Bat Community Composition and Post‐Departure Degradation Patterns of eDNA Shed by Migratory Cave Bats

Leptonycteris nivalis is an endangered species of nectivorous bat known to seasonally occupy Mount Emory Cave in Big Bend National Park, Texas, USA. The endangered status of L. nivalis necessitates regular assessments of population size, habitat use, and roosting behaviors. However, disturbances by researchers may have a negative impact on bat species. In recent years it has been shown that it is possible to characterize a terrestrial vertebrate community using environmental DNA (eDNA) from the air, particularly in an enclosed environment like a cave. Recent studies have surveyed roosts occupied by a small number of bats but have not done so in high‐occupancy, high‐fidelity roosts or when a roost has been vacated by the target species. Our objectives were to use airborne eDNA samples from Mount Emory Cave to evaluate eDNA retention over time and to characterize the bat community inside the cave. We hypothesized that even in their absence, airborne eDNA samples would be able to detect L. nivalis at Mount Emory Cave and identify other species utilizing this roost. We identified DNA from four bat species known to use the habitat around the cave. Our results suggest that the amount of eDNA recovered was not related to the length of time since departure of the target species ( p = 0.4) but was related to the distance from the cave entrance ( p = 0.0002) and the specific location of samplers within the roost ( p < 0.001). We detected L. nivalis DNA inside the cave 162 days after the bats had vacated. These results indicate that airborne eDNA sampling can identify species that have used an environment but cannot reliably reflect current occupancy. We recommend further research into the environmental factors that affect airborne eDNA retention and collection in a cave environment.