Dataset: picophyto_FCM_lab
Deployment: MV1008

Picophytoplankton abundances determined by flow cytometry (post-cruise/on-shore analysis).

Principal Investigator:

Michael R. Landry (University of California-San Diego, UCSD-SIO)

Contact:

Karen E. Selph (University of Hawaii at Manoa, SOEST)

BCO-DMO Data Manager:

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

Project:

Costa Rica Dome FLUx and Zinc Experiments (CRD FLUZiE)

Current State:

Final no updates expected

Version:

02 June 2014

Version Date:

2014-06-02

Data URL:

https://www.bco-dmo.org/dataset-deployment/516302/data

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Description

Picophytoplankton abundances from preserved (0.5% paraformaldehyde) frozen samples run on a Beckman-Coulter Altra flow cytometer after staining with Hoechst 33342 DNA stain and excitation with 200 mW UV and 1W 488 nm laser light. Cell populations include Prochlorococcus, Synechococcus, and Picophytoeukaryotes. Samples were collected on the MV1008 cruise in the Costa Rica Dome (CRD) region of the Eastern Tropical Pacific Ocean.

Methods & Sampling

Dataset acquisition description

Samples were collected from the CTD-Rosette PVC Niskin bottles, then preserved with paraformaldehyde (0.5% final concentration). Preserved samples were then flash frozen in liquid nitrogen, and subsequently stored at -80°C until analysis on-shore in batches. Upon thawing, samples were stained with Hoechst 33342 DNA stain (1 ug/mL final concentration), incubated at room temperature in the dark for 1 h, then analyzed using a Beckman-Coulter Altra flow cytometer, equipped with one 488 nm 1W laser and one UV 200 mM laser for excitation. Samples (100 ul) were delivered quantitatively to the instrument using a Harvard Apparatus syringe pump, at a rate of 50 ul per minute. Signals from the DNA (450±40 nm), Chlorophyll (680±20 nm), Phycoerythrin (575±20 nm), and the forward and side scatter detectors were used to delineate Prochlorococcus, Synechococcus, and Picophytoeukaryotes. Calibration beads (0.5 um and 1.0 um yellow-green and 0.5 um UV) were used to normalize cellular fluorescence values and assure optimal instrument settings. Raw data files (listmode) were processed in FlowJo software (Treestar Inc.).

Data Processing Description

Dataset Processing Description

Raw data, representing 100 ul of sample, was corrected for dilution with preservative, dye, and run volume, to arrive at cellular concentrations (cells/mL).

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0826626	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name: Beckman-Coulter Altra flow cytometer

Supplied Description:

Samples were run on a Beckman-Coulter Altra flow cytometer, equipped with one 488 nm 1W laser and one UV 200 mM laser for excitation.

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)

Niskin bottle

Supplied Description:

Samples were collected from the CTD-Rosette PVC Niskin bottles.

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
event	Number referring to the particular activity (event) on the FluZiE cruise.	integer	event
cast	CTD Cast number from the FluZiE cruise.	integer	cast
niskin	Niskin bottle that the sample was taken from.	integer	bot_Nis
date_local	Date of CTD cast (local time zone of UTC -6). in the format mmddyyyy	unitless	date
lon	Longitude in degrees East.	decimal degrees	lon
lat	Latitude in degrees North.	decimal degrees	lat
depth	Sample depth.	meters	depth
cycle	Type and number of cruise sampling event. Either "Stn_n" or "Cycle_n". A transect of stations was sampled from 29 June to 03 July. Five quasi-Lagrangian experiments called "cycles" were conducted during the remainder of the cruise.	text	no_bcodmo_term
coccus_p	Abundance of Prochlorococcus abundance.	cells per milliliter (cells/mL)	coccus_p
coccus_s	Abundance of Synechococcus abundance.	cells per milliliter (cells/mL)	coccus_s
peuk	Abundance of Picophytoeukaryotes.	cells per milliliter (cells/mL)	pico_euks

Database

Contribute Data

Dataset: picophyto_FCM_lab
Deployment: MV1008

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: picophyto_FCM_labDeployment: MV1008

Dataset acquisition description

Dataset Processing Description

Dataset: picophyto_FCM_lab
Deployment: MV1008