Effect of aerobic exposure on bat guano samples

Bats and their associated microbiota have important impacts on subterranean ecosystems of their roosts, provide important terrestrial ecosystem services, and serve as a reservoir for a wide range of epizootic and zoonotic diseases. Unfortunately, large-scale study of bats and their microbiota is limited by the time and cost of sample collection. To collect fresh guano samples from bats, multiple specially-trained individuals must work long hours at night to capture bats when they are most active. An alternative approach would be to passively collect guano that has already been deposited near roosts which, if effective, could significantly reduce the time, effort, training, and cost required for sample acquisition. To determine if a passive collection strategy is a viable alternative to active sampling, it must first be established whether the post-defecation exposure to an aerobic environment has a large impact on the biodiversity and composition of the guano microbiome. A number of recent studies on mammalian feces have shown that the impact of aerobic exposure is highly species specific; therefore, it is difficult to predict how exposure will affect the bat guano microbiome without empirical data. In our study, we collected fresh guano samples from 24 individuals belonging to 10 different bat species that are common throughout the arid environments of the American southwest and subjected the samples to 0, 1, and 12 hours of exposure. The guano biodiversity decreased rapidly after the shift from an anaerobic to an aerobic environment – much faster what has previously been reported in mammalian species. However, using highly sensitive targeted PCR methods, we found that the microbiota composition of the original non-exposed samples could still be recovered after 12 hours of exposure. These results suggest that with careful sample analysis protocols, a more efficient passive collection strategy is feasible; for example, guano could be collected on tarps placed near the roost entrance. Such passive collection method would greatly reduce the cost of sample collection by allowing more sites/roosts to be surveyed with a fraction of trained personnel, time, and effort investments needed.