http://lod.bco-dmo.org/id/dataset/914387
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2023-11-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Normalized oxygen from incubations conducted with methylcyclohexane using samples collected from the Gulf of Mexico during June 2015 on R/V Atlantis cruise AT29-02
2023-11-07
publication
2023-11-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-10
publication
https://doi.org/10.26008/1912/bco-dmo.914387.1
Eleanor Arrington
University of California-Santa Barbara
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Arrington, E. (2024) Normalized oxygen from incubations conducted with methylcyclohexane using samples collected from the Gulf of Mexico during June 2015 on R/V Atlantis cruise AT29-02. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-11-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.914387.1 [access date]
Normalized oxygen from MCH incubations Dataset Description: Methods and Sampling: <p>Seawater samples were collected aboard R/V Atlantis in June 2015 on cruise AT29-02. Methylcyclohexane (MCH) and methylcyclopentane (MCP) incubations were conducted at stations 1 (27° 30.41ʹ N, 87° 12.41ʹ W), 2 (27° 15.00ʹ N, 89° 05.05ʹ W), 3 (27° 11.60ʹ N, 90° 41.75ʹ W), and 4 (27° 38.40ʹ N, 90° 54.98ʹ W) with seawater collected from 1000 meters (m) depth. Seawater collected from the CTD Niskin bottles was transferred to 250-milliliter (mL) glass serum vials using a small length of Tygon tubing. Vials were filled for at least 3 volumes of water to overflow. Care was taken to ensure no bubbles were present before sealing with a polytetrafluoroethylene (PTFE) coated chlorobutyl rubber stopper and crimp cap seal. All bottles, except for unamended blank controls, immediately received 10 mL of MCH or MCP using a gas-tight syringe (Hamilton) and were maintained in the dark at in-situ temperature (4º Celsius). Before filling, each serum bottle was fixed with a contactless optical oxygen sensor (Pyroscience, Aachen, Germany) on the inner side with silicone glue, and afterward were cleaned from organic contaminants with triple rinses of ethanol, 3% hydrogen peroxide, 10% hydrochloric acid, and MilliQ water, and were sterilized via autoclave. Oxygen concentration was monitored approximately every 8 hours with a fiber optic oxygen meter (Pyroscience, Aachen, Germany). Observed changes in oxygen content were normalized to unamended controls to correct for oxygen loss from background respiration processes and variability due to temperature changes. Bloom onset is operationally defined as three consecutive time points with oxygen loss &gt;0.21 micromoles per hour (µM h-1). Importantly, incubations were conducted with no added headspace and were limited to in-situ availability of oxygen, as well as for key nutrients, such as nitrogen and phosphorous. At the termination of each respiration experiment, samples were harvested and the microbial community was captured on a 0.22-micrometer (μm) polyethersulfone filter. Prior to filtration samples were collected for dissolved inorganic nutrients and bacterioplankton abundance. Samples for prokaryotic cell abundance were fixed with 0.2% paraformaldehyde and quantified using Guava EasyCyte flow cytometer. Dissolved nutrient (nitrate, phosphate, and ammonia) sample collection was conducted following the University of California, Santa Barbara Marine Science Institute Analytical Lab's requirements. Seawater samples from incubations were filtered through a 0.2 μm polyvinylidene into pre-rinsed plastic HDPE 20 mL. Nutrient sample volumes were ∼17 mL water and stored frozen until analysis. Dissolved nutrient concentrations were analyzed by flow injection analysis (FIA) using the QuikChem 8500 Series 2 (Lachat Instruments, Zellweger Analytics Inc.).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756947 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756947
completed
Eleanor Arrington
University of California-Santa Barbara
585-698-6296
1006 Webb Hall
Santa Barbara
CA
93106
USA
earrington@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Station_Latitude
Station_Longitude
ISO_DateTime_Local
ISO_DateTime_UTC
Replicate
Time_hours
Time_days
Oxygen_loss
Millipore Guava EasyCyte 5HT Flow Cytometer
QuikChem 8500 Series 2 (Lachat Instruments)
CTD Niskin bottles
Pyroscience OXSP5 optical oxygen sensors with FireStingO2 oxygen meter
theme
None, User defined
station
latitude
longitude
ISO_DateTime_Local
ISO_DateTime_UTC
replicate
time_elapsed
dissolved Oxygen
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Lachat QuikChem 8500 flow injection analysis system
Niskin bottle
Oxygen Sensor
instrument
BCO-DMO Standard Instruments
AT29-02
service
Deployment Activity
Gulf of Mexico
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Chemical and microbiological studies of water-soluble alkanes in the ocean
https://osprey.bco-dmo.org/project/764256
Collaborative Research: Chemical and microbiological studies of water-soluble alkanes in the ocean
<p><em>NSF Abstract:</em><br />
This research project addresses the fate of hydrocarbons that enter the ocean, using geological oil seeps as a natural scientific laboratory. The key issues of intellectual merit that will be addressed focus on the development and application of methodology to determine how the chemical properties of hydrocarbon molecules dictate whether they will be trapped in the ocean's interior or find their way to the atmosphere. The research will further follow the fate of these molecules in the ocean's interior, determining how the ocean's bacterial population responds, and the extent to which responding bacteria will degrade these molecules. The broader impacts of this research will include the training of undergraduate and graduate students in scientific research and at-sea oceanographic training, as well as the dissemination of findings to policy makers striving to understand the fate and effects of hydrocarbons in the ocean.</p>
<p>Hydrocarbons enter the ocean through a combination of natural seepage, anthropogenic discharge and biological production, with profound impacts on ocean biogeochemistry, ecology, and the atmosphere. This research project addresses the chemical and biological processes affecting water-soluble alkanes in the ocean, using natural seeps to study their fluxes, partitioning between ocean and atmosphere, and the bacterial response to their input. The intellectual merit of this research pertains to the behavior of highly volatile hydrocarbons, a class that is abundant in petroleum reservoirs and many crude and refined products, but is poorly understood in the ocean. Volatile hydrocarbons display distinct behaviors compared with traditional oil in that they will partition to seawater or the atmosphere depending on their molecular structure and the context by which they enter the ocean, a combination of characteristics unsuitable for traditional fate and transport models that govern our understanding of liquid oil. This research project addresses this gap in knowledge through a plan to study volatile, water-soluble hydrocarbons in the context of natural seepage, focusing on key questions about their transport and fate, and the ocean's microbial response. Two key questions include: 1) What factors control the partitioning of water-soluble alkanes between water and the atmosphere at natural seeps, and how does this affect their availability to microbes? 2) What genomic and metabolic factors enable the microbial response to the input of water-soluble alkanes and how does the microbial response vary with regional oceanographic and geologic factors such as proximity to and flux from natural seepage? The hypotheses that result from these questions will be tested through a series of oceanographic and laboratory-based experiments designed around natural oil seeps in the Pacific and in the Gulf of Mexico. The results of these studies promise to inform our understanding of the transport, fate, and effects of water-soluble alkanes in the ocean.</p>
<p>
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
CASA
largerWorkCitation
project
eng; USA
oceans
Gulf of Mexico
-90.9163
-87.2068
27.1933
27.64
2015-06-17
2015-06-18
Coal Oil Point, Santa Barbara, CA and Gulf of Mexico
0
BCO-DMO catalogue of parameters from Normalized oxygen from incubations conducted with methylcyclohexane using samples collected from the Gulf of Mexico during June 2015 on R/V Atlantis cruise AT29-02
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/914566.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/914567.rdf
Name: Station_Latitude
Units: decimal degrees
Description: <p>Station latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/914568.rdf
Name: Station_Longitude
Units: decimal degrees
Description: <p>Station longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/914569.rdf
Name: ISO_DateTime_Local
Units: unitless
Description: <p>Date and time of sampling at the station in ISO 8601 format in local time zone = US Eastern (-5:00/-4:00)</p>
http://lod.bco-dmo.org/id/dataset-parameter/914570.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of sampling at the station in ISO 8601 format in UTC</p>
http://lod.bco-dmo.org/id/dataset-parameter/914571.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate number</p>
http://lod.bco-dmo.org/id/dataset-parameter/914572.rdf
Name: Time_hours
Units: hours
Description: <p>Time in hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/914573.rdf
Name: Time_days
Units: days
Description: <p>Time in days</p>
http://lod.bco-dmo.org/id/dataset-parameter/914574.rdf
Name: Oxygen_loss
Units: micromolar (uM)
Description: <p>Oxygen loss. After sacrificial harvest the oxygen loss values are blank/empty.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
204326
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/febe6ad5-d687-47fd-807b-6295e8e4f02c/content
download
https://doi.org/10.26008/1912/bco-dmo.914387.1
download
onLine
dataset
<p>Seawater samples were collected aboard R/V Atlantis in June 2015 on cruise AT29-02. Methylcyclohexane (MCH) and methylcyclopentane (MCP) incubations were conducted at stations 1 (27° 30.41ʹ N, 87° 12.41ʹ W), 2 (27° 15.00ʹ N, 89° 05.05ʹ W), 3 (27° 11.60ʹ N, 90° 41.75ʹ W), and 4 (27° 38.40ʹ N, 90° 54.98ʹ W) with seawater collected from 1000 meters (m) depth. Seawater collected from the CTD Niskin bottles was transferred to 250-milliliter (mL) glass serum vials using a small length of Tygon tubing. Vials were filled for at least 3 volumes of water to overflow. Care was taken to ensure no bubbles were present before sealing with a polytetrafluoroethylene (PTFE) coated chlorobutyl rubber stopper and crimp cap seal. All bottles, except for unamended blank controls, immediately received 10 mL of MCH or MCP using a gas-tight syringe (Hamilton) and were maintained in the dark at in-situ temperature (4º Celsius). Before filling, each serum bottle was fixed with a contactless optical oxygen sensor (Pyroscience, Aachen, Germany) on the inner side with silicone glue, and afterward were cleaned from organic contaminants with triple rinses of ethanol, 3% hydrogen peroxide, 10% hydrochloric acid, and MilliQ water, and were sterilized via autoclave. Oxygen concentration was monitored approximately every 8 hours with a fiber optic oxygen meter (Pyroscience, Aachen, Germany). Observed changes in oxygen content were normalized to unamended controls to correct for oxygen loss from background respiration processes and variability due to temperature changes. Bloom onset is operationally defined as three consecutive time points with oxygen loss &gt;0.21 micromoles per hour (µM h-1). Importantly, incubations were conducted with no added headspace and were limited to in-situ availability of oxygen, as well as for key nutrients, such as nitrogen and phosphorous. At the termination of each respiration experiment, samples were harvested and the microbial community was captured on a 0.22-micrometer (μm) polyethersulfone filter. Prior to filtration samples were collected for dissolved inorganic nutrients and bacterioplankton abundance. Samples for prokaryotic cell abundance were fixed with 0.2% paraformaldehyde and quantified using Guava EasyCyte flow cytometer. Dissolved nutrient (nitrate, phosphate, and ammonia) sample collection was conducted following the University of California, Santa Barbara Marine Science Institute Analytical Lab's requirements. Seawater samples from incubations were filtered through a 0.2 μm polyvinylidene into pre-rinsed plastic HDPE 20 mL. Nutrient sample volumes were ∼17 mL water and stored frozen until analysis. Dissolved nutrient concentrations were analyzed by flow injection analysis (FIA) using the QuikChem 8500 Series 2 (Lachat Instruments, Zellweger Analytics Inc.).</p>
Specified by the Principal Investigator(s)
<p>The average oxygen loss in unamended controls was averaged. For incubations with hydrocarbons, oxygen loss was normalized to oxygen loss in unamended controls to account for background respiration.</p>
Specified by the Principal Investigator(s)
- Imported original file "bco_dmo_wsa_incubation_oxygen.xlsx" into the BCO-DMO system.
- Marked "NA" as a missing data value (missing data are blank/empty in the final CSV file).
- Concatenated the 4 MCH sheets together into one dataset.
- Added the Station column to denote the station number.
- Added columns for station latitude and longitude, using the location information provided in the metadata.
- Added columns for the sampling date and time in local and UTC time zones.
- Renamed fields to comply with BCO-DMO naming conventions.
- Unpivoted the data, converting replicates from columns to rows, and creating the Oxygen_loss column and the Replicate column.
- Sorted by Station, Replicate, and Time_hours.
- Rounded Time_days to 5 decimal places.
- Saved the final file as "914387_v1_normalized_oxygen_mch.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Millipore Guava EasyCyte 5HT Flow Cytometer
Millipore Guava EasyCyte 5HT Flow Cytometer
PI Supplied Instrument Name: Millipore Guava EasyCyte 5HT Flow Cytometer Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
QuikChem 8500 Series 2 (Lachat Instruments)
QuikChem 8500 Series 2 (Lachat Instruments)
PI Supplied Instrument Name: QuikChem 8500 Series 2 (Lachat Instruments) Instrument Name: Lachat QuikChem 8500 flow injection analysis system Instrument Short Name:QuikChem 8500 Instrument Description: The Lachat QuikChem 8500 Series 2 Flow Injection Analysis System features high sample throughput and simple, but rapid, method changeover. The QuikChem 8500 Series 2 system maximises productivity in determining ionic species in a variety of sample types, from sub-ppb to percent concentrations. Analysis takes 20 to 60 seconds, with a sample throughput of 60 to 120 samples per hour.
CTD Niskin bottles
CTD Niskin bottles
PI Supplied Instrument Name: CTD Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Pyroscience OXSP5 optical oxygen sensors with FireStingO2 oxygen meter
Pyroscience OXSP5 optical oxygen sensors with FireStingO2 oxygen meter
PI Supplied Instrument Name: Pyroscience OXSP5 optical oxygen sensors with FireStingO2 oxygen meter Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
Cruise: AT29-02
AT29-02
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT29-02
David L. Valentine
University of California-Santa Barbara
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel