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Metagenomic data from sand collected from Pensacola Beach, Florida, July 2010-June 2011

Authors: Kostka, Joel
Published On: Jan 15 2016 17:58 UTC
DOI: https://doi.org/10.7266/N7348HCW
UDI: R1.x138.079:0064
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Project Information

Funded By:
Gulf of Mexico Research Initiative

Funding Cycle:
RFP-I

Research Group:
Deepsea to Coast Connectivity in the Eastern Gulf of Mexico (DEEP-C)

Point of Contact

Will Overholt
Georgia Institute of Technology / School of Earth and Atmospheric Sciences
waoverholt@gmail.com

Data Collection Period
2010-05-06
to
2011-06-14
Theme keywords

Metagenomics, Illumina MiSeq, 16s rRNA, Sand microbiome, total community DNA

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Abstract:

This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after Deepwater Horizon oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Total genomic DNA was extracted from beach sands collected on 07/30/2010, 10/20/2010, and 06/14/2011 using MoBio powersoil extraction kits. 16S rRNA gene amplicons from the V4 region were generated using primers 515F/806R, and total community DNA was sequenced using a shotgun sequencing approach.

Suggested Citation:

Kostka, Joel. 2016. Metagenomic data from sand collected from Pensacola Beach, Florida, July 2010-June 2011. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7348HCW

Publications:

Rodriguez-R, L. M., Overholt, W. A., Hagan, C., Huettel, M., Kostka, J. E., & Konstantinidis, K. T. (2015). Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME J, 9(9), 1928–1940. doi:10.1038/ismej.2015.5

Purpose:

To investigate the successional patterns of functional and taxonomic diversity for 1 year after the Deepwater Horizon oil spill.

Data Parameters and Units:

RunID; BioSample ID; Sample name; Library name; # of spots; # of Bases (Mbp); Size (Mb); Assay Type (WGS, Amplicon); Experiment; Insert Size; Oiling Status (Pre-oil, Oiled, Weathered oil), Recovered SRA Sample; Collection Date (Year-Month-Day); Depth (cm); environment biome; environment feature; environment material; geographic location; latitude (decimal degrees); longitude (decimal degrees); sample collection device or method; source material identifiers; oiling status

Methods:

16S rRNA gene amplicon libraries were prepared on both pooled and original samples. Genomic DNA was sequenced at the Argonne National Laboratory using Illumina MiSeq with paired-end strategy and reads of 151bp in length, using custom sequencing primers and procedures as previously described (Caporaso et al., 2012, ISME J 6:1621–1624).