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Study

Study Name: Oil-contaminated marine microbial communities from the Macondo wellhead oil leak, Gulf of Mexico

Projects

Biosamples

Organisms

Biosamples: 0 Seq. Projects: 6
STUDY INFORMATION
GOLD Study ID Gs0103002
Study Name Oil-contaminated marine microbial communities from the Macondo wellhead oil leak, Gulf of Mexico
Other Names Creating a successional model for carbon remediation in the Gulf of Mexico
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 58002
Legacy GOLD ID Gm0058002
Added By Michelle Isbandi on 2013-10-22
Last Modified By Tatiparthi Reddy on 2013-12-10
PI Jack Gilbert
Description The Macondo wellhead oil leak, in the Gulf of Mexico, released a complex mixture of hydrocarbons into the water column that stimulated the growth, metabolic activity, and succession of a diverse, yet distinct, hydrocarbon-degrading microbial community. These samples range from the earliest collection dates in the wellhead area (May 6th 2010) just two weeks after the explosion, to the most recent acquisitions, collected with submersible Alvin from the seafloor, 1 nautical mile south of the now-capped Macondo wellhead (December 2nd 2010), 7 months following the disaster. Sample collection and monitoring at these sites is still continuing in 2011 and 2012, focusing on sediments. Our current and available sample collection has more than 800 unique samples spanning oil-impacted and clean pelagic and sediment samples from a broad temporal and geospatial range. Concomitant to these samples are a suite of vital physicochemical data that contextualize the environment from which these samples were acquired. We propose to sequence and annotate the 16/18S rRNA profile for every sample, to sequence and annotate the whole community DNA from 100 samples, to sequence and assemble the dominant genomes associated with each sample, and to use these combined data to generate descriptive and predictive network models for the taxonomic and functional succession of the bioremediation of the Macondo Wellhead oil leak. This study is driven by four scientific questions; 1) what was the spatial and temporal evolution of the microbial oil spill response? 2) What types of microbial hydrocarbon degradation pathways are involved where and when? 3) What factors determine the differentiation of primary and secondary oil degradation response? 4) Can exploration of the community succession enable predictive, not just retrospective potential, and are observed patterns robust enough to enable application to other oil spills? We wish to generate 100 metagenomic libraries, producing 5 billion base pairs of sequence data from each of these samples using the 2x125bp paired end sequencing strategy on Illumina HiSeq2000. In addition we would like to apply half a 454 GS-flx picotitre plate to each of the enrichment cultures and 1 Pac Bio RS1 platform run per enrichment. In total we request 500 billion base pairs of Illumina sequencing, 10 454 GS-flx plates, and 10 RS1 platform runs with strobe sequencing to minimize errors. These data will be used to compliment 16S and 18S rRNA sequencing performed using the ITAG Illumina approach. In addition we would like to generate 2 genomes from each of the 5 marine enrichments, and 5 sediment enrichments, generating 20 genomes from organisms selected via cell-sorting.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Aquatic
Ecosystem Type Marine
Ecosystem Subtype Oceanic
Specific Ecosystem
STUDY COMPOSITION
Number of Biosamples 0
Number of Organisms 6
Number of Seq Projects 6
Number of Analysis Projects 4
Number of Related Studies 0

 

 

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