Characterizing the Soil Microbial Community Associated with the Fungal Pathogen Coccidioides Immitis

Coccidioidomycosis is a fungal disease affecting humans and other mammals, caused by environmental pathogens of the genusCoccidioides. Understanding the ecological factors that shape the distribution ofCoccidioidesin soils is important for minimizing the risk of human exposure, though this remains challenging due to the pathogen's highly variable spatial distribution. Here, we examined associations between the soil microbial community andCoccidioides immitispresence within the Carrizo Plain National Monument - a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows onC. immitispresence in soils. Using internal transcribed spacer 2 (ITS2) and 16S sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred withCoccidioidesmore frequently than expected by chance.Coccidioides-positive samples were significantly higher in microbial diversity than negative samples, an association partly driven by higherCoccidioidespresence within rodent burrows compared to surface soils. Soil source (i.e., rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher microbial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding associations betweenCoccidioidesand microbial diversity, our study suggests that favorable microhabitats such as rodent burrows can lead to a positive association between soil diversity andCoccidioidespresence, particularly in otherwise resource-limited natural environments.