Long-term management shapes soil microbial communities primarily through modulating soil habitat quality in Swiss croplands

Soil microbial communities are key drivers of soil functioning in agricultural systems. Yet the relative influence of soil properties and cropping practices on their diversity remains insufficiently understood. We investigated 60 cropland sites in western Switzerland, covering a broad range of soil properties and cropping practices, to explore their relationship with soil microbial communities. Rather than classifying fields into broad management systems, we adopted a multifactorial approach, considering both soil properties (soil organic carbon content (SOC), texture, pH, SOC:clay ratio) and cropping practices (tillage intensity, fertilization type and quantity, rotation and cover crop diversity, soil cover, temporary meadow) averaged over ten years. Our results indicate that soil properties are the primary factor influencing microbial habitat, carrying the majority of the explained variance in microbial biomass, activity, and community composition. SOC was positively correlated with microbial biomass and activity. Soil pH also positively correlated with increased microbial activity and was a key factor in shaping prokaryotic community composition. The SOC:clay ratio was significantly associated with fungal community composition. SOC and pH are determined by agriculture over the long term. In contrast, the ten-year agronomic history exhibited weaker direct associations with microbial metrics, even though the agronomic history modulates microbial habitats. The proportion of temporary meadow in the rotation was most consistently linked to changes in soil microbial communities, enhancing microbial biomass, shaping microbial community structure and reducing prokaryotic a-diversity. Taxa with similar ecological functions (e.g. plant beneficial bacteria, symbiotrophic fungi) showed a substantial heterogeneity in their response to soil and agronomic determinants, highlighting the need to investigate functional traits to better understand the link between cropping practices, microbial habitat quality and agroecosystem functioning. Taken together, our findings underscore the need to consider soil habitat quality as the main lever to sustain microbial communities in croplands, jointly shaped by inherent soil properties and the long-term influence of cropping practices. Future research should target microbial functional traits and field-scale habitat characterization to help identify effective levers supporting crop productivity while maintaining sustainable agroecosystems.