Abstract:
Illumina HiSeq (100 bp PE) mRNA sequence from a eukaryotic fraction of the microbial community. Samples were collected from coastal mesocosm studies to assess the response of the planktonic community to exposure to oil and Corexit. The content of this dataset includes the location in NCBI of 6 RNA sequencing samples for eukaryotic plankton for the ADDOMEx mesocosm experiment, a Test of Coastal water with coastal microbial concentrate, TeCOAST (Mesocosm 1). This dataset also includes the SraRunTable (biosample accession SAMN05615432 at https://www.ncbi.nlm.nih.gov/biosample/5615432) for these data.
Suggested Citation:
Zoe Finkel, Andrew Irwin. 2019. Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-kvpb-0878
Purpose:
RNA was extracted from samples at the end of the mesocosm experiment to enable analysis of eukaryotic community structure and relative transcript abundance in response to oil (WAF; water accommodated fraction) and Corexit enhanced WAF (CEWAF and dilute CEWAF; chemically enhanced water accommodated fraction) treatments.
Data Parameters and Units:
Raw reads from Illumina HiSeq
MESO1=mesocosm 1, TeCOAST;
WC=water column;
Bot=bottom, the accumulated marine snow in the bottom of one replicate from each treatment;
1, 2, 3 or 2, 3, 4= replicate number;
Treatments of control, WAF, CEWAF, and dilute CEWAF (DCEWAF) are described in the methods section. Briefly, control is Gulf of Mexico seawater with no additions, WAF is water accommodated fraction, CEWAF is chemically enhanced WAF (Corexit + WAF), and DCEWAF is diluted CEWAF. Concentrations are given in the methods.
All samples were taken at the end of the experiment (74 hours). Samples can be found at NCBI under accession numbers:
MESO1-WC1: water column, control: SRR4238820
MESO1-WC2: water column, WAF: SRR4238822
MESO1-WC3: water column, CEWAF: SRR4238824
MESO1-Bot2: bottom sample, WAF: SRR4238825
MESO1-Bot3: bottom sample, CEWAF: SRR4238826
MESO1-Bot4: bottom sample, dilute CEWAF: SRR4238833
Methods:
TeCOAST (Mesocosm 1): mesocosms for a Test of Coastal water with coastal microbial concentrate
The seawater used in the TeCOAST mesocosm studies was collected on July 30, 2015, from 8 kilometers offshore south of Galveston (TX) in the Gulf of Mexico. The salinity was 34. The seawater was processed through a charcoal filter to remove large particles and debris. Four mesocosm tanks were treated in the following way. The control tank was filled with the seawater directly from the storage tank of filtered seawater. This seawater was also used to fill 130 L recirculating glass flumes to make water accommodated fraction (WAF) and a chemically enhanced water accommodated fraction of oil (CEWAF). The WAF was prepared by mixing a total of 24 mL (2 ml to start, 2 ml after 1 hr, then 5 ml at ~ 2, 3, 4 and 5 hrs total of 24 ml) of Macondo surrogate Marlin oil into 130 L of the seawater. Total mixing time from the start of oil addition to transfer to the mesocosms was 18 hrs. The WAF (79 L) was transferred to the WAF mesocosm tank and mixed. In order to make CEWAF, Corexit 9500 was mixed with Macondo Surrogate oil in a ratio of 1:20 (Corexit to oil) and 24 mL of this mixture (2 ml to start, 2 ml after 1 hr, then 5 ml at ~ 2, 3, 4 and 5 hrs total of 24 ml) of surrogate oil plus Corexit was added to 130 L of seawater and mixed for 18 hrs. The CEWAF (79 L) was transferred to the WAF mesocosm tank and mixed. In addition a dilute CEWAF (DCEWAF) mesocosm treatment was produced by adding 9 L of CEWAF to 70 L of the original seawater for a total volume of 79 L. Light dark bottles were also filled from the WAF and CEWAF. Plankton (≥63 µm) samples were collected using a net and transferred into polycarbonate bottles. This concentrated plankton mass was introduced to each mesocosm and stirred (2 L to each tank for a final volume 81 L) immediately prior to starting the experiments. No plankton was added to the light or dark bottles. The EOE concentration for the control, WAF, DCEWAF and CEWAF at the start of the experiments were estimated as 0 mg/L, 3.4 mg/L, 3.6 mg/L and 36 mg/L, respectively. The EOE concentration of the control, WAF, DCEWAF and CEWAF mesocosms averaged for samples taken during the first 74 hours were 0 mg/L , 1.21 mg/L, 4.28 and 43.4 mg/L, respectively. All mesocosms had loses of EOE from 88 to 100%, while the bottles had losses of 56 to 74%.
Estimated Oil Equivalence (EOE)
The estimated oil equivalents (EOE) were determined by fluorescence (Wade et al. 2011) using Macondo surrogate oil as a standard to produce calibration curves at 5 to 7 concentrations. Water samples (5 to 20 ml) were extracted with 5 ml of dichloromethane. An aliquot of the extract was placed in a cuvette for fluorescence analyses (Horiba Scientific Aqualog Fluorometer). The EOE were determined from the calibration curve (Wade et al. 2011). Samples with fluorescence responses that exceeded the calibration curve were diluted so that their fluorescence was within the calibration range. Samples were taken at the beginning and end of the experiment and at intervals in between and at the same time point as measurements of other parameters during the experiment.
Eukaryotic metatranscriptome sampling and analysis
Samples were taken for RNA extraction and sequencing at time t = 74 h from the mesocosm water column for 3 treatments (control, WAF, CEWAF) and from the bottom sediment of 3 treatments (WAF, CEWAF, DCEWAF). Filters were immediately frozen at –80°C. RNA extraction was performed using standard protocols. Sequencing was performed on an Illumina HiSeq 2000 at the McGill University Genome Quebec Innovation Centre (http://gqinnovationcenter.com/index.aspx) using the TruSeq mRNA stranded mRNA protocols. Raw reads from the sequencing pipeline were deposited in the NCBI SRA.
Provenance and Historical References:
Wade, T. L., Sweet, S. T., Walpert, J. N., Sericano, J. L., Singer, J. J., & Guinasso, N. L. (2011). Evaluation of Possible Inputs of Oil From the Deepwater Horizon Spill to the Loop Current and Associated Eddies in the Gulf of Mexico. Geophysical Monograph Series, 83–90. doi:10.1029/2011gm001095
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