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Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean watersCenter for the Integrated Modeling and Analysis of Gulf Ecosystems II (C-IMAGE II)
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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:
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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
Contact info:
Contact:
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Telephone:
Voice:
8139746220
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4202 E. Fowler Ave.
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Tampa
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Florida
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33620
Country:
USA
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cfotherby@usf.edu
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Role code:
pointOfContact
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.
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All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be
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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
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Linkage:
URL:
https://data.gulfresearchinitiative.org
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distributor
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xls
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inapplicable
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Transfer size:
0.0264
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Online Resource:
Linkage:
URL:
https://data.gulfresearchinitiative.org/data/R4.x267.179:0009
Protocol:
https
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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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