http://lod.bco-dmo.org/id/dataset/564968
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
2015-08-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids project)
2015-08-28
publication
2015-08-28
revision
BCO-DMO Linked Data URI
2015-08-28
creation
http://lod.bco-dmo.org/id/dataset/564968
Sergio A. Sanudo-Wilhelmy
University of Southern California
principalInvestigator
Jed A. Fuhrman
University of Southern California
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: Sanudo-Wilhelmy, S. A., Fuhrman, J. A. (2015) Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 28 Aug 2015) Version Date 2015-08-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/564968 [access date]
Retinoid data from Mediterranean cruise, Hotmix 2014. Dataset Description: Methods and Sampling: <p><strong>Size Fractionation of retinal, bacteriochlorophyll and chlorophyll:</strong><br />
Samples for quantification of light harvesting pigments in eukaryotes and prokaryotes were collected at a number of depths within the euphotic zone (see field study sites). Seawater were collected from each CTD depth using Niskin bottles and immediately filtered. Size fractionated samples were collected using a series of in-line filters using a peristaltic pump (flow rate &lt; 50 ml per minute). Filters of different pore-size (0.2 um for picoplankton, and 3.0 um for nanoplankton) were used for the fractionation. Particulate samples were immediately stored at -80 degrees C until analysis. For analysis, samples were extracted with methanol (retinal, chla, and Bchl) and with hydroxylamine (oxime) and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). The LCMS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system (Seegers et al., in preparation). The mobile phase conditions for the LCMS method for chlorophyll and bacteriochlorophyll analyses were adapted from Goericke (2002). All retinoid samples were analyzed in triplicate using an external calibration curve, though not presented, precision was typically in the 5-15% range.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335269 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1335269
completed
Sergio A. Sanudo-Wilhelmy
University of Southern California
213-821-1302
3616 Trousdale Pkwy Dept. of Biological Sciences, AHF 206, Mail Code: 0371
Los Angeles
CA
90089
USA
sanudo@usc.edu
pointOfContact
Jed A. Fuhrman
University of Southern California
213-740-5757
Dept. Biological Sciences, Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089-0371
USA
fuhrman@usc.edu
pointOfContact
asNeeded
Dataset Version: 28 Aug 2015
Unknown
cruise_name
sample
station
date
time
lon
lat
depth
retinal_pM
retinal_oxime_pM
Bchla_pM
chla_pM
tot_bacteria
retinal_moleculescell
retinal_oxime_moleculescell
Bchla_moleculescell
chla_containing_cells
chla_per_cell_pmolcell
chla_per_cell_moleculescell
EdZ305
EdZ313
EdZ320
EdZ340
EdZ380
EdZ395
EdZ412
EdZ443
EdZ465
EdZ490
EdZ510
EdZ555
EdZ670
EdZ694
EdZ710
EdZPAR
bacterial_prod
ETS_activity
retinal_oxime_energy_ben_Kjcellday
retinal_oxime_energy_ben_KJLday
Bchla_energy_ben_Kjcellday
chla_energy_ben_Kjcellday
ISO_DateTime
CTD
Thermo Accela High Speed Liquid Chromatography system
ThermoTSQ Quantum Access
Niskin bottles
theme
None, User defined
cruise name
sample identification
station
date
time of day
longitude
latitude
depth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD - profiler
High-Performance Liquid Chromatograph
Mass Spectrometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
Hotmix2014
service
Deployment Activity
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.
Environmental regulation of retinal and bacteriochlorophyll biosynthesis
https://osprey.bco-dmo.org/project/564190
Environmental regulation of retinal and bacteriochlorophyll biosynthesis
<p><em>Description from NSF award abstract:</em><br />
Rhodopsins are the simplest energy-harvesting photoproteins and community metagenomics have revealed that their synthesis genes are ubiquitous throughout the world oceans. These include microbial rhodopsin (proteorhodopsin (PR)), which occur in an estimated 75% of marine bacteria and archaea in oceanic surface waters. The discovery of this abundant and widespread photoprotein in the surface ocean has challenged the notion that solar energy can only be converted into chemical energy for growth in marine ecosystems through chlorophyll-based photosynthesis. Although the potential of light-driven energy flux in ocean ecosystems through PR could be significant, the physiological and ecological functions of this type of rhodopsin remains undetermined, mainly due to the lack of a technique for a direct measurement of this photoprotein. To evaluate the ecological relevance of PR in the marine environment, the investigators have developed a new analytical technique to measure the concentrations of the light-sensitive pigment in the PR, the chromophore retinal. Because rhodopsins have a single retinal chromophore associated with the polypeptide opsin, the total number of retinal molecules is equivalent to the total number of PR.</p>
<p>This project will employ the PI's newly developed protocol to examine the effects of light, organic carbon and trace metals availability on PR and bacteriochlorophyll synthesis using field and laboratory manipulations. Such experiments will establish the impact of abiotic factors on the two known bacterial photoheterotrophic metabolisms. The laboratory studies will be complemented with the analyses of those pigments in field samples collected along spatial and temporal gradients in light intensity, organic carbon and trace metals in different oceanographic regimes. Gene expression patterns will be determined in concert with changes in retinal and bacteriochlorophyll concentrations and microbial growth responses in the field and in the laboratory. Therefore, the combination of observational and manipulative approaches, will address fundamental questions in regard to the impact of retinal-based photochemical energy transformation in the ocean, a process that still is not well understood.</p>
Marine Retinoids
largerWorkCitation
project
eng; USA
oceans
2015-08-28
Mediterrean Sea and the North Pacific Ocean
0
BCO-DMO catalogue of parameters from Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids 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
http://lod.bco-dmo.org/id/dataset-parameter/565015.rdf
Name: cruise_name
Units: dimensionless
Description: <p>Name of the cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565016.rdf
Name: sample
Units: dimensionless
Description: <p>Sample identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565017.rdf
Name: station
Units: dimensionless
Description: <p>Station number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565018.rdf
Name: date
Units: mmddYYYY
Description: <p>Date (month, day, year).</p>
http://lod.bco-dmo.org/id/dataset-parameter/565019.rdf
Name: time
Units: HHMM
Description: <p>Time (hours and minutes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/565020.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude in decimal degrees east.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565021.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude in decimal degrees north.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565022.rdf
Name: depth
Units: meters
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565023.rdf
Name: retinal_pM
Units: picomoles per liter (pM)
Description: <p>Retinal.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565024.rdf
Name: retinal_oxime_pM
Units: picomoles per liter (pM)
Description: <p>PR (Retinal Oxime).</p>
http://lod.bco-dmo.org/id/dataset-parameter/565025.rdf
Name: Bchla_pM
Units: picomoles per liter (pM)
Description: <p>Bacteriochlorophyll.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565026.rdf
Name: chla_pM
Units: picomoles per liter (pM)
Description: <p>Chlorophyll-a.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565027.rdf
Name: tot_bacteria
Units: cells per milliliter (cells/mL)
Description: <p>Total bacteria.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565028.rdf
Name: retinal_moleculescell
Units: molecules per cell
Description: <p>Retinal.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565029.rdf
Name: retinal_oxime_moleculescell
Units: molecules per cell
Description: <p>PR (Retinal Oxime).</p>
http://lod.bco-dmo.org/id/dataset-parameter/565030.rdf
Name: Bchla_moleculescell
Units: molecules per cell
Description: <p>Bacteriochlorophyll.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565031.rdf
Name: chla_containing_cells
Units: cells per milliliter (cells/mL)
Description: <p>Chlorophyll-a containing cells.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565032.rdf
Name: chla_per_cell_pmolcell
Units: picomolecules per cell.
Description: <p>Chlorophyll-a per cell.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565033.rdf
Name: chla_per_cell_moleculescell
Units: molecules per cell.
Description: <p>Chlorophyll-a per cell.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565034.rdf
Name: EdZ305
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 305.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565035.rdf
Name: EdZ313
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 313.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565036.rdf
Name: EdZ320
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 320.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565037.rdf
Name: EdZ340
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 340.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565038.rdf
Name: EdZ380
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 380.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565039.rdf
Name: EdZ395
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 395.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565040.rdf
Name: EdZ412
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 412.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565041.rdf
Name: EdZ443
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 443.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565042.rdf
Name: EdZ465
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 465.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565043.rdf
Name: EdZ490
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 490.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565044.rdf
Name: EdZ510
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 510.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565045.rdf
Name: EdZ555
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 555.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565046.rdf
Name: EdZ670
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 670.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565047.rdf
Name: EdZ694
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 694.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565048.rdf
Name: EdZ710
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelength of 710.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565049.rdf
Name: EdZPAR
Units: microwatts per square centimeter-nanometer (uW/(cm2nm))
Description: <p>Light intensity at wavelengths of "photosynthetically active radiation" (PAR).</p>
http://lod.bco-dmo.org/id/dataset-parameter/565050.rdf
Name: bacterial_prod
Units: micrograms Carbon per liter per day (ugC l-1 d-1)
Description: <p>Bacterial production.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565051.rdf
Name: ETS_activity
Units: ?
Description: <p>ETS activity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565052.rdf
Name: retinal_oxime_energy_ben_Kjcellday
Units: kilojoules per cell per day (KJ cell-1 day-1)
Description: <p>PR (Retinal Oxime) energy benefit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565053.rdf
Name: retinal_oxime_energy_ben_KJLday
Units: kilojoules per liter per day (KJ L-1 day-1)
Description: <p>PR (Retinal Oxime) energy benefit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565054.rdf
Name: Bchla_energy_ben_Kjcellday
Units: kilojoules per cell per day (KJ cell-1 day-1)
Description: <p>Bacteriochlorophyll energy benefit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565055.rdf
Name: chla_energy_ben_Kjcellday
Units: kilojoules per cell per day (KJ cell-1 day-1)
Description: <p>Chlorophyll-a energy benefit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/565078.rdf
Name: ISO_DateTime
Units: YYYY-mm-ddTHH:MM:SS.xx
Description: <p>Date and time formatted to ISO8601 standard.</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
36866
https://datadocs.bco-dmo.org/file/JEE1nJOu151Xgn/hotmix2014.csv
hotmix2014.csv
Primary data file for dataset ID 564968
download
https://osprey.bco-dmo.org/dataset/564968/data/download
download
onLine
dataset
<p><strong>Size Fractionation of retinal, bacteriochlorophyll and chlorophyll:</strong><br />
Samples for quantification of light harvesting pigments in eukaryotes and prokaryotes were collected at a number of depths within the euphotic zone (see field study sites). Seawater were collected from each CTD depth using Niskin bottles and immediately filtered. Size fractionated samples were collected using a series of in-line filters using a peristaltic pump (flow rate &lt; 50 ml per minute). Filters of different pore-size (0.2 um for picoplankton, and 3.0 um for nanoplankton) were used for the fractionation. Particulate samples were immediately stored at -80 degrees C until analysis. For analysis, samples were extracted with methanol (retinal, chla, and Bchl) and with hydroxylamine (oxime) and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). The LCMS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system (Seegers et al., in preparation). The mobile phase conditions for the LCMS method for chlorophyll and bacteriochlorophyll analyses were adapted from Goericke (2002). All retinoid samples were analyzed in triplicate using an external calibration curve, though not presented, precision was typically in the 5-15% range.</p>
Specified by the Principal Investigator(s)
<p>Energy Benefit [kJ/cell/day] = Pigment concentration [molecules/cell] × Photosynthetic unit [per cell] × Maximum rate [electron/RC/s] /(PAR [umol photons/m<sup>2</sup>/s] + Half saturation [umol/photons/m<sup>2</sup>/s]) / Avogadro constant [/mol] × 12 [hours] × 60 [min] × 60 [sec] × Energy per photon [kJ/mol]</p>
<p>BCO-DMO Processing Notes:<br />
- Replaced blanks (missing data) with 'nd' to indicate 'no data';<br />
- Modified parameter names to conform with BCO-DMO naming conventions;<br />
- Added ISO_DateTime field using original date and time values provided.</p>
Specified by the Principal Investigator(s)
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
CTD
CTD
PI Supplied Instrument Name: CTD PI Supplied Instrument Description:Seawater were collected from each CTD depth using Niskin bottles and immediately filtered. Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Thermo Accela High Speed Liquid Chromatography system
Thermo Accela High Speed Liquid Chromatography system
PI Supplied Instrument Name: Thermo Accela High Speed Liquid Chromatography system PI Supplied Instrument Description:For analysis, samples were extracted with methanol (retinal, chla, and Bchl) and with hydroxylamine (oxime) and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). The LCMS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
ThermoTSQ Quantum Access
ThermoTSQ Quantum Access
PI Supplied Instrument Name: ThermoTSQ Quantum Access PI Supplied Instrument Description:For analysis, samples were extracted with methanol (retinal, chla, and Bchl) and with hydroxylamine (oxime) and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). The LCMS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Seawater were collected from each CTD depth using Niskin bottles and immediately filtered. 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/
Cruise: Hotmix2014
Hotmix2014
B/O Sarmiento de Gamboa
Community Standard Description
International Council for the Exploration of the Sea
B/O Sarmiento de Gamboa
vessel
B/O Sarmiento de Gamboa
Community Standard Description
International Council for the Exploration of the Sea
B/O Sarmiento de Gamboa
vessel