Disentangling effects of anthropogenic disturbance and community structure on multi-pathogen dynamics in tropical cave-dwelling bat communities

Abstract A major challenge in ecology and evolution is to disentangle the known effects of community structure and habitat degradation on disease prevalence, as they often act simultaneously in natural systems. However, cave-dwelling bats persist in degraded habitats, providing a unique opportunity to examine these dual effects. We evaluated how disturbance and cave complexity influenced bat community composition and the prevalence of multiple pathogens at the community level. During wet and dry season surveys of 15 caves in Costa Rica along a gradient of anthropogenic disturbance, we collected samples from 1,238 adult individuals, representing 17 species from four families. We determined the infection prevalence of four common and divergent pathogens: Bartonella (19.7%), Leptospira (22.7%), Trypanosoma (32.0%), and microfilaria (6.6%). Cave complexity, but not disturbance, predicted bat community composition—however, degraded habitats sustained smaller bat populations. Pathogens responded differently to habitat quality, cave complexity, season, species richness, and bat density. For bat richness, we found a negative association with Bartonella prevalence, but a positive association with Trypanosoma and microfilaria and no association with Leptospira . Our work provides insight into the complex patterns of pathogen dynamics and bat community ecology in changing environments by developing a distinctive framework using a multi-host, multi-pathogen system.