Hartmann, M. & Six, J. Soil structure and microbiome functions in agroecosystems. Nat. Rev. Microbiol. 4, 4–18 (2023).
Schmidt, M. W. I. et al. Persistence of soil organic matter as an ecosystem property. Nature 478, 49–56 (2011).
Gaba, S., Fried, G., Kazakou, E., Chauvel, B. & Navas, M. L. Agroecological weed control using a functional approach: a review of cropping systems diversity. Agron. Sustain. Dev. 34, 103–119 (2014).
Tscharntke, T. et al. Global food security, biodiversity conservation and the future of agricultural intensification. Biol. Conserv. 151, 53–59 (2012).
Zhou, L. & Wang, S. The bright side of ecological stressors. Trends Ecol. Evol. 38, 568–578 (2023).
Cordero, I., Leizeaga, A., Hicks, L. C., Rousk, J. & Bardgett, R. D. High intensity perturbations induce an abrupt shift in soil microbial state. ISME J. 17, 2190–2199 (2023).
Canarini, A. et al. Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community. Nat. Commun. 12, 5308 (2021).
Wilson, S. L., Frazer, C., Cumming, B. F., Nuin, P. A. & Walker, V. K. Cross-tolerance between osmotic and freeze–thaw stress in microbial assemblages from temperate lakes. FEMS Microbiol. Ecol. 82, 405–415 (2012).
Kreyling, J. et al. Geographic origin and past climatic experience influence the response to late spring frost in four common grass species in central Europe. Ecography 35, 268–275 (2012).
Pushpavalli, R. et al. Cross-tolerance for drought, heat and salinity stresses in chickpea (Cicer arietinum L.). J. Agron. Crop Sci. 206, 405–419 (2020).
Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).
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).
Knight, C. G. et al. Soil microbiomes show consistent and predictable responses to extreme events. Nature 636, 690–696 (2024).
Cairns, J., Hogle, S., Alitupa, E., Mustonen, V. & Hiltunen, T. Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities. Nat. Ecol. Evol. 9, 395–405 (2025).
Cui, H. et al. Pre-existing global change legacies regulate the responses of multifunctionality to warming. Appl. Soil Ecol. 204, 105679 (2024).
Jansson, J. K., McClure, R. & Egbert, R. G. Soil microbiome engineering for sustainability in a changing environment. Nat. Biotechnol. 41, 1716–1728 (2023).
Tan, Y. S., Zhang, R. K., Liu, Z. H., Li, B. Z. & Yuan, Y. J. Microbial adaptation to enhance stress tolerance. Front. Microbiol. 13, 888746 (2022).
Malik, A. A. et al. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J. 14, 1–9 (2020).
Piton, G. et al. Life history strategies of soil bacterial communities across global terrestrial biomes. Nat. Microbiol. 8, 2093–2102 (2023).
Peng, Z. et al. Trait-based life history strategies shape bacterial niche breadth. Adv. Sci. 12, 2405947 (2025).
Pacifici, M. et al. Species’ traits influenced their response to recent climate change. Nat. Clim. Change 7, 205–208 (2017).
Ranheim Sveen, T., Hannula, S. E. & Bahram, M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol. 32, 68–78 (2024).
Rillig, M. C., Rolff, J., Tietjen, B., Wehner, J. & Andrade-Linares, D. R. Community priming–effects of sequential stressors on microbial assemblages. FEMS Microbiol. Ecol. 91, fiv040 (2015).
Jiao, S. et al. Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems. Glob. Change Biol. 28, 6653–6664 (2022).
Orwin, K. H. et al. Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions. Funct. Ecol. 30, 1430–1439 (2015).
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).
Xu, Q. et al. Nitrogen enrichment alters multiple dimensions of grassland functional stability via changing compositional stability. Ecol. Lett. 25, 2713–2725 (2022).
Loreau, M. & de Mazancourt, C. Biodiversity and ecosystem stability: a synthesis of underlying mechanisms. Ecol. Lett. 16, 106–115 (2013).
Chen, Q. et al. Multidimensional responses of grassland stability to eutrophication. Nat. Commun. 14, 6375 (2023).
Allsup, C. M., George, I. & Lankau, R. A. Shifting microbial communities can enhance tree tolerance to changing climates. Science 380, 835–840 (2023).
Silverstein, M. R., Segrè, D. & Bhatnagar, J. M. Environmental microbiome engineering for the mitigation of climate change. Global Change Biol. 29, 2050–2066 (2023).
Schmitz, L. et al. Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome. ISME J. 16, 1907–1920 (2022).
Liu, C. et al. Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils. Nat. Food 4, 912–924 (2023).
Xing, Y. et al. Multi-omics reveals the sugarcane rhizosphere soil metabolism-microbiota interactions affected by drought stress. Appl. Soil Ecol. 190, 104994 (2023).
Faist, H. et al. Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation. Environ. Microbiome 18, 18 (2023).
Wu, X. et al. Genome-resolved metagenomics reveals distinct phosphorus acquisition strategies between soil microbiomes. mSystems 7, e01107-21 (2022).
Figueroa-Martinez, F., Nedelcu, A. M., Smith, D. R. & Adrian, R. P. When the lights go out: the evolutionary fate of free-living colorless green algae. New Phytol. 206, 972–982 (2015).
Liu, J. et al. Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils. Environ. Int. 183, 108429 (2024).
Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 00417 (2012).
Laine, A. L. & Leino, S. Plant microbiomes feel the heat. Science 388, 1150–1152 (2025).
Propster, J. R. et al. Distinct growth responses of tundra soil bacteria to short-term and long-term warming. Appl. Environ. Microbiol. 89, e0154322 (2023).
Poppeliers, S. W. M., Sanchez-Gil, J. J. & de Jonge, R. Microbes to support plant health: understanding bioinoculant success in complex conditions. Curr. Opin. Microbiol. 73, 102286 (2023).
Bradford, M. A. et al. Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation. Nat. Ecol. Evol. 3, 223–231 (2019).
Rowell, D. L. Soil Science: Methods & Applications (Routledge, 1994).
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Maestre, F. T. et al. Plant species richness and ecosystem multifunctionality in global drylands. Science 335, 214–218 (2012).
Byrnes, J. E. K. et al. Investigating the relationship between biodiversity and ecosystem multifunctionality: challenges and solutions. Methods Ecol. Evol. 5, 111–124 (2014).
Manning, P. et al. Redefining ecosystem multifunctionality. Nat. Ecol. Evol. 2, 427–436 (2018).
Orwin, K. H. & Wardle, D. A. New indices for quantifying the resistance and resilience of soil biota to exogenous disturbances. Soil Biol. Biochem. 36, 1907–1912 (2004).
Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).
Zhou, G. et al. Resistance of ecosystem services to global change weakened by increasing number of environmental stressors. Nat. Geosci. 17, 882–888 (2024).
Domeignoz-Horta, L. A. et al. Microbial diversity drives carbon use efficiency in a model soil. Nat. Commun. 11, 3684 (2020).
Jiao, S. et al. Core microbiota in agricultural soils and their potential associations with nutrient cycling. mSystems 4, e00313-18 (2019).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Bates, D., Mächler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
Lenth, R. V. emmeans: estimated marginal means, aka least-squares means (Comprehensive R Archive Network, 2024).
Westfall, P. Simultaneous inference in general parametric models. Biom. J. 50, 346–363 (2008).
Archer, E. rfPermute: estimate permutation p-values for random forest importance metrics (Comprehensive R Archive Network, 2023).
Lefcheck, J. S. & Freckleton, R. piecewiseSEM: piecewise structural equation modelling in R for ecology, evolution, and systematics. Methods Ecol. Evol. 7, 573–579 (2015).
Pan, H. et al. Source data and R code from “Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems”. figshare https://doi.org/10.6084/m9.figshare.31451086 (2026).