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)

Aggregation and Degradation of Dispersants and Oil by Microbial Exopolymers 2 (ADDOMEx-2)

DOI:
10.7266/032DBZJY
 
UDI:
R6.x807.000:0040
Last Update:
Jul 29 2019 16:13 UTC
 
Dataset Author(s):
Zoe Finkel, Andrew Irwin, Yue Liang, Deepak Nanjappa
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-VI
 
Extent Description:
Dataset contains laboratory measurements of RNA extracted from filtered mesocosm water samples, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

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

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.

Theme Keywords:

18S rRNA, EPS, hydrocarbon degrading microorganisms, mesocosm, WAF, CEWAF

File Format:

csv

Filename:

R6.x807.0000040.zip (81.73 KB)

Dataset Downloads:

1

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 Information
Distribution Information
Metadata 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 2020-07-02T14:57:02-05:00
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