Copper and synthetic pesticides are major drivers of soil bacterial and fungal communities

Soil microbial communities play a key role in terrestrial ecosystems and provide important agricultural functions. While earlier studies have shown that soil properties, such as pH and soil organic matter, are major drivers of microbial community structure, the roles of copper and synthetic pesticides are poorly understood. Here we focused on intensively managed agricultural systems studying 61 conventional and organic vineyards from three distinct winegrowing regions in Switzerland. We identified the factors shaping bacterial and fungal communities, specifically assessing the importance of copper and synthetic pesticides. Both copper and pesticides were identified as major factors shaping microbial community structure. Copper led to a pronounced reduction in bacterial diversity. Moreover, it affected bacterial and fungal community composition, to a degree comparable to pH. The relative abundances of many large taxonomic groups and functional guilds were positively or negatively impacted by copper, indicating a strong variability in copper sensitivity. Synthetic pesticide concentrations were negatively associated with fungal diversity and community composition, indicating that they are an additional stressor for soil fungi. Finally, we identified several genera negatively related to synthetic pesticides, including the biocontrol fungus Trichoderma, that could be tested for inclusion in improved risk assessments. This is the first study comparing a wide range of field sites which documents consistent negative effects of copper and synthetic pesticides on soil microbial diversity and community composition. Our work points to the need for improved risk assessments, specifically including yet overlooked effects on soil microbes.