Abstract
Global nitrogen (N) enrichment promotes soil organic carbon (SOC) accumulation but often causes biodiversity loss in plants and soil microbes, creating a central challenge for achieving co-benefits of carbon accumulation and biodiversity conservation. The extent to which biodiversity contributes to SOC accumulation, and how these trade-offs can be mitigated under N enrichment remains poorly understood. Here, we conduct a global meta-analysis of N enrichment experiments encompassing 2141 observations from 275 studies to evaluate the contributions of plant, bacterial, and fungal diversity to SOC accumulation and to determine associated ecological thresholds. Our findings indicate that biodiversity, especially in plant communities, is the most important factor for SOC accumulation. We identify three distinct N thresholds characterized by different ecological responses: biodiversity loss accelerates at 50 kg N ha⁻¹ yr⁻¹, soil degradation persists at 200 kg N ha⁻¹ yr⁻¹, and SOC accumulation declines beyond this point. Given that the promoting effects of bacterial, fungal, and plant diversity on SOC diminish or even reverse at 50, 67, and 74 kg N ha⁻¹ yr⁻¹, respectively, we suggest limiting fertilization to around 50 kg N ha⁻¹ yr⁻¹, as the trade-off between biodiversity loss and SOC accumulation under N enrichment is potentially minimized.
Similar content being viewed by others
Data availability
All data generated and analyzed in this study have been deposited in the figshare repository (https://doi.org/10.6084/m9.figshare.30646841). Supplementary Data 1 contains the full citation information for all primary studies included in the meta-analysis. Source data are provided with this paper.
Code availability
The main R code used in this study is available at the figshare repository (https://doi.org/10.6084/m9.figshare.30646841).
References
Amelung, W. et al. Towards a global-scale soil climate mitigation strategy. Nat. Commun. 11, 5427 (2020).
Lehmann, J., Bossio, D. A., Kögel-Knabner, I. & Rillig, M. C. The concept and future prospects of soil health. Nat. Rev. Earth Environ. 1, 544–553 (2020).
Ling, J. et al. Soil organic carbon thresholds control fertilizer effects on carbon accrual in croplands worldwide. Nat. Commun. 16, 3009 (2025).
Yang, X. et al. Nitrogen addition promotes soil carbon accumulation globally. Sci. China Life Sci. 68, 284–293 (2025).
Galloway, J. N. et al. Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 320, 889–892 (2008).
Hiis, E. G. et al. Unlocking bacterial potential to reduce farmland N2O emissions. Nature 630, 421–428 (2024).
Ye, C. et al. Reconciling multiple impacts of nitrogen enrichment on soil carbon: plant, microbial and geochemical controls. Ecol. Lett. 21, 1162–1173 (2018).
Lu, X. et al. Nitrogen addition stimulates soil aggregation and enhances carbon storage in terrestrial ecosystems of China: a meta-analysis. Glob. Change Biol. 27, 2780–2792 (2021).
Tang, B., Rocci, K. S., Lehmann, A. & Rillig, M. C. Nitrogen increases soil organic carbon accrual and alters its functionality. Glob. Change Biol. 29, 1971–1983 (2023).
Feng, X. et al. Nitrogen input enhances microbial carbon use efficiency by altering plant-microbe-mineral interactions. Glob. Change Biol. 28, 4845–4860 (2022).
Neff, J. C. et al. Variable effects of nitrogen additions on the stability and turnover of soil carbon. Nature 419, 915–917 (2002).
Mack, M. C., Schuur, E. A., Bret-Harte, M. S., Shaver, G. R. & Chapin, F. S. Ecosystem carbon storage in arctic tundra reduced by long-term nutrient fertilization. Nature 431, 440–443 (2004).
Janssens, I. A. et al. Reduction of forest soil respiration in response to nitrogen deposition. Nat. Geosci. 3, 315–322 (2010).
Lange, M. et al. Plant diversity increases soil microbial activity and soil carbon storage. Nat. Commun. 6, 6707 (2015).
Li, Y. et al. Microbial diversity losses constrain the capacity of soils to mitigate climate change. Glob. Change Biol. 30, e17601 (2024).
Cardinale, B. J. et al. Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature 443, 989–992 (2006).
Hooper, D. U. et al. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486, 105–108 (2012).
Angst, S., Angst, G., Mueller, K. E., Lange, M. & Eisenhauer, N. Un(der)explored links between plant diversity and particulate and mineral-associated organic matter in soil. Nat. Commun. 16, 5548 (2025).
Liang, C., Schimel, J. P. & Jastrow, J. D. The importance of anabolism in microbial control over soil carbon storage. Nat. Microbiol. 2, 17105 (2017).
Sokol, N. W. et al. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat. Rev. Microbiol. 20, 415–430 (2022).
Domeignoz-Horta, L. A. et al. Microbial diversity drives carbon use efficiency in a model soil. Nat. Commun. 11, 3684 (2020).
Yang, Y. et al. Nitrogen fertilization weakens the linkage between soil carbon and microbial diversity: a global meta-analysis. Glob. Change Biol. 28, 6446–6461 (2022).
Simkin, S. M. et al. Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States. Proc. Natl. Acad. Sci. USA 113, 4086–4091 (2016).
Namuhan et al. Mechanisms of biodiversity loss under nitrogen enrichment: unveiling a shift from light competition to cation toxicity. New Phytol. 243, 1966–1979 (2024).
Tian, Q. et al. An integrated belowground trait-based understanding of nitrogen-driven plant diversity loss. Glob. Change Biol. 28, 3651–3664 (2022).
Band, N., Kadmon, R., Mandel, M. & DeMalach, N. Assessing the roles of nitrogen, biomass, and niche dimensionality as drivers of species loss in grassland communities. Proc. Natl. Acad. Sci. USA 119, e2112010119 (2022).
Wang, X. D. et al. Globally nitrogen addition alters soil microbial community structure, but has minor effects on soil microbial diversity and richness. Soil Biol. Biochem. 179, 108982 (2023).
Fierer, N. et al. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 6, 1007–1017 (2012).
Yu, Q. et al. Decoupled responses of plants and soil biota to global change across the world’s land ecosystems. Nat. Commun. 15, 10369 (2024).
Loreau, M. & Hector, A. J. N. Partitioning selection and complementarity in biodiversity experiments. Nature 412, 72–76 (2001).
Hu, J., Huang, C., Zhou, S. & Kuzyakov, Y. Nitrogen addition to soil affects microbial carbon use efficiency: meta-analysis of similarities and differences in 13C and 18O approaches. Glob. Change Biol. 28, 4977–4988 (2022).
Liu, W., Qiao, C., Yang, S., Bai, W. & Liu, L. Microbial carbon use efficiency and priming effect regulate soil carbon storage under nitrogen deposition by slowing soil organic matter decomposition. Geoderma 332, 37–44 (2018).
Weiskopf, S. R. et al. Biodiversity loss reduces global terrestrial carbon storage. Nat. Commun. 15, 4354 (2024).
Liu, H. Y., Huang, N., Zhao, C. M. & Li, J. H. Responses of carbon cycling and soil organic carbon content to nitrogen addition in grasslands globally. Soil Biol. Biochem. 186, 109164 (2023).
Schuldt, A. et al. Carbon-biodiversity relationships in a highly diverse subtropical forest. Glob. Change Biol. 29, 5321–5333 (2023).
Zhu, L. et al. Regional scalable priorities for national biodiversity and carbon conservation planning in Asia. Sci. Adv. 7, eabe4261 (2021).
Soto-Navarro, C. et al. Mapping co-benefits for carbon storage and biodiversity to inform conservation policy and action. Philos. T. R. Soc. B 375, 20190128 (2020).
Fornara, D. A. & Tilman, D. Soil carbon sequestration in prairie grasslands increased by chronic nitrogen addition. Ecology 93, 2030–2036 (2012).
Zhou, T., Wang, C. K. & Zhou, Z. H. Nitrogen availability regulates tree mixture effects on soil organic carbon in temperate forests: insights from a meta-analysis and long-term experiment. Glob. Ecol. Biogeogr. 34, e70073 (2025).
Shi, T. S. et al. A global meta-analysis on the effects of organic and inorganic fertilization on grasslands and croplands. Nat. Commun. 15, 3411 (2024).
Xia, L. L. et al. Trade-offs between soil carbon sequestration and reactive nitrogen losses under straw return in global agroecosystems. Glob. Change Biol. 24, 5919–5932 (2018).
Berdugo, M. et al. Global ecosystem thresholds driven by aridity. Science 367, 787–790 (2020).
Zhang, J. et al. Water availability creates global thresholds in multidimensional soil biodiversity and functions. Nat. Ecol. Evol. 7, 1002–1011 (2023).
Pan, H. et al. Aridity threshold induces abrupt change of soil abundant and rare bacterial biogeography in dryland ecosystems. mSystems 7, e0130921 (2022).
Egidi, E., Coleine, C., Delgado-Baquerizo, M. & Singh, B. K. Assessing critical thresholds in terrestrial microbiomes. Nat. Microbiol. 8, 2230–2233 (2023).
Frantzeskakis, L. et al. Rapid evolution in plant–microbe interactions–a molecular genomics perspective. New Phytol. 225, 1134–1142 (2020).
Wang, H. et al. Divergent phenological responses of soil microorganisms and plants to climate warming. Nat. Geosci. 18, 753–760 (2025).
Hodge, A., Robinson, D. & Fitter, A. Are microorganisms more effective than plants at competing for nitrogen? Trends Plant Sci. 5, 304–308 (2000).
Lavallee, J. M., Soong, J. L. & Cotrufo, M. F. Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change in the 21st century. Glob. Change Biol. 26, 261–273 (2020).
Midolo, G. et al. Impacts of nitrogen addition on plant species richness and abundance: a global meta-analysis. Glob. Ecol. Biogeogr. 28, 398–413 (2019).
Han, Y. F., Feng, J. G., Han, M. G. & Zhu, B. Responses of arbuscular mycorrhizal fungi to nitrogen addition: a meta-analysis. Glob. Change Biol. 26, 7229–7241 (2020).
Ma, X. C. et al. Global negative effects of nutrient enrichment on arbuscular mycorrhizal fungi, plant diversity and ecosystem multifunctionality. New Phytol. 229, 2957–2969 (2021).
Morrison, E. W. et al. Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest. Fungal Ecol. 23, 48–57 (2016).
Branco, S., Schauster, A., Liao, H. L. & Ruytinx, J. Mechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungi. New Phytol. 235, 2158–2175 (2022).
Zavaleta, E. S., Shaw, M. R., Chiariello, N. R., Mooney, H. A. & Field, C. B. Additive effects of simulated climate changes, elevated CO2, and nitrogen deposition on grassland diversity. Proc. Natl. Acad. Sci. USA 100, 7650–7654 (2003).
Wang, C. Q. & Kuzyakov, Y. Mechanisms and implications of bacterial-fungal competition for soil resources. ISME J. 18, wrae073 (2024).
Hu, Z. et al. Nutrient-induced acidification modulates soil biodiversity-function relationships. Nat. Commun. 15, 2858 (2024).
He, Y. C. et al. Water controls the divergent responses of terrestrial plant photosynthesis under nitrogen enrichment. J. Ecol. 112, 2638–2651 (2024).
Bai, Y. F. & Cotrufo, M. F. Grassland soil carbon sequestration: current understanding, challenges, and solutions. Science 377, 603–608 (2022).
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).
Tian, D. H., Wang, H., Sun, J. & Niu, S. L. Global evidence on nitrogen saturation of terrestrial ecosystem net primary productivity. Environ. Res. Lett. 11, 024012 (2016).
Maestre, F. T. et al. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc. Natl. Acad. Sci. USA 112, 15684–15689 (2015).
Carpenter, D. N., Bockheim, J. G. & Reich, P. F. Soils of temperate rainforests of the North American Pacific Coast. Geoderma 230, 250–264 (2014).
Machmuller, M. B. et al. Arctic soil carbon trajectories shaped by plant-microbe interactions. Nat. Clim. Change 14, 1178–1185 (2024).
Xia, J. & Wan, S. Global response patterns of terrestrial plant species to nitrogen addition. New Phytol. 179, 428–439 (2008).
Ackerman, D., Millet, D. B. & Chen, X. Global estimates of inorganic nitrogen deposition across four decades. Global Biogeochem. Cycles 33, 100–107 (2019).
He, C., Ruan, Y. & Jia, Z. Effects of nitrogen addition on soil microbial biomass: a meta-analysis. Agriculture 14, 1616 (2024).
Treseder, K. K. Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecol. Lett. 11, 1111–1120 (2008).
Forstner, S. J. et al. Vertical redistribution of soil organic carbon pools after twenty years of nitrogen addition in two temperate coniferous forests. Ecosystems 22, 452–452 (2019).
Tian, J. et al. Long-term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil. Glob. Change Biol. 25, 3267–3281 (2019).
Zhou, Z., Wang, C. & Luo, Y. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat. Commun. 11, 3072 (2020).
Meng, C. et al. Global soil acidification impacts on belowground processes. Environ. Res. Lett. 14, 074003 (2019).
Kong, W. et al. Climate and soil pH modulate global negative effects of nitrogen enrichment on soil nematodes. Soil Biol. Biochem. 208, 109860 (2025).
Domeignoz-Horta, L. A. et al. Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils. Nat. Commun. 15, 8065 (2024).
Strassburg, B. B. et al. Global congruence of carbon storage and biodiversity in terrestrial ecosystems. Conserv. Lett. 3, 98–105 (2010).
Thomas, C. D. et al. Reconciling biodiversity and carbon conservation. Ecol. Lett. 16, 39–47 (2013).
Nielsen, U. N., Ayres, E., Wall, D. H. & Bardgett, R. D. Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity–function relationships. Eur. J. Soil Sci. 62, 105–116 (2010).
Zhao, M. et al. Decoupled responses of above- and below-ground beta-diversity to nitrogen enrichment in a typical steppe. Ecol. Lett. 27, e14339 (2024).
Genre, A., Lanfranco, L., Perotto, S. & Bonfante, P. Unique and common traits in mycorrhizal symbioses. Nat. Rev. Microbiol. 18, 649–660 (2020).
Forsmark, B. et al. Anthropogenic nitrogen enrichment increased the efficiency of belowground biomass production in a boreal forest. Soil Biol. Biochem. 155, 108154 (2021).
Hyvönen, R. et al. Impact of long-term nitrogen addition on carbon stocks in trees and soils in northern Europe. Biogeochemistry 89, 121–137 (2008).
Allison, S. D. & Martiny, J. B. Colloquium paper: resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. USA 105, 11512–11519 (2008).
Li, T. et al. Mycorrhizal allies: synergizing forest carbon and multifunctional restoration. Trends Ecol. Evol. 40, 983–994 (2025).
Auer, L. et al. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New Phytol. 242, 1676–1690 (2024).
Kakouridis, A. et al. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. New Phytol. 242, 1661–1675 (2024).
Wu, S. L. et al. Soil organic matter dynamics mediated by arbuscular mycorrhizal fungi - an updated conceptual framework. New Phytol. 242, 1417–1425 (2024).
Tuo, B. et al. Meta-analysis reveals that vertebrates enhance plant litter decomposition at the global scale. Nat. Ecol. Evol. 8, 411–422 (2024).
Takkouche, B. & Norman, G. J. E. PRISMA statement. 22, 128 (2011).
Fan, K. et al. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat. Ecol. Evol. 7, 113–126 (2023).
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Liu, S. W. et al. Response of soil carbon dioxide fluxes, soil organic carbon and microbial biomass carbon to biochar amendment: a meta-analysis. GCB Bioenergy 8, 392–406 (2016).
Liu, T. et al. Forest canopy maintains the soil community composition under elevated nitrogen deposition. Soil Biol. Biochem. 143, 107733 (2020).
Viechtbauer, W. Conducting meta-analyses in R with the metafor package. J. Stat. Softw. 36, 1–48 (2010).
Sáez-Sandino, T. et al. The soil microbiome governs the response of microbial respiration to warming across the globe. Nat. Clim. Change 13, 1382–1387 (2023).
Benito, B. M. spatialRF: Easy Spatial Regression with Random Forest Measurement (R package version,2021).
Pelletier, T. A., Carstens, B. C., Tank, D. C., Sullivan, J. & Espíndola, A. Predicting plant conservation priorities on a global scale. Proc. Natl. Acad. Sci. USA 115, 13027–13032 (2018).
Stekhoven, D. J. & Bühlmann, P. MissForest—non-parametric missing value imputation for mixed-type data. Bioinformatics 28, 112–118 (2012).
Lee, C. H., Cook, S., Lee, J. S. & Han, B. Comparison of two meta-analysis methods: inverse-variance-weighted average and weighted sum of Z-scores. Genom. Inform. 14, 173–180 (2016).
Fong, Y. Y., Huang, Y., Gilbert, P. B. & Permar, S. R. chngpt: threshold regression model estimation and inference. BMC Bioinform. 18, 454 (2017).
Hastie, T. gam: Generalized additive models. R package version 1.20 (2020).
Hu, W. et al. Aridity-driven shift in biodiversity-soil multifunctionality relationships. Nat. Commun. 12, 5350 (2021).
Silva, J. F. Jr. et al. Multivariate split moving windows and magnetic susceptibility for locating soil boundaries of Sao Paulo, Brazil. Geoderma Reg. 26, e00418 (2021).
Jiao, S., Lu, Y. H. & Wei, G. H. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. Glob. Change Biol. 28, 140–153 (2022).
Cai, L. et al. Global models and predictions of plant diversity based on advanced machine learning techniques. New Phytol. 237, 1432–1445 (2023).
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
Abraham, A. et al. Machine learning for neuroimaging with scikit-learn. Front. Neuroinform. 8, 14 (2014).
Childs, C. Interpolating surfaces in ArcGIS spatial analyst. ArcUser 3235, 32–35 (2004).
Lawhead, J. Learning Geospatial Analysis with Python (Packt Publishing Ltd, 2013).
Egger, M. atthias, Martin Schneider, G. D. S. & Minder, C. hristoph Bias in meta-analysis detected by a simple, graphical test. Br. Med. J. 316, 629–634 (1997).
Rosenberg, M. S. The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysis. Evolution 59, 464–468 (2005).
Wong, T. T. Performance evaluation of classification algorithms by k-fold and leave-one-out cross validation. Pattern Recognit. 48, 2839–2846 (2015).
Acknowledgements
This work was supported by the National Key Research and Development Program of China (grant number: 2021YFD1900500; S.J.), National Science Foundation of China (grant number: 42477129; S.J.), and National Science Foundation for Excellent Young Scholars of China (grant number: 42122050; S.J.).
Author information
Authors and Affiliations
Contributions
S.J. and H.P. conceived the ideas and designed the methodology. H.P., Y.H., W.W., and S.L. contributed to the literature inclusion and data collection. H.P. performed the analyses and wrote the original draft. S.J. and G.W. reviewed the paper before submission.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work. A peer review file is available.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Source data
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Pan, H., Hui, Y., Wu, W. et al. Critical thresholds for co-benefits of carbon accumulation and biodiversity conservation under global nitrogen enrichment. Nat Commun (2026). https://doi.org/10.1038/s41467-025-68090-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41467-025-68090-9


