Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.

The European Green Deal puts a healthy environment at the core of policy-making initiatives in the European Union (EU). Soil, due to its nature, is a central actor to be considered when developing and implementing actions in many areas, from biodiversity and agriculture to climate and pollution. New means for monitoring the impact of decisions taken in these sectors are needed. The Land Use and Coverage Area frame Survey (LUCAS modules of Soil Biodiversity and Pesticides provide both policy-makers and the research community with tools in this direction. The first component corresponds to the largest analysis of soil biodiversity across the EU through molecular biology techniques.The second component is the most extensive harmonised pan-European assessment of pesticide residues in agricultural soils. Specific features, together with policy and research potential of these instruments for achieving Green Deals targets under the Biodiversity 2030 Strategy, the Farm to Fork Strategy and the Zero Pollution Action Plan, are presented. All generated data are made available to the public through the EU Soil Observatory and European Soil Data Centre. Highlights• LUCAS Soil Biodiversity is a monitoring survey of biodiversity in the European Union.