Abstract:

Marsh sediment samples were collected from 21 permanent stations that were established in 2011 to include: reference, moderately oiled, and heavily oiled sites (7 replicates each) in Barataria Bay, Louisiana from 2018-05-24 to 2018-10-30. Oil-degrading bacterial populations were determined by plating with BH agar and oil-degrading genes quantified with real-time quantitative PCR assays. The data is essential for accurate assessment of petroleum hydrocarbon biodegradation.

Suggested Citation:

Ren, Jiusheng; Hou, Aixin. 2019. Soil oil-degrading bacterial populations in oil-contaminated sediments collected in Barataria Bay, Louisiana from 2018-05-24 to 2018-10-30. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-3d6f-3010

Purpose:

The purpose of this experiment was to determine if oil-degrading bacterial genes remain elevated in salt marshes that were oiled during the Deepwater Horizon oil spill. Absolute quantities of the genes involved in oil degradation in these samples were also estimated through the use of a standard curve.

Data Parameters and Units:

The dataset consists of one excel file which contains the estimates of oil-degrading populations, as determined with qPCR, in oil-contaminated sediments collected from multiple sites over several time frames. The copy gene numbers per sample are given for the alkane hydroxylase (alkB) gene, Gram positive PAH-ring hydroxylating dioxygenases (GP), and Gram negative (GN) PAH-ring hydroxylating dioxygenases. Parameters: Well, Replicate, Sample (the type of analyte), Cq (quantitation cycle), Cq Mean, Cq Std. Dev, Starting Quantity (SQ), Log Starting Quantity, SQ Mean, SQ Std. Dev, Stations ID, Oiling Level, Sampling Date (YYYY-MM-DD), Lat (Latitude in decimal degrees), Lon (Longitude in decimal degrees).

Methods:

DNA was extracted from 1g of soil by the freeze grind method. qPCR was performed on a BioRad CFX machine. The qPCR protocol for alkB genes was performed according to Powell et al., 2006 with the modification of the denaturing temperature to 95 degrees C, and GP and GN genes according to Cebron et al., 2008.

Instruments:

CFX Connect Real-Time PCR Detection System.

Provenance and Historical References:

Cébron, A., Norini, M.-P., Beguiristain, T., & Leyval, C. (2008). Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from Gram positive and Gram negative bacteria in soil and sediment samples. Journal of Microbiological Methods, 73(2), 148–159. doi:10.1016/j.mimet.2008.01.009 Powell, S. M., Ferguson, S. H., Bowman, J. P., & Snape, I. (2006). Using Real-Time PCR to Assess Changes in the Hydrocarbon-Degrading Microbial Community in Antarctic Soil During Bioremediation. Microbial Ecology, 52(3), 523–532. doi:10.1007/s00248-006-9131-z

Individual Files: