Exploration of CRISPR/Cas systems in the unique Red sea Brine pools can provide insights into host-viral interactions in highly extremophile environments. 454 Metagenomic datasets from different strata of Atlantis II, Discovery deep and Kebrit deep brine pools were mined for CRISPR arrays, and Cas proteins and compared to one another. Overall composition of CRISPR types was inferred by Cas protein HMM data, together with Cas1 phylogenetic placement using RaxML and direct repeat typing. Spacerâ viral interaction was explored using local alignments of mined spacer data to local metagenomic prophage sequences, showing and comparing specific sample CRISPR affected viral occurrences as well as host spacer efficiency. Host prediction was also attempted through the use of the CRISPI database. Results suggest an abundance of Type I CRISPRs and an under representation of Type III CRISPRs throughout our datasets. Type II CRISPRs appear to more readily occupy transitional layers of brine pools. Discovery and Kebrit lower convective brine pool layers appear to show stable biological isolation as reflected by the proportions of representative spacers and affected viral taxa, whereas Atlantis II appears to be more chaotic in nature. 72% of spacers described are of unknown origin, and ~60% appear to be ineffective in the datasets they are found. Results shown here concur with previous physical studies that indicate isolation of the Red Sea brine pools, and offer new insight into the changing nature of host virus interactions in the Red Sea brine pools.


School of Sciences and Engineering

Degree Name

MS in Biotechnology

First Advisor

Siam, Rania

Committee Member 1

Moustafa, Ahmad

Document Type



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