Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils.
Journal
ISME communications
ISSN: 2730-6151
Titre abrégé: ISME Commun
Pays: England
ID NLM: 9918205372406676
Informations de publication
Date de publication:
09 Dec 2021
09 Dec 2021
Historique:
received:
05
02
2021
accepted:
18
10
2021
revised:
14
10
2021
entrez:
10
2
2023
pubmed:
9
12
2021
medline:
9
12
2021
Statut:
epublish
Résumé
Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH
Identifiants
pubmed: 36765259
doi: 10.1038/s43705-021-00068-2
pii: 10.1038/s43705-021-00068-2
pmc: PMC9723554
doi:
Types de publication
Journal Article
Langues
eng
Pagination
74Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 41671249
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 41907026
Organisme : China Postdoctoral Science Foundation
ID : 2020T130387
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2021. The Author(s).
Références
Cheng W, Yagi K, Xu H, Sakai H, Kobayashi K. Influence of elevated concentrations of atmospheric CO
doi: 10.1016/j.chemgeo.2005.01.016
Koka JK. Gas phase activation activation of methane methane molecule molecule with lead lead benzene benzene dication dication complex complex ionion, [Pb (Benzene)
Pratscher J, Vollmers J, Wiegand S, Dumont MG, Kaster AK. Unravelling the identity, metabolic potential and global biogeography of the atmospheric methane‐oxidizing upland soil cluster α. Environ Microbiol. 2018;20:1016–29.
pubmed: 29314604
pmcid: 6849597
doi: 10.1111/1462-2920.14036
Kalyuzhnaya MG, Gomez OA, Murrell JC. The methane-oxidizing bacteria (methanotrophs). In: Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes, 2019; p. 245–78.
Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Mol Biol R. 1996;60:439–71.
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.
pubmed: 7590173
doi: 10.1111/j.1574-6968.1995.tb07834.x
Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MS, Klotz MG. A novel family of functional operons encoding methane/ammonia monooxygenase‐related proteins in gammaproteobacterial methanotrophs. Env Microbiol Rep. 2011;3:91–100.
doi: 10.1111/j.1758-2229.2010.00192.x
Hatzenpichler RS. Identification and characterization of novel ammonia-oxidizing archaea and bacteria. Doctoral dissertation, Uniwien; 2011.
Jones RD, Morita RY. Methane oxidation by Nitrosococcus oceanus and Nitrosomonas europaea. Appl Environ Microbiol. 1983;45:401–10.
pubmed: 16346190
pmcid: 242300
doi: 10.1128/aem.45.2.401-410.1983
O’neill JG, Wilkinson JF. Oxidation of ammonia by methane-oxidizing bacteria and the effects of ammonia on methane oxidation. Microbiology. 1977;100:407–12.
Stein LY, Roy R, Dunfield PF. Aerobic methanotrophy and nitrification: processes and connections. In: Battista J (ed) Encyclopedia of life sciences (eLS). Wiley, Chichester. 2012. www.els.net . https://doi.org/10.1002/9780470015902.a0022213 .
Daebeler A, Bodelier PL, Yan Z, Hefting MM, Jia Z, Laanbroek HJ. Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME J. 2014;8:2397–410.
pubmed: 24858784
pmcid: 4260704
doi: 10.1038/ismej.2014.81
Kou Y, Li J, Wang Y, Li C, Tu B, Yao M, et al. Scale-dependent key drivers controlling methane oxidation potential in Chinese grassland soils. Soil Biol Biochem. 2017;111:104–14.
doi: 10.1016/j.soilbio.2017.04.005
Zheng Y, Huang R, Wang B, Bodelier PLE, Jia Z. Competitive interactions between methane-and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil. Biogeosciences. 2014;11:3353–68.
doi: 10.5194/bg-11-3353-2014
Bodelier PL, Hahn AP, Arth IR, Frenzel P. Effects of ammonium-based fertilisation on microbial processes involved in methane emission from soils planted with rice. Biogeochemistry. 2000;51:225–57.
doi: 10.1023/A:1006438802362
Bodelier PL, Roslev P, Henckel T, Frenzel P. Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature. 2000;403:421–4.
pubmed: 10667792
doi: 10.1038/35000193
Krüger M, Frenzel P. Effects of N-fertilisation on CH
doi: 10.1046/j.1365-2486.2003.00576.x
Rime T, Niklaus PA. Spatio-temporal dynamics of soil CH
doi: 10.1016/j.soilbio.2016.11.001
Van Zwieten L, et al. Biochar effects on nitrous oxide and methane emissions from soil. In: Biochar for environmental management. Routledge; 2015. p. 521–52.
Kravchenko IK. Methane oxidation in boreal peat soils treated with various nitrogen compounds. Plant Soil. 2002;242:157–62.
doi: 10.1023/A:1019614613381
Mutschlechner M, Praeg N, Illmer P. The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils. FEMS Microbiol Ecol. 2018;94:fiy019.
doi: 10.1093/femsec/fiy019
Mishra VK, Shukla R, Shukla PN. Inhibition of soil methane oxidation by fertilizer application: an intriguing but persistent paradigm. EPP. 2018;3:57–69.
doi: 10.22606/epp.2018.32001
Wright AL, Hons FM, Rouquette JrFM. Long-term management impacts on soil carbon and nitrogen dynamics of grazed bermudagrass pastures. Soil Biol Biochem. 2004;36:1809–16.
doi: 10.1016/j.soilbio.2004.05.004
Wang Y, Xue M, Zheng X, Ji B, Du R, Wang Y. Effects of environmental factors on N
pubmed: 15571752
doi: 10.1016/j.chemosphere.2004.04.043
Allen-Dias B. Rangelands in a changing climate: impacts, adaptations and mitigation. In: Watson, RT, et al. (Eds.), Climate change 1995. Impacts, adaptations and mitigation of climate change: scientific-technical analyses. Cambridge University Press, Cambridge, Published for the Intergovernmental Panel on Climate Change; 1996. p.131–58.
Pineiro G, Paruelo JM, Oesterheld M. Potential long-term impacts of livestock introduction on carbon and nitrogen cycling in grasslands of Southern South America. Global Change Biol. 2006;12:1267–84.
doi: 10.1111/j.1365-2486.2006.01173.x
Shi H, Hou L, Yang L, Wu D, Zhang L, Li L. Effects of grazing on CO
doi: 10.1002/ecs2.1760
Wang X, Zhang Y, Huang D, Li Z, Zhang X. Methane uptake and emissions in a typical steppe grazing system during the grazing season. Atmos Environ. 2015;105:14–21.
doi: 10.1016/j.atmosenv.2015.01.036
Tang S, Zhang Y, Zhai X, Wilkes A, Wang C, Wang K. Effect of grazing on methane uptake from Eurasian steppe of China. BMC Ecol. 2018;18:11.
pubmed: 29558936
pmcid: 5859401
doi: 10.1186/s12898-018-0168-x
Li Y, Liu Y, Pan H, Hernández M, Guan X, Wang W, et al. Impact of grazing on shaping abundance and composition of active methanotrophs and methane oxidation activity in a grassland soil. Biol Fert Soils. 2020;56:1–12.
doi: 10.1007/s00374-020-01461-0
Pan H, Xie K, Zhang Q, Jia Z, Xu J, Di H, et al. Archaea and bacteria respectively dominate nitrification in lightly and heavily grazed soil in a grassland system. Biol Fert Soils. 2018;54:1–14.
doi: 10.1007/s00374-017-1236-7
Lampurlanés J, Cantero-Martinez C. Soil bulk density and penetration resistance under different tillage and crop management systems and their relationship with barley root growth. Agron J. 2003;95:526–36.
doi: 10.2134/agronj2003.5260
Kalembasa SJ, Jenkinson DS. A comparative study of titrimetric and gravimetric methods for the determination of organic carbon in soil. J Sci Food Agr. 1973;24:1085–90.
doi: 10.1002/jsfa.2740240910
Olsen SR. Estimation of available phosphorus in soils by extraction with sodium bicarbonate. US Department of Agriculture; 1954.
Zhao Y, Zhang L, Chen Y, Liu X, Xu W, Pan Y, et al. Atmospheric nitrogen deposition to China: a model analysis on nitrogen budget and critical load exceedance. Atmos Environ. 2017;153:32–40.
doi: 10.1016/j.atmosenv.2017.01.018
Whitehead DC. Sources and transformations of organic nitrogen in intensively managed grassland soils//nitrogen fluxes in intensive grassland systems. Springer, Dordrecht; 1986. p. 47–58.
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
pubmed: 21903629
pmcid: 3198573
doi: 10.1093/bioinformatics/btr507
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
pubmed: 24132122
pmcid: 3840312
doi: 10.1093/molbev/mst197
Smets W, Leff JW, Bradford MA, McCulley RL, Lebeer S, Fierer N. A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing. Soil Biol Biochem. 2016;96:145–51.
doi: 10.1016/j.soilbio.2016.02.003
Wang JC, Li Y, Li GY, Xiao Y, Li WM, Ma Q, et al. Simultaneous measurement of bacterial abundance and composition in response to biochar in soybean field soil using 16S rRNA gene sequencing. Land Degrad Dev. 2018;29:2172–82.
doi: 10.1002/ldr.2838
Stämmler F, Gläsner J, Hiergeist A, Holler E, Weber D, Oefner PJ, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome. 2016;4:1–13.
doi: 10.1186/s40168-016-0175-0
Bastian M, Heymann S, Jacomy M. Gephi: An open source software for exploring and manipulating networks. ICWSM. 2009;8:361−2.
doi: 10.1609/icwsm.v3i1.13937
Tang S, Wang K, Xiang Y, Tian D, Wang J, Liu Y, et al. Heavy grazing reduces grassland soil greenhouse gas fluxes: a global meta-analysis. Sci Total Environ. 2019;654:1218–24.
pubmed: 30841396
doi: 10.1016/j.scitotenv.2018.11.082
Pan H, Ying S, Liu H, Zeng L, Zhang Q, Liu Y, et al. Microbial pathways for nitrous oxide emissions from sheep urine and dung in a typical steppe grassland. Biol Fert Soils. 2018;54:717–30.
doi: 10.1007/s00374-018-1297-2
Wolf B, Zheng X, Brüggemann N, Chen W, Dannenmann M, Han X, et al. Grazing-induced reduction of natural nitrous oxide release from continental steppe. Nature. 2010;464:881–4.
pubmed: 20376147
doi: 10.1038/nature08931
Hansen S, Maehlum JE, Bakken LR. N
doi: 10.1016/0038-0717(93)90202-M
Ruser R, Schilling R, Steindl H, Flessa H, Beese F. Soil compaction and fertilization effects on nitrous oxide and methane fluxes in potato fields. Soil Sci Soc Am J. 1998;62:1587–95.
doi: 10.2136/sssaj1998.03615995006200060016x
Sitaula BK, Hansen S, Sitaula JIB, Bakken LR. Effects of soil compaction on N
doi: 10.1016/S1465-9972(00)00040-4
Priemé A, Christensen S. Methane uptake by a selection of soils in Ghana with different land use. J Geophys Res Atmos. 1999;104:23617–22.
doi: 10.1029/1999JD900427
Saggar S, Hedley CB, Giltrap DL, Lambie SM. Measured and modelled estimates of nitrous oxide emission and methane consumption from a sheep-grazed pasture. Agr Ecosyst Environ. 2007;122:357–65.
doi: 10.1016/j.agee.2007.02.006
Cardoso AS, et al. 0653 Grazing intensities and season affect N
doi: 10.2527/jam2016-0653
Yin M, Gao X, Tenuta M, Li L, Gui D, Li X, et al. Enhancement of N
doi: 10.1016/j.geoderma.2020.114511
Li K, Gong Y, Song W, Lv J, Chang Y, Hu Y, et al. No significant nitrous oxide emissions during spring thaw under grazing and nitrogen addition in an alpine grassland. Global Change Biol. 2012;18:2546–54.
doi: 10.1111/j.1365-2486.2012.02704.x
Jia Z, Conrad R. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol. 2009;11:1658–71.
pubmed: 19236445
doi: 10.1111/j.1462-2920.2009.01891.x
Pratscher J, Dumont MG, Conrad R. Ammonia oxidation coupled to CO
pubmed: 21368116
pmcid: 3053987
doi: 10.1073/pnas.1010981108
Hink L, Gubry-Rangin C, Nicol GW, Prosser JI. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J. 2018;12:1084–93.
pubmed: 29386627
pmcid: 5864188
doi: 10.1038/s41396-017-0025-5
Fu TC, Lin YC, Chang CM, Chou WL, Yuan PH, Liu MH, et al. Management practices have a major impact on nitrifier and denitrifier communities in a semiarid grassland ecosystem. J Soil Sediment. 2016;16:896–908.
doi: 10.1007/s11368-015-1321-1
Gubry-Rangin C, Nicol GW, Prosser JI. Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol. 2010;74:566–74.
pubmed: 21039653
doi: 10.1111/j.1574-6941.2010.00971.x
Lu L, Jia Z. Urease gene‐containing Archaea dominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol. 2013;15:1795–809.
pubmed: 23298189
doi: 10.1111/1462-2920.12071
Clark DR, McKew BA, Dong LF, Leung G, Dumbrell AJ, Stott A, et al. Mineralization and nitrification: archaea dominate ammonia-oxidising communities in grassland soils. Soil Biol Biochem. 2020;143:107725.
doi: 10.1016/j.soilbio.2020.107725
Huang R, Wang Y, Gao X, Liu J, Wang Z, Gao M. Nitrous oxide emission and the related denitrifier community: a short-term response to organic manure substituting chemical fertilizer. Ecotox Environ Safe. 2020;192:110291.
doi: 10.1016/j.ecoenv.2020.110291
Webster G, Embley TM, Freitag TE, Smith Z, Prosser JI. Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ Microbiol. 2005;7:676–84.
pubmed: 15819850
doi: 10.1111/j.1462-2920.2005.00740.x
Taylor AE, Bottomley PJ. Nitrite production by Nitrosomonas europaea and Nitrosospira sp. AV in soils at different solution concentrations of ammonium. Soil Biol Biochem. 2006;38:828–36.
doi: 10.1016/j.soilbio.2005.08.001
Shaw LJ, Nicol GW, Smith Z, Fear J, Prosser JI, Baggs EM. Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ Microbiol. 2006;8:214–22.
pubmed: 16423010
doi: 10.1111/j.1462-2920.2005.00882.x
Koch H, van Kessel MA, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biot. 2019;103:177–89.
doi: 10.1007/s00253-018-9486-3
Kits KD, Jung MY, Vierheilig J, Pjevac P, Sedlacek CJ, Liu S, et al. Low yield and abiotic origin of N
doi: 10.1038/s41467-019-09790-x
Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, et al. Conceptualizing functional traits and ecological characteristics of methane‐oxidizing bacteria as life strategies. Environ Microbiol Rep. 2013;5:335–45.
pubmed: 23754714
doi: 10.1111/j.1758-2229.2012.00370.x
Semrau JD, DiSpirito AA, Yoon S. Methanotrophs and copper. FEMS Microbiol Rev. 2010;34:496–531.
pubmed: 20236329
doi: 10.1111/j.1574-6976.2010.00212.x
Mosier A, Schimel D, Valentine D, Bronson K, Parton W. Methane and nitrous oxide fluxes in native, fertilized and cultivated grasslands. Nature. 1991;350:330–2.
doi: 10.1038/350330a0
Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10:538–50.
doi: 10.1038/nrmicro2832
pubmed: 22796884
Daims H, Lücker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol. 2016;24:699–712.
pubmed: 27283264
pmcid: 6884419
doi: 10.1016/j.tim.2016.05.004
Wang B, Wu L, Chen D, Wu Y, Hu S, Li L, et al. Grazing simplifies soil micro-food webs and decouples their relationships with ecosystem functions in grasslands. Global Change Biol. 2020;26:960–70.
doi: 10.1111/gcb.14841