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CWC 2012-2014 Louisiana marsh sediment bacterial communities after the Deepwater Horizon oil spill

Authors: Engel, Annette
Published On: Jan 08 2016 15:47 UTC
DOI: https://doi.org/10.7266/N7W37T8P
UDI: R1.x139.143:0014
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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
2012-06-01
to
2014-12-31
Theme keywords

marsh, bacteria, sediment, 16S rDNA

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Abstract:

This study was done to evaluate changes in microbial communities from coastal marsh subtidal sediments, inland soils, and water in southern Louisiana. These marshes were impacted by the Gulf of Mexico oil spill in 2010, and this project is a continuation and extension of PRJNA232457 (from 2010 - 2013). New samples were acquired from core locations as part of the Coastal Waters Consortium, from June 2012 through October 2014. Bacterial communities were assessed from subtidal sediments collected at 1-2 m from the marsh vegetation edge or from soils collected 5 m inland from the edge (labeled with IN). Water samples were collected from the edge (labeled with EW). Sediment and soil were collected from push cores and sectioned in the field at (A) 0-1 cm, (B) 1-2 cm, (C) 4-5 cm, and (D) 9-10 cm depth intervals. From extracted DNA, the V1-V3 region of the bacterial 16S rRNA gene was amplified and single-direction reads were generated using multiplexed, bar-coded primers for pyrosequencing.

Suggested Citation:

Engel, Annette. 2016. CWC 2012-2014 Louisiana marsh sediment bacterial communities after the Deepwater Horizon oil spill. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7W37T8P

Purpose:

454 tag pyrosequencing of the V1-V3 region of bacterial 16S rRNA genes from marsh sediment and soil environmental samples supports the study of bacterial community diversity and function.

Data Parameters and Units:

Raw sequence reads, collection date (DD-MMM-YYYY), depth (centimeters), elevation (meters), env material (sediment or water), latitude, longitude, water pH, water salinity (parts per thousand), water temperature (degrees Celsius)

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).

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).