[1]

Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences of the United States of America 95:6578−6583

doi: 10.1073/pnas.95.12.6578
[2]

Fierer N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology 15:579−590

doi: 10.1038/nrmicro.2017.87
[3]

Ullah S, Raza MM, Abbas T, Guan X, Zhou W, et al. 2023. Responses of soil microbial communities and enzyme activities under nitrogen addition in fluvo-aquic and black soil of North China. Frontiers in Microbiology 14:1249471

doi: 10.3389/fmicb.2023.1249471
[4]

Zhang YB, Liu F, Wang JT, Hu HW, He JZ, et al. 2022. Effect of straw incorporation and nitrification inhibitor on nitrous oxide emission in three cropland soils. Journal of Sustainable Agriculture and Environment 1:132−141

doi: 10.1002/sae2.12013
[5]

Shade A, Handelsman J. 2012. Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology 14:4−12

doi: 10.1111/j.1462-2920.2011.02585.x
[6]

Jiao S, Liu Z, Lin Y, Yang J, Chen W, et al. 2016. Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns. Soil Biology and Biochemistry 98:64−73

doi: 10.1016/j.soilbio.2016.04.005
[7]

Jiao S, Qi J, Jin C, Liu Y, Wang Y, et al. 2022. Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems. Global Change Biology 28:6653−6664

doi: 10.1111/gcb.16387
[8]

Jiao S, Xu Y, Zhang J, Hao X, Lu Y. 2019. Core microbiota in agricultural soils and their potential associations with nutrient cycling. mSystems 4:e00313-18

doi: 10.1128/msystems.00313-18
[9]

Ravishankara AR, Daniel JS, Portmann RW. 2009. Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123−125

doi: 10.1126/science.1176985
[10]

Masson-Delmotte V, Zhai P, Pirani A, Connors SL, Péan C, et al. 2021. 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, United Kingdom: Cambridge University Press. doi: 10.1017/9781009157896
[11]

López-Aizpún M, Horrocks CA, Charteris AF, Marsden KA, Ciganda VS, et al. 2020. Meta-analysis of global livestock urine-derived nitrous oxide emissions from agricultural soils. Global Change Biology 26:2002−2013

doi: 10.1111/gcb.15012
[12]

Kool DM, Dolfing J, Wrage N, Van Groenigen JW. 2011. Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil. Soil Biology and Biochemistry 43:174−178

doi: 10.1016/j.soilbio.2010.09.030
[13]

Lycus P, Bothun KL, Bergaust L, Shapleigh JP, Bakken LR, et al. 2017. Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy. The ISME Journal 11:2219−2232

doi: 10.1038/ismej.2017.82
[14]

Yu Z, Yang J, Liu L. 2014. Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir. PLoS One 9:e92055

doi: 10.1371/journal.pone.0092055
[15]

Yin C, Fan F, Song A, Cui P, Li T, et al. 2015. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil. Applied Microbiology and Biotechnology 99:5719−5729

doi: 10.1007/s00253-015-6461-0
[16]

Owens J, Clough TJ, Laubach J, Hunt JE, Venterea RT, et al. 2016. Nitrous oxide fluxes, soil oxygen, and denitrification potential of urine- and non-urine-treated soil under different irrigation frequencies. Journal of Environmental Quality 45:1169−1177

doi: 10.2134/jeq2015.10.0516
[17]

Menéndez S, Barrena I, Setien I, González-Murua C, Estavillo JM. 2012. Efficiency of nitrification inhibitor DMPP to reduce nitrous oxide emissions under different temperature and moisture conditions. Soil Biology and Biochemistry 53:82−89

doi: 10.1016/j.soilbio.2012.04.026
[18]

Harter J, Krause HM, Schuettler S, Ruser R, Fromme M, et al. 2014. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. The ISME Journal 8:660−674

doi: 10.1038/ismej.2013.160
[19]

Molstad L, Dörsch P, Bakken LR. 2007. Robotized incubation system for monitoring gases (O2, NO, N2O N2) in denitrifying cultures. Journal of Microbiological Methods 71:202−211

doi: 10.1016/j.mimet.2007.08.011
[20]

Liu B, Mørkved PT, Frostegård Å, Bakken LR. 2010. Denitrification gene pools, transcription and kinetics of NO, N2O and N2 production as affected by soil pH. FEMS Microbiology Ecology 72:407−417

doi: 10.1111/j.1574-6941.2010.00856.x
[21]

Wheatley RE, MacDonald R, Smith AM. 1989. Extraction of nitrogen from soils. Biology and Fertility of Soils 8:189−190

doi: 10.1007/bf00257765
[22]

Tarafder PK, Rathore DPS. 1988. Spectrophotometric determination of nitrite in water. Analyst 113:1073−1076

doi: 10.1039/an9881301073
[23]

Huffman SA, Barbarick KA. 1981. Soil nitrate analysis by cadmium reduction. Communications in Soil Science and Plant Analysis 12:79−89

doi: 10.1080/00103628109367129
[24]

Scheiner D. 1976. Determination of ammonia and Kjeldahl nitrogen by indophenol method. Water Research 10:31−36

doi: 10.1016/0043-1354(76)90154-8
[25]

Qin S, Hu C, Clough TJ, Luo J, Oenema O, et al. 2017. Irrigation of DOC-rich liquid promotes potential denitrification rate and decreases N2O/(N2O+N2) product ratio in a 0–2 m soil profile. Soil Biology and Biochemistry 106:1−8

doi: 10.1016/j.soilbio.2016.12.001
[26]

Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Applied and Environmental Microbiology 66:5488−5491

doi: 10.1128/aem.66.12.5488-5491.2000
[27]

Paulin MM, Nicolaisen MH, Jacobsen CS, Gimsing AL, Sørensen J, et al. 2013. Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils. Soil Biology and Biochemistry 63:37−49

doi: 10.1016/j.soilbio.2013.02.007
[28]

Yang L, Zhang X, Ju X. 2017. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil. Scientific Reports 7:43283

doi: 10.1038/srep43283
[29]

Wu X, Wang Y, Zhu Y, Tian H, Qin X, et al. 2019. Variability in the response of bacterial community assembly to environmental selection and biotic factors depends on the immigrated bacteria, as revealed by a soil microcosm experiment. mSystems 4:e00496-19

doi: 10.1128/msystems.00496-19
[30]

Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10:996−998

doi: 10.1038/nmeth.2604
[31]

Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194−2200

doi: 10.1093/bioinformatics/btr381
[32]

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, et al. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42:D633−D642

doi: 10.1093/nar/gkt1244
[33]

Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460−2461

doi: 10.1093/bioinformatics/btq461
[34]

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335−336

doi: 10.1038/nmeth.f.303
[35]

Jangid K, Williams MA, Franzluebbers AJ, Schmidt TM, Coleman DC, et al. 2011. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties. Soil Biology and Biochemistry 43:2184−2193

doi: 10.1016/j.soilbio.2011.06.022
[36]

Liu C, Xu J, Ding N, Fu Q, Guo B, et al. 2013. The effect of long-term reclamation on enzyme activities and microbial community structure of saline soil at Shangyu, China. Environmental Earth Sciences 69:151−159

doi: 10.1007/s12665-012-1943-1
[37]

Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 103:626−631

doi: 10.1073/pnas.0507535103
[38]

Lladó S, López-Mondéjar R, Baldrian P. 2018. Drivers of microbial community structure in forest soils. Applied Microbiology and Biotechnology 102:4331−4338

doi: 10.1007/s00253-018-8950-4
[39]

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, et al. 2018. Structure and function of the global topsoil microbiome. Nature 560:233−237

doi: 10.1038/s41586-018-0386-6
[40]

Wu B, Zhang M, Zhai Z, Dai H, Yang M, et al. 2024. Soil organic carbon, carbon fractions, and microbial community under various organic amendments. Scientific Reports 14:25431

doi: 10.1038/s41598-024-75771-w
[41]

Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, et al. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal 4:1340−1351

doi: 10.1038/ismej.2010.58
[42]

Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75:5111−5120

doi: 10.1128/aem.00335-09
[43]

Singh BK, Dawson LA, MacDonald CA, Buckland SM. 2009. Impact of biotic and abiotic interaction on soil microbial communities and functions: a field study. Applied Soil Ecology 41:239−248

doi: 10.1016/j.apsoil.2008.10.003
[44]

Hartmann M, Six J. 2023. Soil structure and microbiome functions in agroecosystems. Nature Reviews Earth & Environment 4:4−18

doi: 10.1038/s43017-022-00366-w
[45]

Philippot L, Chenu C, Kappler A, Rillig MC, Fierer N. 2024. The interplay between microbial communities and soil properties. Nature Reviews Microbiology 22:226−239

doi: 10.1038/s41579-023-00980-5
[46]

Anderson TH. 2003. Microbial eco-physiological indicators to asses soil quality. Agriculture, Ecosystems & Environment 98:285−293

doi: 10.1016/S0167-8809(03)00088-4
[47]

Allison SD, Martiny JBH. 2008. Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences of the United States of America 105:11512−11519

doi: 10.1073/pnas.0801925105
[48]

Shade A, Peter H, Allison SD, Baho DL, Berga M, et al. 2012. Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology 3:417

doi: 10.3389/fmicb.2012.00417
[49]

Jia X, Dini-Andreote F, Falcão Salles J. 2018. Community assembly processes of the microbial rare biosphere. Trends in Microbiology 26:738−747

doi: 10.1016/j.tim.2018.02.011
[50]

Jiao S, Chen W, Wei G. 2017. Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils. Molecular Ecology 26:5305−5317

doi: 10.1111/mec.14218
[51]

Barberán A, Ramirez KS, Leff JW, Bradford MA, Wall DH, et al. 2014. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecology Letters 17:794−802

doi: 10.1111/ele.12282
[52]

Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Applied and Environmental Microbiology 68:2391−2396

doi: 10.1128/AEM.68.5.2391-2396.2002
[53]

Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, et al. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. The ISME Journal 3:442−453

doi: 10.1038/ismej.2008.127
[54]

Lee SH, Ka JO, Cho JC. 2008. Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiology Letters 285:263−269

doi: 10.1111/j.1574-6968.2008.01232.x
[55]

Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, et al. 2012. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal 6:1007−1017

doi: 10.1038/ismej.2011.159
[56]

Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, et al. 2006. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genetics 2:e214

doi: 10.1371/journal.pgen.0020214
[57]

Yao Y, Tang H, Su F, Xu P. 2015. Comparative genome analysis reveals the molecular basis of nicotine degradation and survival capacities of Arthrobacter. Scientific Reports 5:8642

doi: 10.1038/srep08642
[58]

Rojas A, Holguin G, Glick BR, Bashan Y. 2001. Synergism between Phyllobacterium sp. (N2-fixer) and Bacillus licheniformis (P-solubilizer), both from a semiarid mangrove rhizosphere. FEMS Microbiology Ecology 35:181−187

doi: 10.1111/j.1574-6941.2001.tb00802.x
[59]

Graf DRH, Jones CM, Hallin S. 2014. Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 9:e114118

doi: 10.1371/journal.pone.0114118
[60]

Song K, Suenaga T, Hamamoto A, Satou K, Riya S, et al. 2014. Abundance, transcription levels and phylogeny of bacteria capable of nitrous oxide reduction in a municipal wastewater treatment plant. Journal of Bioscience and Bioengineering 118:289−297

doi: 10.1016/j.jbiosc.2014.02.028
[61]

Banerjee S, Schlaeppi K, van der Heijden MGA. 2018. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology 16:567−576

doi: 10.1038/s41579-018-0024-1
[62]

Yu S, Wu Q, Ma Y, Bano S, Zhang X. 2026. Keystone bacterial taxa drive denitrification and N2O emission via adaptive genomic and metabolic strategies in contrasting agricultural soils. Environmental Microbiome 21:34

doi: 10.1186/s40793-026-00855-1
[63]

Assémien FL, Cantarel AAM, Florio A, Lerondelle C, Pommier T, et al. 2019. Different groups of nitrite-reducers and N2O-reducers have distinct ecological niches and functional roles in West African cultivated soils. Soil Biology and Biochemistry 129:39−47

doi: 10.1016/j.soilbio.2018.11.003
[64]

Mise K, Masuda Y, Senoo K, Itoh H. 2025. Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms. Journal of Applied Microbiology 136:lxaf055

doi: 10.1093/jambio/lxaf055
[65]

Rummel PS, Oyeogbe AI, Wang H, Urich T, Wrage-Mönnig N. 2025. Nitrous oxide fluxes, their sources, and soil microbial communities depend more on carbon availability than long- and short-term phosphorus addition. Biology and Fertility of Soils 61:955−970

doi: 10.1007/s00374-025-01909-1
[66]

Domeignoz-Horta LA, Spor A, Bru D, Breuil MC, Bizouard F, et al. 2015. The diversity of the N2O reducers matters for the N2O: N2 denitrification end-product ratio across an annual and a perennial cropping system. Frontiers in Microbiology 6:971

doi: 10.3389/fmicb.2015.00971
[67]

Demoling F, Ola Nilsson L, Bååth E. 2008. Bacterial and fungal response to nitrogen fertilization in three coniferous forest soils. Soil Biology and Biochemistry 40:370−379

doi: 10.1016/j.soilbio.2007.08.019
[68]

Firestone MK, Davidson EA. 1989. Microbiological basis of NO and N2O production and consumption in soil. In Exchange of Trace Gases between Terrestrial Ecosystems and the Atmosphere, eds Andreae MO, Schimel DS. New York, US: John Willey and Sons. pp. 7−21
[69]

Bergaust L, Mao Y, Bakken LR, Frostegård A. 2010. Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrogen oxide reductase in Paracoccus denitrificans. Applied and Environmental Microbiology 76:6387−6396

doi: 10.1128/aem.00608-10
[70]

Weier KL, Doran JW, Power JF, Walters DT. 1993. Denitrification and the dinitrogen/nitrous oxide ratio as affected by soil water, available carbon, and nitrate. Soil Science Society of America Journal 57:66−72

doi: 10.2136/sssaj1993.03615995005700010013x
[71]

Philippot L, Spor A, Hénault C, Bru D, Bizouard F, et al. 2013. Loss in microbial diversity affects nitrogen cycling in soil. The ISME Journal 7:1609−1619

doi: 10.1038/ismej.2013.34
[72]

Čuhel J, Šimek M, Laughlin RJ, Bru D, Chèneby D, et al. 2010. Insights into the effect of soil pH on N2O and N2 emissions and denitrifier community size and activity. Applied and Environmental Microbiology 76:1870−1878

doi: 10.1128/AEM.02484-09