Abstract:

This dataset includes high-throughput amplicons for alkane dehydrogenase (alkB) genes, particulate monooxygenase (pmoA) genes, and cytochrome P450, encoded by CYP153, genes amplified and sequenced from subtidal sediment and inland soil samples collected biannually (September 2011 to October 2014) from a marsh near Grand Isle, Louisiana. This marsh was affected by oil deposition following the Deepwater Horizon oil spill in 2010. Other data reported are sample collection information, elevation and water and soil characteristics.

Suggested Citation:

Engel, Annette Summers, Paterson, Audrey. 2018. Alkane oxidation genes alkB, pmoA, and cytochrome P450 CYP153 from inland marsh soil and subtidal sediment, Grand Isle, Louisiana, 2011-2014. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7S75DTK

Purpose:

The goals of this dataset are to 1) track changes in the phylogenetic diversity of genes that code for key enzymes used for bacterial alkane oxidation, short and long chain, from the oil impacted sediments and soil, and 2) to contribute to an understanding of bacterial functional role in the degradation of weathered oil residues in a natural marsh system.

Data Parameters and Units:

Raw sequence reads, collection date (YYYY-MM-DD), depth (centimeters), elevation (meters), environment material (terrigenous or marine sediment), latitude (dec degrees), longitude (dec degrees), sample collection or device (push core or scraping), temperature (degrees Celsius), water salinity (parts per thousand), water content (% weight), water pH, total organic carbon (% dry weight), forward primer sequence, assay type, bioproject, biosample model, organism, platform, SRA study, biome, feature, geographic location

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 alkB, pmoA, and CYP153 genes were done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX). Subtidal sediments were collected 1-2 m offshore from the marsh vegetation edge (labelled A1 for 0-1 cm depth and C1 for 4-5 cm depth), and inland soils were collected 5 m from the edge (labelled MS). From extracted DNA, functional genes were amplified and single-direction reads were generated using multiplexed, barcoded primers for pyrosequencing. Guerry, P., LeBlanc, D.J., & Falkow, S. 1973. General Method for the Isolation of Plasmid Deoxyribonucleic Acid. Journal of Bacteriology, 116(2): 1064-1066. Somerville, C.C., Knight, I.T., Straube, W.L., & Colwell, R.R. 1989. Simple, Rapid Method for Direct Isolation of Nucleic Acids from Aquatic Environments. Applied and Environmental Microbiology, 55(3): 548-554. Zhou, J., Bruns, M.A., & Tiedje, J.M. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 62(2): 316-322. Mitchell, K.R. & Takacs-Vesbach, C.D. 2008. A comparison of methods for total community DNA preservation and extraction from various thermal environments. Journal of Industrial Microbiology & Biotechnology, 35(10): 1139-1147.

Instruments:

Pyrosequencing of the alkB, pmoA, and CYP153 genes were done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX).

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