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Bacterial community diversity on analog site sandy beaches before and after the Deepwater Horizon oil spill in the Gulf of Mexico, Grand Isle, Louisiana, and Dauphin Island, Alabama, 5-3-2010 to 5-20-2011.

Authors: Annette Engel
Published On: Sep 17 2015 15:18 UTC
DOI: https://doi.org/10.7266/N7MK69TM
UDI: R1.x139.143:0016
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No. of Downloads: 0

File Format(s):
NCBI SRA data sff

Project Information

Funded By:
Gulf of Mexico Research Initiative

Funding Cycle:
RFP-I

Research Group:
Coastal Waters Consortium (CWC)

Point of Contact

Jason Weick
Louisiana Universities Marine Consortium (LUMCON) / Data Management
jweick@lumcon.edu

Data Collection Period
2010-05-03
to
2011-05-13
Theme keywords

marine, sand, beach, microbial diversity, oil spill, fecal contamination, sedimentology, 16S rRNA

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Abstract:

Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along the Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changed would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sandwashing and sediment redistribution, would impact microbial ecosystem resiliency. Transects perpendicular to the shoreline were sampled from public beaches on Grand Isle, Louisiana, and Dauphin Island, Alabama, over one year. NCBI data link: http://www.ncbi.nlm.nih.gov/bioproject/170912.

Suggested Citation:

Annette Engel. 2015. Bacterial community diversity on analog site sandy beaches before and after the Deepwater Horizon oil spill in the Gulf of Mexico, Grand Isle, Louisiana, and Dauphin Island, Alabama, 5-3-2010 to 5-20-2011.. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7MK69TM

Publications:

Yin, J., Rekepalli, B., Patel, P., Drennen, C., & Engel, A. S. (2014). Instrumenting Genomic Sequence Analysis Pipeline Mothur on Shared Memory Architecture. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE ’14. doi:10.1145/2616498.2616505

Purpose:

454 tag pyrosequencing of the V1-V3 region of bacterial 16S rRNA genes in sandy beach environmental samples support the study of bacterial community diversity and function, sediment distribution, and physicochemical conditions over a one year period following the Deepwater Horizon oil spill.

Data Parameters and Units:

Bacterial community diversity of sandy beaches before and after the Deepwater Horizon oil spill in the Gulf of Mexico Targeted Locus (Loci) 454 tag pyrosequences of the V1-V3 region of the bacterial 16S rRNA gene Organism: beach sand metagenome (Taxonomy ID 412757) BioProject Accession: PRJNA170912 ID: 170912 Attributes:Scope: Environment; Material: Genome; Capture: Targeted Locus Loci; Method type: Sequencing Relevance:Environmental Data Parameters: Sequence data, SRA Experiments 113, BioSample 113, SRA Data Gbases 1 Lineage:unclassified sequences; metagenomes; ecological metagenomes; beach sand metagenome[Taxonomy ID: 412757] ]

Methods:

Total nucleic acids were extracted in triplicate. Five grams sediment for each sample was subjected to methods modified from Somerville et al. (1989; Appl Environ Microbiol, 55(3): 548-554) and Zhou et al. (1996, Appl Environ Microbiol, 62(2): 316-322) that incorporated sucrose lysis buffer with lysozyme (1 mg/ml), a solution of 5X proteinase K/CTAB/SDS, and overnight incubation at 550 C while shaking at 100 rpm. After protein precipitation, nucleic acids were precipitated in isopropanol overnight at -20?C prior to washing with ethanol and purification.

Instruments:

Pyrosequencing of the V1-V3 region of 16S rRNA genes was done using a 454 GS FLX Titanium at the Research and Testing Laboratory (Lubbock, TX)