Impact of pesticide residues on arable soil microbiomes

Pesticides are widely applied in agriculture to combat disease, pests, and weeds, leading to widespread and chronic contamination of agricultural soils with pesticide residues. However, it is still poorly understood whether continuous exposure to pesticide residues affects the soil microbiome. Here we assessed bacterial and fungal communities and several genes related to nitrogen cycling in soils of 60 wheat fields across Switzerland. We then examined whether pesticide residues are linked to the structure and functioning of the soil microbiome. Pesticides had a significant effect on various traits of the soil microbiome. The diversity of bacteria was negatively linked to the concentration of various pesticide residues, while fungal diversity and abundance were positively affected. Pesticide residues significantly explained the abundance of 1.3% of all bacterial (111 taxa in total) taxa and 8.9% of all fungal taxa (129 taxa in total). Most of these taxa were positively associated to the occurrence of pesticides, possibly because such taxa could use pesticides as food and energy source, while few taxa declined in response to increasing pesticide concentrations. Moreover, specific pesticide residues enriched one taxonomic group (Chloroflexi) and a functional guild (saprotrophic fungi). Nitrogen cycling genes were linked to pesticide residues, with several pesticide residues having a negative influence on the abundance of the gene nifH, involved in biological nitrogen fixation. Interestingly, the effects of pesticides on microbial traits were stronger than effects of cropping system and management practices including tillage, fertilisation and crop rotation. Our results suggest that chronic exposure to pesticide residues is an important factor shaping the composition and functioning of the arable soil microbiome. This indicates that the use of pesticides has long-term effects on agricultural soils, which may interfere with the development of sustainable farming systems.