Dataset: SPOT Vitamins
Deployment: SPOT_Yellowfin_Cruises

Vitamin and methionine quantifications from SPOT cruises during different months

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/753883

Principal Investigator:

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

Co-Principal Investigator:

David A. Hutchins (University of Southern California, USC)

Contact:

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

BCO-DMO Data Manager:

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

Project:

Can the availability of B-vitamins control phyto-and-bacterioplankton successions in a coastal upwelling region? (B-vitamin plankton succession)

Version:

Expand/Collapse All

Description

Methods & Sampling

Dataset acquisition description

Samples for quantification of B-vitamins B1, B7, CB12 and Methionine 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 for chlorophyll quantifications were collected using in-line 0.2um, 3µm and 10um 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. For chlorophyll-a measurements, 100 microliters of the pigment extraction were diluted in acetone (50x dilution) and analyzed using a Turner 10AU fluorometer.

B-vitamins and Methionine samples were analyzed as in Suffridge et al. 2017. Two liters of seawater were filtered through um pore-size filters and then preconcentrated using a C18 resin (HF Bondesil (Agilent Technologies) and 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. The LC system used a stable- bond C18 reversed-phase column (DiscoveryHSC18 10cm × 2.1mm,5 μm column, Supelco Analytical) with a100 uL sample loop. In order to increase the sensitivity and precision, theLC/MS was run in full-loop mode (100 ul/injection).

Bacterial cell counts were heterotrophic prokaryotes were enumerated by flow-cytometry (Becton–Dickinson FACScalibur) (Gasol & del Giorgio, 2000).

Data Processing Description

Dataset Processing Description

Data Processing: The LC-MS data was processed using Xcalibur and LCQUAN quantitative softwares from Thermo Scientific.

Problem report: 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.

BCO-DMO Processing:
- replaced spaces with underscores in cruise names;
- changed date format from m/d/yyyy to yyyy-mm-dd;
- separated time column into Time_start and Time_end
- converted Latitude and Longitude from degrees and minutes to decimal degrees, added new columns and removed original;
- modified parameter names (replaced spaces and decimals with underscores, removed units)
- filled in empty cells with "nd"; replaced NaN with "nd" ("no data").

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1435666	NSF Division of Ocean Sciences

Instruments

Mass Spectrometer

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

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:

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.

Pump

Supplied Name: Peristaltic pump

Supplied Description:

Instrument Type

Generic Name: Pump

Generic Description:

A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps

Turner Designs Fluorometer 10-AU

Supplied Name: Turner 10AU fluorometer

Supplied Description:

Instrument Type

Generic Name: Turner Designs Fluorometer 10-AU

Acronym: Turner Fluorometer 10-AU

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/

Generic Description:

The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer. (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise name	unitless	cruise_id
Date	Date; format: yyyy-mm-dd	unitless	date
Time_range	Time range	unitless	time
Time_start	Start time; format: HH:MM	unitless	time
Time_end	End time; format: HH:MM	unitless	time
Longitude	Longitude of sampling site; postivie values = East	decimal degrees	lon
Latitude	Latitude of sampling site; positive values = North	decimal degrees	lat
Depth	Sample depth	meters (m)	depth
B1	Average Vitamin B1 (Thiamin) concentrations of triplicate analytical replicates using HPLC-MS	picomolar (pM)	no_bcodmo_term
B7	Average Vitamin B7 (Biotin) concentrations of triplicate analytical replicates using HPLC-MS.	picomolar (pM)	no_bcodmo_term
CB12	Average Vitamin B12 (as Cyanocobalamin) concentrations of triplicate analytical replicates using HPLC-MS.	picomolar (pM)	no_bcodmo_term
MET	Average Methionine concentrations of triplicate analytical replicates using HPLC-MS.	picomolar (pM)	no_bcodmo_term
Chla_0_2	Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer. This fraction contains chlorophyll from organisms of 0.2-3 um and was collected onto 0.2 um pore-size filters.	picomolar (pM)	chl_a
Chla_total	Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer. This fraction contains chlorophyll from all microorganisms larger than 0.2 um.	picomolar (pM)	chl_a
Bacterial_cell_counts	Bacterial cell concentration per milliliter of seawater.	cells per milliliter (cells ml-1)	count

Database

Contribute Data

Dataset: SPOT Vitamins
Deployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SPOT VitaminsDeployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Dataset: SPOT Vitamins
Deployment: SPOT_Yellowfin_Cruises