Ibrahim Farag


The Red Sea brine pools are unique environments to assess the biochemical adaptation of marine bacteria. The role of nitrogen in marine biogeochemistry is central and greatly influences the diverse elements including carbon and phosphorus. Anammox communities play a significant role in the total nitrogen loss especially in deep sea and deep ocean ecosystems. Despite this, the biodiversity of Anammox bacteria have not been previously investigated in any brine pool ecosystems. With the advances of the metagenomics based approaches, the exploration of the yet uncultured microbial communities including the Anammox bacteria has taken different perspectives. Anammox communities are currently analyzed using 16srRNA with some unique functional genes e.g. hydrazine oxidase, hydrazine synthase and Cytochrome cd1-containing nitrite reductase encoding gene nirS. In this study, we examined the biodiversity of Anammox microbial communities inhabiting two Red sea brine pools' Atlantis II and Kebrit deep interface layers. Comparative and comprehensive analysis of the unique and specific functional gene, hydrazine oxidase was performed. Anammox hydrazine oxidase gene was amplified from DNA isolated from the 0.1 μm serial fractionation of the water samples of Atlantis II interface layer and Kebrit upper interface layer. hzoA/hzoB libraries were constructed and a total of 81 and 44 specific clones were identified in the interface layers of Atlantis II deep and Kebrit deep, respectively. The identified sequences matched hydrazine oxidases from uncultured Planctomycetes. Alpha and beta diversity analyses were performed using statistical analysis tests and multiple regression analysis was done to assess the level of uniqueness of the Anammox bacteria inhabiting the examined samples using Unifrac. Eight and nine different Anammox related phylotypes were identified in Atlantis II and Kebrit upper interface layers, respectively. Scalindua species predominated the sampled interface brine layers. Moreover, the principle component analysis depicted a unique presence of Anammox communities. This study addresses and identifies the unique microbial community in the interface of the Red Sea Brine Pools.


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date


First Advisor

Siam, Rania



Document Type

Master's Thesis

Library of Congress Subject Heading 1

Biodiversity -- 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


It is an honor to acknowledge all the people who contributed to this work and made it possible. First of all, I would like to thank and express my deepest gratitude to the main supervisor of this dissertation, Associate Prof. Dr. Rania Siam. Dr. Siam was always helpful, supportive and a source of inspiration. I would like also to thank Assistant Prof. Dr. Ahmed Moustafa and Mr. Hazem Sharaf for their help in the computatiol alyses part. Dr. Ahmed A. Sayed, Research Associate Professor, for helping me in the sequencing part. Dr. Mohamed Ghazy and Mr. Amged Ouf for their efforts in D extraction and their continuous guidance in the laboratory. I would like to thank all my colleagues in the Biotechnology master program especially M. Abouelsoud, Rehab, Yasmine and Ghada. I would like to acknowledge both Yousef Jamel Science and Technology Research Center (STRC) and King Abdullah University for Science and Technology (KAUST) for funding my master study and research.