Abstract:

Mesocosm experiments were carried out to test the effect of oil and Corexit on microbial community gene expression over time. Four mesocosm treatments were prepared in triplicate for this study: (1) Control (seawater only); (2) Water accommodated fraction (WAF; oil + seawater); (3) Chemically-enhanced WAF (CEWAF; oil + Corexit + seawater); (4) Diluted CEWAF (DCEWAF; 1:10 dilution). Water was collected from each mesocosm and filtered (47mm, 0.2um PES membranes). Total RNA was extracted from filtered water samples and sequenced using Illumina HiSeq 2500.

Suggested Citation:

Shawn Doyle, Genmei Lin, Jason Sylvan. 2019. Metatranscriptomes: Gulf of Mexico Open Ocean (GOMOO) and Gulf of Mexico Coastal Waters (GOMCOAST). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/9EDJRA3Q

Publications:

Doyle, S. M., Lin, G., Morales-McDevitt, M., Wade, T. L., Quigg, A., & Sylvan, J. B. (2020). Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways. mSystems, 5(4). doi:10.1128/msystems.00668-20

Purpose:

To characterize microbial community gene expression in the Gulf of Mexico Open Ocean (GOMOO) and Gulf of Mexico Coastal Waters (GOMCOAST) experiments.

Data Parameters and Units:

Dataset consists of a text file (GOMOO_and_GOMCOAST_MetaT_SRA_RunTable.txt) and two word documents - “Mesocosm methods M3 GOMOO 2017 07 14.docx” and “Mesocosm methods M4 GOMCOAST 2017 07 14.docx”. The word documents provide details on how the Mesocosm experiments 3 and 4 were prepared and executed. The text document provides details on accession numbers of sequences obtained during the experiment and experimental conditions under which sequences were obtained.

Methods:

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. Mixing ended 24 hrs after the initial oil addition (Knap et al. 1986; Wade et al. 2017 in preparation). 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 (2 L light /dark bottles, 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. Mixing ended 24 hrs after the initial oil addition. The CEWAF was then introduced into the CEWAF mesocosm tanks and filled to 96 L and mixed. From these CEWAF tanks, 13 L was removed for other experiments and analyses (7 L for the DCEWAF mesocosms, 2 L light/dark, 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 (2 L light/dark, 4 L hydrocarbon analyses). The more details on the methods are provided in word documents included in the dataset.

Provenance and Historical References:

Knap, A. H., Burns, K. A., Dawson, R., Ehrhardt, M., & Palmork, K. H. (1986). Dissolved/dispersed hydrocarbons, tarballs and the surface microlayer: Experiences from an IOC/UNEP Workshop in Bermuda, December, 1984. Marine Pollution Bulletin, 17(7), 313–319. doi:10.1016/0025-326x(86)90217-1 Wade, T. L., Morales-McDevitt, M., Bera, G., Shi, D., Sweet, S., Wang, B., … Knap, A. H. (2017). A method for the production of large volumes of WAF and CEWAF for dosing mesocosms to understand marine oil snow formation. Heliyon, 3(10), e00419. doi:10.1016/j.heliyon.2017.e00419

Individual Files: