Dataset: vitamin B particulate - Vitacopss 2015

Name: Particulate B vitamins from Vitacopss, San Pedro Ocean Time series (SPOT), 2015 from R/V Yellowfin near Los Angeles, California from 2015-2016 (B-vitamin plankton succession project)
Published: 2016-08-08
Keywords: oceans

View Data: Data not available yet

Cite This Dataset

Project:

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

Principal Investigator:

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

Co-Principal Investigator:

Feixue Fu (University of Southern California, USC-WIES)

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

Contact:

Lynda Cutter (University of Southern California, USC)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2016-08-08

Restricted:

Yes

Release Date:

2017-12-31

Validated:

Yes

Current State:

Final no updates expected

Particulate B vitamins from Vitacopss, San Pedro Ocean Time series (SPOT), 2015 from R/V Yellowfin near Los Angeles, California from 2015-2016 (B-vitamin plankton succession project)

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Description

Access to this data set is restricted until 2017-12-31. Please contact L. Cutter for further information.

Methods & Sampling

Water was collected from 3 meters depth at the San Pedro Ocean Time-series (SPOT) station (33°33'N, 118°24'W, off the coast of Southern California in March 2015. Six treatments were used: control, nitrate, nitrate+B1, nitrate+B7, nitrate+B12, and nitrate+B1+B7+B12 with triplicate 10L incubations. Growth was tracked daily. Particulate B-vitamin samples were collected initially, and at two points during the experiment: exponential growth and stationary phase. Exponential growth occurred at day 7. Stationary growth varied between treatment ranging from 10-12 days. The incubations were co-limited by nitrate and B12. Samples were collected from two size fractions (0.2um-3um, and >3um) using in-line peristaltic filtration. Samples were flash frozen and stored at -80C until analysis. B-vitamin extraction was performed as described in Suffridge et. al (2017).

Particulate B-vitamins were extracted in acidic methanol (pH 3.5, 5% MeOH, 95% LC/MS Grade water) using bead-beating for cell lysis and a 30C incubation for B-vitamin extraction. A liquid phase extraction using chloroform (1:1 v/v) was used to clean up the samples prior to analysis.

Analysis was conducted using a Thermo TSQ Quantum Access triple quadrupole LC/MS with an ESI interface and a C₁₈ column (Discovery HS C₁₈ 10cm x 2, 1mm, 5μm column, Supelco Analytical) Sanudo 2012. Quantification conducted using an internal standard. Triplicate injections were used to increase precision.

Cited References:

Suffridge, Christopher; Cutter, Lynda; Sanudo-Wilhelmy, Sergio (2017) A New Analytical Method for Direct Measurement of Particulate and Dissolved B-vitamins and Their Congeners in Seawater. Front. Mar. Sci. vol.4 doi.org/10.3389/fmars.2017.00011

Sanudo 2012 - Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14041-5. doi: 10.1073/pnas.1208755109. Epub 2012 Jul 23

Data Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- replaced blank cells with nd (no data)
- added cruise_id, lat, lon, date
- mean_pM and std_dev: reduced digits right of decimal from 9 to 1 to take measurement precision into consideration

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
lab_Sanudo_2015	San Pedro Ocean Time-Series SPOT	2015-03-01	R/V Yellowfin	Sergio A. Sanudo-Wilhelmy (Principal Investigator)	data info

Instruments

CTD - profiler

Supplied Name:

Supplied Description:

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:

Supplied Description:

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:

Supplied Description:

ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer

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:

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
site	sample source	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
analyte	dissolved vitamin-B form: AB12: Adenosyl Cobalamin B1: Thiamine B7: Biotin CB12: Cyanocobalamin HB12: Hydroxycobalamin HMP: 4-Amino-2-methyl-5-pyrimidinyl methanol MB12: Methylcobalamin MET: Methionine TMP: Thiamine monophosphate TPP: Thiamine pyrophosphate	unitless	sample_descrip
sizefrac_um	sample size fraction	microns	samp_fraction
day	days since start of incubation	days	days
treatment	Nutrients added to incubation: Control: no added nutrients N: Nitrogen as sodium nitrate, 20 µmoles/L B1: Thiamine, 300 picomolar/L B7: Biotin, 100 picomoles/L B12: Cyanocobalamin, 100 picomoles/L All: Nitogen + Thiamine,+Cyanocobalamin, concentrations as above	unitless	treatment
mean_pM	particulate analyte concentration	picomoles per liter	no_bcodmo_term
std_dev	concentration standard deviation	picomoles per liter	std_dev

Status message

Database

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Dataset: vitamin B particulate - Vitacopss 2015