Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011

Center for the Integrated Modeling and Analysis of Gulf Ecosystems II (C-IMAGE II)

DOI:
10.7266/N78C9TSB
 
UDI:
R4.x267.000:0098
Last Update:
Mar 06 2018 21:03 UTC
 
Dataset Author(s):
Will A. Overholt
Point of Contact:
Overholt, Will
Georgia Institute of Technology / School of Earth and Atmospheric Sciences
311 Ferst Dr
Atlanta, Georgia  30332
USA
waoverholt@gmail.com
Funding Source:
RFP-IV
Data Collection Period:
2010-07-02 to 2011-07-26

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Will A. Overholt. 2018. Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N78C9TSB

Abstract:

Bacterial abundances were tracked approximately every 6 weeks for one year beginning in June 2010 in Pensacola Beach. Sand samples were visibly assessed as oil contaminated or "clean" and total genomic DNA was extracted using a MoBio powersoil DNA extraction kit. Total bacterial 16S rRNA gene abundances were quantified using taqman qPCR with 331F/772R primers and a 515R probe, while Alcanivorax 16S rRNA gene abundances were quantified with the same probe with 464F/675R primer. This dataset supports the publication: Kostka, J.E., Prakash, O., Overholt, W.A., Green, S.J., Freyer, G., Canion, A., Delgardio, J., Norton, N., Hazen, T.C., & Huettel, M. (2011). Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied and Environmental Microbiology, 77(22): 7962-7974.

Purpose:

To track bacterial abundances in Pensacola Beach following the Deepwater Horizon oil spill.

Theme Keywords:

beach, SSU rRNA gene, 16S gene, bacterial abundance, alcanivorax abundance, quantitative PCR, Deepwater Horizon oil spill

File Format:

xlsx

Filename:

QPCR_pensacola_beach_bac_alcanivorax_griidc.xlsx (310.38 KB)

Dataset Downloads:

4

Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011



Identification Information
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Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x267.000-0098-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Richard McKenzie
      Organisation name: 
          University of South Florida / USF Library System
      Position name: 
          GIS Analyst
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  8139742852
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  4202 E. Fowler Avenue LIB122
              City: 
                  Tampa
              Administrative area: 
                  Florida
              Postal code: 
                  33620
              Country: 
                  USA
              Electronic mail address: 
                  rwmcken2@usf.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-05-04T20:04:57+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.x267.000:0098
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Identification info: Data identification: Citation: Citation: Title: Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011 Alternate title: Date: Date: Date: 2018-04-09 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/N78C9TSB title: DOI doi:10.7266/N78C9TSB Abstract: Bacterial abundances were tracked approximately every 6 weeks for one year beginning in June 2010 in Pensacola Beach. Sand samples were visibly assessed as oil contaminated or "clean" and total genomic DNA was extracted using a MoBio powersoil DNA extraction kit. Total bacterial 16S rRNA gene abundances were quantified using taqman qPCR with 331F/772R primers and a 515R probe, while Alcanivorax 16S rRNA gene abundances were quantified with the same probe with 464F/675R primer. This dataset supports the publication: Kostka, J.E., Prakash, O., Overholt, W.A., Green, S.J., Freyer, G., Canion, A., Delgardio, J., Norton, N., Hazen, T.C., & Huettel, M. (2011). Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied and Environmental Microbiology, 77(22): 7962-7974. Purpose: To track bacterial abundances in Pensacola Beach following the Deepwater Horizon oil spill. Status: Progress code: completed Point of contact: Responsible party: Individual name: Will Overholt Organisation name: Georgia Institute of Technology / School of Earth and Atmospheric Sciences Position name: Graduate Student Contact info: Contact: Phone: Telephone: Voice: Facsimile: Address: Address: Delivery point: 311 Ferst Dr City: Atlanta Administrative area: Georgia Postal code: 30332 Country: USA Electronic mail address: waoverholt@gmail.com Role: Role code: pointOfContact Point of contact: Responsible party: Individual name: Joel E. Kostka Organisation name: Georgia Institute of Technology / School of Earth and Atmospheric Sciences Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 4043853325 Facsimile: Address: Address: Delivery point: 310 Ferst Drive City: Atlanta Administrative area: Georgia Postal code: 30332 Country: USA Electronic mail address: joel.kostka@biology.gatech.edu Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: beach Keyword: SSU rRNA gene Keyword: 16S gene Keyword: bacterial abundance Keyword: alcanivorax abundance Keyword: quantitative PCR Keyword: Deepwater Horizon oil spill Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Pensacola Beach Keyword: Florida Keyword: Gulf of Mexico Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Will A. Overholt. 2018. Tracking total bacterial abundances and Alcanivorax specific abundances with qPCR in Pensacola Beach, June 2010 to June 2011. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N78C9TSB 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. Language: eng; USA Topic category: Topic category code: oceans Topic category: Topic category code: biota Topic category: Topic category code: environment Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -87.1744 East bound longitude: -87.1744 South bound latitude: 30.32563 North bound latitude: 30.32563 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 30.32563 -87.1744 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2010-07-02 End date: 2011-07-26 Supplemental Information: sample_set1: SampleID/Sample Name: Sample Identifier (ID) Date: Sample collection date (MM/DD/YYYY) Location: Sample location (PB-PB6) Depth: Sample depth (cm) Description: Description of sample location) Oil Presence: qualitative scale for degree of oiling (0 = no visible oil, 3 = highest degree of oiling) Weight: Mass of wet sand for DNA extraction DNA: DNA concentration from extraction (ng/µl) Dilution Elution volume (ul) Comment Name Check Volume added to reaction (ul) Plate number Slope and Intercept: Standard curve generated for each qPCR plate Total bacterial abundances (columns P-AF) Alcanivorax specific abundances (columns AG-BA) CT: Critical threshold of the sample; measured in triplicate Conc: Determined number of gene copies in the sample Copies per uL: gene copies per µl extracted (gene copies / total volume DNA eluted into) Copies per g sediment: gene copies per gram sediment extracted from (wet weight) Oil (0-3) BAC (copies/g) ALC (copies/g) %ALC sample_set2: Sample name: Sample identifier Date sampled (MM/DD/YYYY) Depth (cm) Oil presence (0 = no visible oil, 3 = heavily oiled, tar = tarball/surface residual ball Site description DNA concentration (ng/ul) Dilution Sediment wet weight (g) Dilution at sequence DNA added to reaction Slope Intercept CT: Critical threshold of the sample; measured in triplicate Conc: Determined number of gene copies in the sample Copies per uL: gene copies per µl extracted (gene copies / total volume DNA eluted into) Copies per g sediment: gene copies per gram sediment extracted from (wet weight) Average copies/reaction Standard deviation Standard error|||||
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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: xlsx Version: inapplicable File decompression technique: Distributor transfer options: Digital transfer options: Transfer size: 0.3104 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x267.000:0098 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.x267.000:0098 on 2021-09-23T20:05:04-05:00
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