Abstract:
Samples were collected from coastal mesocosm studies to assess the response of the planktonic community to exposure to oil and Corexit. This dataset includes the location of 12 RNA sequencing samples for eukaryotic plankton for the ADDOMEx mesocosm experiment, Coastal water with coastal microbial concentrate, COAST (mesocosm 2). This dataset also includes the SraRunTable (biosample accession SAMN09981213) at https://www.ncbi.nlm.nih.gov/biosample/9981213 for these data.
Suggested Citation:
Zoe Finkel, Andrew Irwin. 2019. Eukaryotic community response to oil and Corexit in a mesocosm, October 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/n7-43q9-xq06
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.
Samples can be found at NCBI under following library name and accession numbers:
MESO2-CTRL_REP1: SRR7796775
MESO2-CTRL_REP2: SRR7796776
MESO2-CTRL_REP3: SRR7796777
MESO2-WAF_REP1: SRR7796778
MESO2-WAF_REP2: SRR7796784
MESO2-WAF_REP3: SRR7796783
MESO2-CEWAF_REP1: SRR7796781
MESO2-CEWAF_REP2: SRR7796782
MESO2-CEWAF_REP3: SRR7796773
MESO2-DCEWAF_REP1: SRR7796774
MESO2-DCEWAF_REP1: SRR7796779
MESO2-DCEWAF_REP1: SRR7796780
For library name: MESO2 = mesocosm 2, COAST; REP1, REP2, REP3 = replicate number; CTRL = Treatments of control; WAF is water accommodated fraction; CEWAF is chemically enhanced WAF (Corexit + WAF) and DCEWAF is diluted CEWAF.
Methods:
Method for COAST, a mesocosm study using Gulf of Mexico coastal waters
The seawater was collected from the same location as that used in TeCOAST mesocosm but was collected on October 17 2015, from 8 kilometers offshore south of Galveston, Texas in the Gulf of Mexico. The salinity was 31. The seawater was processed through a charcoal filter to remove large particles and debris. Four treatments were prepared in triplicate. Control tanks were filled with seawater and a plankton mixture. Water accommodated fraction (WAF) of oil was prepared by mixing 25 mL (5 ml ~ every 30 min for 2.5 hrs) of Macondo surrogate oil into 130 L of seawater then mixing for 12 to 24 hrs. The WAF was then introduced into the WAF mesocosm tanks and filled to 87 L and mixed. From these WAF tanks, 6 L was removed for other experiments and analyses (2L for roller tables, 2 L dark/light, 4 L hydrocarbon analyses). In order to make chemically enhanced water accommodated fraction (CEWAF), Corexit was mixed with oil in a ratio of 1:20 and 25 mL of this mixture (5 ml every 30 min for 2.5 hrs) of surrogate oil plus Corexit was added to 130 L of seawater which was mixed for 8 to 24 hrs prior to being transferred to the mesocosm tanks. The CEWAF was then introduced into the CEWAF mesocosm tanks and filled to 96 L and mixed. From these CEWAF tanks, 15 L was removed for other experiments and analyses (9 L for the DCEWAF mesocosms, 2L for roller tables, 2 L dark/light, 4 L hydrocarbon analyses). Diluted CEWAF (DCEWAF) was prepared by mixing 9 L of CEWAF with 78 L of the original seawater for a total volume of 87 L. From these DCEWAF tanks 6 L was removed for other experiments and analyses (2L for roller tables, 2 L dark/light, 4 L hydrocarbon analyses). Plankton (≥63 µm) were collected using a net and transferred into polycarbonate bottles. This concentrated plankton mass was introduced to the tanks and stirred (2 L to each final volume 83 L) immediately prior to starting the experiments. The EOE mean concentration of the three mesocosms for the control, WAF, DCEWAF and CEWAF at the start of the experiments were 0 mg/L, 0.26 mg/L, 2.74 mg/L and 41.5 mg/L, respectively. The EOE mean concentration of the three for the control, WAF, DCEWAF and CEWAF mesocosms after 72 hours were 0 mg/L, 0.06 mg/L, 1.03, and 17.3 mg/L, respectively.
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 = 72 h from each replicate and treatment (3 replicates x 4 treatments = 12 samples). 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, https://www.ncbi.nlm.nih.gov/biosample/9981213.
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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