Percent relative abundance of the eukaryotic microbial community in the GOMCOAST (Gulf of Mexico, Coastal Water) mesocosm from 8 micron polycarbonate filters

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

DOI:
10.7266/N7JD4V8Z
 
UDI:
R4.x263.000:0042
Last Update:
Aug 01 2018 17:13 UTC
 
Dataset Author(s):
Zoe V. Finkel, Andrew J. Irwin, Yue Liang, Chris M. Brown, Michaël Bradet-Legris, Laura Bretherton, Antonietta Quigg
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-IV
 
Extent Description:
Dataset contains laboratory measurements of percent relative abundance of eukaryotes, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

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

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.

Theme Keywords:

Eukaryotic community composition analysis, 18S, RNAseq, eukaryotes, percent relative abundance, mesocosm

File Format:

csv, txt

Filename:

to GRIIDC 2018 08 01.7z (421.85 KB)

Dataset Downloads:

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Percent relative abundance of the eukaryotic microbial community in the GOMCOAST (Gulf of Mexico, Coastal Water) mesocosm from 8 micron polycarbonate filters



Identification Information
Distribution Information
Metadata Maintenance Information

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
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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
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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, 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
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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.x263.000:0042 on 2020-09-24T10:32:43-05:00
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