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Diversified cropping systems with limited carbon accrual but increased nitrogen supply

Nature Sustainability volume 8, pages 152–161 (2025) Cite this article

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Abstract

Diversified cropping systems offer a chance to mitigate environmental impacts of conventional agriculture, but effects on soil organic carbon (SOC) sequestration and nitrogen (N) dynamics remain debated. We integrated a 20-year field experiment and laboratory measurements with three stable-isotope-enabled mechanistic models to examine SOC stocks and decomposition in a conventional corn–soybean system and two more diversified systems including small grains, legumes and manure inputs, in addition to corn and soybean. Contrary to the prevalent hypothesis that diversified systems increase SOC, we found no differences in 0.3 m topsoil or 1 m profile SOC and N stocks. Diversified systems markedly increased N mineralization rates and decomposition of older SOC from previous corn inputs. Models revealed that increased C decomposition with residence times of months to years counteracted higher C inputs but increased N supply. Our findings highlight a critical trade-off between C storage and N supply in these diversified systems, demonstrating that key climate benefits may arise from decreased N fertilizer use, not SOC sequestration.

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Fig. 1: SOC, TN and C/N among cropping systems.
The alternative text for this image may have been generated using AI.
Fig. 2: Soil C decomposition among cropping systems.
The alternative text for this image may have been generated using AI.
Fig. 3: Soil net N mineralization among cropping systems.
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Fig. 4: Simulated C fluxes from different C pools among cropping systems.
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Data availability

The data that support the findings of this study are available in the Environmental Data Initiative at https://doi.org/10.6073/pasta/7f1dac6bf350221c54d1eb349ca89bbf (ref. 67). Source data for all the figures in the main text are provided with this paper.

Code availability

Code (R and Python scripts) used to generate the figures are deposited to the Environmental Data Initiative at https://doi.org/10.6073/pasta/7f1dac6bf350221c54d1eb349ca89bbf (ref. 67).

References

  1. Paustian, K. et al. Climate-smart soils. Nature 532, 49–57 (2016).

    CAS  Google Scholar 

  2. Minasny, B. et al. Soil carbon 4 per mille. Geoderma 292, 59–86 (2017).

    Google Scholar 

  3. Oldfield, E. E. et al. Crediting agricultural soil carbon sequestration. Science 375, 1222–1225 (2022).

    CAS  Google Scholar 

  4. Bowles, T. M. et al. Long-term evidence shows that crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America. One Earth 2, 284–293 (2020).

    Google Scholar 

  5. Tamburini, G. et al. Agricultural diversification promotes multiple ecosystem services without compromising yield. Sci. Adv. 6, eaba1715 (2020).

    Google Scholar 

  6. Lehman, R. M., Osborne, S. L. & Duke, S. E. Diversified no-till crop rotation reduces nitrous oxide emissions, increases soybean yields, and promotes soil carbon accrual. Soil Sci. Soc. Am. J. 81, 76–83 (2017).

    Google Scholar 

  7. Yang, X. et al. Diversifying crop rotation increases food production, reduces net greenhouse gas emissions and improves soil health. Nat. Commun. 15, 198 (2024).

    CAS  Google Scholar 

  8. Luo, Z., Wang, E. & Sun, O. J. Soil carbon change and its responses to agricultural practices in Australian agro-ecosystems: a review and synthesis. Geoderma 155, 211–223 (2010).

    CAS  Google Scholar 

  9. McDaniel, M. D., Tiemann, L. K. & Grandy, A. S. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis. Ecol. Appl. 24, 560–570 (2014).

    CAS  Google Scholar 

  10. King, A. E. & Blesh, J. Crop rotations for increased soil carbon: perenniality as a guiding principle. Ecol. Appl. 28, 249–261 (2018).

    Google Scholar 

  11. U.S. Soil Enrichment Protocol Version 1.1 (Climate Action Reserve, 2022).

  12. Prairie, A. M., King, A. E. & Cotrufo, M. F. Restoring particulate and mineral-associated organic carbon through regenerative agriculture. Proc. Natl Acad. Sci. USA 120, e2217481120 (2023).

    CAS  Google Scholar 

  13. Rui, Y. et al. Persistent soil carbon enhanced in Mollisols by well-managed grasslands but not annual grain or dairy forage cropping systems. Proc. Natl Acad. Sci. USA 119, e2118931119 (2022).

    CAS  Google Scholar 

  14. Baldwin-Kordick, R. et al. Comprehensive impacts of diversified cropping on soil health and sustainability. Agroecol. Sustain. Food Syst. 46, 331–363 (2022).

    Google Scholar 

  15. Poffenbarger, H. J. et al. Whole-profile soil organic matter content, composition, and stability under cropping systems that differ in belowground inputs. Agric. Ecosyst. Environ. 291, 106810 (2020).

    CAS  Google Scholar 

  16. Balesdent, J. et al. Atmosphere–soil carbon transfer as a function of soil depth. Nature 559, 599–602 (2018).

    CAS  Google Scholar 

  17. Lazicki, P. A., Liebman, M. & Wander, M. M. Root parameters show how management alters resource distribution and soil quality in conventional and low-input cropping systems in central Iowa. PLoS ONE 11, e0164209 (2016).

    Google Scholar 

  18. Drinkwater, L. E., Wagoner, P. & Sarrantonio, M. Legume-based cropping systems have reduced carbon and nitrogen losses. Nature 396, 262–265 (1998).

    CAS  Google Scholar 

  19. Poeplau, C. & Don, A. Carbon sequestration in agricultural soils via cultivation of cover crops – a meta-analysis. Agric. Ecosyst. Environ. 200, 33–41 (2015).

    CAS  Google Scholar 

  20. Dijkstra, F. A., Zhu, B. & Cheng, W. Root effects on soil organic carbon: a double‐edged sword. New Phytol. 230, 60–65 (2021).

    CAS  Google Scholar 

  21. Ros, G. H., Hanegraaf, M. C., Hoffland, E. & van Riemsdijk, W. H. Predicting soil N mineralization: relevance of organic matter fractions and soil properties. Soil Biol. Biochem. 43, 1714–1722 (2011).

    CAS  Google Scholar 

  22. Smith, A., Snapp, S., Dimes, J., Gwenambira, C. & Chikowo, R. Doubled-up legume rotations improve soil fertility and maintain productivity under variable conditions in maize-based cropping systems in Malawi. Agric. Syst. 145, 139–149 (2016).

    Google Scholar 

  23. King, A. E. & Hofmockel, K. S. Diversified cropping systems support greater microbial cycling and retention of carbon and nitrogen. Agric. Ecosyst. Environ. 240, 66–76 (2017).

    Google Scholar 

  24. Osterholz, W. R., Liebman, M. & Castellano, M. J. Can soil nitrogen dynamics explain the yield benefit of crop diversification? Field Crops Res. 219, 33–42 (2018).

    Google Scholar 

  25. Janzen, H. H. The soil carbon dilemma: shall we hoard it or use it? Soil Biol. Biochem. 38, 419–424 (2006).

    CAS  Google Scholar 

  26. Paustian, K. et al. Quantifying carbon for agricultural soil management: from the current status toward a global soil information system. Carbon Manag. 10, 567–587 (2019).

    CAS  Google Scholar 

  27. Chandel, A. K., Jiang, L. & Luo, Y. Microbial models for simulating soil carbon dynamics: a review. J. Geophys. Res. Biogeosci. 128, e2023JG007436 (2023).

    CAS  Google Scholar 

  28. Le Noë, J. et al. Soil organic carbon models need independent time-series validation for reliable prediction. Commun. Earth Environ. 4, 158 (2023).

    Google Scholar 

  29. Ogle, S. M., Breidt, F. J., Easter, M., Williams, S. & Paustian, K. An empirically based approach for estimating uncertainty associated with modelling carbon sequestration in soils. Ecol. Modell. 205, 453–463 (2007).

    Google Scholar 

  30. Singh, P. & Benbi, D. K. Modeling soil organic carbon with DNDC and RothC models in different wheat-based cropping systems in north-western India. Commun. Soil Sci. Plant Anal. 51, 1184–1203 (2020).

    CAS  Google Scholar 

  31. Ehleringer, J. R., Nina, B. & Lawrence, B. F. Carbon isotope ratios in belowground carbon cycle processes. Ecol. Appl. 10, 412–422 (2000).

    Google Scholar 

  32. Farquhar, G. D., Ehleringer, J. R. & Hubick, K. T. Carbon isotope discrimination and photosynthesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 40, 503–537 (1989).

    CAS  Google Scholar 

  33. Camino-Serrano, M. et al. Including stable carbon isotopes to evaluate the dynamics of soil carbon in the land-surface model ORCHIDEE. J. Adv. Model. Earth Syst. 11, 3650–3669 (2019).

    Google Scholar 

  34. Gross, A. & Glaser, B. Meta-analysis on how manure application changes soil organic carbon storage. Sci. Rep. 11, 5516 (2021).

    CAS  Google Scholar 

  35. Keiluweit, M. et al. Mineral protection of soil carbon counteracted by root exudates. Nat. Clim. Change 5, 588–595 (2015).

    CAS  Google Scholar 

  36. Dietz, C. L., Jackson, R. D., Ruark, M. D. & Sanford, G. R. Soil carbon maintained by perennial grasslands over 30 years but lost in field crop systems in a temperate Mollisol. Commun. Earth Environ. 5, 360 (2024).

    Google Scholar 

  37. Stagnari, F., Maggio, A., Galieni, A. & Pisante, M. Multiple benefits of legumes for agriculture sustainability: an overview. Chem. Biol. Technol. Agric. 4, 2 (2017).

    Google Scholar 

  38. Thilakarathna, M. S., McElroy, M. S., Chapagain, T., Papadopoulos, Y. A. & Raizada, M. N. Belowground nitrogen transfer from legumes to non-legumes under managed herbaceous cropping systems. A review. Agron. Sustain. Dev. 36, 58 (2016).

    Google Scholar 

  39. Martin, T. & Sprunger, C. D. Belowground dynamics influence nitrogen cycling and crop productivity in diversified corn systems. Front. Sustain. Food Syst. 5, 705577 (2021).

  40. Hunt, N. D., Hill, J. D. & Liebman, M. Cropping system diversity effects on nutrient discharge, soil erosion, and agronomic performance. Environ. Sci. Technol. 53, 1344–1352 (2019).

    CAS  Google Scholar 

  41. Tomer, M. D. & Liebman, M. Nutrients in soil water under three rotational cropping systems, Iowa, USA. Agric. Ecosyst. Environ. 186, 105–114 (2014).

    CAS  Google Scholar 

  42. Noll, L., Zhang, S., Zheng, Q., Hu, Y. & Wanek, W. Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content. Soil Biol. Biochem. 133, 37–49 (2019).

    CAS  Google Scholar 

  43. Breza, L. C. et al. Complex crop rotations improve organic nitrogen cycling. Soil Biol. Biochem. 177, 108911 (2023).

    CAS  Google Scholar 

  44. Hunt, N. D., Liebman, M., Thakrar, S. K. & Hill, J. D. Fossil energy use, climate change impacts, and air quality-related human health damages of conventional and diversified cropping systems in Iowa, USA. Environ. Sci. Technol. 54, 11002–11014 (2020).

    CAS  Google Scholar 

  45. Hergoualc’h, K. et al. in 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories (eds Calvo Buendia, E. et al.) 11.1–11.48 (IPCC, 2019).

  46. Lawrence, N. C., Tenesaca, C. G., VanLoocke, A. & Hall, S. J. Nitrous oxide emissions from agricultural soils challenge climate sustainability in the US Corn Belt. Proc. Natl Acad. Sci. USA 118, e2112108118 (2021).

    CAS  Google Scholar 

  47. Mathers, C. et al. Validating DayCent-CR for cropland soil carbon offset reporting at a national scale. Geoderma 438, 116647 (2023).

    Google Scholar 

  48. Fry, B. (ed.) in Stable Isotope Ecology 40–75 (Springer, 2006).

  49. Liebman, M. et al. Agronomic and economic performance characteristics of conventional and low‐external‐input cropping systems in the central Corn Belt. Agron. J. 100, 600–610 (2008).

    Google Scholar 

  50. Hunt, N. D., Hill, J. D. & Liebman, M. Reducing freshwater toxicity while maintaining weed control, profits, and productivity: effects of increased crop rotation diversity and reduced herbicide usage. Environ. Sci. Technol. 51, 1707–1717 (2017).

    CAS  Google Scholar 

  51. von Haden, A. C., Yang, W. H. & DeLucia, E. H. Soils’ dirty little secret: depth‐based comparisons can be inadequate for quantifying changes in soil organic carbon and other mineral soil properties. Glob. Change Biol. 26, 3759–3770 (2020).

    Google Scholar 

  52. Fowler, A. F., Basso, B., Millar, N. & Brinton, W. F. A simple soil mass correction for a more accurate determination of soil carbon stock changes. Sci. Rep. 13, 2242 (2023).

    CAS  Google Scholar 

  53. Raffeld, A. M. et al. The importance of accounting method and sampling depth to estimate changes in soil carbon stocks. Carbon Balance Manag. 19, 2 (2024).

    Google Scholar 

  54. Crumpton, W. G., Isenhart, T. M. & Mitchell, P. D. Nitrate and organic N analyses with second-derivative spectroscopy. Limnol. Oceanogr. 37, 907–913 (1992).

    CAS  Google Scholar 

  55. Ye, C. & Hall, S. J. Mechanisms underlying limited soil carbon gains in perennial and cover-cropped bioenergy systems revealed by stable isotopes. Glob. Change Biol. Bioenergy 12, 101–117 (2020).

    CAS  Google Scholar 

  56. Cerling, T. E. et al. Global vegetation change through the Miocene/Pliocene boundary. Nature 389, 153–158 (1997).

    CAS  Google Scholar 

  57. Verberne, E. L. J., Hassink, J., de Willigen, P., Groot, J. J. R. & van Veen, J. A. Modelling organic matter dynamics in different soils. Neth. J. Agric. Sci. 38, 221–238 (1990).

    CAS  Google Scholar 

  58. Whitmore, A. P. et al. Simulating trends in soil organic carbon in long-term experiments using the Verbeme/MOTOR model. Geoderma 81, 137–151 (1997).

    Google Scholar 

  59. Yi, B. et al. Resolving the influence of lignin on soil organic matter decomposition with mechanistic models and continental-scale data. Glob. Change Biol. 29, 5968–5980 (2023).

    CAS  Google Scholar 

  60. Wang, G. et al. Soil moisture drives microbial controls on carbon decomposition in two subtropical forests. Soil Biol. Biochem. 130, 185–194 (2019).

    CAS  Google Scholar 

  61. Jian, S. et al. Multi-year incubation experiments boost confidence in model projections of long-term soil carbon dynamics. Nat. Commun. 11, 5864 (2020).

    CAS  Google Scholar 

  62. Sobol′, I. M. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates. Math. Comput. Simul. 55, 271–280 (2001).

    Google Scholar 

  63. Wang, G., Post, W. M. & Mayes, M. A. Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses. Ecol. Appl. 23, 255–272 (2013).

    Google Scholar 

  64. Xu, T., White, L., Hui, D. & Luo, Y. Probabilistic inversion of a terrestrial ecosystem model: analysis of uncertainty in parameter estimation and model prediction. Glob. Biogeochem. Cycles 20, GB2007 (2006).

    Google Scholar 

  65. Duan, Q., Sorooshian, S. & Gupta, V. Effective and efficient global optimization for conceptual rainfall-runoff models. Water Resour. Res. 28, 1015–1031 (1992).

    Google Scholar 

  66. Wang, G. et al. Microbial dormancy improves development and experimental validation of ecosystem model. ISME J. 9, 226–237 (2015).

    CAS  Google Scholar 

  67. Yi, B. et al. Carbon Decomposition and Nitrogen Mineralization in Marsden Agroecosystem Diversification Experiment, Iowa, 2021 (Environmental Data Initiative, 2024); https://doi.org/10.6073/pasta/7f1dac6bf350221c54d1eb349ca89bbf

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Acknowledgements

We thank C. Tenesaca and M. Leeford for laboratory assistance, and H. Yadav for nitrogen balance calculation. This research was supported in part by the Agricultural and Food Research Initiative Grant 2021-67019-33424 from the USDA National Institute of Food and Agriculture (S.J.H., C.L., S.A., A.V., M.L.). W.H. was partially supported by the intramural research program of the US Department of Agriculture, National Institute of Food and Agriculture, Hatch, IOW0 #3750, and 7000724.

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Author notes

  1. These authors contributed equally: Bo Yi, Wenjuan Huang.

Authors and Affiliations

  1. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA

    Bo Yi, Wenjuan Huang, Chaoqun Lu & Steven J. Hall

  2. Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Wenjuan Huang & Yiqi Luo

  3. Department of Agronomy, Iowa State University, Ames, IA, USA

    Matt Liebman, Matthew Woods, Marshall D. McDaniel, Andy VanLoocke, Sotirios Archontoulis & Bryan Petersen

  4. Institute for Environmental Genomics and School of Biological Sciences, University of Oklahoma, Norman, OK, USA

    Siyang Jian

  5. Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA

    Hanna J. Poffenbarger

  6. State Key Laboratory of Water Resources Engineering and Management, and Institute for Water-Carbon Cycles and Carbon Neutrality, Wuhan University, Wuhan, China

    Gangsheng Wang

  7. Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA

    Steven J. Hall

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Contributions

S.J.H. conceived this study. M.L. initiated and maintained the field experiment. W.H. and S.J.H. conducted the experimental work. B.Y. and W.H. conducted the modelling simulation and analysed the data with S.J.H. M.W. collected soil samples. W.H., B.Y. and S.J.H. wrote the manuscript. M.L., M.W., M.D.M., C.L., A.V., S.A., B.P., S.J., H.J.P., G.W. and Y. L. provided suggestions for substantial revisions.

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Correspondence to Wenjuan Huang.

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Supplementary Methods, Results, Tables 1–14, Figs. 1–19 and References.

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Statistical source data for Fig. 1 in the ‘Fig.1’ sheet. Statistical source data for Fig. 2 in the ‘Fig.2’ sheet. Statistical source data for Fig. 3 in the ‘Fig.3’ sheet. Statistical source data for Fig. 4 in the ‘Fig.4’ sheet.

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Yi, B., Huang, W., Liebman, M. et al. Diversified cropping systems with limited carbon accrual but increased nitrogen supply. Nat Sustain 8, 152–161 (2025). https://doi.org/10.1038/s41893-024-01495-4

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