Dataset: SPOT Cell Counts
Deployment: SPOT_Yellowfin_Cruises

Microbial cell counts in seawater samples from SPOT cruises in 2017

Principal Investigator:

Sergio A. Sanudo-Wilhelmy (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:

The role of organic and metal cofactors on the biogenic synthesis of halogenated volatile hydrocarbons (Volatile_Hydrocarbons)

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/827837/data

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Description

Methods & Sampling

Dataset acquisition description

Samples for microbial cell counts were collected at six depths within the euphotic zone (5-250 m). Seawater was collected from each CTD depth using Niskin bottles, immediately fixed with formalin 2% (0.72% formaldehyde final concentration), and immediately frozen at -80C. Autotrophic picoplankton (Prochlorococcus, Synechococcus, and picoeukaryotes) and heterotrophic prokaryotes were enumerated by flow cytometry (Becton Dickinson FACSCalibur) (Gasol and del Giorgio, 2000).

Data Processing Description

Dataset Processing Description

The flow cytometry data were analyzed and processed using BD FACStation software from Becton Dickinson.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1559276	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name: Becton Dickinson FACSCalibur

Supplied Description:

Autotrophic picoplankton (Prochlorococcus, Synechococcus, and picoeukaryotes) and heterotrophic prokaryotes were enumerated by flow cytometry (Becton Dickinson FACSCalibur).

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 Name: Niskin bottles

Supplied Description:

Seawater was collected from each CTD depth using 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
Cruise	Cruise name, month, and year	unitless	cruise_name
Date	Date; format: YYYY-MM-DD	unitless	date
Time_Start	Start time; format: hh:mm	unitless	time
Time_End	End time; format: hh:mm	unitless	time
Longitude	Longitude	degrees East	lon
Latitude	Latitude	degrees North	lat
Depth	Depth	meters (m)	depth
HNA_bacteria	Number of high nucleic acid content bacterial cells per milliliter of seawater measured with Flow Cytometry	cells per milliter (cell ml-1)	abundance
LNA_bacteria	Number of low nucleic acid content bacterial cells per milliliter of seawater measured with Flow Cytometry	cells per milliter (cell ml-1)	abundance
Total_Bacteria	Number of total bacteria (high + low nucleic acid content) per milliliter of seawater measured with Flow Cytometry	cells per milliter (cell ml-1)	abundance
Pro	Number of Prochlorococcus cells per milliliter of seawater measured with Flow Cytometry	cells per milliter (cell ml-1)	abundance
Syn	Number of Synechococcus cells (regular fluorescence) per milliliter of seawater measured with Flow Cytometry	cells per milliter (cell ml-1)	abundance
Syn_HighF	Number of Synechococcus cells (high fluorescence) per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance
Syn_total	Number of Synechococcus cells (regular fluorescence + high fluorescence) per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance
Pico_small	Number of small picoeukaryotic cells per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance
Pico_large	Number of large picoeukaryotic cells per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance
Pico_total	Number of total picoeukaryotic cells (small + large) per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance
Nano	Number of total nanophytoplanktonic cells per milliliter of seawater measured with Flow Cytometry	picomoles per liter (pico mol L-1)	abundance

Database

Contribute Data

Dataset: SPOT Cell Counts
Deployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SPOT Cell CountsDeployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Dataset: SPOT Cell Counts
Deployment: SPOT_Yellowfin_Cruises