MS Thesis Defense | Halle-Mari D. Santiago

The cave mycobiome is crucial to underground food webs and identifying potential sources of pathogens, novel compounds, and insights into unique subterranean adaptations. However, its characterization depends on comprehensive sampling. Every month for a year, I collected environmental DNA samples (active and passive air, sediment and speleothem swabs, and bat fecal) from three Arkansas caves. I compared survey methods on their ability to capture broad fungal diversity and detect the bat pathogen Pseudogymnoascus destructans (Pd) across sites and zonal microhabitats. Then, I assessed how fungal communities and Pd detection shift over time. I found that active airborne sampling recovers higher genera richness and a core mycofloral community sufficient for baseline surveys. Sampling did not affect Pd detection. While communities were stable over time, genera richness and abundance varied by month and Pd was ever-present. These findings highlight considerations for future speleomycology sampling, either for biodiversity assessments or targeted pathogen surveillance.