Microbial communities that reside in different natural habitats, particularly those of extreme environments, constitute a rich source for novel industrial enzymes and bioactive compounds. Until the advent of metagenomics technique, extreme environments represented a locked area with huge genetic repertoire that remained unexplored. The Atlantis II brine pool of the Red Sea (ATII) is one of such unexplored extreme environment. The lower part of this pool, the lower convective layer (LCL), has a pH of 5.3, high temperature (68C), elevated concentration of toxic heavy metals, and extreme salinity (26% salt). To understand the metabolic and the physiological properties of proteins and enzymes that contribute to the survival of microorganisms in this extreme and hostile environment, the structure and characteristics of their genes should be determined. Metagenomics approach helped in this task through two different techniques: 1) mass sequencing of environmental DNA by high throughput sequencing technique such as pyrosequencing technique; 2) sequencing of environmental DNA fragments from metagenomic fosmid library. The advantage of the first approach is that it produces massive number of reads that can be assembled into long contigs. Its disadvantage is that the majority of the contigs are chimeric i.e. assembled from reads belong to genomes of different microbial species. The second technique has an advantage of establishing the sequence of a contiguous piece of genomic DNA of around 30 to 40 kb‚ that most probably is not a chimeric. The major disadvantages however are the high cost of the sequencing process, it involves elaborate steps, and it has a limited output of nucleotide sequences. In this work we sequenced a contiguous fragment of DNA from the microbial community of the ATII-LCL environment and presenting the structural and potential function of its annotated genes. Interestingly, out of the 39 identified ORFs, 10 ORFs (25%) have no matches in the database. The structure and the function of the potential annotated genes are presented and discussed. In addition, we were able to assembled 28.378 kb out of 33.819 kb of the insert in the recombinant fosmid. The unassembled 5.441 kb is most probably due to the detection of characteristic patterns of low complexity regions, simple repeats as well as gene duplication exists at the end of the assembled sequence.


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date


Submission Date

January 2015

First Advisor

El-Dorry, Hamza

Committee Member 1

El-Sayed, Ahmed

Committee Member 2

Bos, Arthur


74 p.

Document Type

Master's Thesis

Library of Congress Subject Heading 1

Metagenomics -- Red Sea -- Egypt.

Library of Congress Subject Heading 2

Biotechnology -- Red Sea -- Egypt.


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Institutional Review Board (IRB) Approval

Not necessary for this item


KAUST University for providing fund necessary to do the research work