Abstract:

DNA samples for metagenomic reconstruction were obtained from an oil-contaminated sea surface sample (original ID PE5), collected ca. ∼0.86 miles from the DWH spill site (28°44.175′ N, 88°22.335′ W) in the Gulf of Mexico on 5 May 2010. Two samples from the deep hydrocarbon plume (original ID B3 and B6, biological replicates) were collected on 31 May 2010 within 3.5 m of the Macondo wellhead (28°41.686′ N, 88°26.081′ W) at water depths of 1,170 and 1,210 m; these samples were combined for the SIP experiment. In addition, this dataset includes gene counts and annotations from the above genomes

Suggested Citation:

Andreas Teske. 2017. Metagenomic analysis of bacterial Stable-Isotope-Probing enrichments from Deepwater Horizon surface and deep plume, enriched on C13-labelled aromatics and alkanes, May 2010. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7GH9FZ8

Publications:

Dombrowski, N., Donaho, J. A., Gutierrez, T., Seitz, K. W., Teske, A. P., & Baker, B. J. (2016). Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nature Microbiology, 1(7), 16057. doi:10.1038/nmicrobiol.2016.57

Purpose:

Marine microorganisms derive energy and carbon from the degradation of hydrocarbons in oil, which aids in the bioremediation process during anthropogenic oil spills, such as the Deepwater Horizon (DWH) spill. A variety of uncultured bacteria, primarily belonging to Oceanospirillales and other Gammaproteobacteria, were enriched during the DWH spill and are believed to have played a major role in oil degradation. However, this assumption is largely based on the dominance of these organisms in environmental sequencing surveys, whereas the metabolic potential and pathways for degrading oil hydrocarbons in bacterial populations that demonstrably assimilate these compounds remain to be determined. To address this question, we obtained ~113 Gb of shotgun metagenomic data from hydrocarbon-degrading enrichments obtained in previous stable-isotope probing experiments (SIP).

Data Parameters and Units:

Compound (chemical used in enrichment); NCBI Bioproject (NCBI accession number); Date sample collected (day enriched sample collected dd-month-yy); Lat (Latitude, degrees decimal minutes; Long (Longitude, degrees decimal minutes;); Organism accession number (NCBI accession number); Assembly (NCBI accession number); WGS (NCBI accession number); BioSample (NCBI accession number); Isolate (isolate name); Shared gene annotation (gene annotations shared between SIP incubations); Counts (number of hits against the respective gene function); Hexadecane unique genes; Naphthalene unique genes; Phenanthrene unique genes; Subsystem (SEED subsystem annotation); Function (SEED gene function annotation); Gene (gene name); H-Mar (number of total gene hits in the Marinobacter genome assembled from the hexadecane incubation); N-Tha (number of total gene hits in the Thalassospira genome assembled from the hexadecane incubation); N-Alc (number of total gene hits in the Alcanivorax genome assembled from the naphthalene incubation); N-Alt (number of total gene hits in the Alteromonas genome assembled from the naphthalene incubation); P-Cyc (number of total gene hits in the Cycloclasticus genome assembled from the phenanthrene incubation); P-Nep (number of total gene hits in the Neptuniibacter genome assembled from the phenanthrene incubation); P_Col (number of total gene hits in the Colwellia genome assembled from the phenanthrene incubation)

Methods:

The dataset includes ∼113 Gb of shotgun metagenomic data from hydrocarbon-degrading enrichments using stable-isotope probing experiments. The bacterial enrichments were inoculated with weathered hydrocarbons floating on the sea surface and with water samples obtained from the subsurface hydrocarbon plume, collected during the DWH oil spill in May 2010 on RV Pelican. During the SIP experiments, the plume sample was incubated with 13C-labeled n-hexadecane, and the sea surface sample was separately incubated with 13C-labeled naphthalene or phenanthrene. Genomes were obtained by de-novo assembly and tetranucleotide-based binning of metagenomic sequences from the 13C-labeled fractions.

Provenance and Historical References:

DNA samples for metagenomic sequencing and reconstruction of bacterial genomes were obtained from a previously published stable-isotope probing (SIP) experiment using C13-labelled n-hexadecane, naphthalene and phenanthrene as substrates (Gutierrez et al. 2013. ISME Journal 7: 2091-2104). This SIP experiment was started with surface water and deep water samples collected in May 2010. Oil-contaminated sea surface samples were collected near a site of the Deepwater Horizon (DWH) spill (28°44.175′ N, 88°22.335′ W) in the Gulf of Mexico on 5 May 2010, and used for the SIP enrichments on naphthalene and phenanthrene. Two deep hydrocarbon plume samples were collected near the Macondo wellhead (28°41.175′ N, 88°26.081′ W) at a depth of 1170 and 1210 meters on May 31 2010, and combined for the SIP enrichment on n-hexadecane.

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