Bond-Lamberty, B. & Thomson, A. Temperature-associated increases in the global soil respiration record. Nature 464, 579–582 (2010).
Google Scholar
Crippa, M. et al. Food systems are responsible for a third of global anthropogenic GHG emissions. Nat. Food 2, 198–209 (2021).
Google Scholar
Shakoor, A. et al. Effect of animal manure, crop type, climate zone, and soil attributes on greenhouse gas emissions from agricultural soils—A global meta-analysis. J. Clean Prod. 278, 124019. https://doi.org/10.1016/j.jclepro.2020.124019 (2021).
Google Scholar
Wu, L. et al. Soil organic matter priming and carbon balance after straw addition is regulated by long-term fertilization. Soil Biol. Biochem. 135, 383–391 (2019).
Google Scholar
Chen, F. et al. Effects of N addition and precipitation reduction on soil respiration and its components in a temperate forest. Agr. Forest. Meteorol. 271, 336–345 (2019).
Google Scholar
Lei, J. et al. Temporal changes in global soil respiration since 1987. Nat. Commun. 12, 1–9 (2021).
Wang, R. et al. Nitrogen application increases soil respiration but decreases temperature sensitivity: Combined effects of crop and soil properties in a semiarid agroecosystem. Geoderma 353, 320–330 (2019).
Google Scholar
Du, K. et al. Influence of no-tillage and precipitation pulse on continuous soil respiration of summer maize affected by soil water in the North China Plain. Sci. Total Environ. 766, 144384. https://doi.org/10.1016/j.scitotenv.2020.144384 (2021).
Google Scholar
Chen, X. & Chen, H. Y. Plant diversity loss reduces soil respiration across terrestrial ecosystems. Global Change Biol. 25, 1482–1492 (2019).
Google Scholar
Lang, A. K., Jevon, F. V., Ayres, M. P. & Matthes, J. H. Higher soil respiration rate beneath arbuscular mycorrhizal trees in a northern hardwood forest is driven by associated soil properties. Ecosystems 23, 1243–1253 (2020).
Google Scholar
Huang, N. et al. Spatial and temporal variations in global soil respiration and their relationships with climate and land cover. Sci. Adv. 6, eabb8508 (2020).
Google Scholar
Xiao, H. et al. The regulatory effects of biotic and abiotic factors on soil respiration under different land-use types. Ecol. Indic. 127, 107787. https://doi.org/10.1016/j.ecolind.2021.107787 (2021).
Google Scholar
Liu, Y.-R. et al. New insights into the role of microbial community composition in driving soil respiration rates. Soil Biol. Biochem. 118, 35–41 (2018).
Google Scholar
Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E. E. & van der Heijden, M. G. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat. Commun. 10, 1–10 (2019).
Google Scholar
Chen, L.-F. et al. Linkages between soil respiration and microbial communities following afforestation of alpine grasslands in the northeastern Tibetan Plateau. Appl. Soil Ecol. 161, 103882. https://doi.org/10.1016/j.apsoil.2021.103882 (2021).
Google Scholar
Choudhary, M. et al. Long-term effects of organic manure and inorganic fertilization on sustainability and chemical soil quality indicators of soybean-wheat cropping system in the Indian mid-Himalayas. Agr. Ecosyst. Environ. 257, 38–46 (2018).
Google Scholar
Zhang, M. et al. Increasing yield and N use efficiency with organic fertilizer in Chinese intensive rice cropping systems. Field Crop. Res. 227, 102–109 (2018).
Google Scholar
Bonanomi, G. et al. Repeated applications of organic amendments promote beneficial microbiota, improve soil fertility and increase crop yield. Appl. Soil Ecol. 156, 103714. https://doi.org/10.1016/j.apsoil.2020.103714 (2020).
Google Scholar
Gai, X. et al. Long-term benefits of combining chemical fertilizer and manure applications on crop yields and soil carbon and nitrogen stocks in North China Plain. Agr. Water Manage. 208, 384–392 (2018).
Google Scholar
Lai, R. et al. Manure fertilization increases soil respiration and creates a negative carbon budget in a Mediterranean maize (Zea mays L.)-based cropping system. Catena 151, 202–212 (2017).
Google Scholar
Yan, T. et al. Negative effect of nitrogen addition on soil respiration dependent on stand age: Evidence from a 7-year field study of larch plantations in northern China. Agr. Forest Meteorol. 262, 24–33 (2018).
Google Scholar
Peng, Q. et al. Effects of nitrogen fertilization on soil respiration in temperate grassland in Inner Mongolia. China. Environ. Earth Sci. 62, 1163–1171 (2011).
Google Scholar
Zeng, J. et al. Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition. Soil Biol. Biochem. 92, 41–49 (2016).
Google Scholar
Levine, U. Y., Teal, T. K., Robertson, G. P. & Schmidt, T. M. Agriculture’s impact on microbial diversity and associated fluxes of carbon dioxide and methane. ISME J. 5, 1683–1691 (2011).
Google Scholar
Chen, Q., Liu, Z., Zhou, J., Xu, X. & Zhu, Y. Long-term straw mulching with nitrogen fertilization increases nutrient and microbial determinants of soil quality in a maize–wheat rotation on China’s Loess Plateau. Sci. Total. Environ. 775, 145930. https://doi.org/10.1016/j.scitotenv.2021.145930 (2021).
Google Scholar
Wang, J. et al. The impact of fertilizer amendments on soil autotrophic bacteria and carbon emissions in maize field on the semiarid Loess Plateau. Front. Microbiol. https://doi.org/10.3389/fmicb.2021.664120 (2021).
Google Scholar
Subke, J. A., Inglima, I. & Francesca Cotrufo, M. Trends and methodological impacts in soil CO2 efflux partitioning: a metaanalytical review. Global Change Biol. 12, 921–943 (2006).
Google Scholar
Yan, W., Zhong, Y., Liu, J. & Shangguan, Z. Response of soil respiration to nitrogen fertilization: Evidence from a 6-year field study of croplands. Geoderma 384, 114829. https://doi.org/10.1016/j.geoderma.2020.114829 (2021).
Google Scholar
Lamptey, S., Xie, J., Li, L., Coulter, J. A. & Jagadabhi, P. S. Influence of organic amendment on soil respiration and maize productivity in a semi-arid environment. Agronomy 9, 611. https://doi.org/10.3390/agronomy9100611 (2019).
Google Scholar
Chen, Z. et al. Nitrogen fertilization stimulated soil heterotrophic but not autotrophic respiration in cropland soils: A greater role of organic over inorganic fertilizer. Soil Biol. Biochem. 116, 253–264 (2018).
Google Scholar
Zheng, J., Zhang, X., Li, L., Zhang, P. & Pan, G. Effect of long-term fertilization on C mineralization and production of CH4 and CO2 under anaerobic incubation from bulk samples and particle size fractions of a typical paddy soil. Agr. Ecosyst. Environ. 120, 129–138 (2007).
Google Scholar
Shen, J., Zhang, L., Guo, J., Ray, J. & He, J. Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in Northeast China. Appl. Soil Ecol. 46, 119–124 (2010).
Google Scholar
Chen, Q., An, X., Zheng, B., Ma, Y. & Su, J. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. Sci. Total. Environ. 645, 1230–1237 (2018).
Google Scholar
Zhang, W., Yu, C., Wang, X. & Hai, L. Increased abundance of nitrogen transforming bacteria by higher C/N ratio reduces the total losses of N and C in chicken manure and corn stover mix composting. Bioresource Technol. 297, 122410. https://doi.org/10.1016/j.biortech.2019.122410 (2020).
Google Scholar
Chen, X. et al. Microbial carbon use efficiency, biomass turnover, and necromass accumulation in paddy soil depending on fertilization. Agr. Ecosyst. Environ. 292, 106816. https://doi.org/10.1016/j.agee.2020.106816 (2020).
Google Scholar
Wang, J. et al. Nitrogen application increases soil microbial carbon fixation and maize productivity on the semiarid Loess Plateau. Plant Soil https://doi.org/10.1007/s11104-022-05457-7 (2022).
Google Scholar
Li, J. et al. The more straw we deep-bury, the more soil TOC will be accumulated: When soil bacteria abundance keeps growing. J. Soil Sediment 22, 162–171 (2022).
Google Scholar
Siczek, A., Frąc, M., Wielbo, J. & Kidaj, D. Benefits of flavonoids and straw mulch application on soil microbial activity in pea rhizosphere. Int. J. Environ. Sci. Te. 15, 755–764 (2018).
Google Scholar
Zhao, S. et al. Change in straw decomposition rate and soil microbial community composition after straw addition in different long-term fertilization soils. Appl. Soil Ecol. 138, 123–133 (2019).
Google Scholar
Zhang, S. et al. Cow manure application effectively regulates the soil bacterial community in tea plantation. BMC Microbiol. 20, 1–11 (2020).
Google Scholar
Jiang, Y. et al. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95, 250–261 (2016).
Google Scholar
Drenovsky, R., Vo, D., Graham, K. & Scow, K. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microb. Ecol. 48, 424–430 (2004).
Google Scholar
Rath, K. M., Fierer, N., Murphy, D. V. & Rousk, J. Linking bacterial community composition to soil salinity along environmental gradients. ISME J. 13, 836–846 (2019).
Google Scholar
Zhao, F. et al. Changes of the organic carbon content and stability of soil aggregates affected by soil bacterial community after afforestation. CATENA 171, 622–631 (2018).
Google Scholar
Goldfarb, K. C. et al. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front. Microbiol. 2, 94. https://doi.org/10.3389/fmicb.2011.00094 (2011).
Google Scholar
Zhao, J. et al. Response of soil microbial community to vegetation reconstruction modes in mining areas of the Loess Plateau, China. Front. Microbiol. https://doi.org/10.3389/fmicb.2021.714967 (2021).
Google Scholar
Zhang, Y. et al. Fertilization shapes bacterial community structure by alteration of soil pH. Front. Microbiol. 8, 1325. https://doi.org/10.3389/fmicb.2017.01325 (2017).
Google Scholar
Wang, X. et al. Organic amendments drive shifts in microbial community structure and keystone taxa which increase C mineralization across aggregate size classes. Soil Biol. Biochem. 153, 108062. https://doi.org/10.1016/j.soilbio.2020.108062 (2021).
Google Scholar
Lin, Y. et al. Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa. Soil Biol. Biochem. 134, 187–196 (2019).
Google Scholar
Woyke, T. et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950–955 (2006).
Google Scholar
Zhang, B., Zhang, J., Liu, Y., Shi, P. & Wei, G. Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale. Soil Biol. Biochem. 118, 178–186 (2018).
Google Scholar
Wiens, J. J. et al. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol. Lett. 13, 1310–1324 (2010).
Google Scholar
Deng, Y. et al. Molecular ecological network analyses. BMC Bioinf. 13, 1–20 (2012).
Google Scholar
Liao, H. et al. Complexity of bacterial and fungal network increases with soil aggregate size in an agricultural Inceptisol. Appl. Soil Ecol. 154, 103640. https://doi.org/10.1016/j.apsoil.2020.103640 (2020).
Google Scholar
Herren, C. M. & McMahon, K. D. Keystone taxa predict compositional change in microbial communities. Environ. Microbiol. 20, 2207–2217 (2018).
Google Scholar
Zhang, C., Jiao, S., Shu, D. & Wei, G. Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization. Stress Biol. 1, 1–13 (2021).
Google Scholar
Su, Y. G., Huang, G., Lin, Y. J. & Zhang, Y. M. No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert. CATENA 142, 126–133 (2016).
Google Scholar
Yang, C. et al. Assessing the effect of soil salinization on soil microbial respiration and diversities under incubation conditions. Appl. Soil Ecol. 155, 103671. https://doi.org/10.1016/j.apsoil.2020.103671 (2020).
Google Scholar
Banerjee, S. et al. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol. Biochem. 97, 188–198 (2016).
Google Scholar
Chen, L.-F., He, Z.-B., Zhao, W.-Z., Kong, J.-Q. & Gao, Y. Empirical evidence for microbial regulation of soil respiration in alpine forests. Ecol. Indic. 126, 107710. https://doi.org/10.1016/j.ecolind.2021.107710 (2021).
Google Scholar
Liu, S. et al. Decoupled diversity patterns in bacteria and fungi across continental forest ecosystems. Soil Biol. Biochem. 144, 107763. https://doi.org/10.1016/j.soilbio.2020.107763 (2020).
Google Scholar
Lynch, M. D. & Neufeld, J. D. Ecology and exploration of the rare biosphere. Nat. Rev. Microbiol. 13, 217–229 (2015).
Google Scholar
Chen, L. et al. Competitive interaction with keystone taxa induced negative priming under biochar amendments. Microbiome 7, 1–18 (2019).
Chiba, A. et al. Soil bacterial diversity is positively correlated with decomposition rates during early phases of maize litter decomposition. Microorganisms 9, 357 (2021).
Google Scholar
Li, S., Wang, S., Fan, M., Wu, Y. & Shangguan, Z. Interactions between biochar and nitrogen impact soil carbon mineralization and the microbial community. Soil Till. Res. 196, 104437. https://doi.org/10.1016/j.still.2019.104437 (2020).
Google Scholar
Bao, S. Soil agrochemical analysis 30 (China Agricultural Press, Beijing, Chinese, 2000).
Zhai, L., Liu, H., Zhang, J., Huang, J. & Wang, B. Long-term application of organic manure and mineral fertilizer on N2O and CO2 emissions in a red soil from cultivated maize-wheat rotation in China. Agr. Sci. China 10, 1748–1757 (2011).
Google Scholar
Xia, W. et al. Autotrophic growth of nitrifying community in an agricultural soil. ISME J. 5, 1226–1236 (2011).
Google Scholar
Pruesse, E. et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids. Res. 35, 7188–7196 (2007).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 57, 289–300 (1995).
Google Scholar
Layeghifard, M., Hwang, D. M. & Guttman, D. S. Disentangling interactions in the microbiome: A network perspective. Trends Microbiol. 25, 217–228 (2017).
Google Scholar
Liaw, A. & Wiener, M. Classification and regression by randomForest. R news 2, 18–22 (2002).
Archer, E. rfPermute: Estimate permutation p-values for random Forest importance metrics. R package version 2(1), 81 (2020).
Google Scholar
Hooper, D., Coughlan, J. & Mullen, M. Structural equation modelling: Guidelines for determining model fit. Electron. J. Bus. Res. Methods 6(1), 53–60 (2008).
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