Diversity and potential roles of cave and bat fungi in Yunnan province, China

Abstract

Caves represent unique and underexplored ecological environments characterized by permanent darkness, high humidity, stable temperatures, and limited nutrient availability. These conditions promote the growth of specialized and diverse fungal communities with important taxonomic, ecological, and biotechnological potential. According to current statistics, approximately 2,290 species belonging to 269 families have been reported from cave environments worldwide. While Yunnan Province is known for its numerous caves —more than 1,000 have been discovered —little information is available on the fungi associated with them. To study fungi associated with caves, 11 caves across Yunnan Province, China, were investigated, and fungal diversity was characterized using morphological and multi-gene phylogenetic analyses. A total of 802 culturable fungal strains, representing 216 species across 79 genera, were isolated from 264 cave environmental samples. Among these, 15 genera, comprising 10 Ascomycota genera and 5 Basidiomycota ones, were recorded for the first time from cave environments. Phylogenetic and morphological analyses revealed 16 species new to science and 94 taxa newly associated with cave habitats. The dominant phylum was Ascomycota, followed by Basidiomycota and Mucoromycota. The most commonly encountered genera included Penicillium, Aspergillus, Fusarium, Trichoderma, Mucor, Talaromyces, and Chaetomium. In parallel, this study also examined fungi associated with bats, the second-largest order of mammals, which are of significant ecological and economic importance due to their roles in pollination, seed dispersal, and insect control. However, bats can also serve as reservoirs and vectors for pathogenic microorganisms. In this study, fieldwork was conducted at four bat roosting sites in Yunnan Province. A total of 175 fungal strains were isolated from the wing membranes, feet, and fur of 164 individual bats representing 19 species. These isolates comprised 75 culturable fungal species belonging to 36 genera, 16 newly described species and 59 new host records. Among these genera, 21 were reported for the first time from bats, and four had never been reported from caves. Notably, 36 of the identified species have previously been reported as pathogens of plants, animals, or humans, while the remaining 39 were non-pathogenic or have not been associated with pathogenicity. Of these species, 77% (58 species) belonged to Ascomycota, 9% (seven species) to Basidiomycota, and 13% (10 species) to Mucoromycota. Our study revealed that smaller, cave-dwelling Rhinolophus individuals were more likely to harbor identical fungal species, whereas larger and more aggressive Hipposideros individuals exhibited a lower prevalence of culturable fungi. This disparity may be attributed to differences in roosting behavior, as Hipposideros species typically maintain greater inter-individual distances. Due to incomplete sampling, particularly the underrepresentation of bats with diverse dietary preferences and the predominance of insectivorous species in our dataset, no clear correlation was observed between fungal communities and bat taxa or diet. Furthermore, we observed partial specificity of fungal species for particular bat hosts and tissue types, with notably more species isolated from wing membranes. Interestingly, the distribution of fungi across body parts varied among bat taxa. Rhinolophus species exhibited the highest fungal incidence and diversity on their wings, whereas Hipposideros and Myotis species showed substantially lower fungal loads in the same region. This pattern may reflect habitat differences, as Rhinolophus species primarily inhabit forested environments, while Hipposideros and Myotis generally occupy more open habitats. An exception was observed in Rhinolophus rex, which harbored greater fungal diversity on the body rather than on the wings—a trend that may be attributed to its relatively longer fur, providing a more favorable substrate for fungal colonization. Given that bats frequently move between multiple habitat types, including forests, agricultural fields, and livestock enclosures, they may serve as effective vectors for the dispersal of fungal pathogens across regions, raising concerns about the potential spread of pathogenic fungi. Pathogenicity assays further confirmed that Penicillium glabrum isolated from bats could cause fruit rot in pomegranate (Punica granatum), highlighting the ecological and agricultural risks posed by bat-borne fungi. This study represents the first systematic survey of cave fungi in Yunnan Province, and the first documented isolation of fungi from live bats in China. It effectively bridges the knowledge gap between cave- and bat-associated mycobiota in the region. Notably, this is also the first comprehensive taxonomic investigation of bat-associated fungi incorporating both morphological and multigene phylogenetic analyses. The work establishes a critical foundation for future research and is expected to serve as a catalyst for continued exploration in this understudied field. This research significantly enriches the global inventory of cave- and bat-associated fungi and deepens our understanding of fungal diversity in karst ecosystems in Yunnan Province. It also highlights the dual ecological roles of bats as vital ecosystem service providers and potential reservoirs of pathogenic fungi. The findings offer valuable insights into fungal taxonomy, microbial ecology, cave conservation, and pathogen spillover risks between wildlife and agricultural systems.