Soil microbiome signatures are associated with pesticide residues in arable landscapes

Pesticides are widely applied in agriculture to combat disease, pests, and weeds, leading to long-lasting contamination of agricultural soils with pesticide residues. While classical risk assessment experiments have repeatedly addressed immediate pesticide effects, we employ an ecological approach to investigate how pesticide residues persisting in soils influence the soil microbiome under realistic agricultural conditions. We assessed a wide range of soil characteristics, including the occurrence of 48 widely-used pesticides in 60 fields under conventional, no-tillage and organic management. We then tested which factors best explain soil microbiome traits. Environmental factors, including climate, geography, and soil characteristics, were the soil microbiome’s leading drivers. Remarkably, of all management factors, pesticide residues showed the strongest associations with soil microbiome traits, which were even more pronounced than the effects of cropping systems. Pesticide residues were almost exclusively positively associated with the relative abundance of 113 bacterial and 130 fungal taxa, many of them being assigned to taxa of known pesticide degraders. While fungal diversity and abundance were primarily positively associated with pesticide residues, bacterial diversity and abundance of the gene nifH - essential for biological nitrogen fixation - were negatively linked to the concentration of individual pesticide residues. Our results suggest that pesticide residues alter the soil microbiome, with potential long-term implications for the functioning of agricultural soils.