Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015
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Metadata:
File identifier:
R4.x263.189-0010-metadata.xml
Language:
eng; USA
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utf8
Hierarchy level:
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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:
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Address:
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P.O. Box 1675
City:
Galveston
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Texas
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77553
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USA
Electronic mail address:
schwehrk@tamug.edu
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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:
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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.
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Legal constraints:
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All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be
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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
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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:
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Delivery point:
6300 Ocean Drive
City:
Corpus Christi
Administrative area:
TX
Postal code:
78412
Country:
USA
Electronic mail address:
griidc@gomri.org
Online Resource:
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URL:
https://data.gulfresearchinitiative.org
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distributor
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File decompression technique:
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Transfer size:
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Online:
Online Resource:
Linkage:
URL:
https://data.gulfresearchinitiative.org/data/R4.x263.189:0010
Protocol:
https
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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 2021-03-02T01:58:18-06:00
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<gco:CharacterString>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</gco:CharacterString>
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