Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters

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

DOI:
10.7266/n7-df3b-bq71
 
UDI:
R4.x267.179:0009
Last Update:
Jan 03 2019 14:24 UTC
 
Dataset Author(s):
Xiaoxu Sun and Joel Kostka
Point of Contact:
Kostka, Joel E.
Georgia Institute of Technology / School of Earth and Atmospheric Sciences
310 Ferst Drive
Atlanta, Georgia  30332
USA
joel.kostka@biology.gatech.edu
Funding Source:
RFP-IV
Data Collection Period:
2015-08-03 to 2015-08-20

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Xiaoxu Sun and Joel Kostka. 2019. Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-df3b-bq71

Abstract:

Samples were collected from three different origins (two from the subtropical area and one from the Arctic ocean) were used for generating geochemical data, including microbial respiration rates and percentage hydrocarbon degraded during the incubation period. Following the incubation, 16s rRNA library was generated. Experiments were divided into multiple groups, with a systemic combination of different temperature and nutrients addition.

Purpose:

The objective of this study was to quantify the potential for hydrocarbon biodegradation in surface waters of three sites that represent geographic regions of major oil exploration in a systematic experimental design that incorporates gradients in temperature and the availability of major nutrients.

Theme Keywords:

hydrocarbon degradation, bacteria, microbial ecology, IXTOC, Deepwater horizon, microcosm, MC252 oil, Colwellia, quantitative PCR, 16s rRNA, nifH gene, microbial respiration rates

File Format:

xls

Filename:

Temperature_summary_0725_1.xlsx (26.44 KB)

Dataset Downloads:

5

Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x267.179-0009-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Carla Fotherby
      Organisation name: 
          University of South Florida
      Position name: 
          Collections Specialist
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        Contact: 
          Phone: 
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                  8139746220
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                  4202 E. Fowler Ave.
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                  Tampa
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                  Florida
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                  33620
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                  USA
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                  cfotherby@usf.edu
      Role: 
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  Date stamp: 
      2019-06-05T13:58:00+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.x267.179:0009
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Identification info: Data identification: Citation: Citation: Title: Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters Alternate title: Date: Date: Date: 2019-02-10 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/n7-df3b-bq71 title: DOI doi:10.7266/n7-df3b-bq71 Abstract: Samples were collected from three different origins (two from the subtropical area and one from the Arctic ocean) were used for generating geochemical data, including microbial respiration rates and percentage hydrocarbon degraded during the incubation period. Following the incubation, 16s rRNA library was generated. Experiments were divided into multiple groups, with a systemic combination of different temperature and nutrients addition. Purpose: The objective of this study was to quantify the potential for hydrocarbon biodegradation in surface waters of three sites that represent geographic regions of major oil exploration in a systematic experimental design that incorporates gradients in temperature and the availability of major nutrients. Status: Progress code: completed 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 Point of contact: Responsible party: Individual name: Xiaoxu Sun 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: austin0613@gmail.com Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: hydrocarbon degradation Keyword: bacteria Keyword: microbial ecology Keyword: IXTOC Keyword: Deepwater horizon Keyword: microcosm Keyword: MC252 oil Keyword: Colwellia Keyword: quantitative PCR Keyword: 16s rRNA Keyword: nifH gene Keyword: microbial respiration rates Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Gulf of Mexico Keyword: Beaufort Sea Keyword: Arctic ocean Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Xiaoxu Sun and Joel Kostka. 2019. Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-df3b-bq71 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: Sun, X., & Kostka, J. E. (2019). Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters. Applied and Environmental Microbiology. doi:10.1128/aem.00443-19 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1128/aem.00443-19 title: DOI doi:10.1128/aem.00443-19 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: oceans Topic category: Topic category code: environment Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -129.17 East bound longitude: -88.23 South bound latitude: 19 North bound latitude: 75.47 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 75.47 -129.17 gml:pointMember: Point: gml:pos: 28.43 -88.23 gml:pointMember: Point: gml:pos: 19 -92 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2015-08-03 End date: 2015-08-20 Supplemental Information: TB_rate_original: calculated respiration rates for each individual microcosm. Sample collection site, incubation temperature (temp; degrees C), microcosm treatment (Nutrient Amended (NA)/Unamended (UN)), maximum CO2 accumulation rate (mu.TB.spline; micromol CO2/day), mu.TB.spline converted to per Liter seawater per day (R; micromol CO2/L seawater/day).
          
TB_all_rates_avg: averages of the measured respiration rated in replicates. Sample collection site, incubation temperature (temp; degrees C), microcosm treatment (Nutrient Amended (NA)/Unamended (UN)), averaged respiration rates (respiration; micromol CO2/L seawater/day), averaged respiration rates standard deviation (respiration_std), NA/UN (rate increase (ratio) between NA and UN treatment at the same temperature from the same site, averaged respiration rate at maximum (30C for CB2 and 38 for DWH01 and IXTOC01) comparing to that at 4C (Ropt/R4), Ropt/R4 standard deviation (Ropt/R4_STDEV), statistical results (p-value and significance for sample pairs for T-test comparison between sites for Ropt/R4.
          
Ea: calculation results for activation energies. Sample collection site, microcosm treatment (Nutrient Amended (NA)/Unamended (UN)), mean activation energy calculated based on respiration rates (Mean; kJ/mol), standard deviation of activation energy (Std), calculated Q10 value (rate change when temperature increases 10C) at 20 C (Q10@20C).
          
qPCR: quantitative PCR results for 16s rRNA, nifH gene, and their ratio. Sample collection site, incubation temperature (temp; degrees C), microcosm treatment (Nutrient Amended (NA)/Unamended (UN)), average abundance of 16s gene copy number (abund_16s; copy of 16s/L of seawater), standard deviation of the abundance of 16s gene copy number (stdev_16s), average abundance of nifH gene copy number (abund_nifH; copy of 16s/L of seawater), standard deviation of the abundance of nifH gene copy number (stdev_nifH), averaged relative abundance of nifH gene in microbial community (nifH/16s, percent), standard deviation of averaged relative abundance of nifH gene in microbial community (stdev_nifH/16s, percent).
          
Colwellia: the sequence of the most abundant Colwellia strain found in the microcosms. Sequence id (row 1), nucleic acid sequence (row 2), blast result of the most closely related sequences in the NCBI database (rows 4-7).
          
Sample collection sites: latitude and longitude (decimal degrees), and collection date (mm/dd/yyyy): Site CB2: 75.470000, 129.17000, 08/03/2015 Site DWH01: 28.430000, -88.230000, 08/20/2015 Site IXTOC01: 19.000000, -92.000000, 08/03/2015|For each site, microcosms were constructed by amending 5 ml of seawater with 5 μl of surrogate MC252 oil in 30 ml sealed glass tubes. The surrogate oil is a sweet light crude with similar analytical and toxicological properties to the MC252 oil discharged during the Deepwater Horizon disaster that was set aside by BP as a tractable model oil for experimentation. Experimental treatments included: unamended (UN) microcosms to which no nutrient was added and nutrient amended (NA) microcosms that received 32 μM ammonium and 2 μM phosphate (final concentration). Microcosms with no oil addition were constructed and incubated at 25 °C to indicate the amount of respiration supported by recently-produced natural organic matter present in seawater at the time of sampling. Triplicate microcosms were incubated in the dark at 6 different temperatures spanning the temperature range of polar to tropical climates (4, 8, 19, 25, 30, and 38 °C) for 15 days. Microcosms were sampled at regular intervals for respiration rate measurements.
          
Five milliliters of seawater from each site were incubated with 0.5% Macondo surrogate oil at 6 different temperatures (4, 8, 19, 25, 30, 38 degrees C) and two different nutrient conditions (no nutrient addition, 32 uM Nh4Cl, and 2uM K2HPO4) in triplicates. No oil addition control of each site was incubated at 25C without oil and nutrient addition.|Respiration measurement- GC-FID|||
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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: xls Version: inapplicable File decompression technique: Distributor transfer options: Digital transfer options: Transfer size: 0.0264 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x267.179:0009 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.x267.179:0009 on 2021-01-22T23:05:34-06:00
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