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

ABSTRACT 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 modeling 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 waterways, 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 1,178 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. IMPORTANCE This study demonstrates that Coccidioides is present in urban riparian corridors within major population centers in California’s San Joaquin Valley. By analyzing 1,178 soil and dust samples, we show that the pathogen exhibits strong spatial structure, occurring at low elevations, associating with drier soils, and appearing in rodent burrows within cities. In contrast to expectations for a free-living soil fungus, Coccidioides shows limited association with the broader fungal community but co-occurs with taxa linked to animal-derived substrates, supporting a host-associated ecological niche. These findings identify urban waterways as underrecognized habitats for Coccidioides and highlight ecological constraints on its distribution. Incorporating these factors into predictive models will improve risk mapping under changing climate and land use conditions. The results directly influence public health, indicating that disturbance of rodent burrows in urban environments may represent a previously underappreciated source of exposure.