Metadata: 
  File identifier: 
      R4.x263.000-0042-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: 
      2018-08-27T21:03:38+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.x263.000:0042
Return To Index
  Identification info: 
    Data identification: 
      Citation: 
        Citation: 
          Title: 
              Percent relative abundance of the eukaryotic microbial community in the GOMCOAST (Gulf of Mexico, Coastal 
              Water) mesocosm from 8 micron polycarbonate filters
          Alternate title: 
              Relative abundance of eukaryotic microbes as part of the GOMCOAST mesocosm experiment
          Date: 
            Date: 
              Date: 
                  2018-08-27
              Date type: 
                Date type code: 
                  publication
          Identifier: 
            Identifier: 
              Code: 
                Anchor: xlink: https://dx.doi.org/10.7266/N7JD4V8Z title: DOI
                  doi:10.7266/N7JD4V8Z
      Abstract: 
          This dataset provides an estimate of the relative abundance of active microbial eukaryotes within and across 3 
          treatments (oil, oil and Corexit, and a dilute oil and Corexit treatment) in the GOMCOAST mesocosm 
          experiment based on 18S RNA sequences from RNAseq data. The data reflects the relative presence, activity 
          and detectability of eukaryotic species captured on an 8 micron polycarbonate filter.
      Purpose: 
          To determine how oil and oil and dispersant mixtures influence eukaryotic microbial community composition.
      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
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              Eukaryotic community composition analysis
          Keyword: 
              18S
          Keyword: 
              RNAseq
          Keyword: 
              eukaryotes
          Keyword: 
              percent relative abundance
          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 V. Finkel, Andrew J. Irwin, Yue Liang, Chris M. Brown, Michaël Bradet-Legris, Laura Bretherton, 
              Antonietta Quigg. 2018. Percent relative abundance of the eukaryotic microbial community in the GOMCOAST 
              (Gulf of Mexico, Coastal Water) mesocosm from 8 micron polycarbonate filters. Distributed by: Gulf of 
              Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas 
              A&M University–Corpus Christi. doi:10.7266/N7JD4V8Z
      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: 
                  Bretherton, L., Kamalanathan, M., Genzer, J., Hillhouse, J., Setta, S., Liang, Y., … Quigg, A. (2019). 
                  Response of natural phytoplankton communities exposed to crude oil and chemical dispersants during a 
                  mesocosm experiment. Aquatic Toxicology, 206, 43–53. doi:10.1016/j.aquatox.2018.11.004
              Date: 
                inapplicable
          Aggregate Data Set Identifier:  title: Related Publication DOI
            Identifier: 
              Code: 
                Anchor: xlink: https://dx.doi.org/10.1016/j.aquatox.2018.11.004 title: DOI
                  doi:10.1016/j.aquatox.2018.11.004
          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 percent relative abundance of eukaryotes, no field sampling 
              involved.
      Supplemental Information: 
          Raw data_GOMCOAST-taxonomic-composition-data-analysis.csv
          KPC: Kingdom, Phylum, or Class, derived from columns 2-4 and chosen to produce a useful decomposition of total 
          diversity in a small number of categories
          Kingdom: The Kingdom of the taxon, from World Registry of Marine Species (WoRMS, marinespecies.org)
          Phylum: The phylum of the taxon from WoRMS
          Class: The class of the taxon from WoRMS
          Genus: The genus ot the taxon from WoRMS
          target_id: The ID from the silva SSU non-redundant database version 123
          qval.WAF: The multiple-comparisons corrected p-value for the hypothesis that relative abundance is the same in 
          control and WAF treatments
          b.WAF: The log2 fold change in relative abundance between WAF and control (> 0 means higher relative abundance 
          in WAF)
          sig.WAF: A flag of 0 or 1 to indicate if there is a change due to the treatment (1= change); used to produce 
          the summary table
          qval.dCEWAF: The multiple-comparisons corrected p-value for the hypothesis that relative abundance is the same 
          in control and dilute CEWAF treatments
          b.dCEWAF: The log2 fold change in relative abundance between dilute CEWAF and control (> 0 means higher 
          relative abundance in WAF)
          sig.dCEWAF: A flag of 0 or 1 to indicate if there is a change due to the treatment (1= change); used to 
          produce the summary table
          qval.CEWAF: The multiple-comparisons corrected p-value for the hypothesis that relative abundance is the same 
          in control and CEWAF treatments
          b.CEWAF: The log2 fold change in relative abundance between CEWAF and control (> 0 means higher relative 
          abundance in WAF)
          sig.CEWAF: A flag of 0 or 1 to indicate if there is a change due to the treatment (1= change); used to produce 
          the summary table
          control: The estimated relative abundance (as %) of this taxon from kallisto in the control
          WAF: The estimated relative abundance of this taxon from kallisto in the WAF treatment
          DCEWAF: The estimated relative abundance of this taxon from kallisto in the dilute CEWAF treatment
          CEWAF: The estimated relative abundance of this taxon from kallisto in the CEWAF treatment
          
          Summary_GOMCOAST-taxonomic-composition-data-analysis.csv
          Number with significant differential abundance relative to control: Category, n, WAF, dCEWAF, CEWAF
          Proportion of total abundance (%): Control, WAF, DCEWAF, CEWAF
          Kingdom-Phylum-Class: The taxonomic affiliation derived from column 1 of the raw data table
          Count of Genus: The number of taxa (rows) aggregated from the raw data table to produce this summary
          Sum of sig.WAF: The number of these taxa with significant differential abundance in WAF relative to control
          Sum of sig.dCEWAF: The number of these taxa with significant differential abundance in dilute CEWAF relative 
          to control
          Sum of sig.CEWAF: The number of these taxa with significant differential abundance in CEWAF relative to control
          Sum of control: The proportion (as a %) of total abundance attributed to this taxon in the control
          Sum of WAF: The proportion (as a %) of total abundance attributed to this taxon in the WAF treatment
          Sum of DCEWAF: The proportion (as a %) of total abundance attributed to this taxon in the dilute CEWAF treatment
          Sum of CEWAF: The proportion (as a %) of total abundance attributed to this taxon in the CEWAF 
          treatment|Twelve 100L mesocosm tanks were filled with Gulf of Mexico seawater collected from the Texas 
          coastline, near TABS buoy R (29° 38.1000'N, 93° 38.5020'W) which is located ~100 miles away from Galveston 
          (TX). Four treatments were prepared in triplicate. Control tanks were filled with seawater. 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. Mixing ended 24 hrs. after the initial oil addition (Knap et al. 1986; 
          Wade et al. 2017in preparation). 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 (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. Mixing ended 24 hrs after the initial oil addition. The CEWAF 
          was then introduced into the CEWAF mesocosm tanks and filled to 96 L and mixed. From these CEWAF tanks 13 L 
          was removed for other experiments and analyses (7 L for the DCEWAF mesocosms, 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 (2 L dark/light, 4 L hydrocarbon analyses). To the water in the 12 mesocosms, nutrients were added 
          (final concentration f/20) and the tanks stirred. Banks of lights were placed behind each of the glass 
          mesocosm tanks and a 12:12 light/dark cycle employed. Sampling commenced and defined as time zero. 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.
          The estimate of the relative abundance of active microbial eukaryotes within and across treatments is based on 
          18S RNA sequences from RNAseq data and reflects the relative presence and activity and detectability of each 
          species. RNA was harvested from each of the 12 mesocosm tanks (3 replicate tanks for each treatment: 
          control, WAF, CEWAF, DECWAF) 72 hours after the initiation of the experiment. Several hundred mL (250 to 
          4000 mL) were rapidly and gently filtered onto two 47mm, 8 m polycarbonate filters. We limited the total 
          filtration time to 20 minutes. It took more time to filter water from the CEWAF tanks, and therefore less 
          volume was filtered from this treatment. The filters and denaturation solution (Ambion Simply RNA) was added 
          to Y-matrix bead beater tubes (MoBio). The samples were lysed using a SuperFastprep2 bead beater (30 seconds 
          at the maximum setting) and immediately stored in a -80°C freezer. RNA was extracted by exposing samples 
          immediately after thawing to 2 additional 30 second rounds in the SuperFastprep2 bead beater. The Ambion 
          Total RNA kit (ThermoFisher AM1910) was used to extract RNA followed by DNA removal with the Ambion Turbo 
          DNAfree kit (ThermoFisher AM1907) as per manufacturer instructions.
          RNA was sequenced as 125 base pair paired-end reads using Illumina HiSeq 250 RNAseq by Genome Quebec. PolyA 
          selection was used to remove the majority of the rRNA using the NEBNext Poly(A) mRNA magnetic isolation 
          module kit from New England Biolabs. Approximately 2-10% of the original rRNA sequences pass through this 
          step are sequenced (Abernathy and Overturf 2016). Trimmomatic was used to remove Illumina adapters and low 
          quality bases were identified using Phred scores (Bolger, Lohse et al. 2014). Kraken and the Silva SSU rRNA 
          Ref NR 99 database (release 123) were used to filter reads matching 18S sequences (Quast, Pruesse et al. 
          2013, Wood and Salzberg 2014). Kallisto and Sleuth were used to match, count and perform differential 
          expression and relative abundance analysis for reads against the Silva 18S database (Bray, Pimentel et al. 
          2016, Pimentel, Bray et al. 2017). Three replicate mesocosms were sequenced for the control and WAF 
          treatment, but following quality control only two replicates were available for the DCEWAF treatment and one 
          replicate for the CEWAF treatment.
          Each 18S sequence in the Silva database is identified with an accession code and a hierarchical taxonomic 
          identification. All non-Eukaryota, Metazoa and Embryophyta sequences were removed from the analyses. The 
          taxonomic identification in Silva is hierarchical but the identifications do not all have the same number of 
          levels in the hierarchy so the phylum, order, or class, for example, are not readily extracted. Where 
          possible we use the taxonomic hierarchy used by WoRMS in 2016/17. The genus and species name for each taxon 
          in the Silva database (the last entry in the hierarchy) was used to search the World Registry of Marine 
          Species (WoRMS, marinespecies.org). A variety of secondary sources were used to identify the taxonomic 
          hierarchy for taxa without a match in WoRMS including the Global Names Index (GNI), the Pan-European Species 
          Infrastructure (PESI), the Paleobiology database (Paleo), and the taxonomic hierarchy used by 
          Wikipedia/Wikispecies. An automatic search for all taxa was performed using lifewatch.be on 2016 December 31 
          using WoRMS, GNI, PESI, and Paleo.||One sampling point was taken and analysed as described in the methods 
          above.|There is no error quantified for the individual point estimates of relative abundance across 
          treatments. The average relative abundance was estimated from replicate samples when available as described 
          in the methods.|The original raw sequence data from the Illumina sequencer have been deposited at NCBI’s 
          Short read archive (SRA) under BioProject PRJNA338185. The data are archived as BioSample SAMN08118040 and 
          are accessible at http://www.ncbi.nlm.nih.gov/biosample/8118040
          
          Jason Abernathy
Return To Index
  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, txt
              Version: 
                inapplicable
              File decompression technique: 
                  7z
          Distributor transfer options: 
            Digital transfer options: 
              Transfer size: 
                  0.4218
              Online: 
                Online Resource: 
                  Linkage: 
                    URL: 
                      https://data.gulfresearchinitiative.org/data/R4.x263.000:0042
                  Protocol: 
                      https
                  Name: 
                      Data Landing Page
                  Description: 
                      GRIIDC dataset landing page
                  Function: 
                    Online function code: 
                      information
Return To Index
  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.x263.000:0042 on 2020-12-01T12:27:05-06:00
Return To Index