In recent years, host-associated microbial communities have received extensive attention due to their important role in host wellness (Cho and Blaser 2012). Host-associated microbial taxa can modulate the host immune response through direct effects on the host (i.e. inflammatory response, Moloney et al. 2014, Byrd et al. 2018), as well as through the production of antimicrobial compounds (Donia et al. 2011). Bacteria are commonly investigated components of host microbiomes; however, information about fungal-host interactions is lacking. In this study, we investigated the composition and diversity of fungi associated with 186 bats in the American Southwest. Our results revealed strong effects of geography and bat species, as well as a significant effect of location where the bats were caught (outside/inside a cave) on community composition. This suggests that the mycobiome of bats is dynamic over the course of a day, despite no significant effect of seasonality (Spring-Fall) or year sampled. Host-associated microbial communities can be highly dynamic on short (day) or long (months to years) time scales due to natural variations including host activity, diet, or health (Caporaso et al. 2011). While we have documented the variability of the bat mycobiome, more information is needed on the dynamics and immune interactions (Banerjee et al. 2020). While FunGuild analysis suggests that most taxa employ a saprotrophic lifestyle, the functional capacity of these communities is not well understood, in particular with respect to interactions with white-nose syndrome.
The strongest drivers of bat skin/fur mycobiome were geography and bat species. Host microbiomes commonly exhibit patterns of morphological, functional, and genetic differentiation concurrent with the distribution of their hosts (Yatsunenko et al. 2012). Further, environmental microbes display similar variations over spatial scales and, as with host-associated taxa, are governed by local environmental conditions that select for composition, diversity, and abundance (Oh et al. 2014). Despite a similar roosting environment (cave), the skin microbiome of bats was most strongly driven by the local abiotic conditions of each site, suggesting local cues and reservoirs of fungi drive fungal community composition of bat-associated fungi. In addition to geography, the species of bat also had a significant effect on fungal composition. Host microbiomes display host specificity at broad (Knief et al. 2010; Thomas et al. 2016), narrow (Kearns et al. 2017; Pietrangelo et al. 2018), and subspecies (Bowen et al. 2017; Sapkota et al. 2015) taxonomic resolutions. Within a given site, bat species was a significant driver of fungal composition suggesting, despite no effect of bat size or sex, each species of bat harbors a distinct community. Physiological differences between bat species such as skin secretions (Rios-Sotelo et al. 2018), the physical properties of the skin (Swartz et al. 1996), and host-microbe immune interactions (Banerjee et al. 2020) likely play a role in differentiating fungal communities among bat species.
A key service that host microbiomes provide to their host is the protection against invasion by foreign and potentially pathogenic microorganisms. While these interactions can often be mediated by competition for niche space (Phillips et al. 2017), host-associated taxa can produce antimicrobial compounds to inhibit or kill off potential invaders (Cornelison et al. 2014a, b; Hamm et al. 2017, Garcia-Bayona et al. 2018 ). Analysis of widely distributed fungi revealed several taxa, including fungal taxa from the genera Alternaria and Metschnikowia have been demonstrated to have antimicrobial properties (Csutak et al. 2007, Lee et al. 2015). For example, members of the genus Metschnikowia display antagonism towards other fungi (Sisti et al. 2014) and Alternaria produce numerous toxic compounds (Lee et al. 2015). Furthermore, a parallel study of the bacterial microbiome of the same group of bats (Winter et al. 2017) revealed Actinobacteria to be a dominant component of the microbiome. Actinobacteria have long been known to produce antimicrobial compounds (i.e. Streptomycin) including antifungal compounds (Hamm et al. 2017; Choudoir et al. 2018; Watve et al. 2001).
Many of the taxa identified (e.g. fungi from the order Chaetothyriales) are closely related to recently identified fungi that display significant inhibitory activity against the amphibian killing fungus, Batrachochytrium dendrobatidis (Kearns et al. 2017). Furthermore, recent work by Vanderwolf et al. (2021) revealed a handful of fungal taxa from the genus Aureobasidium (Class: Dothideomycetes, Family: Dothioraceae). While the read-length of ITS fragments from this study did not allow for high-levels of taxonomic classification, many of the bats sampled in this study had >75% of their fungal communities from the class Dothideomycetes (SI Figure 2). In addition, it is important to note that no taxa from thefamily of Pseudogymnoascus destructans (Pseudeurotiaceae), the causative agent of white-nose syndrome, were found. Furthermore, recent work in these cave systems detected ideal habitat for Pd in 50% of surveyed caves and species from the genus Pseudogymnoascus were detected with PCR/culturing in 70% of caves, but no sampled soils (Torres-Cruz et al. 2019). Overall this suggests that the while the conditions are right for the proliferation of Pd in the American Southwest, it simply hasn’t taken off. While more work is necessary to elucidate the presence of potential WNS inhibiting fungal taxa on wild bats, overall, our results suggest that bats may recruit potentially pathogen-inhibiting taxa.
In conclusion, our study has demonstrated the important role of geography and species in structuring fungal communities. Bat associated fungi were highly variable; however, we’ve identified cosmopolitan Ascomycetes that are likely important to the healthy bat mycobiome. Further, our results demonstrate co-occurring bacterial and fungal taxa that display anti-microbial capabilities to both bacterial and fungal pathogens. Our results suggest that despite the heterogeneity of bat associated fungal communities, bats harbor anti-microbial taxa that likely play key roles in host defense. As WNS progresses across the Western United States, it will be of great importance to understand the host-pathogen-microbiome dynamics and the role that potential probiotic taxa play in the alleviation of WNS.