Abstract:

Bacterial abundances were tracked approximately every 6 weeks for one year beginning in June 2010 in Pensacola Beach. Sand samples were visibly assessed as oil contaminated or "clean" and total genomic DNA was extracted using a MoBio powersoil DNA extraction kit. Total bacterial 16S rRNA gene abundances were quantified using taqman qPCR with 331F/772R primers and a 515R probe, while Alcanivorax 16S rRNA gene abundances were quantified with the same probe with 464F/675R primer. This dataset supports the publication: Kostka, J.E., Prakash, O., Overholt, W.A., Green, S.J., Freyer, G., Canion, A., Delgardio, J., Norton, N., Hazen, T.C., & Huettel, M. (2011). Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied and Environmental Microbiology, 77(22): 7962-7974.

Suggested Citation:

Will A. Overholt. 2018. Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N78C9TSB

Purpose:

To track bacterial abundances in Pensacola Beach following the Deepwater Horizon oil spill.

Data Parameters and Units:

sample_set1: SampleID/Sample Name: Sample Identifier (ID) Date: Sample collection date (MM/DD/YYYY) Location: Sample location (PB-PB6) Depth: Sample depth (cm) Description: Description of sample location) Oil Presence: qualitative scale for degree of oiling (0 = no visible oil, 3 = highest degree of oiling) Weight: Mass of wet sand for DNA extraction DNA: DNA concentration from extraction (ng/µl) Dilution Elution volume (ul) Comment Name Check Volume added to reaction (ul) Plate number Slope and Intercept: Standard curve generated for each qPCR plate Total bacterial abundances (columns P-AF) Alcanivorax specific abundances (columns AG-BA) CT: Critical threshold of the sample; measured in triplicate Conc: Determined number of gene copies in the sample Copies per uL: gene copies per µl extracted (gene copies / total volume DNA eluted into) Copies per g sediment: gene copies per gram sediment extracted from (wet weight) Oil (0-3) BAC (copies/g) ALC (copies/g) %ALC sample_set2: Sample name: Sample identifier Date sampled (MM/DD/YYYY) Depth (cm) Oil presence (0 = no visible oil, 3 = heavily oiled, tar = tarball/surface residual ball Site description DNA concentration (ng/ul) Dilution Sediment wet weight (g) Dilution at sequence DNA added to reaction Slope Intercept CT: Critical threshold of the sample; measured in triplicate Conc: Determined number of gene copies in the sample Copies per uL: gene copies per µl extracted (gene copies / total volume DNA eluted into) Copies per g sediment: gene copies per gram sediment extracted from (wet weight) Average copies/reaction Standard deviation Standard error

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