High-throughput sequencing (HTS) of bees and pollen for biosurveillance of bacterial and fungal pathogens and invasive species

The European honey bee, Apis mellifera, is Canada’s most prevalent managed pollinator. Honey bee pollination services are valued up to 5.5 billion dollars annually in Canada. Being associated with microorganisms in their environment, they have the potential to interact with and acquire pathogens. As a result, they can serve as vectors, transporting bee pathogens back to their hive or transferring pathogens between individual plants. In our proof-of-concept experiment, we exploited this bee-pathogen relationship to develop a new way to rapidly detect pathogens in the environment and assess the health of plant-pollinator systems. High-throughput sequencing (HTS) of the conserved ITS1 and 16S regions in samples from pollen collected in hive-mounted pollen traps, hive-stored pollen, and bee foragers was used to categorize fungi and bacteria, respectively. Over 19 million reads per run were generated from 44 samples. The QIIME2 pipeline was used to do quality control, produce amplicon sequence variants, and conduct taxonomic classification. Using this method, we created community pathogen profiles for apples and blueberries from British Columbia and Ontario. Identified plant pathogens include fungi Monilinia spp. and Podosphaera leucotricha. Bee pathogens include the fungus responsible for chalkbrood disease, Ascosphaera apis, as well as the bacteria Melissococcus plutonius, the causative agent of European foulbrood disease, and its secondary invader Paenibacillus alvei. With this pilot project, we seek to determine the capacity of this approach to evaluate plant-pollinator ecosystem health, identify limitations, and set up a foundation from which future screening programs may be built.