Defense Date


Document Type


Degree Type

Master of Science

Degree Name

Biological Sciences

First Advisor

Jose V. Lopez, Ph.D.

Second Advisor

Jacob F. Warner, Ph.D.

Third Advisor

Travis Craddock, Ph.D.


Bioindicator, Cinachyrella, Dispersant, Deep Water Horizon, Gene Expression, Oil, Sponges, Transcriptomics


Because of their filter-feeding lifestyle, sponges (Phylum Porifera) have shown to be bio-accumulators of heavy metals, and bio-monitors for polychlorobiphenyl (PCB) contaminants. Furthermore, marine sponges have been shown to be regulators of reef ecosystems by fulfilling many ecological functions. However, very little is known about their behavior in the face of environmental changes. Consequently, our lab has developed the reef sponge Cinachyrella spp. as novel experimental model. We have designed an experiment to study the effects of WAF (Water Accommodated Fraction), Corexit 9500 dispersant, and CE-WAF (Chemically Enhanced Water Accommodated Fraction)mixtures, in an effort to mimic the conditions of the Deepwater Horizon oil spill of 2010. Three replicate of dosing experiments (labeled as X1, X2, X3) were performed on Cinachyrella based on standard CROSERF protocols. Over 80 different sponges were exposed to sublethal amounts (0.5 ppm) of oil, oil mixed with 10% Corexit dispersant (OD), and dispersant for 1 and 24 hours.

This thesis took up the characterization by using RNA-Seq data to determine the differential expression genetic response on a Florida reef native sponge from the Cinachyrella genus. Overall, from 24 Cinachyrella individuals, 31,571 total transcripts were eligible for genetic profiling. Overall, 12,913 transcripts have shown significant differential expression, among which 7,863 were upregulated, and 5,058 were down regulated. These differentially expressed transcripts included transcripts from the sponge holotranscriptome, coding for protein structure and integrity, cancer related proteins, cell survival proteins, apoptosis along with other essential protein for the organism’s survival. A large number of “orphan” uncharacterized sponge genes (and putative protein products) with no previously known function were identified, providing a scope for future work. Overall down-regulation of genes was dominant over upregulation of genes. Major genetic responses to oil had started mostly after 1 hour of exposure and higher response was seen after 24 hours of exposure for dispersant and oil:dispersant mixtures. CE-WAF Oil:dispersant mixtures appeared most harmful to the sponge after longer exposure This study confirmed Cinachyrella as a suitable research model organism from Florida reefs.