cooper M, Wilford J. The pH of Australian soils: field results from a national survey. Soil Res. 2011;49:173–82.
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