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).
Google Scholar
Qiao, L. et al. Soil quality both increases crop production and improves resilience to climate change. Nat. Clim. Change 12, 574–580 (2022).
Google Scholar
Bünemann, E. K. et al. Soil quality—a critical review. Soil Biol. Biochem. 120, 105–125 (2018).
Google Scholar
Banerjee, S. & van der Heijden, M. G. A. Soil microbiomes and one health. Nat. Rev. Microbiol. 21, 6–20 (2023).
Google Scholar
Rawls, W. J., Pachepsky, Y. A., Ritchie, J. C., Sobecki, T. M. & Bloodworth, H. Effect of soil organic carbon on soil water retention. Geoderma 116, 61–76 (2003).
Google Scholar
Maron, J. L., Marler, M., Klironomos, J. N. & Cleveland, C. C. Soil fungal pathogens and the relationship between plant diversity and productivity. Ecol. Lett. 14, 36–41 (2011).
Google Scholar
Tilak, K. V. B. R. et al. Diversity of plant growth and soil health supporting bacteria. Curr. Sci. 89, 136–150 (2005).
Google Scholar
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).
Shah, A. N. et al. Soil compaction effects on soil health and crop productivity: an overview. Environ. Sci. Pollut. Res. 24, 10056–10067 (2017).
Google Scholar
Kibblewhite, M. G., Ritz, K. & Swift, M. J. Soil health in agricultural systems. Philos. Trans. R. Soc. B 363, 685–701 (2008).
Google Scholar
Panagos, P. et al. Soil priorities in the European Union. Geoderma Reg. 29, e00510 (2022).
Google Scholar
Rinot, O., Levy, G. J., Steinberger, Y., Svoray, T. & Eshel, G. Soil health assessment: a critical review of current methodologies and a proposed new approach. Sci. Total Environ. 648, 1484–1491 (2019).
Google Scholar
Fernández-Martínez, M. et al. Nutrient availability as the key regulator of global forest carbon balance. Nat. Clim. Change 4, 471–476 (2014).
Google Scholar
Krishna, M. P. & Mohan, M. Litter decomposition in forest ecosystems: a review. Energy Ecol. Environ. 2, 236–249 (2017).
Google Scholar
Wang, J. et al. Vegetation type controls root turnover in global grasslands. Glob. Ecol. Biogeogr. 28, 442–455 (2019).
Google Scholar
Gill, R. A. & Jackson, R. B. Global patterns of root turnover for terrestrial ecosystems. New Phytol. 147, 13–31 (2000).
Google Scholar
Labouyrie, M. et al. Patterns in soil microbial diversity across Europe. Nat. Commun. 14, 3311 (2023).
Google Scholar
Kindler, R. et al. Dissolved carbon leaching from soil is a crucial component of the net ecosystem carbon balance. Glob. Change Biol. 17, 1167–1185 (2011).
Google Scholar
Nouri, A., Lukas, S., Singh, S., Singh, S. & Machado, S. When do cover crops reduce nitrate leaching? A global meta-analysis. Glob. Change Biol. 28, 4736–4749 (2022).
Google Scholar
Bauer, J. T., Kleczewski, N. M., Bever, J. D., Clay, K. & Reynolds, H. L. Nitrogen-fixing bacteria, arbuscular mycorrhizal fungi and the productivity and structure of prairie grassland communities. Oecologia 170, 1089–1098 (2012).
Google Scholar
van der Heijden, M. G. A., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present and the future. New Phytol. 205, 1406–1423 (2015).
Google Scholar
Gujre, N., Soni, A., Rangan, L., Tsang, D. C. W. & Mitra, S. Sustainable improvement of soil health utilizing biochar and arbuscular mycorrhizal fungi: a review. Environ. Pollut. 268, 115549 (2021).
Google Scholar
Liang, Y., Pan, F., He, X., Chen, X. & Su, Y. Effect of vegetation types on soil arbuscular mycorrhizal fungi and nitrogen-fixing bacterial communities in a karst region. Environ. Sci. Pollut. Res. 23, 18482–18491 (2016).
Google Scholar
Guerra, C. A. et al. Tracking, targeting and conserving soil biodiversity. Science 371, 239–241 (2021).
Google Scholar
Heintz-Buschart, A. et al. Microbial diversity–ecosystem function relationships across environmental gradients. Res. Ideas Outcomes 6, e52217 (2020).
Google Scholar
Couto, W. in Handbook of Agricultural Productivity (ed. Rechcigl, M.) 71–84 (CRC Press, 2018).
Banerjee, S. et al. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol. Biochem. 97, 188–198 (2016).
Google Scholar
Kielak, A. M., Cipriano, M. A. P. & Kuramae, E. E. Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Arch. Microbiol. 198, 987–993 (2016).
Google Scholar
Sikorski, J. et al. The evolution of ecological diversity in Acidobacteria. Front. Microbiol. 13, 78 (2022).
Google Scholar
Fan, K. et al. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME J. 15, 550–561 (2021).
Google Scholar
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Google Scholar
Hashmi, I., Bindschedler, S. & Junier, P. in Beneficial Microbes in Agro-Ecology (eds Amaresan, N. et al.) 363–396 (Academic Press, 2020); https://doi.org/10.1016/B978-0-12-823414-3.00018-6
van de Vossenberg, B. T. L. H., Prodhomme, C., Vossen, J. H. & van der Lee, T. A. J. Synchytrium endobioticum, the potato wart disease pathogen. Mol. Plant Pathol. 23, 461–474 (2022).
Google Scholar
Yang, Y., Tilman, D., Furey, G. & Lehman, C. Soil carbon sequestration accelerated by restoration of grassland biodiversity. Nat. Commun. 10, 718 (2019).
Google Scholar
Lange, M. et al. Plant diversity increases soil microbial activity and soil carbon storage. Nat. Commun. 6, 6707 (2015).
Google Scholar
Xu, S. et al. Species richness promotes ecosystem carbon storage: evidence from biodiversity–ecosystem functioning experiments. Proc. R. Soc. B 287, 20202063 (2020).
Google Scholar
Osburn, E. D., Yang, G., Rillig, M. C. & Strickland, M. S. Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress. ISME Commun. 3, 66 (2023).
Google Scholar
Anthony, M. A. et al. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. ISME J. 16, 1327–1336 (2022).
Google Scholar
Krause, A. et al. Quantifying the impacts of land cover change on gross primary productivity globally. Sci. Rep. 12, 18398 (2022).
Google Scholar
Collalti, A. et al. Forest production efficiency increases with growth temperature. Nat. Commun. 11, 5322 (2020).
Google Scholar
Morin, X. et al. Long-term response of forest productivity to climate change is mostly driven by change in tree species composition. Sci. Rep. 8, 5627 (2018).
Google Scholar
Walder, F. et al. Synergism between production and soil health through crop diversification, organic amendments and crop protection in wheat-based systems. J. Appl. Ecol. 60, 2091–2104 (2023).
Google Scholar
Delgado-Baquerizo, M. et al. Microbial richness and composition independently drive soil multifunctionality. Funct. Ecol. 31, 2330–2343 (2017).
Google Scholar
Sünnemann, M. et al. Climate change and cropland management compromise soil integrity and multifunctionality. Commun. Earth Environ. 4, 394 (2023).
Google Scholar
Wagg, C., Jansa, J., Stadler, M., Schmid, B. & van der Heijden, M. G. A. Mycorrhizal fungal identity and diversity relaxes plant–plant competition. Ecology 92, 1303–1313 (2011).
Google Scholar
van der Heijden, M. G. A. et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396, 69–72 (1998).
Google Scholar
Lutz, S. et al. Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat. Microbiol. 8, 2277–2289 (2023).
Google Scholar
Orgiazzi, A., Ballabio, C., Panagos, P., Jones, A. & Fernández-Ugalde, O. LUCAS Soil, the largest expandable soil dataset for Europe: a review. Eur. J. Soil Sci. 69, 140–153 (2018).
Google Scholar
Orgiazzi, A. et al. LUCAS Soil Biodiversity and LUCAS Soil Pesticides, new tools for research and policy development. Eur. J. Soil Sci. 73, e13299 (2022).
Google Scholar
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108, 4516–4522 (2011).
Google Scholar
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).
Google Scholar
Tedersoo, L. & Anslan, S. Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences. Environ. Microbiol Rep. 11, 659–668 (2019).
Google Scholar
Özkurt, E. et al. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome 10, 176 (2022).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Google Scholar
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Google Scholar
Pertea, G. fqtrim: v0. 9.4 release. Zenodo https://doi.org/10.5281/zenodo.20552 (2015).
Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642 (2014).
Google Scholar
Tedersoo, L. et al. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Divers. 111, 573–588 (2021).
Google Scholar
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 421 (2009).
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).
Google Scholar
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).
Google Scholar
Põlme, S. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).
Google Scholar
Liu, S. et al. Phylotype diversity within soil fungal functional groups drives ecosystem stability. Nat. Ecol. Evol. 6, 900–909 (2022).
Google Scholar
Ballabio, C. et al. Mapping LUCAS topsoil chemical properties at European scale using Gaussian process regression. Geoderma 355, 113912 (2019).
Google Scholar
Smith, L. C. et al. Large‐scale drivers of relationships between soil microbial properties and organic carbon across Europe. Glob. Ecol. Biogeogr. 30, 2070–2083 (2021).
Google Scholar
Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).
Google Scholar
Fan, K. et al. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat. Ecol. Evol. 7, 113–126 (2023).
Google Scholar
Running, S. W., Nemani, R., Glassy, J. M. & Thornton, P. E. MODIS daily photosynthesis (PSN) and annual net primary production (NPP) product (MOD17). Algorithm Theoretical Basis Document (Univ. Montana,1999); www.umt.edu/numerical-terradynamic-simulation-group/files/modis/atbd_mod17_v21.pdf
Ballabio, C., Panagos, P. & Monatanarella, L. Mapping topsoil physical properties at European scale using the LUCAS database. Geoderma 261, 110–123 (2016).
Google Scholar
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Google Scholar
Rillig, M. C. et al. Increasing the number of stressors reduces soil ecosystem services worldwide. Nat. Clim. Change 13, 478–483 (2023).
Google Scholar
Cutler, D. R. et al. Random forests for classification in ecology. Ecology 88, 2783–2792 (2007).
Google Scholar
Eisenhauer, N., Bowker, M. A., Grace, J. B. & Powell, J. R. From patterns to causal understanding: structural equation modeling (SEM) in soil ecology. Pedobiologia 58, 65–72 (2015).
Google Scholar
Wei, T. & Simko, V. corrplot: Visualization of a correlation matrix. R package version 0.84. GitHub https://github.com/taiyun/corrplot (2017).
Archer, E. rfPermute: estimate permutation p-values for random forest importance metrics. R package version 1. CRAN http://CRAN.R-project.org/package=rfPermute (2016).
Lefcheck, J., Byrnes, J. & Grace, J. piecewiseSEM: piecewise structural equation modeling. R package version 2.1.2. CRAN https://cloud.r-project.org/web/packages/piecewiseSEM/piecewiseSEM.pdf (2020).
Romero, F. Soil health is associated with higher primary productivity across Europe. figshare https://doi.org/10.6084/m9.figshare.26272657.v1 (2024).