Comparison of Fungal and Bacterial Microbiomes of Bats and Their Cave Roosting Environments at El Malpais National Monument, New Mexico, USA

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.

白鼻综合征(white-nose syndrome, WNS)是一种可造成蝙蝠大规模死亡的毁灭性真菌病害，其传入北美凸显了全面解析蝙蝠体外皮肤微生物群(external skin microbiota)的必要性。本研究聚焦WNS暴发前蝙蝠天然微生物群的组成及其获得路径，于新墨西哥州两处熔岩洞穴中采集了12只栖息蝙蝠的体表绒毛、邻近洞穴岩壁及洞穴腔内空气样本，并采用Illumina MiSeq测序技术对样本中的细菌与真菌多样性进行表征。尽管不同样本类型间共享诸多分类单元，但各群落内部及群落间的α多样性与β多样性均存在显著差异。细菌序列中，放线菌门(Actinobacteriota，39.1%)与变形菌门(Proteobacteria，27.9%)合计占比达三分之二。真菌群落则以子囊菌门(Ascomycota，78.9%)为绝对优势类群，其次为担子菌门(Basidiomycota，14.7%)与毛霉菌门(Mucoromycota，4.3%)。细菌群落分析结果显示，洞穴岩壁与洞穴空气可对蝙蝠微生物群产生调控作用，同时蝙蝠微生物群也可反向影响洞穴岩壁的微生物群落；而洞穴岩壁、空气与蝙蝠的真菌微生物群之间几乎不存在相互影响。本研究结果初步阐明了洞穴环境可为蝙蝠提供天然微生物防御机制的潜在路径，为预测WNS对北美西部蝙蝠种群的影响提供了关键研究维度。