UCSC-GEOPATHS Summer Internship: Analyzing the Microbiome Community of Diseased Coral

Abstract:

UCSC GEOPATHS is an NSF-supported initiative to improve student success in the geosciences, driven by a desire to broaden participation. One component of the program is undergraduate student internships that provide authentic, career-relevant experiences – across all employment sectors – to increase student engagement in the geoscience pipeline.

My GEOPATHS Internship with Ph.D. Candidate Stephan Bitterwolf at UCSC focused on analyzing the microbiome of partially diseased coral to investigate microbial differences between the diseased and healthy portions. Coral diseases are resulting in a decline in coral populations worldwide. The coral is made up of the coral animal and endosymbiotic Symbiodiniacea algae, whereas the microbiome is made up of multiple bacterial species. The bacterial population can stress the symbiotic relationship between the coral and algae by being composed of invading pathogens or lacking beneficial microbes, resulting in disease. When lab grown corals at UCSC became diseased with no outside intervention, DNA was extracted from the diseased and healthy portions of the coral for further investigation. In my internship, I learned how to analyze microbial sequences from the V4 region of the 16s rRNA gene using programs and computer languages including R, Bash, and QIIME2. I used these tools to classify Operational Taxonomic Units(OTUs) and compared the microbial community of diseased and healthy tissues using alpha and beta diversity indices. The results of this process showed the bacterial community composition of the diseased coral. I will share the results of my project and experiences in the program.