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

Area of Science:

• Environmental microbiology
• Mycology
• Ecology

Background:

• Coccidioidomycosis is a fungal disease caused by *Coccidioides* species, contracted through inhaling soil-borne spores.
• Understanding the ecological factors influencing *Coccidioides* distribution is crucial for mitigating human exposure, but its spatial variability poses challenges.
• Rodent burrows are known microhabitats that can influence soil pathogen presence and microbial communities.

Purpose of the Study:

• To investigate the relationship between soil microbial community composition and the presence of *Coccidioides immitis*.
• To determine if microhabitats like rodent burrows affect soil microbial diversity and *C. immitis* distribution.
• To identify ecological factors associated with *C. immitis* presence in a grassland ecosystem.

Main Methods:

• Soil samples were collected from surface soils and rodent burrows in the Carrizo Plain National Monument.
• Internal transcribed spacer 2 (ITS2) and 16S amplicon sequencing were used to characterize fungal and bacterial communities.
• Statistical analyses were performed to assess associations between microbial diversity, community composition, and *C. immitis* presence.

Main Results:

• Over 30 fungal species, including other Onygenales, frequently co-occurred with *C. immitis*.
• *Coccidioides*-positive soil samples exhibited significantly higher fungal and bacterial diversity compared to negative samples.
• Rodent burrows showed higher fungal and bacterial diversity and a greater presence of *C. immitis* than surface soils, with soil source being the primary driver of variation.

Conclusions:

• Favorable microhabitats, such as rodent burrows, create a positive association between soil microbial diversity and *Coccidioides* presence.
• Rodent burrow environments may act as ecological niches supporting both diverse microbial communities and *C. immitis*.
• These findings highlight the importance of microhabitat heterogeneity in shaping pathogen distribution in natural environments.