The arrival of white-nose syndrome (WNS), a devastating fungal disease, has highlighted the need to better understand bat microbiota and how bats acquire their microbiota. To address this need, we investigated how bat microbiota compare to microbiota from the cave walls in two El Malpais National Monument caves. The external surfaces of six roosting bats from each cave, representing four different bat species, and their associated microbial mats were sampled. One to three air samples were taken in each cave. Samples were sequenced using Illumina MiSeq sequencing of the 16S rRNA gene for bacterial diversity and the ITS region for fungal diversity. Many bacterial and fungal operational taxonomic units (OTUs) were shared among the sample types. Within the bacterial OTUs, Actinobactria were highest overall in all samples, but were higher in bats than mats. The most prevalent actinobacterial genera recovered were Rhodococcus, Streptomyces, Arthrobacter, and Rubrobacter. SourceTracker suggested bat bacterial communities may originate from mat and air samples. Within the fungal OTUs, Ascomycota were highest overall in all samples, but higher in bats than mats. Prevalent fungal families included Cladosporiaceae, Pleosporaceae, Pseudeurotiaceae, Microascaceae, Leucosporidiaceae, and Mortierellaceae. A top fungal OTU recovered was a close relative of Pseudogymnoascus destructans, the cause of WNS. Our results shed light on a relatively understudied area that could have implications for understanding the source of potential natural defenses of bats, which could be important in predicting which western bats species are most vulnerable to WNS
