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. Author SummaryCoccidioidomycosis, or Valley fever, is caused by a fungus that primarily infects people when its spores become airborne and are inhaled. Although the fungus is found in the burrows of rodents, its presence in cities has been unclear. We investigated whether urban environments in Californias San Joaquin Valley, an area with high Valley fever incidence, harbor the fungus. By sampling more than a thousand soils and settled dust samples along riparian areas (waterways and adjacent environments) in Bakersfield and Coalinga, we found that the fungus that causes Valley fever, Coccidioides, occurs in urban riparian zones. The fungus was restricted to low elevations and was more likely to be detected in drier soils. We also compared positive and negative soils using DNA-based surveys of fungi. While the broader fungal community showed no strong relationship to Coccidioides, several species tied to animal activity were more common in positive samples, supporting a link to rodent hosts. These findings show that urban waterways can serve as habitat for Coccidioides. Because these areas lie within major population centers, identifying and avoiding disturbance of rodent burrows may reduce exposure risk, and future models of Valley fever should account for riparian corridors and local ecological conditions.