Dataset: 13C incubation cell counts
Deployment: KOK1605

Counts of Prochlorococcus from on-deck incubations with 13C-bicarbonate as part of DNA-SIP experiments

Principal Investigator:

Anne W. Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

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

Project:

Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal? (ProEco)

Current State:

Final no updates expected

Version:

23 May 2017

Deployment Synonyms:

HOT283, HOT-283, KOK16-05

Version Date:

2017-05-23

Data URL:

https://www.bco-dmo.org/dataset-deployment/700779/data

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Description

Counts of Prochlorococcus from on-deck incubations with 13C-bicarbonate as part of DNA-SIP experiments; conducted on Hawaii Ocean Time-series (HOT) cruises 283 and 288.

Methods & Sampling

Dataset acquisition description

Water was sampled from the CTD under trace metal clean conditions into 2 L polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate. Flow cytometry samples were collected from triplicate bottles at several time points between 0 hours (unlabeled control) and 36 hours after the initiation of incubation. Flow cytometry samples were collected in 1 mL volumes and fixed immediately with 25% TEM-grade glutaraldehyde to a final concentrations of 0.125%. Samples were inverted 10 times to mix, incubated at room temperature in the dark for 10 minutes, then flash frozen in liquid nitrogen to archive. Samples were stored at -80C until analysis. For analysis, each sample was thawed at room temperature then analyzed by flow cytometry.

Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter. A 488 nm laser was used in addition to chlorophyll and phycoerythrin filters, forward scatter relative to 1 um beads, and side scattered light.

Data Processing Description

Dataset Processing Description

The program BD Software was used to collect flow cytometry data and generate distinct files for analysis. The program Flow Jo (version 7.6.5) was used to process flow cytometry files.

BCO-DMO Data Processing:
- modified parameter names to conform with BCO-DMO naming conventions;
- replaced spaces with underscores and removed parentheses (in depth column).

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1646709	NSF Division of Ocean Sciences

Instruments

CTD - profiler

Supplied Name: CTD

Supplied Description:

Water was sampled from the CTD under trace metal clean conditions into 2L polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate.

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Flow Cytometer

Supplied Name: BD Biosciences Influx high speed cell sorter

Supplied Description:

Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter.

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)

Trace Metal Bottle

Supplied Name:

Supplied Description:

Water was sampled from the CTD under trace metal clean conditions into 2L polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate.

Instrument Type

Generic Name: Trace Metal Bottle

Acronym: TM Bottle

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

Generic Description:

Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise	Cruise name/identifier	unitless	cruise_id
incubation	Incubation identifier	unitless	exp_id
depth	Sample depth; DCM = deep chlorophyll maxium	unitless	depth_comment
timepoint	Time point in the incubation	hours	time_sample
replicate	Replicate identifier	unitless	replicate
prochlorococcus	Count of Prochlorococcus cells	cells per milliliter (cells/mL)	coccus_p

Database

Contribute Data

Dataset: 13C incubation cell counts
Deployment: KOK1605

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: 13C incubation cell countsDeployment: KOK1605

Dataset acquisition description

Dataset Processing Description

Dataset: 13C incubation cell counts
Deployment: KOK1605