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Eukaryotic community response to oil and Corexit in a mesocosm, October 2015Aggregation and Degradation of Dispersants and Oil by Microbial Exopolymers (ADDOMEx)
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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:
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Filename:
to GRIIDC R4.x263.1890011.zip (1.86 KB)
Dataset Downloads:
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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:
2021-05-04T20:04:56+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
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URL:
https://data.gulfresearchinitiative.org
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distributor
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inapplicable
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URL:
https://data.gulfresearchinitiative.org/data/R4.x263.189:0011
Protocol:
https
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Data Landing Page
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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 2021-07-29T19:40:34-05:00
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