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 (2016) 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:

15

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 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: -89 East bound longitude: -86.50765 South bound latitude: 26.88267 North bound latitude: 29.065 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 29.065 -88.036 gml:pointMember: Point: gml:pos: 28.853 -87.413 gml:pointMember: Point: gml:pos: 28.853 -87.413 gml:pointMember: Point: gml:pos: 28.925 -87.52 gml:pointMember: Point: gml:pos: 28.02 -87.51 gml:pointMember: Point: gml:pos: 27.99 -87.38 gml:pointMember: Point: gml:pos: 28.056 -87.38 gml:pointMember: Point: gml:pos: 28.056 -88.065 gml:pointMember: Point: gml:pos: 28.16 -88.54 gml:pointMember: Point: gml:pos: 26.96667 -89 gml:pointMember: Point: gml:pos: 26.88267 -88.99883 gml:pointMember: Point: gml:pos: 27.03282 -88.15602 gml:pointMember: Point: gml:pos: 27.5635 -87.54633 gml:pointMember: Point: gml:pos: 28.11392 -87.47123 gml:pointMember: Point: gml:pos: 28.46958 -87.48992 gml:pointMember: Point: gml:pos: 29.00127 -87.48806 gml:pointMember: Point: gml:pos: 28.9271 -87.39687 gml:pointMember: Point: gml:pos: 28.532 -87.024 gml:pointMember: Point: gml:pos: 27.9768 -86.97892 gml:pointMember: Point: gml:pos: 28.49218 -86.97455 gml:pointMember: Point: gml:pos: 27.45757 -86.98505 gml:pointMember: Point: gml:pos: 27.0179 -87.0031 gml:pointMember: Point: gml:pos: 27.51498 -86.55363 gml:pointMember: Point: gml:pos: 26.96091 -87.00187 gml:pointMember: Point: gml:pos: 27.52662 -86.50765 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 2019-12-06T02:59:30-06:00
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