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    Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids project)
    
  
  
    
    

Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids project)

Website: https://www.bco-dmo.org/dataset/564968
Version: 28 Aug 2015
Version Date: 2015-08-28

Project
» Environmental regulation of retinal and bacteriochlorophyll biosynthesis (Marine Retinoids)
ContributorsAffiliationRole
Sanudo-Wilhelmy, Sergio A.University of Southern California (USC-WIES)Principal Investigator
Fuhrman, Jed A.University of Southern California (USC-WIES)Co-Principal Investigator
Cutter, LyndaUniversity of Southern California (USC)Contact
Gómez-Consarnau, LauraUniversity of Southern California (USC)Contact
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Acquisition Description

Size Fractionation of retinal, bacteriochlorophyll and chlorophyll:
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 < 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.


Processing Description

Energy Benefit [kJ/cell/day] = Pigment concentration [molecules/cell] × Photosynthetic unit [per cell] × Maximum rate [electron/RC/s] /(PAR [umol photons/m2/s] + Half saturation [umol/photons/m2/s]) / Avogadro constant [/mol] × 12 [hours] × 60 [min] × 60 [sec] × Energy per photon [kJ/mol]

BCO-DMO Processing Notes:
- Replaced blanks (missing data) with 'nd' to indicate 'no data';
- Modified parameter names to conform with BCO-DMO naming conventions;
- Added ISO_DateTime field using original date and time values provided.


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Parameters

ParameterDescriptionUnits
cruise_nameName of the cruise. dimensionless
sampleSample identification number. dimensionless
stationStation number. dimensionless
dateDate (month, day, year). mmddYYYY
timeTime (hours and minutes). HHMM
lonLongitude in decimal degrees east. decimal degrees
latLatitude in decimal degrees north. decimal degrees
depthSample depth. meters
retinal_pMRetinal. picomoles per liter (pM)
retinal_oxime_pMPR (Retinal Oxime). picomoles per liter (pM)
Bchla_pMBacteriochlorophyll. picomoles per liter (pM)
chla_pMChlorophyll-a. picomoles per liter (pM)
tot_bacteriaTotal bacteria. cells per milliliter (cells/mL)
retinal_moleculescellRetinal. molecules per cell
retinal_oxime_moleculescellPR (Retinal Oxime). molecules per cell
Bchla_moleculescellBacteriochlorophyll. molecules per cell
chla_containing_cellsChlorophyll-a containing cells. cells per milliliter (cells/mL)
chla_per_cell_pmolcellChlorophyll-a per cell. picomolecules per cell.
chla_per_cell_moleculescellChlorophyll-a per cell. molecules per cell.
EdZ305Light intensity at wavelength of 305. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ313Light intensity at wavelength of 313. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ320Light intensity at wavelength of 320. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ340Light intensity at wavelength of 340. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ380Light intensity at wavelength of 380. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ395Light intensity at wavelength of 395. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ412Light intensity at wavelength of 412. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ443Light intensity at wavelength of 443. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ465Light intensity at wavelength of 465. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ490Light intensity at wavelength of 490. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ510Light intensity at wavelength of 510. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ555Light intensity at wavelength of 555. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ670Light intensity at wavelength of 670. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ694Light intensity at wavelength of 694. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZ710Light intensity at wavelength of 710. microwatts per square centimeter-nanometer (uW/(cm2nm))
EdZPARLight intensity at wavelengths of "photosynthetically active radiation" (PAR). microwatts per square centimeter-nanometer (uW/(cm2nm))
bacterial_prodBacterial production. micrograms Carbon per liter per day (ugC l-1 d-1)
ETS_activityETS activity. ?
retinal_oxime_energy_ben_KjcelldayPR (Retinal Oxime) energy benefit. kilojoules per cell per day (KJ cell-1 day-1)
retinal_oxime_energy_ben_KJLdayPR (Retinal Oxime) energy benefit. kilojoules per liter per day (KJ L-1 day-1)
Bchla_energy_ben_KjcelldayBacteriochlorophyll energy benefit. kilojoules per cell per day (KJ cell-1 day-1)
chla_energy_ben_KjcelldayChlorophyll-a energy benefit. kilojoules per cell per day (KJ cell-1 day-1)
ISO_DateTimeDate and time formatted to ISO8601 standard. YYYY-mm-ddTHH:MM:SS.xx


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Instruments

Dataset-specific Instrument Name
Niskin bottles
Generic Instrument Name
Niskin bottle
Dataset-specific Description
Seawater were collected from each CTD depth using Niskin bottles and immediately filtered.
Generic 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.

Dataset-specific Instrument Name
CTD
Generic Instrument Name
CTD profiler
Dataset-specific Description
Seawater were collected from each CTD depth using Niskin bottles and immediately filtered.
Generic 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 and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the 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 instrument designation is used when specific make and model are not known.

Dataset-specific Instrument Name
Thermo Accela High Speed Liquid Chromatography system
Generic Instrument Name
High Performance Liquid Chromatograph
Dataset-specific 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
Generic 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.

Dataset-specific Instrument Name
ThermoTSQ Quantum Access
Generic Instrument Name
Mass Spectrometer
Dataset-specific 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.
Generic 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.


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Deployments

Hotmix2014

Website
Platform
B/O Sarmiento de Gamboa
Start Date
2014-04-29
End Date
2014-05-28


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Project Information

Environmental regulation of retinal and bacteriochlorophyll biosynthesis (Marine Retinoids)

Coverage: Mediterrean Sea and the North Pacific Ocean


Description from NSF award abstract:
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.

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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database.    2021-04-10  15:42:01