Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments

Abstract

The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.

Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival

“…To correlate the microbial communities and how their taxonomic profiles contribute to specialized metabolites production, archaeal and bacterial phyla were investigated and were related to the SMGCs found in each site (Figure 5, Tables S4–S6). The abundance of major archaeal and bacterial phyla in the dataset was previously reported, albeit for the sequence reads not for the assembled contigs [22,36]. However, in this study we focused on bacterial phyla with the potentiality to produce bioactive products; as certain bacterial phyla were reported to produce bioactive compounds such as antibacterial and anticancer agents.…”

“…Metagenomic read sequences were previously reported for ATII water column samples [19], brine ATII, DD and KD water samples [20], as well as for the sediment samples [36]; 16S rRNA and taxonomic analysis of the different sediment sections were previously discussed [28]. In this study we utilized the assembled metagenomes for all the previously mentioned samples, in order to detect and thoroughly analyze the specialized metabolism gene clusters encoded in the Red Sea brine pool metagenomic dataset.…”

“…Distinct assembly files were generated for all the water samples, from particular sites and depths [19,20]. However, sediment (SDM) reads from the same brine pool were cross-assembled, i.e., ATII SDM cross-assembly comprised samples obtained from seven different ATII sediment depths, and DD SDM cross-assembly from seven different DD sediment depths [36]. NB sediments cross-assembly was derived from samples obtained from two brine-influenced sites [28].…”

“…In this study we investigated specialized metabolism gene clusters in Red Sea brine water and sediment samples through metagenomic mining. Metagenomes from different sites in the Atlantis II, Discovery Deep and Kebrit Deep brine pools [28,36] were comprehensively studied to determine quantitatively and qualitatively SMGCs in the selected Red Sea brine prokaryotic metagenomes. Red Sea brine SMGCs’ homology to known biosynthetic gene clusters, predicted functions and structures of the encoded potential specialized metabolites are addressed, and their potential contribution in shaping the microbial communities in such harsh environments are discussed.…”

Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool

“…LCL is the hottest, saltiest, deepest and most secluded layer of the Atlantis II Deep (Winckler et al ., ). Several studies investigated various functional and phylogenetic aspects of ATIID brine (Abdallah et al ., ; Ferreira et al ., ; Antunes et al ., ; Adel et al ., ). The extreme conditions in LCL stimulated the search for extremophilic organisms and enzymes in this unique environment (Mohamed et al ., ; Sayed et al ., ; Sonbol et al ., ).…”