Dataset: BLOOFINZ-IO Flow Cytometry Abundance

Name: Abundances of phytoplankton and non-pigmented bacteria determined by flow cytometry from water samples collected on R/V Roger Revelle cruise RR2201 in the Eastern Indian Ocean during February and March 2022
Published: 2024-01-09
Keywords: phytoplankton abundance, bacteria abundance, eukaryotes, mixotrophs, cytometry, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.916288.1

Spatial Extent: N:-13.174 E:121.49767 S:-17.12632 W:114.13514

Temporal Extent: 2022-02-03 - 2022-03-02

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 Hawaii at Manoa, SOEST)

BCO-DMO Data Manager:

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

Version:

Version Date:

2024-01-09

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Abundances of phytoplankton and non-pigmented bacteria determined by flow cytometry from water samples collected on R/V Roger Revelle cruise RR2201 in the Eastern Indian Ocean during February and March 2022

Abstract:

This dataset is from CTD-based water collections of samples for phytoplankton and non-pigmented bacteria in the Indian Ocean on an R/V Roger Revelle cruise in Feb-March 2022 led by Dr. Michael Landry to investigate the plankton dynamics and impacts on growth and survival of larval Southern Bluefin Tuna (SBT). These flow cytometry results include abundances of phytoplankton taxa (Prochlorococcus, Synechococcus, photosynthetic eukaryotes), non-pigmented bacteria (HBACT), heterotrophic eukaryotes (HEUK), and potential mixotrophic eukaryotes (MEUK). Photosynthetic eukaryote (PEUK) abundance includes the MEUK cells reported (e.g., MEUK are a subset of the PEUK cells with chlorophyll and acidic-vacuoles). Note that MEUK cells likely also include some HEUK with intact chlorophyll-bearing prey, but there is no way to definitively separate these cells from each other.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2024-01-09	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.916288.1	2024-01-09

Methods & Sampling

Flow cytometry samples were collected from each CTD rosette or individual Go-Flo bottles. All samples were analyzed on board the ship with a Beckman Coulter CytoFlex S flow cytometer, equipped with 4 lasers (375 nanometers (nm), 405 nm, 488 nm, and 536 nm) and CytExpert software. Preserved (0.5% paraformaldehyde final) samples (500 microliters (µL)) were stained with Hoechst 34580 (1 microgram per milliliter (µg mL⁻¹)) and run (50 microliters per minute (µl min⁻¹)) within 3 hours of collection (Selph 2021). The data presented here for all populations, except heterotrophic eukaryotes (HEUK) and potential mixotrophs (MEUK), are from these preserved samples. At many stations, a live sample (500 µL) was also analyzed after staining with Hoechst (1 µg mL⁻¹ final) and Lysotracker Green (LTG, acidic vacuole stain, 75 nanomolar (nM) final, Rose et al. 2004) to obtain estimates of HEUK and MEUK. Data files (Lismode 3.0) were generated and analyzed using FlowJo software (Tree Star, Inc.).

Data Processing Description

Gating analyses of the listmode files followed those in Selph 2021 for the Hoechst-stained samples. For samples stained with Hoechst and LTG, the gating involved many steps as follows. LTG positive and negative particles were separated assuming that the maximum negative signal was that of co-occurring prokaryotes (Prochlorococcus, Synechococcus, and non-pigmented bacteria). Thus, all particles that had LTG signals greater than that of prokaryotes were designated LTG POS. LTG POS particles were further separated by the signal of the forward light scatter (FSC) of a 1 micrometer (µm) yellow-green fluorescent plastic beads (Polysciences, Inc.). Those particles with less FSC than a 1 µm bead were designated "PICO" sized particles and plotted as chlorophyll vs. phycoerythrin to eliminate any cyanobacteria, whereas the remaining cells were designated as potential mixotrophic cells. Those with more scatter than a 1 µm bead were designated "NANO+" sized particles and plotted as a single parameter chlorophyll histogram, where those with more chlorophyll than Prochlorococcus were considered potential mixotrophic eukaryotic cells. LTG POS PICO and NANO+ particles comprise the MEUK category reported. NANO+ (LTG POS) particles with less chlorophyll than Prochlorococcus were designated as heterotrophic eukaryotes (HEUK).

BCO-DMO Processing

- Imported original file "Selph FCM IO.xlsx" into the BCO-DMO system.
- Flagged "nd" as a missing data value (missing data are blank/empty in the final CSV file).
- Renamed fields to comply with BCO-DMO naming conventions.
- Corrected Station numbers where needed so dates match those in Date column, as instructed by data provider.
- Converted the Date column to YYYY-MM-DD format.
- Created the ISO 8601 date-time column by extracting date-times from the Station column.
- Saved the final data file as "916288_v1_bloofinz-io_flow_cytometry.csv".

Data Files

File
916288_v1_bloofinz-io_flow_cytometry.csv (Comma Separated Values (.csv), 15.53 KB) MD5:3d606be4cfddb78fe1175529662c5eda Primary data file for dataset ID 916288, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851381

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
RR2201	BLOOFINZ-IO	2022-01-20	R/V Roger Revelle	Michael R. Landry (Chief Scientist)	data info

Instruments

Flow Cytometer

Supplied Name: Beckman Coulter CytoFlex S

Supplied Description:

Samples were analyzed with a Beckman Coulter CytoFlex S flow cytometer with a 96-well sample plate and 4 lasers (375 nm, 405 nm, 488 nm, and 536 nm).

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)

GO-FLO Bottle

Supplied Name: Go-Flo bottles

Supplied Description:

Samples were collected using a CTD-rosette with Niskin Bottles or Go-Flo bottles deployed by hand on a line.

Instrument Type

Generic Name: GO-FLO Bottle

Acronym: GO-FLO

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

GO-FLO bottle cast used to collect water samples for pigment, nutrient, plankton, etc. The GO-FLO sampling bottle is specially designed to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths.

Niskin bottle

Supplied Name: Niskin Bottles

Supplied Description:

Samples were collected using a CTD-rosette with Niskin Bottles or Go-Flo bottles deployed by hand on a line.

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
Cruise	R/V Revelle cruise ID number	unitless	cruise_id
Station	Station designation incorporating date and UTC time	unitless	station
ISO_DateTime_UTC	Date and time (UTC) in ISO 8601 format Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
Date	Date Format: %Y-%m-%d	unitless	date
Latitude	Latitude; negative values = South	decimal degrees	lat
Longitude	Longitude; positive values = East	decimal degrees	lon
CTD_Number	Sequential CTD number on the cruise	unitless	cast
Depth	Depth of water collection	meters (m)	depth
PRO	Prochlorococcus abundance	cells per milliliter	abundance
SYN	Synechococcus abundance	cells per milliliter	abundance
PEUK	Photosynthetic Eukaryote abundance (includes MEUK abundance)	cells per milliliter	abundance
HBACT	Heterotrophic bacteria abundance	cells per milliliter	abundance
HEUK	Heterotrophic eukaryote abundance	cells per milliliter	abundance
MEUK	Mixotrophic eukaryote abundance	cells per milliliter	abundance

Database

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Dataset: BLOOFINZ-IO Flow Cytometry Abundance