Abstract
Soil health affects both food production and environmental quality. However, quantifying its impact poses a substantial global challenge due to the scarcity of comprehensive soil health data and the complexity of disentangling its effects from other variables. Here we integrate high-resolution global data on soil, climate and farm management practices to assess the contribution of soil health to agricultural productivity. We show that soil health is responsible for approximately 12% and 22% of global variations in crop production and nitrogen use efficiency, respectively. While the influence of climate on crop yields is comparable to that of soil health, it is substantially overshadowed by the role of agricultural management, which accounts for roughly 70% of the global yield variation. In regions such as China, India and the central United States, the influence of soil health on crop yields and nitrogen use efficiency is less pronounced due to the dominant effects of farming practices, including the intensive use of fertilizers. Enhancing global soil health could increase crop yields by 7.8 Mt while reducing nitrogen surplus by 8.1 Mt worldwide by 2050. It is crucial to achieve global sustainable development through managing soil health beyond traditional agricultural practices and climate adaptation.
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Data availability
We utilized nitrogen budget data at a 0.5° × 0.5° spatial resolution, including fertilizer input, biological nitrogen fixation, deposition and manure, from the IMAGE–GNM database (https://doi.org/10.5194/gmd-8-4045-2015)28. Cropland data, measured in square kilometres per grid at the same resolution, were obtained from HYDE v. 3.2 (https://doi.org/10.5194/essd-9-927-2017)29. Rural population data were sourced from the WorldPop dataset (https://www.worldpop.org/)30. Soil physical properties, including bulk density, pH and organic carbon density, were extracted from the surface layer (0–30 cm) at a 1 km × 1 km resolution (ISRIC dataset; https://files.isric.org/). Phosphorus content was sourced from figshare (https://doi.org/10.6084/m9.figshare.14583375)50. Biotic data were from ref. 51, covering fungal richness data from ref. 52, bacterial richness data from ref. 20, viral abundance data from ref. 53, and nematode and worm abundance data from ref. 54. Soil pesticide data, including fungicides, herbicides and insecticides, were sourced from ref. 55. Climate data for 2020, including temperature and precipitation at a 0.5° × 0.5° resolution, were obtained from CRU TS v. 4.06 (https://doi.org/10.1038/s41597-020-0453-3)34. For scenario analysis, we collected cropland area, population, temperature and precipitation data under three SSP–RCP scenarios (SSP1–RCP2.6, SSP2–RCP4.5 and SSP5–RCP8.5). Cropland area projections until 2050 were sourced from the LUH2 dataset (https://luh.umd.edu/data.shtml). Population projections until 2050 were obtained from gridded datasets for population and economy under SSPs (https://doi.org/10.57760/sciencedb.01683)36. Monthly temperature and precipitation data (2015–2050) at 0.9° × 1.25° resolution were sourced from CMIP6 (https://esgf-node.llnl.gov/projects/cmip6/). Data supporting this study’s findings are included in the article and Supplementary Information. Additional data are sourced from publicly available databases and literature, as cited in the reference list. Source data are provided with this paper.
Code availability
Statistical analyses and computations were conducted using Stata 16.0. All model code is available in the Supplementary Information.
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Acknowledgements
This study was supported by the National Natural Science Foundation of China (42325707 and 42261144001) and National Key Research and Development Project of China (2022YFE0138200).
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B.G. and J.X. designed the study. C.R., X.Z. and C.W. conducted the research and analysed the data. B.G. interpreted the findings and wrote the first draft of the paper. B.M., Y.H., L.H., X.L., S.W., F.Z., L.L. and S.L. provided support for the data availability and processed the raw data. J.Z., Y.-G.Z. and P.V. revised the paper. All authors contributed to the discussion and revision of the paper.
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Nature Food thanks Hai-Lin Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Xu, J., Ren, C., Zhang, X. et al. Soil health contributes to variations in crop production and nitrogen use efficiency. Nat Food 6, 597–609 (2025). https://doi.org/10.1038/s43016-025-01155-6
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DOI: https://doi.org/10.1038/s43016-025-01155-6
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