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 2021-04-14T22:06:05-05:00
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