Trace amounts of insecticide, herbicide, and their combination disrupt the bacterial and fungal microbiome of a nontarget aquatic invertebrate

The ubiquitous contamination of freshwater by pesticides contributes substantially to the ongoing diversity crisis. The animal microbiome affects a range of important functions, including host immunity and resilience to pesticide stress. Therefore, understanding how pesticides impact the microbiome of nontarget organisms is critical; however, this topic remains understudied in freshwater invertebrates. We investigated the effect of sublethal concentrations of pesticides on the host-associated microbiomes of larval Sympetrum vulgatum (Odonata: Libellulidae). Fifth-instar larvae reared in the laboratory and collected in the field were experimentally exposed to the herbicide metazachlor, the insecticide etofenprox, and their combination, and their bacterial and fungal microbiomes were profiled using 16S and ITS2 rRNA gene metabarcoding. Exposure to pesticides, particularly the insecticide, reduced bacterial richness, altered microbial community composition, reduced the complexity of co-occurrence networks, and neutral model deviations were more consistent with increased deterministic structuring. Simultaneously, our results suggested a loss of potentially beneficial taxa and an increase in pathogens, but also xenobiotic-degrading bacteria. The herbicide–insecticide mixture did not cause more profound effects than the insecticide alone, although it modified community assembly patterns. We found a shared set of prevalent genera persisting across treatments, alongside smaller treatment-associated subsets. Using a prevalence-based definition (detected in ≥3 samples per treatment), 91 bacterial and 22 fungal genera were shared across all treatments. The potentially contrasting responses of bacteria and fungi and the lab-reared and field-collected larvae to pesticides highlight the need to integrate the fungal component into microbiome research and suggest the importance of the naturally assembled microbiomes for host resilience. • Pesticides, mainly insecticide, negatively impact bacterial and fungal communities • Pesticide mixture does not cause more profound effect, excepting community assembly • Pesticides trigger deterministic processes and simplify co-occurrence networks • Substantial core bacterial and fungal community persists under pesticide stress • Naturally-assembled microbiome is more resilient to pesticide stress