Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015

Aggregation and Degradation of Dispersants and Oil by Microbial Exopolymers (ADDOMEx)

DOI:
10.7266/n7-kvpb-0878
 
UDI:
R4.x263.189:0010
Last Update:
Dec 11 2018 17:18 UTC
 
Dataset Author(s):
Zoe Finkel, Andrew Irwin
Point of Contact:
Finkel, Zoe
Mount Allison University / Department of Geography and Environment
144 Main St.
Sackville, New Brunswick  E4L 1A8
CAN
zfinkel@mta.ca
Funding Source:
RFP-IV
 
Extent Description:
Dataset contains Illumina HiSeq (100 bp PE) mRNA sequence from eukaryotes in coastal water mesocosm, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

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

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.

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.

Theme Keywords:

Illumina HiSeq (100 bp PE) mRNA sequence, Eukaryotic community response, oil, WAF, CEWAF, Corexit, phytoplankton response

File Format:

txt

Filename:

to GRIIDC R4.x263.1890010.zip (1.63 KB)

Dataset Downloads:

2

Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x263.189-0010-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Kathleen (Kathy) Schwehr
      Organisation name: 
          Texas A&M University at Galveston / Marine Sciences Department
      Position name: 
          Associate Research Scientist
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  4097404452
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  P.O. Box 1675
              City: 
                  Galveston
              Administrative area: 
                  Texas
              Postal code: 
                  77553
              Country: 
                  USA
              Electronic mail address: 
                  schwehrk@tamug.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2019-02-22T21:18:49+00:00
  Metadata standard name: 
      ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
  Metadata standard version: 
      ISO 19115-2:2009(E)
  Dataset URI: 
      https://data.gulfresearchinitiative.org/metadata/R4.x263.189:0010
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Identification info: Data identification: Citation: Citation: Title: Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015 Alternate title: Illumina HiSeq (100 bp PE) raw reads from coastal mesocosm study Date: Date: Date: 2019-02-22 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/n7-kvpb-0878 title: DOI doi:10.7266/n7-kvpb-0878 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. 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. Status: Progress code: completed Point of contact: Responsible party: Individual name: Zoe Finkel Organisation name: Mount Allison University / Department of Geography and Environment Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 5063642615 Facsimile: Address: Address: Delivery point: 144 Main St. City: Sackville Administrative area: New Brunswick Postal code: E4L 1A8 Country: CAN Electronic mail address: zfinkel@mta.ca Role: Role code: pointOfContact Point of contact: Responsible party: Individual name: Andrew Irwin Organisation name: Mount Allison University / Mathematics and Computer Science Position name: Associate Professor Contact info: Contact: Phone: Telephone: Voice: 5063645747 Facsimile: Address: Address: Delivery point: 62 York St. City: Sackville Administrative area: New Brunswick Postal code: E4L 1E2 Country: CAN Electronic mail address: airwin@mta.ca Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: Illumina HiSeq (100 bp PE) mRNA sequence Keyword: Eukaryotic community response Keyword: oil Keyword: WAF Keyword: CEWAF Keyword: Corexit Keyword: phytoplankton response Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: inapplicable Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: 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 Resource constraints: title: CC0 License Legal constraints: Use constraints: Restriction code: licenceUnrestricted Other constraints: This information is released under the Creative Commons license - No Rights Reserved - CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/). The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Resource constraints: title: Liability and Warranty Legal constraints: Other constraints: All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be submitted by an individual who represents and warrants that s/he has sufficient rights to be able to make the content available under a CC0 waiver. There is no warranty (expressed or implied) to these materials, their title, accuracy, non-infringement of third party rights, or fitness for any particular purpose, including the performance or results you may obtain from their use. Use these materials at your own risk. Under no circumstances shall GRIIDC be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use or the inability to use either this website or the materials available via this website. If you are dissatisfied with any website feature, content, or terms of use, your sole and exclusive remedy is to discontinue use. Language: eng; USA Topic category: Topic category code: oceans Topic category: Topic category code: biota Topic category: Topic category code: environment Extent: Extent: Description: Dataset contains Illumina HiSeq (100 bp PE) mRNA sequence from eukaryotes in coastal water mesocosm, no field sampling involved. Supplemental Information: 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|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.||Two samples were taken from each mesocosm (control, WAF, CEWAF, dilute CEWAF) at the end of the experiment, one in the water column and one from the bottom layer with accumulated detritus.||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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Distribution info: Distribution: Distributor: Distributor: Distributor contact: Responsible party: Organisation name: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) Contact info: Contact: Phone: Telephone: Voice: 3618253604 Address: Address: Delivery point: 6300 Ocean Drive City: Corpus Christi Administrative area: TX Postal code: 78412 Country: USA Electronic mail address: griidc@gomri.org Online Resource: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org Role: Role code: distributor Distributor format: Format: Name: txt Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 0.0016 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x263.189:0010 Protocol: https Name: Data Landing Page Description: GRIIDC dataset landing page Function: Online function code: information
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Metadata maintenance: Maintenance information: Maintenance and update frequency: unknown Maintenance note: This ISO metadata record was automatically generated from information provided to GRIIDC for dataset: R4.x263.189:0010 on 2020-12-01T12:15:50-06:00
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