Effects of Neonicotinoid Seed Treatments on Soil Microbial Gene Expression Vary with Time in an Agricultural Ecosystem

Neonicotinoids, a class of systemic insecticides, have been widely used for decades against various insect pests. Past studies have reported non-target effects of neonicotinoids on some beneficial macro- and micro-organisms. Given the crucial role that the soil microbiota plays in sustaining soil fertility, it is critical to understand how microbial taxonomic composition and gene expression respond to neonicotinoid exposure. To date, few studies have focused on this question, and these studies have evaluated the shifts in soil microbial taxonomic composition or used soil biochemical analyses to assess the changes in microbial functions. In this study, we have applied a metatranscriptomic approach to quantify the variability in soil microbial gene expression in a two-year soybean/corn crop rotation in Quebec, Canada. We identified weak and temporally inconsistent effects of neonicotinoid application on soil microbial gene expression, as well as a strong temporal variation in soil microbial gene expression among months and years. Neonicotinoid seed treatment altered the expression of a small number of microbial genes, including genes associated with heat shock proteins, regulatory functions, metabolic processes and DNA repair. These changes in gene expression varied during the growing season and between years. Overall, the composition of soil microbial expressed genes seems to be more resilient and less affected by neonicotinoid application than soil microbial taxonomic composition. Our study is among the first to document the effects of neonicotinoid seed treatment on microbial gene expression and highlights the strong temporal variability of soil microbial gene expression and its responses to neonicotinoid seed treatments. IMPORTANCEThis work provides the first example of the impacts of neonicotinoid seed treatment on community-wide soil microbial gene expression in an experimental design representing real farming conditions. Neonicotinoid pesticides have attracted a great deal of attention in recent years due to their potential non-target impacts on ecological communities and their functions. Our paper represents the first use of metatranscriptomic sequencing to offer real-time and in-depth insights into the non-target effects of this pesticide on soil microbial gene expression and on potentially beneficial soil microorganisms.