Dataset: BLOOFINZ-GoM flow cytometry abundance

Name: Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018
Published: 2021-01-05
Keywords: phytoplankton, bacteria, Prochlorococcus, Synechococcus, Gulf of Mexico, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.835414.1

Spatial Extent: N:28.3358 E:-84.434 S:24.96 W:-90.1775

Temporal Extent: 2017-05-11 - 2018-05-19

Project:

Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean (BLOOFINZ-IO)

Program:

Second International Indian Ocean Expedition (IIOE-2)

Principal Investigator:

Karen E. Selph (University of Hawaiʻi at Mānoa, SOEST)

Contact:

Karen E. Selph (University of Hawaiʻi at Mānoa, SOEST)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-01-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018

Abstract:

Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-01-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.835414.1	2021-01-12

Description

This dataset is being discussed in Selph et al. 2021.

Methods & Sampling

This dataset is from CTD-based water collections of samples for phytoplankton and non-pigmented bacteria in the Gulf of Mexico on R/V Nancy Foster cruises in May 2017 and May 2018, which were part of a NOAA RESTORE project (aka: BLOOFINZ-GoM) led by Dr. John Lamkin to investigate the epipelagic marine nitrogen cycle, plankton dynamics, and impacts on growth and survival of larval Atlantic Bluefin Tuna (ABT). These data are meant to be used in inter-species, interregional comparisons to data from the BLOOFIN-IO study of larval larval Southern Bluefin Tuna in the Indian Ocean spawning region. Flow cytometry results include abundances of phytoplankton taxa (Prochlorococcus, Synechococcus, Photosynthetic Eukaryotes) and non-pigmented bacteria (HBACT).

Flow cytometry samples were collected at sea from each CTD rosette on the NOAA Ship Nancy Foster (NF) from cruises from 30 April to 19 May 2017 and from 11 May to 30 May 2018. For phytoplankton and heterotrophic bacteria enumeration, 2 ml sample volumes are collected, preserved (0.5% paraformaldehyde, final concentration) and flash frozen in liquid nitrogen. On shore, the samples are transferred to a –80°C freezer for storage until analysis on the flow cytometer. Samples are thawed in batches, then stained with Hoechst 34442 (1 µg/ml, final concentration) (Monger and Landry, 1993; Campbell and Vaulot, 1993; Campbell et al., 1994).

Data Processing Description

The data generated is in the form of listmode files (FCS 2.0 format) acquired from the flow cytometer using Expo32 software (Beckman-Coulter). These data are processed, designating populations from their fluorescence and scatter signals, using FlowJo software (Tree Star, Inc., www.flowjo.com), which generates excel-spreadsheet files.

BCO-DMO processing info:

Adjusted column headers to comply with database requirements
Converted date to ISO format

Data Files

File
flow_cytometry.csv (Comma Separated Values (.csv), 12.54 KB) MD5:394e977f3ca0b2bfb2cbbcbf36bb24a7 Primary data file for dataset ID 835414

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851558
National Oceanic and Atmospheric Administration	NA16NMF4320058

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NF1704	BLOOFINZ-GoM	2017-05-07	R/V Nancy Foster	Estrella Malca (Chief Scientist)	data info
NF1802	BLOOFINZ-GoM	2018-04-27	R/V Nancy Foster	John Lamkin (Chief Scientist)	data info

Instruments

Flow Cytometer

Supplied Name: Beckman-Coulter Altra

Supplied Description:

The flow cytometer used is a Beckman-Coulter Altra (operated by the SOEST Flow Cytometry Facility, www.soest.hawaii.edu/sfcf), mated to a Harvard Apparatus syringe pump for quantitative analyses, and it is equipped with two argon ion lasers, tuned to UV (200 mW) and 488 nm (1 W) excitation. Scatter (side and forward) and fluorescence signals are collected using filters as appropriate, including those for Hoechst-bound DNA, phycoerythrin and chlorophyll.

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)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise ID	unitless	cruise_id
Station	Station number	unitless	station
Date	Sampling date Format: %Y-%m-%d	unitless	date
Longitude	Station longitude, west is negative	decimal degrees	lon
Latitude	Station latitude, south is negative	decimal degrees	lat
CTD_Number	CTD cast number	unitless	sample_descrip
Depth	Sample depth	meters (m)	depth
Prochlorococcus	Prochlorococcus	cells per milliliters (cells/ml)	count
Synechococcus	Synechococcus	cells per milliliters (cells/ml)	count
Photosynthetic_eukaryotes	Photosynthetic eukaryotes	cells per milliliters (cells/ml)	count
Heterotrophic_bacteria	Heterotrophic bacteria	cells per milliliters (cells/ml)	count

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Database

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Dataset: BLOOFINZ-GoM flow cytometry abundance