Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015

Deep-Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND)

DOI:
10.7266/N7P55KWX
 
UDI:
R4.x257.228:0001		 Last Update:
Feb 13 2017 16:47 UTC
 
Dataset Author(s):
Cole Easson, Jose Lopez		 Point of Contact:
Lopez, Jose V.
Nova Southeastern University / Halmos College of Natural Sciences and Oceanography
3301 College Ave
Fort Lauderdale, Florida  33314
USA
Joslo@Nova.edu
Funding Source:
RFP-IV
Data Collection Period:
2015-05-01 to 2015-08-31

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Cole Easson, Jose Lopez (2017) Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University-Corpus Christi. doi:10.7266/N7P55KWX

Abstract:

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – 1500 m, across the spatial extent of the northern GOM, and over time. Microbiome analyses also considered environmental variables unique to the GOM, including the Mississippi river inputs, mesoscale cyclonic and anticyclonic eddies, and in relation to measured environmental parameters at collection time using the CTD.

Purpose:

The dataset was generated to characterize the composition and dynamics of pelagic microbial communities in the northern Gulf of Mexico.

Theme Keywords:

microbial, sequencing, microbiome, depth, microbial diversity, CTD, seawater

File Format:

csv, docx, fna, biom, word, txt

Filename:

DEEPEND_Year1_microbial_data_GRIIDC.zip (1.03 GB)

Dataset Downloads:

17

Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015



Identification Information
Distribution Information
Metadata Maintenance Information
Metadata: 
  File identifier: 
      R4.x257.228-0001-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Jose V. Lopez
      Organisation name: 
          Nova Southeastern University / Halmos College of Natural Sciences and Oceanography
      Position name: 
          Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  9542623665
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  3301 College Ave
              City: 
                  Fort Lauderdale
              Administrative area: 
                  Florida
              Postal code: 
                  33314
              Country: 
                  USA
              Electronic mail address: 
                  Joslo@Nova.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2018-08-11T13:28:58+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.x257.228:0001

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  Identification info: 
    Data identification: 
      Citation: 
        Citation: 
          Title: 
              Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, 
              Cruises DP01 and DP02 from May 2015 - August 2015
          Alternate title: 
          Date: 
            Date: 
              Date: 
                  2016-08-22
              Date type: 
                Date type code: 
                  publication
          Identifier: 
            Identifier: 
              Code: 
                Anchor: xlink: https://dx.doi.org/doi:10.7266/N7P55KWX title: DOI
                  doi:10.7266/N7P55KWX
      Abstract: 
          Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various 
          depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for 
          total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon 
          libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced 
          on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality 
          filter and assess microbial community diversity and taxonomic composition. These baseline characterizations 
          track alpha and beta diversity at different depths ranging from 0 – 1500 m, across the spatial extent of the 
          northern GOM, and over time. Microbiome analyses also considered environmental variables unique to the GOM, 
          including the Mississippi river inputs, mesoscale cyclonic and anticyclonic eddies, and in relation to 
          measured environmental parameters at collection time using the CTD.
      Purpose: 
          The dataset was generated to characterize the composition and dynamics of pelagic microbial communities in the 
          northern Gulf of Mexico.
      Status: 
        Progress code: 
          completed
      Point of contact: 
        Responsible party: 
          Individual name: 
              Jose V. Lopez
          Organisation name: 
              Nova Southeastern University / Halmos College of Natural Sciences and Oceanography
          Position name: 
              Professor
          Contact info: 
            Contact: 
              Phone: 
                Telephone: 
                  Voice: 
                      9542623665
                  Facsimile: 
              Address: 
                Address: 
                  Delivery point: 
                      3301 College Ave
                  City: 
                      Fort Lauderdale
                  Administrative area: 
                      Florida
                  Postal code: 
                      33314
                  Country: 
                      USA
                  Electronic mail address: 
                      Joslo@Nova.edu
          Role: 
            Role code: 
              pointOfContact
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              microbial
          Keyword: 
              sequencing
          Keyword: 
              microbiome
          Keyword: 
              depth
          Keyword: 
              microbial diversity
          Keyword: 
              CTD
          Keyword: 
              seawater
          Type: 
            Keyword type code: 
              theme
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              Gulf of Mexico
          Type: 
            Keyword type code: 
              place
      Language: 
          eng; USA
      Topic category: 
        Topic category code: 
          environment
      Topic category: 
        Topic category code: 
          oceans
      Extent: 
        Extent: 
          Geographic element: 
            Geographic bounding box: 
              West bound longitude: 
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              East bound longitude: 
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              North bound latitude: 
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          Temporal element: 
            Temporal extent: 
              Extent: 
                Time period: 
                  Description: 
                    ground condition
                  Begin date: 
                    2015-05-01
                  End date: 
                    2015-08-31
      Supplemental Information: 
          SampleID_in_OTU_table – sample label corresponding to OTU table columns and Sequence labels Original Tube 
          label – Label on original sample New Tube label - sample label corresponding to OTU table columns and 
          Sequence labels Cruise number – Sequential cruise number Sample_depth – depth in meters from which sample 
          was collected Site - Site name from which the sample was collected. LAT – Latitude of collection site in 
          decimal degrees LONG – Longitude of collection site in decimal degrees Pelagic_zone – Pelagic depth zone in 
          which the sample was collected Identifier – Unique sample identifier SampleID-Long – Complete SampleID 
          Feature – Depth feature from which sample was taken|||||

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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, docx, fna, biom, word, txt
              Version: 
                inapplicable
              File decompression technique: 
                  zip
          Distributor transfer options: 
            Digital transfer options: 
              Transfer size: 
                  1026.8291
              Online: 
                Online Resource: 
                  Linkage: 
                    URL: 
                      https://data.gulfresearchinitiative.org/data/R4.x257.228:0001
                  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.x257.228:0001 on 2020-04-03T15:56:05-05:00

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