Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community.

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiomes due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiome communities, and the lack of white-nose syndrome (a newly emergent fungal disease of bats) presence in the Southwest. We studied the extent to which changes in distributions of bacteria on external bat surfaces are a function of geographic location and ecoregion, and whether the sampled bats were caught in caves or surface-netted. To test these variables we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 186 bats from 14 species sampled across southeastern New Mexico to northwestern Arizona. Community similarity patterns and random forest models, and generalized linear mixed-effects models show that factors such as location (e.g. cave-caught vs. surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of external bat bacteria in a WNS-free environment and provide a baseline of bat external microbiomes that can be explored for potential natural defenses against pathogens.

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiomes due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiome communities, and the lack of white-nose syndrome (a newly emergent fungal disease of bats) presence in the Southwest. We studied the extent to which changes in distributions of bacteria on external bat surfaces are a function of geographic location and ecoregion, and whether the sampled bats were caught in caves or surface-netted. To test these variables we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 186 bats from 14 species sampled across southeastern New Mexico to northwestern Arizona. Community similarity patterns and random forest models, and generalized linear mixed-effects models show that factors such as location (e.g. cave-caught vs. surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of external bat bacteria in a WNS-free environment and provide a baseline of bat external microbiomes that can be explored for potential natural defenses against pathogens.

White-nose syndrome (WNS) is a bat disease caused by the fungal pathogen Pseudogymnoascus destructans, which thrives in cold and very humid environments where bats frequently hibernate. Conidia of Pseudogymnoascus species are often documented on bats prior to the onset of WNS, but characterization of high-risk areas defined by microclimate cave conditions have been lacking. Investigating the occurrence of this fungal genus and appropriate environmental conditions to support P. destructans in southwestern U.S. caves is key to understanding the sites most likely to be impacted by WNS. Microclimate conditions in ten caves at El Malpais (ELMA) National Monument in New Mexico, USA were recorded using i-Button data loggers during the winters of 2011-2014 to assess appropriate environmental conditions (temperature and relative humidity) for P. destructans and other Pseudogymnoascus species. Optimal microclimate conditions for P. destructans and other psychrophilic fungi were found in all the caves with at least 50% of the caves identified as high-risk areas. Pseudogymnoascus species were detected in 70% of the caves using culturing methods and PCR, but no soil samples were positive for P. destructans using realtime PCR in soil and guano samples. Pseudogymnoascus destructans has a recognized range of appropriate temperatures and relative humidity for growth and cave microclimate can help define high-risk areas. This study offers resource managers guidance for establishing priority monitoring areas in their bat caves to determine which bat species are at higher risk. bats, cave microclimate, guano, Pseudogymnoascus destructans, white-nose syndrome