Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011).
Foley, J. A. et al. Solutions for a cultivated planet. Nature 478, 337–342 (2011).
Oliveira, E. M. et al. Effects of conventional, organic and conservation agriculture on soil physical properties, root growth and microbial habitats in a long-term field experiment. Geoderma 447, 116927 (2024).
Global Assessment Report of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Debating Nature’s Value (IPBES, 2019).
Gomiero, T., Pimentel, D. & Paoletti, M. G. Environmental impact of different agricultural management practices: conventional vs. organic agriculture. CRC Crit. Rev. Plant Sci. 30, 95–124 (2011).
Tuck, S. L. et al. Land-use intensity and the effects of organic farming on biodiversity: a hierarchical meta-analysis. J. Appl. Ecol. 51, 746–755 (2014).
Reganold, J. P. & Wachter, J. M. Organic agriculture in the twenty-first century. Nat. Plants 2, 15221 (2016).
Status of the World’s Soil Resources (Food and Agriculture Organization, 2015).
Smith, P. et al. Global change pressures on soils from land use and management. Glob. Change Biol. 22, 1008–1028 (2016).
Pretty, J. et al. Global assessment of agricultural system redesign for sustainable intensification. Nat. Sustain. 1, 441–446 (2018).
Qiao, L. et al. Soil quality both increases crop production and improves resilience to climate change. Nat. Clim. Change 12, 574–580 (2022).
Toda, M., Walder, F. & van der Heijden, M. G. A. Organic management and soil health promote nutrient use efficiency. J. Sustain. Agric. Environ. 2, 215–224 (2023).
Krause, H. M. et al. Organic cropping systems balance environmental impacts and agricultural production. Sci. Rep. 14, 25537 (2024).
Farm to Fork Strategy (EU Commission, 2020).
de la Cruz, V. Y. V., Tantriani, Cheng, W. & Tawaraya, K. Yield gap between organic and conventional farming systems across climate types and sub-types: a meta-analysis. Agric. Syst. 211, 103732 (2023).
Seufert, V., Ramankutty, N. & Foley, J. A. Comparing the yields of organic and conventional agriculture. Nature 485, 229–232 (2012).
Ponisio, L. C. et al. Diversification practices reduce organic to conventional yield gap. Proc. R. Soc. B 282, 20141396 (2015).
Muller, A. et al. Strategies for feeding the world more sustainably with organic agriculture. Nat. Commun. 8, 1290 (2017).
Godfray, H. C. J. et al. Food security: the challenge of feeding 9 billion people. Science 327, 812–818 (2010).
Barbieri, P. et al. Global option space for organic agriculture is delimited by nitrogen availability. Nat. Food 2, 363–372 (2021).
Gong, S. et al. Biodiversity and yield trade-offs for organic farming. Ecol. Lett. 25, 1699–1710 (2022).
Barral, M. P., Rey Benayas, J. M., Meli, P. & Maceira, N. O. Quantifying the impacts of ecological restoration on biodiversity and ecosystem services in agroecosystems: a global meta-analysis. Agric. Ecosyst. Environ. 202, 223–231 (2015).
Jiao, S., Lu, Y. & Wei, G. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. Glob. Change Biol. 28, 140–153 (2022).
Ostandie, N. et al. Multi-community effects of organic and conventional farming practices in vineyards. Sci. Rep. 11, 11979 (2021).
Tiwari, S., Singh, C. & Singh, J. S. Land use changes: a key ecological driver regulating methanotrophs abundance in upland soils. Energy Ecol. Environ. 3, 355–371 (2018).
Anthony, M. A., Bender, S. F. & van der Heijden, M. G. A. Enumerating soil biodiversity. Proc. Natl Acad. Sci. USA 120, e2304663120 (2023).
Kremen, C. & Miles, A. Ecosystem services in biologically diversified versus conventional farming systems: benefits, externalities, and trade-offs. Ecol. Soc. http://www.jstor.org/stable/26269237 (2012).
Rehberger, E., West, P. C., Spillane, C. & McKeown, P. C. What climate and environmental benefits of regenerative agriculture practices? An evidence review. Environ. Res. Commun. 5, 052001 (2023).
Wittwer, R. A. et al. Organic and conservation agriculture promote ecosystem multifunctionality. Sci. Adv. 7, eabg6995 (2021).
Knapp, S. & van der Heijden, M. G. A. A global meta-analysis of yield stability in organic and conservation agriculture. Nat. Commun. 9, 3632 (2018).
Allan, E. et al. Interannual variation in land-use intensity enhances grassland multidiversity. Proc. Natl Acad. Sci. USA 111, 308–313 (2014).
Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).
de Graaff, M. A., Hornslein, N., Throop, H. L., Kardol, P. & van Diepen, L. T. A. in Advances in Agronomy 1–44 (Elsevier, 2019).
Armas, C., Ordiales, R. & Pugnaire, F. I. Measuring plant interactions: a new comparative index. Ecology 85, 2682–2686 (2004).
Lal, R. Restoring soil quality to mitigate soil degradation. Sustainability 7, 5875–5895 (2015).
George, P. B. L. et al. Evaluation of mesofauna communities as soil quality indicators in a national-level monitoring programme. Soil Biol. Biochem. 115, 537–546 (2017).
Lopezosa, P., Soliveres, S., Serra, L., Constán-Nava, S. & Berdugo, M. Land use determines Mediterranean ecosystems’ multifunctionality more than plant richness or habitat composition. J. Appl. Ecol. https://doi.org/10.1111/1365-2664.14568 (2024).
Schall, P. et al. Can multi-taxa diversity in European beech forest landscapes be increased by combining different management systems? J. Appl. Ecol. 57, 1363–1375 (2020).
Neyret, M. et al. Landscape management strategies for multifunctionality and social equity. Nat. Sustain. 6, 391–403 (2023).
Clark, M. & Tilman, D. Comparative analysis of environmental impacts of agricultural production systems, agricultural input efficiency, and food choice. Environ. Res. Lett. 12, 064016 (2017).
Krajewski, S., Žukovskis, J., Gozdowski, D., Cieśliński, M. & Wójcik-Gront, E. Evaluating the path to the European Commission’s organic agriculture goal: a multivariate analysis of changes in EU countries (2004–2021) and socio-economic relationships. Agriculture 14, 064016 (2024).
The World of Organic Agriculture: Statistics and Emerging Trends 2022 (FiBL and IFOAM – Organics International, 2022).
Sapbamrer, R. & Thammachai, A. A systematic review of factors influencing farmers’ adoption of organic farming. Sustainability 13, 3842 (2021).
van der Esch, S. et al. Exploring Future Changes in Land Use and Land Condition and the Impacts on Food, Water, Climate Change and Biodiversity (PBL Netherlands Environmental Assessment Agency, 2017).
Delgado-Baquerizo, M. et al. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. Ecol. Lett. 20, 1295–1305 (2017).
de Vries, F. T. & Shade, A. Controls on soil microbial community stability under climate change. Front. Microbiol. 4, 265 (2013).
Gomiero, T. Soil degradation, land scarcity and food security: reviewing a complex challenge. Sustainability 8, 281 (2016).
GarcÃa-Velázquez, L. et al. Dataset from: Optimizing biodiversity, multifunctionality and yield when transitioning to organic farming. figshare https://doi.org/10.6084/m9.figshare.27302391 (2026).
Bligh, E. G. & Dyer, W. J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).
Ellis, S. & Ritz, K. A modified high-throughput analysis of PLFAs in soil. MethodsX 5, 1491–1497 (2018).
Oostenbrink, M. in Nematology (eds Sasser, J. N. & Jenkins, W. R.) 85–102 (Univ. North Carolina Press, 1960).
Yeates, G. W., Bongers, T., De Goede, R. G. M., Freckman, D. W. & Georgieva, S. S. Feeding habits in soil nematode families and genera—an outline for soil ecologists. J. Nematol. 25, 315–331 (1993).
Macfadyen, A. Improved funnel-type extractors for soil arthropods. J. Anim. Ecol. 30, 171–184 (1961).
Longepierre, M. et al. Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management. ISME Commun. 1, 44 (2021).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. https://doi.org/10.14806/ej.17.1.200 (2011).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Bengtsson-Palme, J. et al. metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol. Ecol. Resour. 15, 1403–1414 (2015).
Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).
Gamfeldt, L., Hillebrand, H. & Jonsson, P. R. Multiple functions increase the importance of biodiversity for overall ecosystem functioning. Ecology 89, 1223–1231 (2008).
Maestre, F. T. et al. Plant species richness and ecosystem multifunctionality in global drylands. Science 335, 214–218 (2012).
Henry, S. et al. Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J. Microbiol. Methods 59, 327–335 (2004).
Throbäck, I. N., Enwall, K., Jarvis, Å & Hallin, S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49, 401–417 (2004).
Domeignoz-Horta, L. A. et al. Peaks of in situ N2O emissions are influenced by N2O-producing and reducing microbial communities across arable soils. Glob. Change Biol. 24, 360–370 (2018).
Harris, D., Horwáth, W. R. & van Kessel, C. Acid fumigation of soils to remove carbonates prior to total organic carbon or CARBON-13 isotopic analysis. Soil Sci. Soc. Am. J. 65, 1853–1856 (2001).
Schimel, J. P. & Bennet, J. Nitrogen mineralization: challenges of a changing paradigm. Ecology 85, 591–602 (2004).
Sollins, P., Paul, E. A., Heil, J. W. & Elliott, E. T. in Standard Soil Methods for Long-term Ecological Research (eds Robertson, G. P. et al.) 89–106 (Oxford Univ. Press, 1991).
Ochoa Esteban, V. Soil N transformation rates protocol. Zenodo https://doi.org/10.5281/zenodo.10354902 (2023).
Olsen, S., Cole, C., Watanabe, F. & Dean, L. Estimation of Available Phosphorus in Soils by Extraction with Sodium Bicarbonate USDA Circular No. 939 (US Government Printing Office, 1954).
Fernández, J. A., Niell, F. X. & Lucena, J. A rapid and sensitive automated determination of phosphate in natural waters. Limnol. Oceanogr. 30, 227–230 (1985).
Dick, R. P. et al. Cross-laboratory comparison of fluorimetric microplate and colorimetric bench-scale soil enzyme assays. Soil Biol. Biochem. 121, 240–248 (2018).
Keuskamp, J. A., Dingemans, B. J. J., Lehtinen, T., Sarneel, J. M. & Hefting, M. M. Tea Bag Index: a novel approach to collect uniform decomposition data across ecosystems. Methods Ecol. Evol. 4, 1070–1075 (2013).
Tongway, D. & Hindley, N. Landscape Function Analysis Manual : Procedures for Monitoring and Assessing Landscapes with Special Reference to Minesites and Rangelands (CSIRO, 2004); http://hdl.handle.net/102.100.100/186491?index=1
Robertson, G. P., Coleman, D. C., Bledsoe, C. S. & Sollins, P. (eds) Standard Soil Methods for Long-Term Ecological Research (Oxford Univ. Press, 1999).
Mills, A., Fey, M., Donaldson, J., Todd, S. & Theron, L. Soil infiltrability as a driver of plant cover and species richness in the semi-arid Karoo, South Africa. Plant Soil 320, 321–332 (2009).
Wang, L., Xin, J., Nai, H. & Zheng, X. Effects of different fertilizer applications on nitrogen leaching losses and the response in soil microbial community structure. Environ. Technol. Innov. 23, 101608 (2021).
Johnson, D., Schmidt, K., Scholz, C. & Chowdhury, L. Valuation of soil-mediated contributions to people (SmCPs) – a systematic review of values and methods. Ecosyst. People 20, 2401945 (2024).
Allan, E. et al. Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition. Ecol. Lett. 18, 834–843 (2015).
Sánchez-Cueto, P. et al. Impacts of climate, organic management, and degradation status on soil biodiversity in agroecosystems worldwide. Glob. Change Biol. 31, e70486 (2025).
Oksanen, A. J. et al. Package ‘vegan’. Community ecology package. CRAN https://cran.r-project.org/web/packages/vegan/vegan.pdf (2020).
Wickham, H. Reshaping data with the reshape package. J. Stat. Softw. 21, 1–20 (2007).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020); https://www.r-project.org/