Discipline: Ecology Environmental and Earth Sciences
Natalia Rangel - California State University, Bakersfield
Co-Author(s): Antje Lauer, 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 disease called valley fever in California. As a spore former, this fungus may have some advantages over other microorganisms in arid soils throughout southern and central California. The focus of this project is to identify the habitat that supports the growth of C. immitis and also to identify all dominant members of the fungal community that thrive in soils in the endemic area of the pathogen using a culture independent approach to better understand the ecology of C. immitis in California. The methods used in this study will be based on DNA and RNA extractions from ~20 soil samples collected near the City of Lancaster and Edwards Air Force Base in the Western Mojave Desert. 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. We have successfully identified positive samples of the pathogen within the city of Lancaster with the nested PCR. We were also able to extract the RNA from the samples and will soon quantify the amount of RNA found. Furthermore, we have identified members from the following fungal orders: Onygenales, Eurotiales, Pleosporales and Capnodiales by sequencing DGGE bands. The results of this project will be of great interest to communities where the valley fever epidemic is rampant, such as the Antelope Valley in the Western Mojave Desert where Lancaster and Edwards Airforce Base are located. The Antelope Valley in Northern Los Angeles County is an area that 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 general public and construction workers by not disturbing those soils in the first place. Future work might also 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.
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 was supported by funding from the NASA Armstrong Flight Research Center in Edwards, CA, and from LSAMP.
Faculty Advisor: Antje Lauer, email@example.com
Role: I began this research by collecting soil samples with Antje Lauer. Once, the soil samples were collected, I pursued the following tasks: determined the amount of DNA and RNA extracted from all soil samples from each location using a Nano-spectrophotometer, converted all extracted RNA into cDNA using a kit manufactured by Invitrogen, and lately I have been following a nested PCR approach based on the protocol published by Baptista-Rosas et al. (2012) which was modified in our laboratory to detect C. immitis in DNA and cDNA. Under Dr. Lauer's supervision, I have began performing PCRs on DNA and cDNA followed by Denaturing Gradient Gel Electrophoresis (DGGE) to indicate dominant members of the fungal community in the soil and to compare cDNA (RNA) vs DNA as well.