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. 2016 Sep 6:6:32704.
doi: 10.1038/srep32704.

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

Mustafa Adel  1 , Ali H A Elbehery  1 , Sherry K Aziz  1 , Ramy K Aziz  2 , Hans-Peter Grossart  3   4 , Rania Siam  1
Affiliations

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

Mustafa Adel et al. Sci Rep. .

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 × 10(9) 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.

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Figures

Figure 1
Figure 1. Sampling sites of Red Sea Atlantis II area.
Samples were collected during KAUST Red Sea Expedition on April 2010. Sampling locations of the 1-Atlantis II (ATII), 2-Discovery Deep (DD), 3-Chain Deep (CD) and 4-the brine-influenced (BI) sites are presented. The figure was generated using Google Earth v 7.1.4.1529 © 2015 Google and data provided to the software by Basarsoft, US Dept. of Sate Geographer, Image Landsat, Data SIO, NOAA, U.S. Navy, NGA GEBCO. The overlaid bathymetric contours © 2014, GRID-Arendal.
Figure 2
Figure 2. Domain distribution of metagenomic reads in ATIID, DD, CD and BI sediment sections.
Classification of the metagenomic reads at the domain level, following elimination of water column reads. The bar graph shows the prevalence reads of bacterial, viral and archaeal origin. Unknown reads for each sample (not illustrated) represent the rest of the bar up to 100%. The classified bacterial community in ATIID-1a and ATIID-1b sections is high compared to the remaining samples. Reads of viral origin are higher in the remaining ATIID, DD, CD and BI samples. The figure was generated by MEGAN software v. 4.70.4 with modifications.
Figure 3
Figure 3. Sulfur metabolism, nucleotides metabolism, DNA replication and repair in all sediment metagenomic reads.
Visualization of (a) Sulfur metabolism utilizing the SEED classification and (b) Differentially represented KEGG orthologous groups in nucleotides metabolism, DNA replication and repair categories. Frequencies are normalized to total identified reads per sample. The figure was generated by MEGAN software v. 4.70.4 with modifications.
Figure 4
Figure 4. Abundance and diversity of mobile genetic elements in the Red Sea metagenomes.
(a) Abundance of mobile genetic elements. (b) Diversity of mobile genetic elements. (c) Heat map based on the abundance of insertion sequence families. ATIID, Atlantis II Deep; DD, Discovery Deep; CD; Chain Deep, BI, Brine Influenced; IS, Insertion sequences. Charts (a,b) were generated by GraphPad Prism software, while heatmap (c) was generated by heatmap package in R environment.
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