Sensitive Environmental DNA Methods for Low-Risk Surveillance of At-Risk Bumble Bees

Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.