Dataset: Vitacopss: cell counts and chla
Deployment: lab_Sanudo_2015

Picoplankton growth with nitrate and B vitamins from San Pedro Ocean Timeseries (SPOT), 2015

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/725929

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)

Project:

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

Version:

Deployment Synonyms:

San Pedro Ocean Time-Series, SPOT

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Description

This dataset includes chlorophyll-a concentrations and cell counts for picoplankton collected in water samples from the San Pedro Ocean Time-series (SPOT), 2015. They were incubated with six treatments of nitrate and vitamin B.

Methods & Sampling

Dataset acquisition description

Water samples were 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. Samples were collected initially, and at two points during the experiment: exponential growth and stationary phase. Exponential growth occurred at day 7 and stationary growth varied between treatment ranging from 10-12 days. The incubations were co-limited by nitrate and B12. Samples were flash frozen and stored at -80C until analysis. For further details on the methodology, see Suffridge et al (2017).

Samples for flow cytometry were collected, fixed with 2% formalin, and frozen at -80C. Analysis for the cellular abundance of heterotrophic bacteria, Synechococcus, and pircoeukaryotes was conducted using a BD Accuri C6 flow cytometer (Becton Dickerson and Company).

Chl-a concentrations were measured using the protocol described by Welschmeyer (1994). 40 ml of water samples from each replicate were filtered through GF/F glass fiber filters, 3.0-μm and 8.0-μm polycarbonate membrane for size fractionated Chl-a analyses. After adding 6 ml of 90% acetone, Chl-a was extracted in the freezer at -20°C and measured using the non-acidification method with a Turner Designs 10-AUTM fluorometer after 24 hours.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- reformatted columns by adding chla, organism, and cell_count -replacing type, units, and value in order to keep one type of data in each column
- changed 'syn' to 'Synechococcus', 'picoeuk' to 'picoeukaryotes'
- changed B1, B7, B12 to N+B1, N+B7, N+B12

More information about this dataset deployment

Funding

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

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.

Flow Cytometer

Supplied Name: BD Accuri C6 flow cytometer (Becton Dickerson and Company)

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Fluorometer

Supplied Name:

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.

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

Supplied Name	Supplied description	Supplied Units	Standard Name
treatment	treatments: control; nitrate (N); nitrate+B1 (N+B1); nitrate+B7 (N+B7); nitrate+B12 (N+B12); and nitrate+B1+B7+B12 (All)	unitless	treatment
date	date of experiment formatted as yyyy-mm-dd	unitless	date
time_point_code	code for sampling period during one of three growth phases of the population: 0=initial sampling; 1=exponential phase; 2=stationary phase. Dates: 2015-03-12 (time 0); 2015-03-20 (time 1); 2015-03-25 (time 2)	unitless	time_point
organism	type of microorganism counted	unitless	taxon
chla	chl-a Rf value	unitless	chl_a
cell_count	cell count of microorganism	cells/milliliter	count

Database

Contribute Data

Dataset: Vitacopss: cell counts and chla
Deployment: lab_Sanudo_2015

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Vitacopss: cell counts and chlaDeployment: lab_Sanudo_2015

Dataset acquisition description

Dataset Processing Description

Dataset: Vitacopss: cell counts and chla
Deployment: lab_Sanudo_2015