Abstract:

Twelve 100 L tanks were filled with Gulf of Mexico seawater collected from the Texas coastline, near the TABS buoy R. Four treatments (WAF, CEWAF, DCEWAF, Control) were prepared in triplicate. A coastal plankton slurry was used to seed the tanks. Immediately prior to starting the experiment, 2 L of slurry was stirred into each tank. Gene counts, annotations, differential expression, and KEGG pathway enrichment analysis of eukaryotic genes from a mesocosm experiment. Raw reads and assembled transcripts are deposited at NCBI.

Suggested Citation:

Irwin, Andrew. 2021. Mesocosm: Eukaryotic community response to oil and oil-dispersant mixtures in the COAST (Gulf of Mexico, COASTal water mesocosms amended with coastal microbial concentrate). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/2JWNDY5F

Purpose:

This experiment was done to evaluate the metabolic analysis, based on metatranscriptome, of marine eukaryotic community in response to oil and oil-dispersant mixture.

Data Parameters and Units:

Table S1 presented as excel spreadsheet file. Summary statistics for the metatranscriptome assembly, annotation, and differential expression analysis of annotated genes. Genes (detected and annotated transcripts with distinct KO IDs) were tested for differential expression. All numbers are counts. Data S1: KEGG pathway enrichment analysis results. Each observation corresponds to a KEGG pathway tested for enrichment in up- or downregulated genes. For each pathway we list the level A, B, C annotation, the number of KO genes in the pathway analyzed for each treatment relative to the control, the number of up- and downregulated genes, the p-value and false discovery rate corrected p-values for the hypergeometric tests of enrichment in up- and downregulated genes. Enriched pathways (FDR < 0.05) are highlighted in yellow (upregulated) or purple (downregulated) matching Table 1. Data S2: All genes with KO ID annotation that were differentially expressed in at least one treatment (WAF, DCEWAF, CEWAF) relative to the control. The table lists the KO ID, the Level A, B, and C KEGG pathway or BRITE membership, the gene names and definitions, the median TPM across replicates for the control and three treatments, the false discovery rate corrected p-value (q-value) for the differential expression analysis, and the loge-fold change in the treatment relative to the control (b-value; negative means lower expression in the treatment). Significantly upregulated genes are highlighted in green and downregulated genes highlighted in red (FDR < 0.05); the color scheme matches the KEGG pathway diagrams in Fig. S2 and S3. Genes can appear in multiple KEGG pathways or BRITEs leading to some genes appearing more than once in different pathways. Data S3: Count table for each transcript in each treatment and replicate. Columns are transcript IDs (transcript_ID) and the Kallisto counts (TPM) for each treatment and replicate (Control_A, Control_B, Control_C, and similarly labeled columns for WAF, DCEWAF, and CEWAF). The sequences for each assembled transcript are available at NCBI TSA (www.ncbi.nlm.nih.gov/nuccore) under the accession GICR00000000. Data S4: Annotations for each transcript identified by Trinity ID. Columns are Trinity transcript ID (target_id), KO gene ID (KO), Gene name (Name), Gene description (Definition), BRITE description (Brite), KEGG Pathway description (Pathway), and Module description (Module).

Methods:

Twelve 100 L tanks were filled with Gulf of Mexico seawater collected from the Texas coastline, near the TABS buoy R. Four treatments were prepared in triplicate, after the method described in Wade et al. (2017). WAF was introduced into the tanks and filled to 87 L and mixed. In order to make chemically enhanced water accommodated fraction (CEWAF), Corexit was mixed with Macondo surrogate oil in a ratio of 1:20 and 25 mL of this mixture (5 mL every 30 min for 2.5 h) was added to 130 L of seawater. The CEWAF was then introduced into the CEWAF tanks and filled to 96 L and mixed. 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. Control tanks were filled with untreated seawater. A coastal plankton slurry was used to seed the tanks. Immediately prior to starting the experiment, 2 L of slurry was stirred into each tank. RNA extraction and sequencing: At the end of each experiment (t = 72 h), plankton from the tanks were filtered on 0.8 µm polycarbonate filter and RNA was extracted and sequenced using Illumina HiSeq 2000. Sequence processing, taxonomic classification, assembly and analysis: Reads were filtered for quality and trimmed. Kraken was used to filter out likely prokaryotic or rRNA reads so that only the eukaryotic mRNA reads could be analyzed. Reads were assembled using Trinity. Transcripts were counted with Kallisto, annotated with Diamond, and differential expression analysis performed using Sleuth. We analyzed KEGG pathways to determine if they were enriched in differentially expressed genes with a focus on metabolism pathways.

Provenance and Historical References:

Wade, Terry L., Maya Morales-McDevitt, Gopal Bera, Dawai Shi, Stephen Sweet, Binbin Wang, Gerado Gold-Bouchot, Antonietta Quigg, and Anthony H. Knap. 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):3e00419. DOI: 10.1016/j.heliyon.2017.e00419

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