Vieira, D. et al. Pesticides Residues in European Agricultural Soils – Results from LUCAS 2018 Soil Module (European Union, 2023).
Riedo, J. et al. Concerted evaluation of pesticides in soils of extensive grassland sites and organic and conventional vegetable fields facilitates the identification of major input processes. Environ. Sci. Technol. 56, 13686–13695 (2022).
Liu, Y.-R. et al. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat. Commun. 14, 1706 (2023).
Wang, C.-N. et al. Effects of pesticide residues on bacterial community diversity and structure in typical greenhouse soils with increasing cultivation years in Northern China. Sci. Total Environ. 710, 136321 (2020).
Panico, S. C. et al. Field mixtures of currently used pesticides in agricultural soil pose a risk to soil invertebrates. Environ. Pollut. 305, 119290 (2022).
Edlinger, A. et al. Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts. Nat. Ecol. Evol. 6, 1145–1154 (2022).
Walder, F. et al. Soil microbiome signatures are associated with pesticide residues in arable landscapes. Soil Biol. Biochem. 174, 108830 (2022).
El Mujtar, V., Muñoz, N., Mc Cormick, B. P., Pulleman, M. & Tittonell, P. Role and management of soil biodiversity for food security and nutrition; where do we stand?. Glob. Food Secur. 20, 132–144 (2019).
Anthony, M. A., Bender, S. F. & van der Heijden, M. G. Enumerating soil biodiversity. Proc. Natl Acad. Sci. USA 120, e2304663120 (2023).
Tang, F. H. & Maggi, F. Pesticide mixtures in soil: a global outlook. Environ. Res. Lett. 16, 044051 (2021).
Wauchope, R. D. et al. Pesticide soil sorption parameters: theory, measurement, uses, limitations and reliability. Pest Manag. Sci. 58, 419–445 (2002).
Hallmann, C. A., Foppen, R. P., Van Turnhout, C. A., De Kroon, H. & Jongejans, E. Declines in insectivorous birds are associated with high neonicotinoid concentrations. Nature 511, 341–343 (2014).
Rigal, S. et al. Farmland practices are driving bird population decline across Europe. Proc. Natl Acad. Sci. USA 120, e2216573120 (2023).
Nicholson, C. C. et al. Pesticide use negatively affects bumble bees across European landscapes. Nature 628, 355–358 (2024).
Rundlöf, M. et al. Seed coating with a neonicotinoid insecticide negatively affects wild bees. Nature 521, 77–80 (2015).
Henry, M. et al. A common pesticide decreases foraging success and survival in honey bees. Science 336, 348–350 (2012).
Hallmann, C. A. et al. More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLoS ONE 12, e0185809 (2017).
Brühl, C. A. et al. Direct pesticide exposure of insects in nature conservation areas in Germany. Sci. Rep. 11, 24144 (2021).
Maggi, F., Tang, F. H. & Tubiello, F. N. Agricultural pesticide land budget and river discharge to oceans. Nature 620, 1013–1017 (2023).
Zheng, X. et al. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. ISME J. 16, 1397–1408 (2022).
Beaumelle, L. et al. Pesticide effects on soil fauna communities—a meta-analysis. J. Appl. Ecol. 60, 1239–1253 (2023).
Pelosi, C., Barot, S., Capowiez, Y., Hedde, M. & Vandenbulcke, F. Pesticides and earthworms. Agron. Sustain. Dev. 34, 199–228 (2014).
Riedo, J. et al. Widespread occurrence of pesticides in organically managed agricultural soils—the ghost of a conventional agricultural past?. Environ. Sci. Tech. 55, 2919–2928 (2021).
Rivera-Becerril, F. et al. Impact of a pesticide cocktail (fenhexamid, folpel, deltamethrin) on the abundance of Glomeromycota in two agricultural soils. Sci. Total Environ. 577, 84–93 (2017).
Ke, M. et al. Development of a machine-learning model to identify the impacts of pesticides characteristics on soil microbial communities from high-throughput sequencing data. Environ. Microbiol. 24, 5561–5573 (2022).
Gunstone, T., Cornelisse, T., Klein, K., Dubey, A. & Donley, N. Pesticides and soil invertebrates: a hazard assessment. Front. Environ. Sci. https://doi.org/10.3389/fenvs.2021.643847 (2021).
Tejada, M., García, C., Hernández, T. & Gómez, I. Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide. Arch. Environ. Contamin. Toxicol. 69, 8–19 (2015).
Franco, A. et al. Evaluation of the ecological risk of pesticides residues from the European LUCAS soil monitoring 2018 survey. Integr. Environ. Assess. Manag. 20, 1639–1653 (2024).
EFSA Panel, C. et al. Scientific opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms. EFSA Journal 15, e04690 (2017).
Riedo, J., Rillig, M. C. & Walder, F. Beyond dosage: the need for more realistic research scenarios to understand pesticide impacts on agricultural soils. J. Agric. Food Chem. 73, 10093–10100 (2025).
Karpouzas, D. G., Vryzas, Z. & Martin-Laurent, F. Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report). Pure Appl. Chem. 94, 1161–1194 (2022).
Storck, V., Karpouzas, D. G. & Martin-Laurent, F. Towards a better pesticide policy for the European Union. Sci. Total Environ. 575, 1027–1033 (2017).
Silva, V. et al. Pesticide residues in European agricultural soils–a hidden reality unfolded. Sci. Total Environ. 653, 1532–1545 (2019).
Active Substances, Safeners and Synergists (European Commission, accessed 17 October 2025); https://ec.europa.eu/food/plant/pesticides/eu-pesticides-database/start/screen/active-substances.
Baćmaga, M., Wyszkowska, J. & Kucharski, J. The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth. Ecotoxicology 25, 1575–1587 (2016).
Zhang, H. et al. Exposure to fungicide difenoconazole reduces the soil bacterial community diversity and the co-occurrence network complexity. J. Hazard. Mater. 405, 124208 (2021).
Martin, F. M. & van Der Heijden, M. G. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytol. 242, 1486–1506 (2024).
Trap, J., Bonkowski, M., Plassard, C., Villenave, C. & Blanchart, E. Ecological importance of soil bacterivores for ecosystem functions. Plant Soil 398, 1–24 (2016).
Sim, J. X. et al. Impact of twenty pesticides on soil carbon microbial functions and community composition. Chemosphere 307, 135820 (2022).
Staley, Z. R., Harwood, V. J. & Rohr, J. R. A synthesis of the effects of pesticides on microbial persistence in aquatic ecosystems. Crit. Rev. Toxicol. 45, 813–836 (2015).
Ni, B. et al. Increasing pesticide diversity impairs soil microbial functions. Proc. Natl Acad. Sci. USA 122, e2419917122 (2025).
Romero, F., Jiao, S. & van der Heijden, M. G. Impact of microbial diversity and pesticide application on plant growth, litter decomposition and carbon substrate use. Soil Biol. Biochem. 208, 109866 (2025).
PLAN/2023/1497 RR – Rev. 1 (European Commission, 2024).
Karas, P. et al. Assessment of the impact of three pesticides on microbial dynamics and functions in a lab-to-field experimental approach. Sci. Total Environ. 637, 636–646 (2018).
Tsiafouli, M. A. et al. Intensive agriculture reduces soil biodiversity across Europe. Glob. Chang. Biol. 21, 973–985 (2015).
de Vries, F. T. et al. Soil food web properties explain ecosystem services across European land use systems. Proc. Natl Acad. Sci. USA 110, 14296–14301 (2013).
Adriaanse, P. I., Buddendorf, W. B., Holterman, H. J. & ter Horst, M. M. Supporting the development of exposure assessment scenarios for non-target terrestrial organisms to plant protection products: development of exposure assessment goals. EFSA Support. Publ. 19, 7661E (2022).
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).
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).
Pihlström, T. et al. Analytical quality control and method validation procedures for pesticide residues analysis in food and feed. Sante 11813, 21–22 (2017).
Sabzevari, S. & Hofman, J. A worldwide review of currently used pesticides’ monitoring in agricultural soils. Sci. Total Environ. 812, 152344 (2022).
Geissen, V. et al. Cocktails of pesticide residues in conventional and organic farming systems in Europe–legacy of the past and turning point for the future. Environ. Pollut. 278, 116827 (2021).
Lewis, K. A., Tzilivakis, J., Warner, D. J. & Green, A. An international database for pesticide risk assessments and management. Hum. Ecol. Risk Assess. 22, 1050–1064 (2016).
Forouzesh, A., Zand, E., Soufizadeh, S. & Samadi Foroushani, S. Classification of herbicides according to chemical family for weed resistance management strategies—an update. Weed Res. 55, 334–358 (2015).
Hermann, D. & Stenzel, K. FRAC mode-of-action classification and resistance risk of fungicides. Modern Crop Protect. Compound. 2, 589–608 (2019).
Sparks, T. C. & Nauen, R. IRAC: mode of action classification and insecticide resistance management. Pesticide Biochem. Physiol. 121, 122–128 (2015).
Labouyrie, M. et al. Patterns in soil microbial diversity across Europe. Nat. Commun. 14, 3311 (2023).
Köninger, J. et al. Ecosystem type drives soil eukaryotic diversity and composition in Europe. Glob. Chang. Ecol. 29, 5706–5719 (2023).
Bahram, M. Intensive land use enhances soil ammonia-oxidising archaea at a continental scale. Soil Biol. Biochem. 213, 110024 (2026).
Weigand, H. et al. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: gap-analysis and recommendations for future work. Sci. Total Environ. 678, 499–524 (2019).
Wang, Q., Wang, W., Liu, L., Tang, S. & Yang, Y. Temporal and spatial dynamics of rotifer communities in the Pearl River Delta (China) with emphasis on DNA metabarcoding versus morphology to assess rotifer diversity. Hydrobiologia 851, 2999–3012 (2024).
Topstad, L., Guidetti, R., Majaneva, M. & Ekrem, T. Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats. Genome 64, 217–231 (2021).
Beule, L. & Karlovsky, P. Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities. PeerJ 8, e9593 (2020).
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).
Liu, C., Cui, Y., Li, X. & Yao, M. microeco: an R package for data mining in microbial community ecology. FEMS Microbiol. Ecol. 97, fiaa255 (2021).
Põlme, S. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).
van den Hoogen, J. et al. A global database of soil nematode abundance and functional group composition. Sci. Data 7, 103 (2020).
Mazel, F. et al. Soil protist function varies with elevation in the Swiss Alps. Environ. Microbiol. 24, 1689–1702 (2022).
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
Oliverio, A. M. et al. The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6, eaax8787 (2020).
Ferris, H., Bongers, T. & de Goede, R. G. A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Appl. Soil Ecol. 18, 13–29 (2001).
Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Clum, A. et al. DOE JGI metagenome workflow. mSystems 6, e00804-00820 (2021).
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).
Kuhn, M. Building predictive models in R using the caret package. J. Stat. Softw. 28, 1–26 (2008).
Domene, X. et al. Applying a GLM-based approach to model the influence of soil properties on the toxicity of phenmedipham to Folsomia candida. J. Soils Sediments 12, 888–899 (2012).
Obregon, D., Guerrero, O. R., Stashenko, E. & Poveda, K. Natural habitat partially mitigates negative pesticide effects on tropical pollinator communities. Glob. Ecol. Conserv. 28, e01668 (2021).
Szöcs, E. et al. Analysing chemical-induced changes in macroinvertebrate communities in aquatic mesocosm experiments: a comparison of methods. Ecotoxicology 24, 760–769 (2015).
Hartig, F. DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models. R packag version 020 cran.r-project.org/web/packages/DHARMa (2018).
Fox, J. & Weisberg, S. An R Companion to Applied Regression (Sage publications, 2018).
Ribeiro, P. J. Jr, Diggle, P. J. The geoR package. R News 1, 14–18 (2007).
Grömping, U. Variable importance in regression models. WIREs Comput. Stat. 7, 137–152 (2015).
Legendre, P. & Legendre, L. in Numerical Ecology Vol. 24, 3rd edn Ch. 10.3 (Elsevier, 2012).
Oksanen, J. Vegan: community ecology package. R package version 2.5.7 http://vegan.r-forge.r-project.org/ (2010).
R Core Team. R: A Language and Environment for Statistical Computing. www.R-project.org/ (R Foundation for Statistical Computing, 2020).
Guidance Document on Terrestrial Ecotoxicology Under Council Directive 91/414/EEC (European Commission, 2002).
