Eukaryotic phytoplankton community composition in the COAST (Gulf of Mexico, COASTal water mesocosms amended with coastal microbial concentrate) mesocosm as identified by 18S sequence from RNA-seq whole transcriptome sequencing for four treatments (control, WAF, CEWAF, dilute CEWAF)
Identification InformationDistribution InformationMetadata Maintenance Information
Metadata:
File identifier:
R6.x807.000-0040-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:
2020-01-17T22:09:28+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/R6.x807.000:0040
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Identification info:
Data identification:
Citation:
Citation:
Title:
Eukaryotic phytoplankton community composition in the COAST (Gulf of Mexico, COASTal water mesocosms
amended with coastal microbial concentrate) mesocosm as identified by 18S sequence from RNA-seq whole
transcriptome sequencing for four treatments (control, WAF, CEWAF, dilute CEWAF)
Alternate title:
Eukaryotic phytoplankton community composition
Date:
Date:
Date:
2020-01-17
Date type:
Date type code:
publication
Identifier:
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.7266/032DBZJY title: DOI
doi:10.7266/032DBZJY
Abstract:
A mesocosm experiment was conducted October 2015 (COAST, Mesocosm 2) using coastal water collected near
Galveston Bay, Texas. Four mesocosm treatments were prepared in triplicate for this study: (1) Control
(seawater only); (2) WAF (oil + seawater); (3) Chemically-enhanced WAF (CE-WAF; oil + Corexit + seawater);
(4) Diluted CE-WAF (1:10 dilution). Initial mesocosm volumes were 79L. Prior to experiment initiation,
phytoplankton were collected from coastal Galveston, TX waters and added to each tank to stimulate
interactions between phytoplankton, oil, and Corexit. One sample was taken from all four treatments, three
replicate mesocosms each, at time 72 h in clean, opaque Nalgene bottles with PTFE-lined diaphragm pumps. RNA
was extracted from filtered water samples and sequenced using Illumina HiSeq. The sequences were deposited
at the NCBI short read archive, SRA bioproject code PRJNA489497;
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489497
Purpose:
Characterize the microbial community composition and structure in the COAST Mesocosm.
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:
Antonietta Quigg
Organisation name:
Texas A&M University at Galveston / Marine Biology Department
Position name:
Professor
Contact info:
Contact:
Phone:
Telephone:
Voice:
4097404990
Facsimile:
Address:
Address:
Delivery point:
P.O. Box 1675
City:
Galveston
Administrative area:
Texas
Postal code:
77553
Country:
USA
Electronic mail address:
quigga@tamug.edu
Role:
Role code:
pointOfContact
Descriptive keywords:
Keywords:
Keyword:
18S rRNA
Keyword:
EPS
Keyword:
hydrocarbon degrading microorganisms
Keyword:
mesocosm
Keyword:
WAF
Keyword:
CEWAF
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, Yue Liang, Deepak Nanjappa. 2020. Eukaryotic phytoplankton community composition
in the COAST (Gulf of Mexico, COASTal water mesocosms amended with coastal microbial concentrate)
mesocosm as identified by 18S sequence from RNA-seq whole transcriptome sequencing for four treatments
(control, WAF, CEWAF, dilute CEWAF). Distributed by: Gulf of Mexico Research Initiative Information and
Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi.
doi:10.7266/032DBZJY
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.
Aggregation Info:
AggregateInformation:
Aggregate Data Set Name: title: Related Publication Citation
Citation:
Title:
Finkel, Z. V., Liang, Y., Nanjappa, D., Bretherton, L., Brown, C. M., Quigg, A., & Irwin, A. J.
(2020). A ribosomal sequence-based oil sensitivity index for phytoplankton groups. Marine Pollution
Bulletin, 151, 110798. doi:10.1016/j.marpolbul.2019.110798
Date:
inapplicable
Aggregate Data Set Identifier: title: Related Publication DOI
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.1016/j.marpolbul.2019.110798 title: DOI
doi:10.1016/j.marpolbul.2019.110798
Association Type:
Association type code:
crossReference
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 laboratory measurements of RNA extracted from filtered mesocosm water samples, no field
sampling involved.
Supplemental Information:
The two csv files are the output of KrakenUniq, one using the full-length 18S sequences from the PR2 database,
and the other using the PR2 database sequences cropped to include just the V4 hypervariable region. This
second analysis is intended to be a simulation of the analysis results that would be obtained from a
amplicon sequencing approach. The columns of the tables provide the taxonomic labels from the PR2 database,
a simplified functional group level (diatoms, dinoflagellates, Chrysophytes, green algae), the raw counts,
and the normalized TPM counts. There are 12 columns for each of the raw and TPM counts: control 1-3, waf
1-3, dcewaf 1-3, and cewaf 1-3 corresponding to the 12 biological samples analyzed.|Mesocosm methods –
COASTal water with coastal microbial concentrate, COAST: Twelve 100L mesocosm tanks were filled with Gulf of
Mexico seawater collected 5 miles offshore from Galveston (TX) that had been pre-treated with a charcoal
filter to remove large particles and debris. Plankton (<63 µm) were collected using a net and transferred
into polycarbonate bottles. This concentrated plankton mass was introduced to the tanks (2 L to each final
volume 83 L) immediately prior to starting the experiments. Four treatments were prepared in triplicate.
Control tanks were filled with seawater and 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. (Knap et al. 1983). 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 loaded into 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). The estimated oil equivalents (EOE) were determined using
Macondo surrogate oil as the calibration standard (Wade et al. 2011) for the fluorescence analyses (Horiba
Scientific Aqualog Fluorometer). 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 mesocosms for the in the control, WAF, DCEWAF and
CEWAF after 72 hours were 0 mg/L , 0.06 mg/L, 1.03. and 17.3 mg/L, respectively.
Data treatment for the 18S sequence from RNA-seq whole transcriptome: The data are the results of counting raw
reads (deposited at the NCBI short read archive, SRA bioproject code PRJNA489497;
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489497) against the PR2 protist rRNA database using the
software KrakenUniq. This tool is a k-mer based counting approach which identifies the level in the
taxonomic hierarchy at which each k-mer in the target database is unique (i.e., at the species, genus,
phylum, order, or kingdom level). Matches between k-mers in the source raw reads and the target database,
together with this taxonomic hierarchy, are used to identify species or counts at other levels of the
taxonomy.||||Knap, A.H., Sleeter, T.D., Dodge, R.E., Wyers, S.C., Frith, H.R. and Smith, S.R., 1983. The
effects of oil spills and dispersant use on corals: A review and multidisciplinary experimental approach.
Oil and Petrochemical Pollution, 1(3), pp.157-169. doi:10.1016/s0143-7127(83)90134-5
Wade, T.L., Sweet S.T., Sericano, J.L., N.L. Guinasso Jr., Diercks, A.-R., Highsmith, R.C., Asper, V.L.,
Joung, D., Shiller, A.M., Lohrenz, S.E. and Joye, S.B., 2011. Analyses of Water Samples From the Deepwater
Horizon Oil Spill: Documentation of the Subsurface Plume. Geophysical Monograph Series, 77–82.
doi:10.1029/2011gm001103
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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:
csv
Version:
inapplicable
File decompression technique:
zip
Distributor transfer options:
Digital transfer options:
Transfer size:
0.0817
Online:
Online Resource:
Linkage:
URL:
https://data.gulfresearchinitiative.org/data/R6.x807.000:0040
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:
R6.x807.000:0040 on 2021-01-26T00:43:38-06:00
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<gco:CharacterString>Zoe Finkel, Andrew Irwin, Yue Liang, Deepak Nanjappa. 2020. Eukaryotic phytoplankton community composition in the COAST (Gulf of Mexico, COASTal water mesocosms amended with coastal microbial concentrate) mesocosm as identified by 18S sequence from RNA-seq whole transcriptome sequencing for four treatments (control, WAF, CEWAF, dilute CEWAF). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/032DBZJY</gco:CharacterString>
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<gco:CharacterString>Finkel, Z. V., Liang, Y., Nanjappa, D., Bretherton, L., Brown, C. M., Quigg, A., & Irwin, A. J. (2020). A ribosomal sequence-based oil sensitivity index for phytoplankton groups. Marine Pollution Bulletin, 151, 110798. doi:10.1016/j.marpolbul.2019.110798
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<gco:CharacterString>The two csv files are the output of KrakenUniq, one using the full-length 18S sequences from the PR2 database, and the other using the PR2 database sequences cropped to include just the V4 hypervariable region. This second analysis is intended to be a simulation of the analysis results that would be obtained from a amplicon sequencing approach. The columns of the tables provide the taxonomic labels from the PR2 database, a simplified functional group level (diatoms, dinoflagellates, Chrysophytes, green algae), the raw counts, and the normalized TPM counts. There are 12 columns for each of the raw and TPM counts: control 1-3, waf 1-3, dcewaf 1-3, and cewaf 1-3 corresponding to the 12 biological samples analyzed.|Mesocosm methods – COASTal water with coastal microbial concentrate, COAST: Twelve 100L mesocosm tanks were filled with Gulf of Mexico seawater collected 5 miles offshore from Galveston (TX) that had been pre-treated with a charcoal filter to remove large particles and debris. Plankton (<63 µm) were collected using a net and transferred into polycarbonate bottles. This concentrated plankton mass was introduced to the tanks (2 L to each final volume 83 L) immediately prior to starting the experiments. Four treatments were prepared in triplicate. Control tanks were filled with seawater and 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. (Knap et al. 1983). 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 loaded into 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). The estimated oil equivalents (EOE) were determined using Macondo surrogate oil as the calibration standard (Wade et al. 2011) for the fluorescence analyses (Horiba Scientific Aqualog Fluorometer). 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 mesocosms for the in the control, WAF, DCEWAF and CEWAF after 72 hours were 0 mg/L , 0.06 mg/L, 1.03. and 17.3 mg/L, respectively.
Data treatment for the 18S sequence from RNA-seq whole transcriptome: The data are the results of counting raw reads (deposited at the NCBI short read archive, SRA bioproject code PRJNA489497; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489497) against the PR2 protist rRNA database using the software KrakenUniq. This tool is a k-mer based counting approach which identifies the level in the taxonomic hierarchy at which each k-mer in the target database is unique (i.e., at the species, genus, phylum, order, or kingdom level). Matches between k-mers in the source raw reads and the target database, together with this taxonomic hierarchy, are used to identify species or counts at other levels of the taxonomy.||||Knap, A.H., Sleeter, T.D., Dodge, R.E., Wyers, S.C., Frith, H.R. and Smith, S.R., 1983. The effects of oil spills and dispersant use on corals: A review and multidisciplinary experimental approach. Oil and Petrochemical Pollution, 1(3), pp.157-169. doi:10.1016/s0143-7127(83)90134-5
Wade, T.L., Sweet S.T., Sericano, J.L., N.L. Guinasso Jr., Diercks, A.-R., Highsmith, R.C., Asper, V.L., Joung, D., Shiller, A.M., Lohrenz, S.E. and Joye, S.B., 2011. Analyses of Water Samples From the Deepwater Horizon Oil Spill: Documentation of the Subsurface Plume. Geophysical Monograph Series, 77–82. doi:10.1029/2011gm001103</gco:CharacterString>
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