Host Development and Environment Influence the Microbiomes of Aquatic Insects and Riparian Spiders

ABSTRACT Larval aquatic insects harbour diverse microbiomes critical for physiology and development, yet the effects of metamorphosis combined with environmental exposures on this community remain unknown. Herein we examined bacterial microbiome composition and predicted function across larval and adult stages of three families of aquatic insects and riparian spider predators, collected upstream and downstream of wastewater treatment plants (WWTPs) in Ontario, Canada. Insect host developmental stage was the primary driver of microbiome structure. Larval microbiomes were more diverse and showed higher abundances in pathways reflecting active feeding. Larval and adult populations of holometabolous insects shared few ASVs (3.8%–12.6% of the combined ASV pool), whereas a larger proportion was shared in hemimetabolous insects (23.4%). WWTP effluent exposures led to selective microbial filtering rather than broad community restructuring. Macroinvertebrate and spider microbiomes sampled downstream were characterized by higher abundances in bacterial taxa associated with wastewaters and increased xenobiotic degradation pathways. Such impacts on spider microbiomes provide evidence that ecological impacts of effluents cross the aquatic‐terrestrial boundary. Lastly, a significant decrease of vertically transmitted endosymbionts ( Rickettsiella , Wolbachia ) was detected in aquatic insects, representing a pathway through which effluent pollution may affect host fitness without detectably altering overall microbiome diversity.