Comparison of Fungal and Bacterial Microbiomes of Bats and Their Cave Roosting Environments at El Malpais National Monument, New Mexico, USA

Abstract

The arrival in North America of white-nose syndrome (WNS), a devastating fungal disease in bats, has emphasized the necessity of a comprehensive understanding of the bats’ external skin microbiota. Here, we investigated the composition of the natural bat microbiota pre-WNS and how they are acquired. The fur surfaces of 12 roosting bats, adjacent cave walls, and cave chamber air were sampled in two New Mexican lava caves. Bacterial and fungal diversity were assessed using Illumina MiSeq sequencing. Although many taxa were shared among the sample types, there were significant differences in alpha and beta diversity within and among communities. Bacterial phyla Actinobacteriota (39.1%) and Proteobacteria (27.9%) comprised two-thirds of the sequences. Fungal communities were dominated by Ascomycota (78.9%), followed by Basidiomycota (14.7%), and Mucoromycota (4.3%). Results for bacterial communities suggested that cave walls and cave air influence the bat microbiome and that the bat microbiome can have a reciprocal influence on the microbiome of cave walls. Fungal microbiomes of cave walls, air, and bats appear to have very low impact on each other. Our results begin to elucidate how cave environments may provide natural microbial defenses for bats, one facet in predicting the effect of WNS on western bats.