Soil biota significantly contributes to ecosystem services like food production, climate regulation, and pest control. Soil microbes are crucial for decomposing organic matter, regulating carbon stocks and nutrient cycling, and facilitating plant nutrient uptake. Changes in soil microbial communities and their functions can alter these services. While land-use perturbation's impact on above-ground biodiversity is well-documented, less is known about its effects on below-ground diversity and functions, particularly at large spatial scales. Land-use perturbation is a major anthropogenic pressure affecting soil microbial diversity, causing shifts in community composition. Other factors influencing soil microbial communities include climate, soil properties, and vegetation. Changes in climate and soil properties (pH, texture, nitrogen availability) also lead to changes in microbial assemblages. Plant community attributes and functional traits also predict variations in soil microbial diversity and composition. Previous studies often focus on major determinants separately, lacking continental-scale surveys to assess the drivers of taxonomic and functional diversity changes in bacterial and fungal soil assemblages. This study addresses these knowledge gaps by analyzing DNA sequences from soil samples across Europe, assessing the effects of vegetation cover (and associated land-use), soil properties, climate, and their interactions on soil microbial communities and potential functional groups.

Extensive research has established that land-use perturbation significantly impacts soil microbial diversity and community structure. Studies have shown that land-use intensification reduces soil biodiversity across Europe, leading to community composition shifts. Climate, soil properties (pH, texture, nitrogen), and vegetation have also been identified as major factors influencing soil microbial communities. Changes in these factors lead to shifts in microbial assemblages. The interplay between aboveground and belowground biodiversity is also recognized, with plant diversity being a significant predictor of soil microbial beta diversity. However, most studies have focused on localized scales or individual drivers, limiting a comprehensive understanding of the complex interplay of factors at continental scales. Studies comparing microbial domains (bacteria and fungi) across a range of land-use types (from undisturbed to intensively managed) are scarce, hindering a comprehensive assessment of the impact of land-use intensification on key soil functions.

This study analyzed DNA sequences from 715 soil samples collected across 23 European Union countries and the United Kingdom as part of the 2018 LUCAS Soil module. The samples represent six vegetation cover types along a gradient of increasing land-use perturbation: coniferous and broadleaved woodlands, extensively and intensively managed grasslands, and permanent and non-permanent croplands. Microbial biodiversity was assessed using metabarcoding, generating over 79,000 bacterial and 25,000 fungal operational taxonomic units (OTUs). Nine soil physicochemical properties and six climatic variables were also measured. Statistical analyses included variation partitioning to determine the unique contributions of vegetation cover, soil properties, and climate to microbial alpha (richness, Shannon diversity) and beta diversity (community structure). Functional groups (chemoheterotrophs, N-fixers, pathogens for bacteria; ectomycorrhizal, arbuscular mycorrhizal fungi, saprotrophs, plant pathogens for fungi) were inferred from taxonomy using FAPROTAX and FungalTraits databases. The impacts of single factors and their interactions were assessed using multivariate models and ordination methods. Specifically, dbRDA was used to test for the effect of land-use on microbial beta diversity. Variation partitioning analyses were implemented to identify the unique contributions of vegetation, soil and climate as well as two-way interaction terms on alpha and beta diversity.

The study revealed that microbial richness and diversity increased along the land-use perturbation gradient, from woodlands to croplands and grasslands. Woodlands had the lowest bacterial and fungal diversity, while croplands and grasslands showed significantly higher diversity. Bacterial chemoheterotrophs were significantly more abundant in highly disturbed environments, while N-fixing bacteria were more abundant in woodlands and extensively managed grasslands. Similarly, fungal plant pathogens and saprotrophs were more prevalent in disturbed areas, while ectomycorrhizal fungi dominated woodlands and arbuscular mycorrhizal fungi were more abundant in extensively managed grasslands. Variation partitioning analysis revealed that soil properties primarily drove bacterial alpha and beta diversity, whereas vegetation cover was the most important driver of fungal alpha diversity, with soil properties being most important for beta diversity. Climate variables had a relatively smaller influence on overall diversity patterns. Importantly, models incorporating interactions between vegetation cover, soil properties, and climate explained a greater proportion of the variance in microbial diversity and functional group distribution compared to models considering single factors alone. Specific interactions, such as the combination of pH and temperature seasonality, had substantial influence on fungal communities and functional groups.

The findings highlight the significant impact of land-use perturbation on soil microbial diversity and functional potential. The observed increase in microbial diversity in disturbed habitats does not necessarily equate to improved ecosystem functioning. The higher prevalence of potential pathogens in croplands and grasslands raises concerns about potential negative effects on plant health and ecosystem services. The importance of soil properties for bacterial communities and vegetation cover for fungal communities underscores the need for tailored management strategies that consider both aboveground and belowground interactions. The stronger explanatory power of models including interaction effects reveals the complexity of soil microbial responses and the limitations of focusing on single factors. These results highlight the need for more holistic approaches to soil biodiversity conservation, considering both taxonomic and functional aspects.

This study demonstrates that land-use perturbation significantly alters soil microbial diversity, community structure, and functional group distribution across Europe. High taxonomic diversity does not guarantee beneficial ecosystem functions, as disturbed areas show a higher prevalence of potentially harmful taxa. Soil properties and vegetation cover are key drivers of bacterial and fungal diversity, respectively, but the interactions among soil, climate, and vegetation best explain diversity patterns. Effective monitoring and conservation strategies should incorporate both taxonomic and functional diversity assessments, considering the interactive effects of multiple environmental drivers. Future research should expand the scope of considered environmental variables and incorporate multi-omics approaches to refine functional annotations.

Despite the comprehensive nature of this study, certain limitations exist. The unexplained variance in the models suggests the influence of other factors not included in the analysis, such as specific micronutrients or soil moisture. The reliance on taxonomic inference for functional group assignment introduces uncertainty, and the relatively low proportion of functionally assigned OTUs, especially for bacteria, limits the depth of functional analyses. The lack of quantified data on plant community structure could also contribute to the unexplained variance, particularly regarding the relationships between plants and biotrophic organisms. Future research should address these limitations by incorporating additional variables and adopting advanced omics techniques.