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Microbial Cycling of Greenhouse Gases and Their Impact on Climate Change

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Advances in Soil Microbiology: Recent Trends and Future Prospects

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 3))

Abstract

Greenhouse gas (GHG) emission from agriculture contributes significantly to the global climate change. The major greenhouse gases emitted from agriculture are methane (CH4) and nitrous oxide (N2O). These two greenhouse gases have higher global warming potential than carbon dioxide (CO2). The manuscript embodies biogeochemical cycling of CH4 and N2O. Microbial pathways of methanogenesis, CH4 oxidation, nitrification, and denitrification are outlined. Information on the agricultural strategies to mitigate GHG emission from soils are discussed. The review highlights significance of low-affinity methanotrophs that can be activated by repeated enrichment of high CH4 concentration, as global climate regulators. Iron redox cycling is also linked with soil CH4 uptake as repeated Fe3+ reduction and Fe2+ oxidation decline crystalline Fe fraction that enhances CH4 consumption by stimulating pmoA gene of methanotrophs. Studies suggested alternate flooding and drying as a potential approach to mediate atmospheric CH4 uptake in flooded soil. N2O emission from soil is the outcome of both nitrification and denitrification. However, in upland soil N2O emission occurs through nitrification and through denitrification from flooded soil ecosystem. Nitrogen-fixing Rhizobium sp. also produces N2O, and these bacteria can be manipulated to mitigate N2O emission by activating N2O reductase (nosZ gene). It is concluded that apart from regular agricultural resource management strategies, there is need of genetically manipulated soil microorganisms to effectively mitigate climate change.

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References

  • Angel R, Conrad R (2009) In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environ Microbiol 11:2598–2610

    Article  CAS  PubMed  Google Scholar 

  • Angel R, Claus P, Conrad R (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6:847–862

    Article  CAS  PubMed  Google Scholar 

  • Arevalo-Martinez DL, Beyer M, Krumbholz M, Piller I, Kock A, Steinhoff T, Körtzinger A, Bange HW (2013) A new method for continuous measurements of oceanic and atmospheric N 2 O, CO and CO 2: performance of off-axis integrated cavity output spectroscopy (OA-ICOS) coupled to non-dispersive infrared detection (NDIR). Ocean Sci 9:1071–1087

    Article  Google Scholar 

  • Baani M, Liesack W (2008) Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci 105:10203–10208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ball BC (2013) Soil structure and greenhouse gas emissions: a synthesis of 20 years of experimentation. Eur J Soil Sci 64:357–373

    Article  CAS  Google Scholar 

  • Bao Q-L, Xiao K-Q, Chen Z, Yao H-Y, Zhu Y-G (2014) Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw. FEMS Microbiol Ecol 88:372–385

    Article  CAS  PubMed  Google Scholar 

  • Bedard C, Knowles R (1989) Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers. Microbiol Mol Biol Rev 53:68–84

    CAS  Google Scholar 

  • Bock E, Koops HP (2000) The genus nitrobacter and related genera. Prokaryotes Dworkin M (ed) Springer, New York

    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 

  • Butterbach-Bahl K, Baggs EM, Dannenmann M, Kiese R, Zechmeister-Boltenstern S (2013) Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Phil Trans R Soc B 368:20130122

    Article  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  • Cantera S, Lebrero R, García-Encina PA, Muñoz R (2016) Evaluation of the influence of methane and copper concentration and methane mass transport on the community structure and biodegradation kinetics of methanotrophic cultures. J Environ Manag 171:11–20

    Article  CAS  Google Scholar 

  • Conrad R (1999) Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microb Ecol 28:193–202

    Article  CAS  Google Scholar 

  • Dong D, Yang M, Wang C, Wang H, Li Y, Luo J, Wu W (2013) Responses of methane emissions and rice yield to applications of biochar and straw in a paddy field. J Soils Sediments 13:1450–1460

    Article  CAS  Google Scholar 

  • Eller G, Deines P, Grey J, Richnow H-H, Krüger M (2005) Methane cycling in lake sediments and its influence on chironomid larval δ13C. FEMS Microbiol Ecol 54:339–350. https://doi.org/10.1016/j.femsec.2005.04.006

    Article  CAS  PubMed  Google Scholar 

  • Forster P, Ramaswamy V, Artaxo P, Berntsen T, Betts R, Fahey DW, Haywood J, Lean J, Lowe DC, Myhre G (2007) Changes in atmospheric constituents and in radiative forcing. Clim Chang 20

    Google Scholar 

  • Fortin D, Langley S (2005) Formation and occurrence of biogenic iron-rich minerals. Earth-Sci Rev 72:1–19

    Article  CAS  Google Scholar 

  • Han X, Sun X, Wang C, Wu M, Dong D, Zhong T, Thies JE, Wu W (2016) Mitigating methane emission from paddy soil with rice-straw biochar amendment under projected climate change. Sci Rep 6:1–10. https://doi.org/10.1038/srep24731

  • Haque MFU, Gu W, DiSpirito AA, Semrau JD (2016) Marker exchange mutagenesis of mxaF, encoding the large subunit of the Mxa methanol dehydrogenase, in Methylosinus trichosporium OB3b. Appl Environ Microbiol 82:1549–1555

    Article  Google Scholar 

  • Hernández M, Conrad R, Klose M, Ma K, Lu Y (2017) Structure and function of methanogenic microbial communities in soils from flooded rice and upland soybean fields from Sanjiang plain, NE China. Soil Biol Biochem 105:81–91

    Article  Google Scholar 

  • Ho A, Lüke C, Reim A, Frenzel P (2013) Selective stimulation in a natural community of methane oxidizing bacteria: effects of copper on pmoA transcription and activity. Soil Biol Biochem 65:211–216. https://doi.org/10.1016/j.soilbio.2013.05.027

    Article  CAS  Google Scholar 

  • Holmes RM, Fisher SG, Grimm NB (1994) Parafluvial nitrogen dynamics in a desert stream ecosystem. J N Amer Benthol Soc 13:468–478

    Article  Google Scholar 

  • Hooper K, Petreas MX, Chuvakova T, Kazbekova G, Druz N, Seminova G, Sharmanov T, Hayward D, She J, Visita P, Winkler J, McKinney M, Wade TJ, Grassman J, Stephens RD (1998) Analysis of breast milk to assess exposure to chlorinated contaminants in Kazakstan: high levels of 2,3,7, 8-tetrachlorodibenzo-p-dioxin (TCDD) in agricultural villages of southern Kazakstan. Environ Health Perspect 106:797–806

    CAS  PubMed  PubMed Central  Google Scholar 

  • Horz HP, Rich V, Avrahami S, Bohannan BJM (2005) Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Appl Environ Microbiol 71:2642–2652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu H-W, Chen D, He J-Z (2015) Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol Rev 39:729–749

    Article  CAS  PubMed  Google Scholar 

  • Huang B, Yu K, Gambrell RP (2009) Effects of ferric iron reduction and regeneration on nitrous oxide and methane emissions in a rice soil. Chemosphere 74:481–486

    Article  CAS  PubMed  Google Scholar 

  • Huang T, Gao B, Christie P, Ju X (2013) Net global warming potential and greenhouse gas intensity in a double-cropping cereal rotation as affected by nitrogen and straw management. Biogeosciences 10:7897–7911

    Article  Google Scholar 

  • Huang T, Gao B, Hu X-K, Lu X, Well R, Christie P, Bakken LR, Ju X-T (2014) Ammonia-oxidation as an engine to generate nitrous oxide in an intensively managed calcareous Fluvo-aquic soil. Sci Rep 4

    Google Scholar 

  • Itakura M, Uchida Y, Akiyama H, Hoshino YT, Shimomura Y, Morimoto S, Tago K, Wang Y, Hayakawa C, Uetake Y (2013) Mitigation of nitrous oxide emissions from soils by Bradyrhizobium japonicum inoculation. Nat Clim Chang 3:208–212

    Article  CAS  Google Scholar 

  • Kang TJ, Lee EY (2016) Metabolic versatility of microbial methane oxidation for biocatalytic methane conversion. J Ind Eng Chem 35:8–13

    Article  CAS  Google Scholar 

  • Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of Methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69:6703–6714. https://doi.org/10.1128/AEM.69.11.6703-6714.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knief C, Kolb S, Bodelier PLE, Lipski A, Dunfield PF (2006) The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environ Microbiol 8:321–333

    Article  CAS  PubMed  Google Scholar 

  • Knox SH, Sturtevant C, Matthes JH, Koteen L, Verfaillie J, Baldocchi D (2015) Agricultural peatland restoration: effects of land-use change on greenhouse gas (CO2 and CH4) fluxes in the Sacramento-san Joaquin Delta. Glob Chang Biol 21:750–765

    Article  PubMed  Google Scholar 

  • Koops HP, Purkhold U, Pommerening-Roser A, Timmermann G, Wagner M (2000) The lithoautotrophic ammonia-oxidizing bacteria. Prokaryotes Dworkin M (ed). New York, Springer

    Google Scholar 

  • Lee SJ, McCormick MS, Lippard SJ, Cho U-S (2013) Control of substrate access to the active site in methane monooxygenase. Nature 494:380–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Y-L, Konhauser KO, Kappler A, Hao X-L (2013) Experimental low-grade alteration of biogenic magnetite indicates microbial involvement in generation of banded iron formations. Earth Planet Sci Lett 361:229–237

    Article  CAS  Google Scholar 

  • Lohila A, Aalto T, Aurela M, Hatakka J, Tuovinen J-P, Kilkki J, Penttilä T, Vuorenmaa J, Hänninen P, Sutinen R (2016) Large contribution of boreal upland forest soils to a catchment-scale CH4 balance in a wet year. Geophys Res Lett 43:2946–2953

    Article  CAS  Google Scholar 

  • Mau S, Blees J, Helmke E, Niemann H, Damm E (2013) Vertical distribution of methane oxidation and methanotrophic response to elevated methane concentrations in stratified waters of the Arctic fjord Storfjorden (Svalbard, Norway). Biogeosciences 10:6267–6278

    Article  CAS  Google Scholar 

  • Mohanty SR, Bandeepa GS, Dubey G, Ahirwar U, Patra AK, Kollah B (2016) Methane oxidation in response to iron reduction-oxidation metabolism in tropical soils. Eur J Soil Biol 78:75–81

    Google Scholar 

  • Raupach MR, Marland G, Ciais P, Le Quéré C, Canadell JG, Klepper G, Field CB (2007) Global and regional drivers of accelerating CO2 emissions. Proc Natl Acad Sci 104:10288

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reay DS, Davidson EA, Smith KA, Smith P, Melillo JM, Dentener F, Crutzen PJ (2012) Global agriculture and nitrous oxide emissions. Nat Clim Chang 2:410–416

    Article  CAS  Google Scholar 

  • Rice AL, Butenhoff CL, Teama DG, Röger FH, Khalil MAK, Rasmussen RA (2016) Atmospheric methane isotopic record favors fossil sources flat in 1980s and 1990s with recent increase. Proc Natl Acad Sci 113:10791–10796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ricke P, Erkel C, Kube M, Reinhardt R, Liesack W (2004) Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2. Appl Environ Microbiol 70:3055–3063. https://doi.org/10.1128/AEM.70.5.3055-3063.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rissanen AJ, Karvinen A, Nykänen H, Peura S, Tiirola M, Mäki A, Kankaala P (2016) Effects of inorganic electron acceptors on methanogenesis and methanotrophy and on the community structure of bacteria and archaea in sediments of a boreal lake, in: EGU General Assembly Conference Abstracts, p. 3726

    Google Scholar 

  • Roden EE, Zachara JM (1996) Microbial reduction of crystalline iron(III) oxides: influence of oxide surface area and potential for cell growth. Environ Sci Technol 30:1618–1628

    Article  CAS  Google Scholar 

  • Steger K, Premke K, Gudasz C, Boschker HTS, Tranvik LJ (2015) Comparative study on bacterial carbon sources in lake sediments: the role of methanotrophy. Aquat Microb Ecol 76:39–47

    Article  Google Scholar 

  • Strand S, Bruce N, Rylott L, Zhang L (2013) Phytoremediation of atmospheric methane. DTIC Document

    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 

  • Tobler NB, Hofstetter TB, Straub KL, Fontana D, Schwarzenbach RP (2007) Iron-mediated microbial oxidation and abiotic reduction of organic contaminants under anoxic conditions. Environ Sci Technol 41:7765–7772

    Article  CAS  PubMed  Google Scholar 

  • Ťupek B, Minkkinen K, Pumpanen J, Vesala T, Nikinmaa E (2014) CH4 and N2O dynamics in the boreal forest–mire ecotone. Biogeosci Discuss 11(6):8049–8084

    Article  Google Scholar 

  • Vanitchung S, Chidthaisong A, Conrad R (2014) Methane uptakes and emissions in upland tropical Forest and agricultural soils. J Sustain Energy Environ 5

    Google Scholar 

  • Weber EB, Lehtovirta-Morley LE, Prosser JI, Gubry-Rangin C (2015) Ammonia oxidation is not required for growth of Group 1.1 c soil Thaumarchaeota. FEMS Microbiol Ecol 91. fiv001

    Google Scholar 

  • Yuan J, Ding W, Liu D, Xiang J, Lin Y (2014a) Methane production potential and methanogenic archaea community dynamics along the Spartina Alterniflora invasion chronosequence in a coastal salt marsh. Appl Microbiol Biotechnol 98:1817–1829

    Article  CAS  PubMed  Google Scholar 

  • Yuan Q, Pump J, Conrad R (2014b) Straw application in paddy soil enhances methane production also from other carbon sources. Biogeosciences 11:237–246

    Article  Google Scholar 

  • Zhang B, Pang C, Qin J, Liu K, Xu H, Li H (2013) Rice straw incorporation in winter with fertilizer-N application improves soil fertility and reduces global warming potential from a double rice paddy field. Biol Fertil Soils 49:1039–1052

    Article  Google Scholar 

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Acknowledgment

This manuscript is part of the project “Greenhouse gas emission from composting systems and characterization of GHG regulating microbes.” Authors declare no conflict of interest of any type.

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Correspondence to Santosh Ranjan Mohanty .

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Kollah, B., Patra, A.K., Mohanty, S.R. (2018). Microbial Cycling of Greenhouse Gases and Their Impact on Climate Change. In: Adhya, T., Lal, B., Mohapatra, B., Paul, D., Das, S. (eds) Advances in Soil Microbiology: Recent Trends and Future Prospects. Microorganisms for Sustainability, vol 3. Springer, Singapore. https://doi.org/10.1007/978-981-10-6178-3_7

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