Discipline: Biological Sciences
Natalia Rangel - California State University, Bakersfield
Coccidioides immitis is a soil-dwelling fungal pathogen, which can become airborne when soil is disturbed, and when inhaled can cause a respiratory disease called valley fever. As a spore former, this fungus may have some advantages over other microorganisms in arid soils throughout southern and central California. With a combined approach of DNA and RNA extractions from soil samples, we will investigate if C. immitis and other fungi are active or dormant. This approach will allow us to identify growth sites of the pathogen and distinguish them from sites where the pathogen is inactive. We will extract DNA and RNA from soil samples collected near the City of Antelope Acres located in the Western Mojave Desert, the City of Lemoore located in the San Joaquin Valley, and Tejon Ranch, where several ecoregions overlap, such as the Tehachapi Mountains and Antelope Valley. We are focusing on i) a nested PCR with a diagnostic PCR step to detect the pathogen in soils and ii) perform a PCR reaction followed by Denaturing Gradient Gel Electrophoresis (DGGE) to obtain fingerprints of the active members of the fungal communities in the soil (RNA-based) and of the overall fungal diversity in the soil (DNA-based). We hypothesize that the fungal communities in soils that support or not support the growth of the pathogen will be different. So far, we have successfully identified the pathogen in soils from all three sites. Members of the following fungal orders were present in our soil samples: Onygenales, Eurotiales, Pleosporales and Capnodiales, as identified by sequencing DGGE bands. The results of this project will be of interest to communities where the valley fever epidemic is rampant, such as Antelope Valley in the Western Mojave Desert which experiences increased population growth, urbanization, and recently increased soil disturbance and fugitive dust development due to the construction of solar ranches. Knowing more about the ecology of the pathogen and the habitat where it thrives might help to prevent incidence of valley fever among the public by not disturbing those soils in the first place. Future work will include the search for microbial species that can act as antagonists to the pathogen, especially those fungal species that are dominant in C.immitis negative soil samples from the same environment and our PCR/DGGE approach is a first step in this direction. This project is supported by funding from LSAMP. References Baptista-Rosas RC, Catalan-Dibene J, Romero-Olivares AL, Hinojosa A, Cavazos T, Riquelme M. Molecular detection of Coccidioides spp. from environmental samples in Baja California: linking Valley Fever to soil and climate conditions. Fungal Ecology. 2012 Apr 30;5(2):177-90. Vargas-Gastélum L, Romero-Olivares AL, Escalante AE, Rocha-Olivares A, Brizuela C, Riquelme M. Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing. FEMS microbiology ecology. 2015 May 1;91(5):fiv044.
Funder Acknowledgement(s): This project is supported by funding from LSAMP.
Faculty Advisor: Antje Lauer, email@example.com
Role: I have participated in soil sampling trips and completed the DNA and RNA extractions for all three sites. I have quantified the extracted DNA and RNA and have completed the nested PCR sequence for the DNA, and was able to identify the fungal pathogen in all three sites by sequencing the diagnostic PCR products. I have converted the RNA to cDNA by conducting a reverse transcriptase PCR and will complete the nested PCR sequence with the cDNA. I have helped in running the DGGE for several samples and am currently learning to complete this process on my own.