Canadell JG, Monteiro PMS, Costa, MH, Cotrim da Cunha L, Cox PM, Eliseev AV, et al. Global carbon and other biogeochemical cycles and feedbacks. In: Masson-Delmotte V, Zhai P, Pirani A, Connors SL, Péan C, Berger S, et al. editors. Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press; 2021, in press.
Rosentreter JA, Borges AV, Deemer BR, Holgerson MA, Liu S, Song C, et al. Half of global methane emissions come from highly variable aquatic ecosystem sources. Nat Geosci. 2021;14:225–30.
Google Scholar
Saunois M, Stavert AR, Poulter B, Bousquet P, Canadell JG, Jackson RB, et al. The global methane budget 2000 – 2017. Earth Syst. Sci Data. 2020;12:1561–623.
Lamentowicz M, Gałka M, Pawlyta J, Lamentowicz Ł, Goslar T, Miotk-Szpiganowicz G. Climate change and human impact in the southern Baltic during the last millennium reconstructed from an ombrotrophic bog archive. Stud Quat. 2011;28:3–16.
Davidson NC. How much wetland has the world lost? Long-term and recent trends in global wetland area. Mar Freshw Res. 2014;65:934–41.
Oertel C, Matschullat J, Zurba K, Zimmermann F, Erasmi S. Greenhouse gas emissions from soils – a review. Geochemistry. 2016;76:327–52.
Google Scholar
Liesack W, Schnell S, Revsbech NP. Microbiology of flooded rice paddies. FEMS Microbiol Rev. 2000;24:625–45.
Google Scholar
Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep. 2009;1:285–92.
Google Scholar
Lyu Z, Shao N, Akinyemi T, Whitman WB. Methanogenesis. Curr Biol. 2018;28:R727–R732.
Google Scholar
Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S, Jetten MSM, et al. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. 2021;15:3549–65.
Google Scholar
Mayumi D, Mochimaru H, Tamaki H, Yamamoto K, Yoshioka H, Suzuki Y, et al. Methane production from coal by a single methanogen. Science. 2016;354:222–6.
Google Scholar
Bridgham SD, Cadillo-Quiroz H, Keller JK, Zhuang Q. Methane emissions from wetlands: Biogeochemical, microbial, and modeling perspectives from local to global scales. Glob Chang Biol. 2013;19:1325–46.
Google Scholar
Narrowe AB, Borton MA, Hoyt DW, Smith GJ, Daly RA, Angle JC, et al. Uncovering the diversity and activity of methylotrophic methanogens in freshwater wetland soils. mSystems. 2019;4:e00320–19.
Google Scholar
Zalman CA, Meade N, Chanton J, Kostka JE, Bridgham SD, Keller JK. Methylotrophic methanogenesis in Sphagnum-dominated peatland soils. Soil Biol Biochem. 2018;118:156–60.
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.
Google Scholar
Le Mer J, Roger P. Production, oxidation, emission and consumption of methane by soils: a review. Eur J Soil Biol. 2001;37:25–50.
Wieczorek AS, Drake HL, Kolb S. Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs. FEMS Microbiol Ecol. 2011;77:28–39.
Google Scholar
Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, et al. Nitrate- and nitrite-dependent anaerobic oxidation of methane. Environ Microbiol Rep. 2016;8:941–55.
Google Scholar
Cui M, Ma A, Qi H, Zhuang X, Zhuang G. Anaerobic oxidation of methane: An ‘active’ microbial process. Microbiol Open. 2015;4:1–11.
Ettwig KF, Zhu B, Speth D, Keltjens JT, Jetten MSM, Kartal B. Archaea catalyze iron-dependent anaerobic oxidation of methane. Proc Natl Acad Sci USA. 2016;113:12792–6.
Google Scholar
Stiehl-Braun PA, Hartmann AA, Kandeler E, Buchmann N, Niklaus PA. Interactive effects of drought and N fertilization on the spatial distribution of methane assimilation in grassland soils. Glob Chang Biol 2011;17:2629–39.
Bodelier PLE, Meima-Franke M, Hordijk CA, Steenbergh AK, Hefting MM, Bodrossy L, et al. Microbial minorities modulate methane consumption through niche partitioning. ISME J. 2013;7:2214–28.
Google Scholar
Karbin S, Hagedorn F, Dawes MA, Niklaus PA. Treeline soil warming does not affect soil methane fluxes and the spatial micro-distribution of methanotrophic bacteria. Soil Biol Biochem. 2015;86:164–71.
Google Scholar
Stiehl-Braun PA, Powlson DS, Poulton PR, Niklaus PA. Effects of N fertilizers and liming on the micro-scale distribution of soil methane assimilation in the long-term Park Grass experiment at Rothamsted. Soil Biol Biochem. 2011;43:1034–41.
Google Scholar
Menyailo OV, Hungate BA, Abraham WR, Conrad R. Changing land use reduces soil CH4 uptake by altering biomass and activity but not composition of high-affinity methanotrophs. Glob Chang Biol. 2008;14:2405–19.
Ciais P, Sabine C, Bala G, Bopp L, Brovkin V, Canadell J, et al. Carbon and Other Biogeochemical Cycles. In: Stocker TF, Qin D, Plattner G-K, Tignor M, Allen SK, Boschung J, et al. editors. Climate Change 2013 the Physical Science Basis: Working Group I Contribution to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. New York, NY: Cambridge University Press; 2013, 465–570.
Täumer J, Kolb S, Boeddinghaus RS, Wang H, Schöning I, Schrumpf M, et al. Divergent drivers of the microbial methane sink in temperate forest and grassland soils. Glob Chang Biol. 2021;27:929–40.
Google Scholar
Kolb S. The quest for atmospheric methane oxidizers in forest soils. Environ Microbiol Rep. 2009;1:336–46.
Google Scholar
Kolb S, Horn MA. Microbial CH4 and N2O consumption in acidic wetlands. Front Microbiol. 2012;3:78.
Google Scholar
Cai Y, Zheng Y, Bodelier PLE, Conrad R, Jia Z. Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat Commun. 2016;7:11728.
Google Scholar
Dean JF, Middelburg JJ, Röckmann T, Aerts R, Blauw LG, Egger M, et al. Methane feedbacks to the global climate system in a warmer world. Rev Geophys. 2018;56:207–50.
Levy-Booth DJ, Giesbrecht IJW, Kellogg CTE, Heger TJ, D’Amore DV, Keeling PJ, et al. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil. ISME J. 2019;13:950–63.
Google Scholar
Lombard N, Prestat E, van Elsas JD, Simonet P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol Ecol. 2011;78:31–49.
Google Scholar
Carini P, Marsden PJ, Leff JW, Morgan EE, Strickland MS, Fierer N. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol. 2016;2:16242.
Google Scholar
Blazewicz SJ, Barnard RL, Daly RA, Firestone MK. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J. 2013;7:2061–8.
Google Scholar
Sukenik A, Kaplan-Levy RN, Welch JM, Post AF. Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria). ISME J. 2012;6:670–9.
Google Scholar
Schwartz E, Hayer M, Hungate BA, Koch BJ, McHugh TA, Mercurio W, et al. Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples. Curr Opin Biotechnol. 2016;41:14–18.
Google Scholar
Angel R, Conrad R. Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event. Environ Microbiol. 2013;15:2799–815.
Google Scholar
Papp K, Mau RL, Hayer M, Koch BJ, Hungate BA, Schwartz E. Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA. ISME J. 2018;12:3043–5.
Google Scholar
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One. 2008;3:e2527.
Google Scholar
Peng J, Wegner CE, Liesack W. Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups. Front Microbiol. 2017;8:400.
Google Scholar
Peng J, Wegner CE, Bei Q, Liu P, Liesack W. Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. Microbiome. 2018;6:169.
Google Scholar
Abdallah RZ, Wegner CE, Liesack W. Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life. Soil Biol Biochem. 2019;132:131–42.
Google Scholar
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017;8:2224.
Google Scholar
Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan LK, et al. Sizing up metatranscriptomics. ISME J. 2013;7:237–43.
Google Scholar
Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA. Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J. 2011;5:461–72.
Google Scholar
Söllinger A, Tveit AT, Poulsen M, Noel SJ, Bengtsson M, Bernhardt J, et al. Holistic assessment of rumen microbiome dynamics through quantitative metatranscriptomics reveals multifunctional redundancy during key steps of anaerobic feed degradation. mSystems 2018;3:e00038–18.
Google Scholar
Fischer M, Bossdorf O, Gockel S, Hänsel F, Hemp A, Hessenmöller D, et al. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl Ecol. 2010;11:473–85.
IUSS Working Group WRB. World reference base for soil resources 2014, update 2015 international soil classification system for naming soils and creating legends for soil maps. World Soil Resour Reports No 106. Rome: FAO; 2015.
Vance ED, Brookes PC, Jenkinson DS. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem. 1987;19:703–7.
Google Scholar
Joergensen RG, Mueller T. The fumigation-extraction method to estimate soil microbial biomass: calibaration of the kEN value. Soil Biol Biochem. 1996;28:33–37.
Google Scholar
Brookes PC, Landman A, Pruden G, Jenkinson DS. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem. 1985;17:837–42.
Google Scholar
Bamminger C, Zaiser N, Zinsser P, Lamers M, Kammann C, Marhan S. Effects of biochar, earthworms, and litter addition on soil microbial activity and abundance in a temperate agricultural soil. Biol Fertil Soils. 2014;50:1189–1200.
Google Scholar
Koch O, Tscherko D, Kandeler E. Seasonal and diurnal net methane emissions from organic soils of the Eastern Alps, Austria: Effects of soil temperature, water balance, and plant biomass. Arct Antarct Alp Res. 2007;39:438–48.
Tveit AT, Urich T, Svenning MM. Metatranscriptomic analysis of arctic peat soil microbiota. Appl Environ Microbiol. 2014;80:5761–72.
Google Scholar
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
Google Scholar
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.
Google Scholar
Kopylova E, Noé L, Touzet H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, et al. CREST – Classification resources for environmental sequence tags. PLoS One. 2012;7:e49334.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. MEGAN community edition – interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12:e1004957.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59–60.
Google Scholar
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.
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2018.
Oksanen J, Blanchet f. G, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community ecology package. 2020. R package version 2.5-7. https://CRAN.R-project.org/package=vegan.
Graves S, Piepho H-P, Selzer L. multcompView: Visualizations of paired comparisons. 2019. R package version 0.1-8. https://CRAN.R-project.org/package=multcompView.
Günther A, Barthelmes A, Huth V, Joosten H, Jurasinski G, Koebsch F, et al. Prompt rewetting of drained peatlands reduces climate warming despite methane emissions. Nat Commun. 2020;11:1644.
Google Scholar
IPCC Task Force on National Greenhouse Gas Inventories. Methodological guidance on lands with wet and drained soilds, and constructed wetlands for wastewater treatment. 2013 Supplement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories: Wetlands. 2014.
Tiemeyer B, Albiac Borraz E, Augustin J, Bechtold M, Beetz S, Beyer C, et al. High emissions of greenhouse gases from grasslands on peat and other organic soils. Glob Chang Biol. 2016;22:4134–49.
Google Scholar
Kirschbaum MUF. The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biol Biochem. 1995;27:753–60.
Google Scholar
Knorr W, Prentice IC, House JI, Holland EA. Long-term sensitivity of soil carbon turnover to warming. Nature 2005;433:298–301.
Google Scholar
Dutaur L, Verchot LV. A global inventory of the soil CH4 sink. Glob Biogeochem Cycles. 2007;21:GB4013.
McDaniel MD, Saha D, Dumont MG, Hernández M, Adams MA. The effect of land-use change on soil CH4 and N2O fluxes: A global meta-analysis. Ecosystems. 2019;22:1424–43.
Google Scholar
Gulledge J, Schimel JP. Moisture control over atmospheric CH4 consumption and CO2 production in diverse Alaskan soils. Soil Biol Biochem. 1998;30:1127–32.
Google Scholar
Tveit AT, Urich T, Frenzel P, Svenning MM. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proc Natl Acad Sci USA. 2015;112:E2507–E2516.
Google Scholar
Conrad R. Methane production in soil environments – anaerobic biogeochemistry and microbial life between flooding and desiccation. Microorganisms 2020;8:881.
Google Scholar
Lyu Z, Lu Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME J. 2018;12:411–23.
Google Scholar
Smith KS, Ingram-Smith C. Methanosaeta, the forgotten methanogen? Trends Microbiol. 2007;15:150–5.
Google Scholar
Whitman WB, Bowen TL, Boone DR. The methanogenic bacteria. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F editors. The prokaryotes: other major lineages of bacteria and the archaea. Berlin, Heidelberg: Springer; 2014, pp 123–63.
Conrad R. Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: a mini review. Pedosphere. 2020;30:25–39.
Söllinger A, Urich T. Methylotrophic methanogens everywhere – physiology and ecology of novel players in global methane cycling. Biochem Soc Trans. 2019;47:1895–907.
Google Scholar
Yang S, Liebner S, Winkel M, Alawi M, Horn F, Dörfer C, et al. In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands. Soil Biol Biochem. 2017;111:66–77.
Google Scholar
Weil M, Wang H, Bengtsson M, Köhn D, Günther A, Jurasinski G, et al. Long-term rewetting of three formerly drained peatlands drives congruent compositional changes in pro- and eukaryotic soil microbiomes through environmental filtering. Microorganisms. 2020;8:550.
Google Scholar
Söllinger A, Seneca J, Dahl MB, Motleleng LL, Prommer J, Verbruggen E, et al. Down-regulation of the microbial protein biosynthesis machinery in response to weeks, years, and decades of soil warming. Sci Adv. 2022;8:eabm3230.
Google Scholar
Luesken FA, Wu ML, Op den Camp HJM, Keltjens JT, Stunnenberg H, Francoijs KJ, et al. Effect of oxygen on the anaerobic methanotroph ‘Candidatus Methylomirabilis oxyfera’: Kinetic and transcriptional analysis. Environ Microbiol. 2012;14:1024–34.
Google Scholar
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. 2008;105:10203–8.
Google Scholar
Yimga MT, Dunfield PF, Ricke P, Heyer J, Liesack W. Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2. Appl Environ Microbiol. 2003;69:5593–602.
Google Scholar
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.
Google Scholar
Freitag TE, Toet S, Ineson P, Prosser JI. Links between methane flux and transcriptional activities of methanogens and methane oxidizers in a blanket peat bog. FEMS Microbiol Ecol. 2010;73:157–65.
Google Scholar
Qin H, Tang Y, Shen J, Wang C, Chen C, Yang J, et al. Abundance of transcripts of functional gene reflects the inverse relationship between CH4 and N2O emissions during mid-season drainage in acidic paddy soil. Biol Fertil Soils. 2018;54:885–95.
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