The causative agents of coccidioidomycosis, also known as valley fever, are Coccidioides immitis and C. posadasii, two species of ascomycete fungi in the order of the Onygenales. Although it is known that these fungi grow in the soil of endemic areas, that military personnel are impacted by the disease, and that infection occurs through inhalation, relatively little is known about the specific conditions under which exposure occurs. Cases of valley fever have been reported among military personnel in Coccidioides endemic areas of the desert Southwest since World War II, indicating an ongoing threat to military staff and families.

This limited scope project aimed to determine the prevalence of the fungus in regions that may impact military and civilian DoD personnel, if some associations between soil properties and the presence of the pathogen could be established, and if additional information about potential pathways for exposure could be identified. The specific objectives were to determine/identify:

  • any measurable soil-, or environmental variables or combinations thereof that are promising as proxies for the presence of live Coccidioides spp. in soils.
  • if potential for wind erosion and dust emission can be related to exposure to the pathogen.
  • if dust suspended from travel on unpaved roads is related to exposure to the pathogen.
  • if there are promising parameters that can be linked to large-scale datasets, maps, and satellite retrievals for the purpose of scaling field results up to the installation- or regional-scale.

Technical Approach

Methods employed to accomplish the stated objective included a combination of bulk soil sampling (5-7 cm depth in general, and several core samples down to 30 cm), collection of wind suspendable dust from soil surfaces that tested positive for the presence of Coccidioides using a portable wind tunnel-like device (PI-SWERL®), and collection of road dust suspended by the travel of a vehicle on unpaved roads using an established mobile platform (TRAKER™). Bulk soil sampling occurred three times over the course of the project year to capture temporal variations in the vicinity of three DoD installations in endemic areas of the southwestern US. Those were the Naval Air Station (NAS) at Lemoore, Edwards Air Force Base (EAFB), and the Marine Corps Air Ground Combat Center (MCAGCC) at Twentynine Palms including a few locations from nearby Joshua Tree National Park. After the first collection period in winter, sites that tested positive for Coccidioides were targeted for core sample collection, wind-suspendable dust collection, and suspended road dust collection during the ensuing spring and summer sampling campaigns.

Samples collected during field work were subjected to standard analysis for selected physical and chemical parameters such as grain size, pH, electrical conductivity, and total dissolved salts, as well as inorganic ions. All samples were analyzed for the presence of the pathogen using DNA extraction and nested polymerase chain reaction (PCR) methods. Two different diagnostic primer pairs that were rather specific to Coccidioides spp. were used to test for the presence of the pathogen. Additionally, fingerprints of the broader fungal community in the samples were obtained using standard environmental microbiological techniques. Although RNA extraction was embarked upon for the purpose of identifying pathogen active growth sites, that effort was resource intensive and had to be postponed for a possible future research project.


Coccidioides spp. were detected in soil and dust samples collected near all three military installations, with most of the positive soil samples associated with the wet season (end of January – beginning of February). The Twentynine Palms area showed the highest percentage of Coccidioides positive samples. Soil core samples collected at Coccidioides positive sites revealed the presence of the pathogen predominantly, but not exclusively near the soil surface (A and B horizon). Soil fungal communities were composed of few species that varied with soil depth.

The sample analyses indicated that elevated pH (7.1 – 8.1), electrical conductivity, total dissolved salts, and silt and clay content can be helpful in describing a suitable Coccidioides habitat, but none of these appeared to be first order parameters in controlling the occurrence of the fungus. There is inferential evidence that microbial antagonists to the pathogen and the type of organic matter in the soil may have an influence. Of interest were also the results of soil ion chromatography, indicating high amounts of soluble calcium and potassium in desert soils where Coccidioides seemed to be more prevalent. The range of soil parameters measured provide an envelope of necessary conditions for the growth of Coccidioides, but do not prescribe the conditions that are sufficient for the fungus to thrive. One important finding is that the fungus is nearly absent from agricultural fields with high levels of sulfate and nitrate, suggesting that once lands have been severely disturbed from their original state, resultant changes in nutrients and a shift in soil microbial diversity becomes unsuitable for fungal growth.

The pathogen was detected via diagnostic PCR in several wind-suspendable dust samples that were collected with the PI-SWERL method. However, most of the sites that tested positive for the presence of Coccidioides with a bulk surface sample tested negative for material that was resuspended from the surface using the PI-SWERL. This suggests that soils where the fungus is relatively abundant are also soils that are less prone to erosion. With regard to suspended road dust, the limited number of samples collected does not allow for in-depth understanding of the relationship between road dust and exposure to Coccidioides. However, road dust from the Twentynine Palms area did test positive for the fungus, confirming that simply traveling on unpaved roads in endemic areas is a potential pathway for exposure, possibly a very important one given the extensive exposure to road dust that troops are subjected to during training activities.

One outcome of this study was the observation that Coccidioides growth sites appear to be restricted to where vegetation such as creosote and salt bush are still in place. Possibly, soils from these sites where rodents are frequently observed contain animal derived organic matter and the fungus prefers to catabolize rodent keratin instead of plant detritus. When the landscape is reworked to the point of becoming an agricultural field, the soil is of course, more prone to erosion and apparently no longer hospitable to Coccidioides growth, perhaps because of changes in soil chemical parameters and microbiota. This implies that exposure to the fungus can happen in the immediate vicinity of land disturbance activity at the time of the activity, for a finite amount of time following disturbance due to erosional events, or within a small buffer zone along the border between a vegetated growth site and an area that is prone to erosion by wind or vehicular traffic.


This conceptual framework, if shown to be true, can result in tools that are immediately useful for minimizing exposure to the fungus. Satellite imagery can be used to identify large highly degraded locations or ongoing and planned construction within the setting of endemic areas of the pathogen that together with wind data indicate high risk areas for Coccidioides exposure. Maps can be retrieved for past years as well, which allows the documentation of changes in risk of exposure to the pathogen due to changes in environmental conditions including human activities. Together with more information about the lifecycle of the fungus, these tools can be used to inform management decisions about certain activities to reduce exposure and ultimately disease burden.