Dataset: Microbial abundance
Deployment: TAN1810

Microbial abundance

Principal Investigator:

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

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Quantifying trophic roles and food web ecology of salp blooms of the Chatham Rise (Salp Food Web Ecology)

Deployment Synonyms:

SalpPOOP

Data URL:

https://www.bco-dmo.org/dataset-deployment/809731/data

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Description

Methods & Sampling

Dataset acquisition description

Sampling and analytical procedures: Samples (15 mL) were collected from hydrographic casts with Niskin bottles on a CTD-rosette for live ship-board and preserved shore-based flow cytometry analyses for profiles of phytoplankton and heterotrophic (non-pigmented) bacteria abundance. Live samples (~800 uL) were analyzed within 2 hours of collection (and usually sooner), kept in the dark at room temperature prior to analysis. Samples (2 mL) for shore-based analyses were aliquoted into cryovials, preserved with a final concentration of 0.5% paraformaldehyde (Electron Microscopy Sciences, methanol-free), then flash frozen in liquid nitrogen. After freezing, samples were transferred to a -80°C freezer. Upon completion of the cruise, samples were transferred to a charged dry shipper for transport to the University of Hawaii. Samples were thawed in batches, stained with the DNA stain Hoechst 34580 for 1 hour (1 ug/ml, final concentration), then quantitatively analyzed (100 uL).

Offline analysis software: FlowJo Software (Mac) Version 10.6.1. Ashland, OR: Becton Dickinson and Company; 2019.Offline analysis software: FlowJo Software (Mac) Version 10.6.1. Ashland, OR: Becton Dickinson and Company; 2019.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- reformatted date from m/d/yy to yyyy-mm-dd
- converted latitude and longitude to decimal degrees

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1756465	NSF Division of Ocean Sciences
OCE-1756610	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name: Becton Dickinson Accuri C6 Plus with CSampler Plus

Supplied Description:

Used for cell counts on board ship.

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)

Flow Cytometer

Supplied Name: Beckman Coulter CytoFLEX S, with Near UV (375 nm), Violet (405 nm), Blue (488 nm), and Yellow-Green (561 nm) lasers, with 96-well plate loader

Supplied Description:

Used for shore-based cell counts

Instrument Type

Generic Name: Flow Cytometer

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

Generic Description:

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
DATE	Date collected; formatted as yyyy-mm-dd	unitless	date
LAT	Latitude; north is positive	decimal degrees	lat
LONG	Longitude; east is positive	decimal degrees	lon
CAST	Cruise-based cast number	unitless	cast
STATION	Station number as recorded by the bridge	unitless	station
DEPTH	Depth of water collection	meters (m)	depth
PRO	Prochlorococcus abundance determined via preserved shore-based flow cytometry	cells/milliliter	coccus_p_cyt
SYN	Synechococcus abundance determined via preserved shore-based flow cytometry	cells/milliliter	coccus_s_cyt
PEUK	Photosynthetic eukaryotes determined via live ship-board flow cytometry	cells/milliliter	cell_concentration
HBACT	Heterotrophic (non-pigmented) bacteria determined via preserved shore-based flow cytometry	cells/milliliter	bact_het_cyt

Database

Contribute Data

Dataset: Microbial abundance
Deployment: TAN1810

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Microbial abundanceDeployment: TAN1810

Dataset acquisition description

Dataset Processing Description

Dataset: Microbial abundance
Deployment: TAN1810