Novel eDNA approaches to monitor Western honey bee (Apis mellifera L.) microbial and arthropod communities

Pests and pathogens are a continuous threat to the health of Western honey bee Apis mellifera L. Monitoring honey bee colonies for arthropod pests, disease-causing bacteria and fungi, and early detection of new invasions is essential to maintain the pollination services provided by honey bees. We investigated the feasibility of using eDNA metabarcoding to detect honey bee pests and pathogens in their hives and across their foraging environment. We sampled 13 different sample sources of eDNA within and outside hives from our test apiary to determine where the most informative eDNA could be obtained, with most sources sampled thrice. We used DNA metabarcoding with universal primers tagged with unique dual indexes targeting arthropod (16S and COI mitochondrial genes), bacterial (16S gene) and fungal communities (16S gene). Our results showed that most sample sources yielded usable and informative DNA. Collectively, our data show that eDNA metabarcoding can accurately detect DNA from arthropods and microbes honey bees contact and can be used as a comprehensive molecular predictor tool for colony health surveys.