The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

Abstract

It has long been known that the air harbours microorganisms following Eherenberg's discovery of "infusoria" in dust samples collected off the coast of Africa nearly 200 years ago (Ehrenberg, 1830).

Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land

“…The relationship between Coccidioides detection and soil fungal community β-diversity from Hwy33 rodent burrows, as represented through Bray-Curtis dissimilarity, was trivial (r 2 = 0.01) although statistically significant (p = 0.004). Instead, the soil fungal community composition was more strongly associated with sampling site (r 2 = 0.17, p = 0.001), and to a lesser extent, sampling month (r 2 = 0.08, p = 0.001), as previously reported [ 17 ] ( Fig 4 and Table 4 ). Adjusting for environmental covariates did not meaningfully change the relationship between Coccidioides detection and the composition of the soil fungal community ( S6 Table ).…”

“…The single positive settled dust sample collected at the Kearney agricultural site showed detection in 4/4 wells and no other settled dust sample collected at Kearney showed detection in any well. Coccidioides detection using ITS2 metabarcoding from sites along Hwy33 found 4 positive rodent burrow soil samples, as previously described [ 17 ], all of which had tested positive using the CocciEnv qPCR assay. Coccidioides was not detected using ITS2 metabarcoding from any of the agricultural soil samples from Kearney, nor from any settled dust sample, whether from Hwy33 sites or Kearney, via ITS2 metabarcoding.…”

“…We collected a total of 975 samples across nine sites spanning the San Joaquin Valley, including 472 soil samples from agricultural land (Kearney, West Side, Shafter and Weedpatch), 90 settled dust samples from agricultural land (Kearney), and 238 soil samples from rodent burrows and 175 settled dust samples from undeveloped land at five sites along Hwy33. All samples were tested for Coccidioides using the CocciEnv qPCR assay ( Fig 1 ) and fungal communities had been characterized for all Hwy33 and Kearny samples using ITS2 barcoding [ 17 , 57 , 58 ].…”

“…As there is no cure or vaccine for coccidioidomycosis [ 16 ], prevention is paramount, and a better understanding of the distribution of Coccidioides in the environment is needed to inform strategies to prevent infection. Our previous comparison of fungal communities from agricultural and undisturbed soils used metabarcoding, which rarely detected Coccidioides [ 17 ]. Here we combine a sensitive qPCR method of detecting Coccidioides with our data on fungal communities to investigate the presence of Coccidioides in soil and air in the SJV on both agricultural and undeveloped land (which we define as generally uninhabited land showing no evidence of recent cultivation or irrigation).…”

“…Finally, we examine Coccidioides presence in the context of the greater soil fungal community using metabarcoding of fungal ribosomal DNA, leveraging recent work we undertook investigating relationships between the soil and airborne mycobiomes in the SJV [ 17 ]. Early studies comparing Coccidioides with other soil microbes are scant and have focused on individual taxa that inhibit the growth of Coccidioides .…”