Amidst the global biodiversity crisis, efforts to assess population trends for bat species are hampered by a lack of data. Bats are cryptic, nocturnal, and may leave no visible evidence of their roosting. In addition, some species use habitats that are unfeasible or unsafe to enter to conduct survey work. Environmental DNA, or eDNA, survey methods involve sampling environmental media (water, soil, air) and testing for exogenous DNA shed by organisms into their environments to infer species presence. eDNA air sampling is the active collection and filtration of air as a source of eDNA and it has been demonstrated to have utility for surveying tropical bat roosts. This study assesses the readiness of eDNA air sampling, paired with both target-taxa assays and metabarcoding, as a tool for bat conservation and management in a western North American context. eDNA air sampling methods successfully captured bat eDNA in mixed-Myotis maternity roosts, an artificial bat cave used as a night roost, and at a known underground mine hibernaculum in winter. This is the first field validation of three new target-taxa eDNA assays developed for western Myotis bats. Results of this study are as follows: validation of a genus-wide Myotis assay to the level of operational for routine species monitoring; essential validation completed for a species-specific assay for the federally Endangered Myotis lucifugus; field validation of a species-specific assay for a morphologically similar co-occurring species, M. yumanensis. However, this assay did not successfully detect M. yumanensis DNA in any environmental samples so redesign and further laboratory validation is required. Information obtained via eDNA air sampling complemented bat activity patterns recorded using a traditional passive acoustic monitoring approach. With further optimization of eDNA capture from air in low bat abundance and activity sites, eDNA air sampling has the potential to become an efficient, non-invasive, and sensitive way to identify subterranean or inaccessible bat habitats and document species presence in mixed-species roosts.
