Mobile genetic elements in microbial communities are mainly composed of plasmids, transposons and viruses. They are collectively referred to as the mobilome and serve as agents that facilitate horizontal gene transfer, which plays an important role in evolution and adaptation of microorganisms. In order to study the abundance and distribution of mobile genetic elements in different marine environments and to clarify whether certain environmental conditions could explain such distribution, sequence similarity searches using protein family signatures against diverse marine metagenomic datasets were used to determine the relative frequency of coding sequences associated with transposases, integrases, plasmids and viruses, or phages. In this work, a total of 24 marine metagenomic datasets were employed, comprising those obtained in the AUC/KAUST Red Sea Microbiome Project in addition to publicly available datasets representing environments that were assessed in the North Pacific Subtropical Gyre, the Mediterranean Sea  and during the Global Ocean Sampling project  . Metagenomic datasets from the Red Sea derived from samples collected at three different sites: Atlantis II Deep, Discovery Deep, and Kebrit Deep, and comprised samples from a marine water column and three deep marine brine pools. The results showed that the abundance of mobile genetic elements is higher in Atlantis II Deep brine pool than in Atlantis II Deep bathypelagic zone (1500 m sample), and is higher in the bathypelagic zone than in the mesopelagic zone (700 m and 200 m samples). This pattern can be attributed to the relaxed purifying selection due to the stressful condition of the brine and deep waters which would lead to the accumulation of features that can help microorganisms to survive in such environments, resulting in larger average genome size and elevated content of selfish genes. However, the total abundance of mobile genetic elements is higher in the epipelagic zone (50 m sample) in comparison to mesopelagic zone samples because a large increase in the abundance of sequence related to viruses and phages.this can be associated with the much larger population of cyanobacteria which are specifically infected by cyanophages in 50 m sample than in any other sample. The results also show that the abundance of mobile genetic elements is higher in Atlantis II Deep brine pool than in Kebrit and Discovery Deep brines. Although Kebrit and Discovery Deep brines show similar total abundance of mobile genetic elements, the relative frequency of each type of mobile genetic elements is different between them. Discovery Deep brine is richer in sequence related to plasmids and poorer in those related to viruses and phages than Kebrit Deep brine. The different composition of the two brines particularly with respect to heavy metal ions concentration (higher in Discovery than in Kebrit) could be responsible for such discrepancy.
School of Sciences and Engineering
MS in Biotechnology
Ferreira, Ari J. S.
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El Rifai, M. M.
(2021).Metagenomic assessment of the mobilomes of Red Sea's Atlantis II, Discovery and Kebrit Deeps [Thesis, the American University in Cairo]. AUC Knowledge Fountain.
El Rifai, Mohamed Mohamed. Metagenomic assessment of the mobilomes of Red Sea's Atlantis II, Discovery and Kebrit Deeps. 2021. American University in Cairo, Thesis. AUC Knowledge Fountain.