Molecular Surveillance of Honey Bee Hives Using <scp>eDNA</scp> Metabarcoding During Pollination Season

ABSTRACT Healthy honey bees are critical in safeguarding our food supply, but monitoring their health presents a significant challenge to apiarists, biosecurity agencies and animal health experts. Our objective was to investigate the feasibility of using environmental DNA (eDNA) metabarcoding to characterize the arthropod, fungal and bacterial diversity of hives with a focus on taxa that contribute to hive health such as pests and pathogens, beneficials, and biocontrol agents. We collected hive debris from four hives approximately every 2 weeks during the pollination season, first at a research almond orchard and then at a small hobby farm. A single sample was also collected from a feral colony that was relocated to the hobby farm part way through the experiment. eDNA metabarcoding detected species from all the arthropod and microbial communities targeted in debris samples, including hive pests and pathogens as well as hive beneficials. Additionally, we detected DNA from other important agricultural pest and beneficial species not commonly associated with hives, as well as taxa that can impact human health. In total, 4480 unique amplicon sequence variants were recorded across the three taxonomic groups (arthropod, fungi and bacteria) considered in this study. Our results suggest that eDNA metabarcoding can be used to monitor different aspects of hive health, such as presence or absence of pests, pathogens, and beneficial organisms. Additionally, the whole community data collected could be used to detect and monitor agriculturally relevant species more broadly. Our findings contribute to a small but growing body of research laying the foundation for using hive diversity and indicator taxa as a measure of hive health.