Sub-lethal pesticide exposure in field trials may alter microbial composition of the honey bee gut microbiome

In colony level field trials we determine the impact of pesticides on the gut microbiome of the European honey bee (Apis mellifera). The gut microbiome plays an important role in bee health and immunity; serving as an indicator of colony exposure to environmental stressors. We found a significant association between pesticide risk (proportion of LD50) in bee bodies and the microbiome composition of honey bees sampled in highbush blueberry (Vaccinium corymbosum) fields. In particular, we observed a positive association between the sum of pesticide risk and the relative abundance of core microbiome members: Lactobacillus spp. and Bifidobacterium spp.. These results are in alignment with cage and colony trials performed by the BeeCSI consortium that have also demonstrated agrochemical associated dysbiosis. Field trials took place across two years where colonies were situated in either highbush blueberry fields or wild forage environments and sampled throughout the pollination period. We found significant associations between pesticide risk and microbial composition in blueberry pollinating colonies. While overall correlation between risk and composition was not statistically significant in wild forage environments, similar trends for risk and individual taxa were also observed. Microbiome composition was determined by isolating the intestinal tract from sampled bees in the lab followed by shotgun metagenomics sequencing and taxonomic assignment via kraken 2 to our curated bee microbiome database. Statistical analysis included examining the correlation between pesticide and microbiome matrices via the Mantel test, as well as linear regression on the sum of pesticide risk and individual taxa abundance. This work demonstrates that sub-lethal levels of pesticide exposure may alter the composition of the gut microbiome in honey bees; targeting members responsible for core functions.