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.

Keywords:

• White-nose syndrome
• lava caves
• microbial mats
• Myotis
• Corynorhinus townsendii

Acknowledgments

Thank you to Terry Torres-Cruz and the Northup laboratory members, namely Joseph Medley and Ana Pittis, for their thoughtful comments, which greatly improved this manuscript. We thank the park staff at El Malpais National Monument, especially Eric Weaver and Laura Baumann, for their help with this project. We also would like to thank the UNM Center for Evolutionary & Theoretical Immunology (CETI) for support under National Institutes of Health grant P30GM110907. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Disclosure statement

The authors declare no competing interests.

Data availability statement

The data that support the findings of this study are openly available in figshare at https://doi.org/10.6084/m9.figshare.22203688.

Additional information

Funding

Research reported in this publication was supported in part by the Western National Parks Association, T & E Inc., FightWNS, and the National Institute of General Medical Sciences of the National Institutes of Health under award number [P30 GM110907].