COS 315-1 - Of rodents and riverways: exploring the biogeography of Coccidioides fungus in riparian habitats of the San Joaquin Valley.

Abstract: Coccidioides spp., the fungi that cause coccidioidomycosis, are routinely found in soils collected from rodent burrows. In arid and semi-arid environments, rodent and small-mammal populations are found in higher abundance in riparian ecosystems than in adjacent upland ecosystems. Bakersfield and Coalinga, two cities in California, represent two human population centers with riparian habitats running though or directly adjacent to their urban cores, each with a high annual incidence of coccidioidomycosis. From a total of 52 sites in the vicinity of Bakersfield and Coalinga, in the San Joaquin Valley in California, a region endemic to Coccidioides and high in coccidioidomycosis incidence, we surveyed 1030 rodent burrow soil samples for Coccidioides presence. We collected 825 samples from along two riparian habitats: the Kern River in Kern County and Los Gatos Creek in Fresno County, 205 samples from in and around Bakersfield, California and an additional 100 urban surface samples from Coalinga, California. Sampling along the Kern river occurred over one year at four timepoints, with a subset of samples spanning the entire period. Of these, 68 rodent burrow soil samples (28 from the Kern River and 40 from Los Gatos Creek) were selected for sequencing of the internal transcribed (ITS2) region of fungal rDNA. Coccidioides was more commonly found closer to population centers, less commonly found on land showing less evidence of human habitation and never found in higher elevation, mountainous terrain. Coccidioides detection was geographically sporadic, being found at only 12 of 52 sites, with few clear patterns. However, Coccidioides detection was temporally consistent, being reliably detected at sites previously showing high levels of detection, and, importantly, showing no seasonal pattern. Finally, few associations were present between Coccidioides and the greater soil fungal community. Coccidioides can be found abundantly and consistently in rodent burrow soils situated in urban and urban-adjacent riparian habitats in the San Joaquin Valley. The lack of seasonality in Coccidioides detection, and its sporadic geographic distribution, may indicate that characteristics of rodent subpopulations may drive Coccidioides biogeography in soils.