Dataset: SPOT- Retinoid
Deployment: SPOT_20170711

Principal Investigator:

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

Co-Principal Investigator:

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

Contact:

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

BCO-DMO Data Manager:

Megan Switzer (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Environmental regulation of retinal and bacteriochlorophyll biosynthesis (Marine Retinoids)

Data URL:

https://www.bco-dmo.org/dataset-deployment/723543/data

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Description

Location: San Pedro Ocean Time Series (SPOT) station (33°33′N, 118°24′W)

Samples for quantification of retinal oxime were collected at a six of depths within the euphotic zone (5-250m). Seawater was collected from each CTD depth using Niskin bottles and immediately filtered. Particulate samples were collected using in-line 0.2µm, 3µm and 10µm pore-size filters and a peristaltic pump (flow rate < 50 ml per minute), transferred into sterile cryovials and were immediately stored at -80 degrees C until analysis.

Pigments were extracted from the filters in 3 mL of methanol, BHT (butylated hydroxytoluene) was added and placed in a -20 degrees C freezer overnight. The retinal oxime was formed by the addition of hydroxylamine hydrochloride and irradiated under yellow light for 2 hours before analysis. Retinal oxime samples were analyzed by liquid chromatography/triple mass spectrometry (LC/MS/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.

For chlorophyll-a measurements, 100 microliters of the pigment extraction were diluted in acetone (50x dilution) and analyzed using a Turner 10AU fluorometer.

Bacterial production was estimated by incorporation of [3H] thymidine and [3H] leucine into DNA and protein, respectively, as earlier described (Simon & Azam, 1989, Fuhrman and Azam 1982).

Methods & Sampling

Dataset acquisition description

Deployment: SPOT
Platform: RV Yellowfin and RV Nerissa
Platform Type: vessel
Start Date: 09/14/2016
End Date: 07/11/2017

The SPOT sampling for the months of May and July were carried out on the research vessel Nerissa of the Orange County Sanitation District. This was because the RV Yellowfin was in the dry dock for maintenance and repairs. Unfortunately, the light intensity for those two months is missing due to problems with the sensor.

Data Processing Description

Dataset Processing Description

The LC-MS data was processed using LCQUAN quantitative software from Thermo Scientific.

More information about this dataset deployment

Funding

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

Instruments

Fluorometer

Supplied Name: Turner 10AU fluorometer

Supplied Description:

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Mass Spectrometer

Supplied Name: ThermoTSQ Quantum Access electro-spray ionization triple quadupole mass spectrometer

Supplied Description:

The LC-MS system used for the pigment quantification consists of a Thermo TSQ Quantum Access electro-spray ionization triple quadruple mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography pump and auto-sampler.

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise ID	SPOT month and year	cruise_id
Date	Sampling date	mm/dd/yy	date
Time	Start and end times of sampling	hh:mm-hh:mm	time
Longitude	SPOT longitude	decimal degrees	lon
Latitude	SPOT latitude	decimal degrees	lat
Depth	Sampling depth	meters	depth
Microbial_Size_fraction	Size range of particles collected	micrometers(µm)	no_bcodmo_term
PR_retinal_Oxime_sw	Average Proteorhodopsin concentrations of triplicate analytical replicates of retinal oxime using HPLC-MS	picomolar (pico mol L-1)	no_bcodmo_term
STDEV_retinal_oxime_sw	Standard deviation of Proteorhodopsin concentrations of triplicate analytical replicates of retinal oxime using HPLC-MS	picomolar (pico mol L-1)	no_bcodmo_term
Chl_a_sw_avg	Average Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer	picomolar (pico mol L-1)	no_bcodmo_term
STDEV_Chl_a_sw	Standard deviation of Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer	picomolar (pico mol -L)	no_bcodmo_term
Leucine_BP	Bacterial production calculated from Leucine uptake	lls ml-1 day-1	no_bcodmo_term
Thymidine_BP	Bacterial production calculated from Thymidine uptake	cells ml-1 day-1	no_bcodmo_term
PAR	Photosynthetically active radiation (400-700nm)	micro Einsteins per square meter per second	no_bcodmo_term
ISO_DateTime_start	Time at sampling start	yyyy-mm-ddThh:mm:ss	time

Database

Contribute Data

Dataset: SPOT- Retinoid
Deployment: SPOT_20170711

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SPOT- RetinoidDeployment: SPOT_20170711

Dataset acquisition description

Dataset Processing Description

Dataset: SPOT- Retinoid
Deployment: SPOT_20170711