Abstract:

This dataset includes an inventory of processed, taxonomically classified bacterial amplicons from marsh sediment collected in May 2013, a component of a longitudinal study of marsh microbial diversity and sediment stability before, during, and after oil deposition associated with the Deepwater Horizon oil spill. Data include the results of 454 tag pyrosequencing of the V1-V3 region of bacterial 16S rRNA genes from marsh sediment and soil environmental samples. Inland soil and subtidal sediment samples were collected 5 m inland from the marsh edge and 1-2m offshore, respectively. Complementary field data for the May 2013 collection are reported separately (R1.x139.143:0013).

Suggested Citation:

Annette Summers Engel, Audrey Paterson. 2016. May 2013 bacterial diversity data supporting changes in Louisiana marsh sediment microbial communities after the Deepwater Horizon oil spill. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N73N21BJ

Purpose:

The goals of the dataset are 1) to assess and track bacterial community composition in Louisiana marshes over time and 2) to contribute to a biophysical model of marsh ecosystem processes in the context of petrogenic and biogenic hydrocarbon exposures.

Data Parameters and Units:

Data are reported as classified 454 amplicon abundance at the bacterial phylum and proteobacterial class levels. For each sample, data are reported as follows: sample ID, latitude (decimal degrees N), longitude (decimal degrees W), collection date (DD-MMM-YYYY), sample description, geographic location name, total classified amplicons.

Methods:

Total nucleic acids were extracted in triplicate. Three to six grams of marsh sediment or soil were subjected to DNA isolation methods that incorporated sucrose lysis buffer with lysozyme (1 mg/ml) and a solution of 5X proteinase K/CTAB/SDS; incubation at 55 degrees C while shaking at 40-120 rpm; nucleic acids precipitation in isopropanol at -20 degrees C; and ethanol washing. This approach was modified from Guerry et al. (1973), Somerville et al.(1989), Zhou et al. (1996), and Mitchell and Takacs-Vesbach (2008). Amplification and pyrosequencing of the V1-V3 region of 16S rRNA genes were done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX). Raw 16S rRNA gene sequences were processed using the microbial ecology community software Mothur (http://www.mothur.org/wiki/Download_mothur) (Schloss et al., 2011). Amplicons were trimmed for length (200-500bp) and quality (average quality score of 35 over a sliding window of 50bp), aligned and classified using the SILVA reference database (https://www.arb-silva.de/silva-license-information), screened and filtered, and removed of chimera detected by UCHIME (http://drive5.com/uchime)(Schloss et al., 2011). Inventories of processed reads classified at the bacterial phylum and proteobacterial class levels are provided for each sediment sample.

Instruments:

Pyrosequencing of the V1-V3 region of 16S rRNA genes was done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX).

Individual Files: