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Metagenomic analysis of bacterial Stable-Isotope-Probing enrichments from Deepwater Horizon surface and deep plume, enriched on C13-labelled aromatics and alkanes, May 2010

Ecosystem Impacts of Oil and Gas Inputs to the Gulf-2 (ECOGIG-2)

DOI:
10.7266/N7GH9FZ8
 
UDI:
R4.x268.185:0005
Last Update:
Mar 29 2017 16:31 UTC
 
Dataset Author(s):
Andreas Teske
Point of Contact:
Teske, Andreas P.
University of North Carolina at Chapel Hill / Department of Marine Sciences
3202 Venable Hall, CB 3300
Chapel Hill, North Carolina  27599
USA
teske@email.unc.edu
Funding Source:
RFP-IV
Data Collection Period:
2010-05-05 to 2010-05-31

Identified Submitted Metadata Available
3 3 3 3

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

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).

Theme Keywords:

Metagenomics, stable isotope probing, metabolic pathways, hydrocarbon-degrading bacteria, MC252, Deepwater Horizon wellhead

File Format:

xlsx

Dataset Downloads:

2

Metagenomic analysis of bacterial Stable-Isotope-Probing enrichments from Deepwater Horizon surface and deep plume, enriched on C13-labelled aromatics and alkanes, May 2010



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x268.185-0005-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Matthew Saxton
      Organisation name: 
          University of Georgia / Department of Marine Sciences
      Position name: 
          ECOGIG Managing Director
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  7065426818
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  325 Sanford Dr
              City: 
                  Athens
              Administrative area: 
                  Georgia
              Postal code: 
                  30602
              Country: 
                  USA
              Electronic mail address: 
                  msaxton@uga.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2017-04-18T20:03:17+00:00
  Metadata standard name: 
      ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
  Metadata standard version: 
      ISO 19115-2:2009(E)
  Dataset URI: 
      https://data.gulfresearchinitiative.org/metadata/R4.x268.185:0005
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Identification info: Data identification: Citation: Citation: Title: Metagenomic analysis of bacterial Stable-Isotope-Probing enrichments from Deepwater Horizon surface and deep plume, enriched on C13-labelled aromatics and alkanes, May 2010 Alternate title: Date: Date: Date: 2017-03-29 Date type: Date type code: publication 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 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). Status: Progress code: completed Point of contact: Responsible party: Individual name: Andreas P. Teske Organisation name: University of North Carolina at Chapel Hill / Department of Marine Sciences Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 9198432463 Facsimile: Address: Address: Delivery point: 3202 Venable Hall, CB 3300 City: Chapel Hill Administrative area: North Carolina Postal code: 27599 Country: USA Electronic mail address: teske@email.unc.edu Role: Role code: principalInvestigator Descriptive keywords: Keywords: Keyword: Metagenomics Keyword: stable isotope probing Keyword: metabolic pathways Keyword: hydrocarbon-degrading bacteria Keyword: MC252 Keyword: Deepwater Horizon wellhead Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Gulf of Mexico Type: Keyword type code: place Language: eng; USA Topic category: Topic category code: environment Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -88.43468 East bound longitude: -88.37225 South bound latitude: 28.68625 North bound latitude: 28.73625 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 28.68625 -88.43468 gml:pointMember: Point: gml:pos: 28.73625 -88.37225 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2010-05-05 End date: 2010-05-31 Supplemental Information: 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)|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.||||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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Distribution info: Distribution: Distributor: Distributor: Distributor contact: Responsible party: Organisation name: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) Contact info: Contact: Phone: Telephone: Voice: +1-361-825-3604 Facsimile: +1-361-825-2050 Address: Address: Delivery point: 6300 Ocean Drive Unit 5869 City: Corpus Christi Administrative area: Texas Postal code: 78412-5869 Country: USA Electronic mail address: griidc@gomri.org Online Resource: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org Role: Role code: distributor Distributor format: Format: Name: xlsx Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 0.1865 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x268.185:0005 Protocol: https
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Metadata maintenance: Maintenance information: Maintenance and update frequency: unknown Maintenance note: This ISO metadata record was automatically generated from information provided to GRIIDC for dataset: R4.x268.185:0005 on 2017-04-06T19:31:51+00:00
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