The Influence of Agroecological Intensification on Dominant and Rare Microbial Communities Across Diverse European Countries

Intensive land use leads to the degradation of agroecosystems, resulting in long-term losses in agricultural productivity. In contrast, sustainable management is known to improve soil fertility directly and indirectly through changes in the soil microbiota, which plays a fundamental role in agroecosystems by influencing nutrient biogeochemical processes and through symbiotic relationships with crops. In this study, we used amplicon sequencing to investigate changes occurring in dominant and rare sub-communities of bacteria and fungi in agricultural soils from seven European countries under different number of agroecological cropping systems: one and two sustainability-promoting practices or none. Both sub-communities were structured along a latitude gradient, reflecting bioclimatic differences across Europe, especially the fungal communities. Differences in the bacterial and fungal sub-communities’ structure were greater under the 2SP treatment than under 1SP, particularly within the fungal dominant sub-community, which changed by sustainability-promoting practices across more sites. In both fungal and bacterial communities, we identified specific taxa associated with carbon and nutrient cycling, pathogen suppression, or plant growth promotion.