A mesocosm experiment was conducted October 2015 (COAST, Mesocosm 2) using coastal water collected near Galveston Bay, Texas. Four mesocosm treatments were prepared in triplicate for this study: (1) Control (seawater only); (2) WAF (oil + seawater); (3) Chemically-enhanced WAF (CE-WAF; oil + Corexit + seawater); (4) Diluted CE-WAF (1:10 dilution). Initial mesocosm volumes were 79L. Prior to experiment initiation, phytoplankton were collected from coastal Galveston, TX waters and added to each tank to stimulate interactions between phytoplankton, oil, and Corexit. One sample was taken from all four treatments, three replicate mesocosms each, at time 72 h in clean, opaque Nalgene bottles with PTFE-lined diaphragm pumps. RNA was extracted from filtered water samples and sequenced using Illumina HiSeq. The sequences were deposited at the NCBI short read archive, SRA bioproject code PRJNA489497; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489497
Zoe Finkel, Andrew Irwin, Yue Liang, Deepak Nanjappa. 2020. Eukaryotic phytoplankton community composition in the COAST (Gulf of Mexico, COASTal water mesocosms amended with coastal microbial concentrate) mesocosm as identified by 18S sequence from RNA-seq whole transcriptome sequencing for four treatments (control, WAF, CEWAF, dilute CEWAF). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/032DBZJY
Finkel, Z. V., Liang, Y., Nanjappa, D., Bretherton, L., Brown, C. M., Quigg, A., & Irwin, A. J. (2020). A ribosomal sequence-based oil sensitivity index for phytoplankton groups. Marine Pollution Bulletin, 151, 110798. doi:10.1016/j.marpolbul.2019.110798
Characterize the microbial community composition and structure in the COAST Mesocosm.
Data Parameters and Units:
The two csv files are the output of KrakenUniq, one using the full-length 18S sequences from the PR2 database, and the other using the PR2 database sequences cropped to include just the V4 hypervariable region. This second analysis is intended to be a simulation of the analysis results that would be obtained from a amplicon sequencing approach. The columns of the tables provide the taxonomic labels from the PR2 database, a simplified functional group level (diatoms, dinoflagellates, Chrysophytes, green algae), the raw counts, and the normalized TPM counts. There are 12 columns for each of the raw and TPM counts: control 1-3, waf 1-3, dcewaf 1-3, and cewaf 1-3 corresponding to the 12 biological samples analyzed.
Mesocosm methods – COASTal water with coastal microbial concentrate, COAST: Twelve 100L mesocosm tanks were filled with Gulf of Mexico seawater collected 5 miles offshore from Galveston (TX) that had been pre-treated with a charcoal filter to remove large particles and debris. Plankton (<63 µm) were collected using a net and transferred into polycarbonate bottles. This concentrated plankton mass was introduced to the tanks (2 L to each final volume 83 L) immediately prior to starting the experiments. Four treatments were prepared in triplicate. Control tanks were filled with seawater and 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. (Knap et al. 1983). 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 loaded into 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). The estimated oil equivalents (EOE) were determined using Macondo surrogate oil as the calibration standard (Wade et al. 2011) for the fluorescence analyses (Horiba Scientific Aqualog Fluorometer). 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 mesocosms for the in the control, WAF, DCEWAF and CEWAF after 72 hours were 0 mg/L , 0.06 mg/L, 1.03. and 17.3 mg/L, respectively.
Data treatment for the 18S sequence from RNA-seq whole transcriptome: The data are the results of counting raw reads (deposited at the NCBI short read archive, SRA bioproject code PRJNA489497; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489497) against the PR2 protist rRNA database using the software KrakenUniq. This tool is a k-mer based counting approach which identifies the level in the taxonomic hierarchy at which each k-mer in the target database is unique (i.e., at the species, genus, phylum, order, or kingdom level). Matches between k-mers in the source raw reads and the target database, together with this taxonomic hierarchy, are used to identify species or counts at other levels of the taxonomy.
Provenance and Historical References:
Knap, A.H., Sleeter, T.D., Dodge, R.E., Wyers, S.C., Frith, H.R. and Smith, S.R., 1983. The effects of oil spills and dispersant use on corals: A review and multidisciplinary experimental approach. Oil and Petrochemical Pollution, 1(3), pp.157-169. doi:10.1016/s0143-7127(83)90134-5
Wade, T.L., Sweet S.T., Sericano, J.L., N.L. Guinasso Jr., Diercks, A.-R., Highsmith, R.C., Asper, V.L., Joung, D., Shiller, A.M., Lohrenz, S.E. and Joye, S.B., 2011. Analyses of Water Samples From the Deepwater Horizon Oil Spill: Documentation of the Subsurface Plume. Geophysical Monograph Series, 77–82. doi:10.1029/2011gm001103