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.
Purpose
To track bacterial abundances in Pensacola Beach following the Deepwater Horizon oil spill.
Keywords
beach, SSU rRNA gene, 16S gene, bacterial abundance, alcanivorax abundance, quantitative PCR, Deepwater Horizon oil spill
UDI
R4.x267.000:0098
Date
April 2018
Point of Contact
Name
Will Overholt
Organization
Georgia Institute of Technology / School of Earth and Atmospheric Sciences
Name
Joel E. Kostka
Organization
Georgia Institute of Technology / School of Earth and Atmospheric Sciences
Funding Source
RFP-4
DOI
10.7266/N78C9TSB
Rights Information
This work is licensed under a
Creative Commons Public Domain Dedication 1.0 License.
Scholar Commons 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: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N78C9TSB
Comments
Supplemental Information
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|||||