Eukaryotic community response to oil and Corexit in a mesocosm, October 2015

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

DOI:
10.7266/n7-43q9-xq06
 
UDI:
R4.x263.189:0011
Last Update:
Dec 11 2018 20:09 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 eukaryotic metatranscriptome analysis for plankton response to oil and Corexit, 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 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

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.

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:

Eukaryotic metatranscriptomes, Illumina HiSeq, Eukaryotic RNA, WAF, CEWAF, DCEWAF, oil, Corexit, mesocosm

File Format:

txt

Filename:

to GRIIDC R4.x263.1890011.zip (1.86 KB)

Dataset Downloads:

2

Eukaryotic community response to oil and Corexit in a mesocosm, October 2015



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x263.189-0011-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: 
      2019-02-25T20:38:34+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.x263.189:0011
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Identification info: Data identification: Citation: Citation: Title: Eukaryotic community response to oil and Corexit in a mesocosm, October 2015 Alternate title: Illumina HiSeq (100 bp PE) raw reads from coastal mesocosm study Date: Date: Date: 2019-02-25 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/n7-43q9-xq06 title: DOI doi:10.7266/n7-43q9-xq06 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. 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: Eukaryotic metatranscriptomes Keyword: Illumina HiSeq Keyword: Eukaryotic RNA Keyword: WAF Keyword: CEWAF Keyword: DCEWAF Keyword: oil Keyword: Corexit Keyword: mesocosm 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 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 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 eukaryotic metatranscriptome analysis for plankton response to oil and Corexit, no field sampling involved. Supplemental Information: 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.|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.||||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: 0.0019 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x263.189:0011 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.x263.189:0011 on 2020-12-01T11:55:03-06:00
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