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Comment
. 2016 Jul 5:3:160050.
doi: 10.1038/sdata.2016.50.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

Mohamed F Haroon  1 , Luke R Thompson  1   2 , Donovan H Parks  3 , Philip Hugenholtz  3   4 , Ulrich Stingl  1
Affiliations
Comment

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

Mohamed F Haroon et al. Sci Data. .

Abstract

Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Experimental workflow for this study.
The circles superimposed on the Red Sea 3D map shows the sampling points during the King Abdullah University of Science and Technology Red Sea Expedition 2011. The green lines represent the three Gulf of Aden Intermediate Water (GAIW) sampling points. The numbers within the circles represent the number of genomes recovered from each of the sample. Colors represent the high (dark red) to low (dark blue) water temperature. A total of 45 samples of 20 l each were collected and filtered through a series of filters. For this study, DNA extraction was performed on the small microbial fractions (between 0.1 to 1.2 μm). Extracted DNA was sequenced on the Illumina HiSeq 2,000 generating paired-end reads (2×93 bp). Reads from each metagenome were cleaned and assembled individually. Genomes were binned based on tetranucleotide and coverage-based method, refined and quality checked. All 136 genomes were annotated by IMG/ER and taxonomically assigned based on genome trees inferred from single-copy genes.
Figure 2
Figure 2. Phylogenetic trees for the archaeal (green lines; top left) and bacterial (blue lines; bottom right) domains based on 122 and 120 single-copy marker genes, respectively.
The clades represented by the triangles are collapsed at the phylum (P) level except for phyla containing genomes from this study which are expanded at the class (C) level and highlighted in red. Certain phyla have genome representatives only at the phylum level (Thaumarchaeota, Marinimicrobia, Cyanobacteria, and Bdellovibrionaeota). Numbers in parentheses indicate the count of recovered genomes from a particular taxonomic level. Dashed lines indicate nodes for class level. Robustness of the tree is indicated by black circles (size of circles scaled from 80 to 100% bootstrap support values). Trees were inferred independently. The archaeal tree was rooted with the DPANN superphylum while the bacterial tree was ‘arbitrarily’ rooted with the phylum Chloroflexi but should be treated as unrooted.
See this image and copyright information in PMC

Comment on

  • IMG: the Integrated Microbial Genomes database and comparative analysis system.
    Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. Markowitz VM, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D115-22. doi: 10.1093/nar/gkr1044. Nucleic Acids Res. 2012. PMID: 22194640 Free PMC article.

References

Data Citations

    1. Haroon M. F. 2015. National Center for Biotechnology Information (NCBI) BioProject database. PRJNA289734
    1. Haroon M. F. 2016. Figshare. https://dx.doi.org/10.6084/m9.figshare.3362899.v1 - DOI

References

    1. Thompson L. R. et al. Metagenomic covariation along densely sampled environmental gradients in the Red Sea. bioRxiv doi:10.1101/055012 (2016). - PMC - PubMed
    1. Churchill J. H., Bower A. S., McCorkle D. C. & Abualnaja Y. The transport of nutrient-rich Indian Ocean water through the Red Sea and into coastal reef systems. Journal of Marine Research 72, 165–181 (2014).
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    1. Jimenez-Infante F. et al. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. FEMS microbiology ecology 89, 181–197 (2014). - PubMed
    1. Zhang G., Haroon M. F., Zhang R., Hikmawan T. & Stingl U. Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea. Genome Announcements 4, e00109–16 (2016). - PMC - PubMed

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