Urban soils along the Kern River and Los Gatos Creek are hotspots for Coccidioides in the San Joaquin Valley of California.

Coccidioidomycosis (Valley fever) is acquired through inhalation of spores produced by fungi in the genus Coccidioides. Coccidioides is commonly detected in, and cultivated from, the lung tissue of native rodents and the soils within their burrows. Coccidioidomycosis is acquired by exposure to environmentally produced spores and is not spread between hosts. Thus, determining the location of rodent burrows with soils harboring Coccidioides will be critical for understanding coccidioidomycosis incidence and modelling how Coccidioides distributions will be affected by global change. Coccidioides is readily detected in rodent burrows on undisturbed land, has not been detected on agricultural land, and is unstudied on urban land. To test the hypothesis that Coccidioides is in urban soil, we sampled rodent burrow soils from the banks of two water ways, the Kern River and Los Gatos Creek, which transect two cities, Bakersfield and Coalinga, in the San Joaquin Valley of California. To test the hypothesis that Coccidioides would not be detected at higher elevations, we extended our sampling of rodent burrows along waterways into the mountains of California. From 1178 soil and settled dust samples, we find that Coccidioides is found in urban riparian environments in Bakersfield and Coalinga, on riparian land on the floor of the San Joaquin Valley but not at higher elevations and is negatively correlated with modeled soil moisture. Coccidioides shows significant co-occurrence patterns with animal-associated fungal taxa, but no broader relationships with the greater fungal community. Our results warrant caution when excavating urban rodent burrows in the region.