Dataset: Hotmix 2014 Retinoids

Name: Retinoid data from Niskin bottle samples from B/O Sarmiento de Gamboa cruise Hotmix2014 in the Mediterranean in 2014 (Marine Retinoids project)
Published: 2015-08-28
Keywords: oceans

Cite This Dataset

Spatial Extent: N:41.49 E:31.41 S:31.25 W:-12.98

Project:

Environmental regulation of retinal and bacteriochlorophyll biosynthesis (Marine Retinoids)

Principal Investigator:

Sergio A. Sanudo-Wilhelmy (University of Southern California, USC-WIES)

Co-Principal Investigator:

Jed A. Fuhrman (University of Southern California, USC-WIES)

Contact:

Lynda Cutter (University of Southern California, USC)

Laura Gómez-Consarnau (University of Southern California, USC)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

28 Aug 2015

Version Date:

2015-08-28

Restricted:

Validated:

Current State:

Final no updates expected

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

Expand/Collapse All

Methods & Sampling

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.

Data 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.

Data Files

File
hotmix2014.csv (Comma Separated Values (.csv), 36.00 KB) MD5:6dd68caae40e8bf6adb807adf874705f Primary data file for dataset ID 564968

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1335269

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Hotmix2014		2014-04-29	B/O Sarmiento de Gamboa		data info

Instruments

CTD - profiler

Supplied Name: CTD

Supplied Description:

Seawater were collected from each CTD depth using Niskin bottles and immediately filtered.

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic 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.

High-Performance Liquid Chromatograph

Supplied Name: Thermo Accela High Speed Liquid Chromatography system

Supplied 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 Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic 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.

Mass Spectrometer

Supplied Name: ThermoTSQ Quantum Access

Supplied Description:

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic 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.

Niskin bottle

Supplied Name: Niskin bottles

Supplied Description:

Seawater were collected from each CTD depth using Niskin bottles and immediately filtered.

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_name	Name of the cruise.	dimensionless	cruise_name
sample	Sample identification number.	dimensionless	sample
station	Station number.	dimensionless	station
date	Date (month, day, year).	mmddYYYY	date
time	Time (hours and minutes).	HHMM	time
lon	Longitude in decimal degrees east.	decimal degrees	lon
lat	Latitude in decimal degrees north.	decimal degrees	lat
depth	Sample depth.	meters	depth
retinal_pM	Retinal.	picomoles per liter (pM)	no_bcodmo_term
retinal_oxime_pM	PR (Retinal Oxime).	picomoles per liter (pM)	no_bcodmo_term
Bchla_pM	Bacteriochlorophyll.	picomoles per liter (pM)	no_bcodmo_term
chla_pM	Chlorophyll-a.	picomoles per liter (pM)	no_bcodmo_term
tot_bacteria	Total bacteria.	cells per milliliter (cells/mL)	no_bcodmo_term
retinal_moleculescell	Retinal.	molecules per cell	no_bcodmo_term
retinal_oxime_moleculescell	PR (Retinal Oxime).	molecules per cell	no_bcodmo_term
Bchla_moleculescell	Bacteriochlorophyll.	molecules per cell	no_bcodmo_term
chla_containing_cells	Chlorophyll-a containing cells.	cells per milliliter (cells/mL)	no_bcodmo_term
chla_per_cell_pmolcell	Chlorophyll-a per cell.	picomolecules per cell.	no_bcodmo_term
chla_per_cell_moleculescell	Chlorophyll-a per cell.	molecules per cell.	no_bcodmo_term
EdZ305	Light intensity at wavelength of 305.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ313	Light intensity at wavelength of 313.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ320	Light intensity at wavelength of 320.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ340	Light intensity at wavelength of 340.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ380	Light intensity at wavelength of 380.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ395	Light intensity at wavelength of 395.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ412	Light intensity at wavelength of 412.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ443	Light intensity at wavelength of 443.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ465	Light intensity at wavelength of 465.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ490	Light intensity at wavelength of 490.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ510	Light intensity at wavelength of 510.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ555	Light intensity at wavelength of 555.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ670	Light intensity at wavelength of 670.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ694	Light intensity at wavelength of 694.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZ710	Light intensity at wavelength of 710.	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
EdZPAR	Light intensity at wavelengths of "photosynthetically active radiation" (PAR).	microwatts per square centimeter-nanometer (uW/(cm2nm))	no_bcodmo_term
bacterial_prod	Bacterial production.	micrograms Carbon per liter per day (ugC l-1 d-1)	no_bcodmo_term
ETS_activity	ETS activity.	?	no_bcodmo_term
retinal_oxime_energy_ben_Kjcellday	PR (Retinal Oxime) energy benefit.	kilojoules per cell per day (KJ cell-1 day-1)	no_bcodmo_term
retinal_oxime_energy_ben_KJLday	PR (Retinal Oxime) energy benefit.	kilojoules per liter per day (KJ L-1 day-1)	no_bcodmo_term
Bchla_energy_ben_Kjcellday	Bacteriochlorophyll energy benefit.	kilojoules per cell per day (KJ cell-1 day-1)	no_bcodmo_term
chla_energy_ben_Kjcellday	Chlorophyll-a energy benefit.	kilojoules per cell per day (KJ cell-1 day-1)	no_bcodmo_term
ISO_DateTime	Date and time formatted to ISO8601 standard.	YYYY-mm-ddTHH:MM:SS.xx	no_bcodmo_term

Status message

Database

Contribute Data

Dataset: Hotmix 2014 Retinoids