Metabarcoding reveals fungal community structure and presence of opportunistic pathogens in Brazilian touristic caves

Le résumé fourni par la source

Caves are nutrient-limited and environmentally stable ecosystems that host specialized microbial communities. Fungal diversity in Brazilian karst systems remains poorly explored. We used ITS2 metabarcoding to characterize mycobiomes from different substrates and luminosity zones in two limestone caves in the Bonito region, Brazil: Lago Azul (LA), which receives regulated tourism, and Nossa Senhora Aparecida (NSA), closed to visitation. Across 15 samples, we recovered 1,042 ASVs assigned to 219 genera and seven fungal phyla, with Ascomycota and Basidiomycota dominating both caves. Although overall diversity was comparable, the two caves shared few genera, indicating distinct ecological conditions. Functional annotation revealed a high proportion of pathotrophic guilds, including animal, plant, and insect pathogens, reflecting strong ecological connectivity between surface inputs and subterranean environments. Notably, members of Ajellomycetaceae (Histoplasma, Emergomyces, Emmonsiellopsis) occurred primarily in shadow and aphotic sediments and guano. This study includes the first environmental detection of Emergomyces in Brazil, suggesting that subterranean habitats may act as reservoirs for dimorphic opportunistic fungi with clinical overlap with histoplasmosis. Although tourism is restricted to upper zones, airborne spores and sediment transport highlight the relevance of continued microbial monitoring. These findings advance the ecological understanding of Brazilian cave mycobiomes and support the need for integrated microbial and conservation strategies in karst environments.

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