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The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior

  • Fungal Microbiology
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Abstract

Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.

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Data Availability

Data and code from this study are available on GitHub: https://github.com/pattyjk/bat_mycobiome.

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Acknowledgements

We are very grateful to Debbie Buecher, Buecher Biological Consulting for her netting and handling of bats in our sites across New Mexico and Arizona under her permits, and to Dr. Ernie Valdez for his assistance in netting and processing bats in the El Malpais Cerro Rendeja II and El Malpais Cerrito Comadre. We are also very grateful to the many field assistants from the various parks and BLM units who assisted with note taking and other tasks, to the Resources staff who worked with us to arrange permits and field support, to Northup Lab personnel who performed DNA extractions, and to MR DNA for sequencing services.

Permits

Permits were approved by the 2014 Arizona and New Mexico Game and Fish Department Scientific Collecting Permit (SP670210, SCI#3423, SCI#3350); National Park Service Scientific Collecting Permit (CAVE-2014-SCI-0012, ELMA-2013-SCI-0005, ELMA-2014-SCI-0001, and PARA-2012-SCI-0003).

Funding

This work was supported by Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU)—Carlsbad, Caverns National Park (CAVE) Award #P14AC00793, UNM-101; Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU)—El Malpais National Monument (ELMA) Award #P14AC00588, UNM-99; Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU)—Grand Canyon Parashant National Monument (PARA) Award #P12AC10812, UNM-80; Fort Stanton Cave Study Project (FSCSP) and Bureau of Land Management Agreement No. 13–0484; T&E, Inc. Award #TE-EAA-01222014; New Mexico Game & Fish Department Share with Wildlife Award #12516000000045; Western National Parks Association. DCW was supported by the National Science Foundation (IOS-1845634).

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Authors and Affiliations

  1. Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA

    Patrick J. Kearns & Douglas C. Woodhams

  2. Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA

    Ara S. Winter & Diana E. Northup

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  1. Patrick J. Kearns
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Contributions

ASW and DEN collected and processed all samples in coordination with other local scientists and bat biologists. PJK and DCW performed all sequences/statistical analyses with input from ASW and DEN. All authors contributed to authorship of the manuscript.

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Correspondence to Patrick J. Kearns.

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Kearns, P.J., Winter, A.S., Woodhams, D.C. et al. The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior. Microb Ecol 86, 1565–1574 (2023). https://doi.org/10.1007/s00248-023-02230-w

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