Dataset: Cell abundance and chlorophyll content

Name: Cell abundance, forward scatter, chlorophyll, growth rate, and FvFm.0 measurements from reciprocal transplant assays
Published: 2021-06-17
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.854010.1

Project:

BEE: Testing the evolutionary responses of mixotrophs to future ocean conditions (MixoEvo)

Principal Investigator:

Holly V. Moeller (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-06-17

Restricted:

Validated:

Yes

Current State:

Final with updates expected

Cell abundance, forward scatter, chlorophyll, growth rate, and FvFm.0 measurements from reciprocal transplant assays

Abstract:

This dataset includes cell abundance, forward scatter, chlorophyll, growth rate and FvFm.0 measurements from reciprocal transplant assays.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2021-06-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.854010.1	2021-06-29

Methods & Sampling

Six lineages of each of two strains of the genus Ochromonas (CCMP1393, and CCMP2951) have been evolving at three temperatures, the ancestral temperature of 24C, and cooler and warmer temperatures of 18C and 30C. A third strain, CCMP 1391 does not survive at 30C and is only evolving at 18C and 24C. The experiment is run at two light levels, 100uE and 50uE. Cultures are maintained in batch culture in K medium made by adding pre‐mixed nutrients (ordered from the NCMA) to 0.2 μm filtered Santa Barbara coastal seawater in three light- and temperature-controlled incubators.

Evolving lineages are regularly tested for several characteristics including growth rate, cell size, chlorophyll content, and photosynthetic efficiency. To show that characteristic changes are indeed from an evolutionary response as opposed to phenotypic plasticity, reciprocal transplant assays are conducted every three months. This involved placing subsamples of each evolving lineage into all three temperatures, and comparing their performance in characteristic tests (growth rate, photosynthetic efficiency etc.).

Sampling and analytical procedures:

Guava count:
Cell density and relative size are measured every day for a 4-day growth period using a Guava easyCyte Flow Cytometer (Luminex Corporation, Austin, TX).

Chlorophyll Extractions:
Cellular chlorophyll-a (chl-a) content is measured by filtering cells onto a 25mm-diameter GF/F filter (Whatman) and extracting for 24 hours in a 90% acetone solution. Chl-a concentration in the acetone solution is read using a Trilogy fluorometer (Turner Designs, San Jose, CA).

FIRe Dark-acclimated Fv/Fm measurement:
Photosynthetic efficiency is measured using a mini Fluorescence Induction and Relaxation (FIRe) system (custom built by M. Gorbunov, Rutgers University).

Known Issues/Problems:
There was no chlorophyll collected during the first three backtransfers. Some FvFm data is missing because the FIRe was unable to process the data.

Data Processing Description

Data processing:
Guava Suite Software 3.4 (Luminex Corporation, Austin, TX), fpro.exe

FIRe Analysis: To run the analysis program on a separate PC, copy the program (fpro.exe), together with the file EGAVGA.bgi (a graphic driver). The program fprope.exe must be stored in the same directory as the raw FIRe data files. Use DOSBox emulator to run fpro.exe.

BCO-DMO Processing:
- concatenated separate .csv files into one dataset;
- re-named fields to comply with BCO-DMO naming conventions (replaced special characters with underscores).

Data Files

File
cell_abund.csv (Comma Separated Values (.csv), 300.30 KB) MD5:6b11b1a999f7902bebd3f1e7080ea812 Primary data file for dataset ID 854010

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851194

Deployments

None available yet

Instruments

Flow Cytometer

Supplied Name: Guava easyCyte flow cytometer

Supplied Description:

Guava easyCyte flow cytometer (Luminex Corporation, Austin, TX)

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)

Fluorometer

Supplied Name: mini-FIRe

Supplied Description:

mini-FIRe (Fluorescence Induction and Relaxation System) custom built by M. Gorbunov, Rutgers University.

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Fluorometer

Supplied Name: Trilogy fluorometer

Supplied Description:

Trilogy fluorometer (Turner Designs, San Jose, CA)

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Strain	The strain of Ochromonas	unitless	taxon
Light	Light intensity	micromoles quanta per square meter per second (umol quanta m-2 s-1)	no_bcodmo_term
Ev	Temperature that the strain was evolved at	degrees Celsius (°C)	temperature
Acc	Temperature that the strain was briefly acclimated to (for 5 days) prior to measurements	degrees Celsius (°C)	temperature
Rep	Replicate; Which of 6 replicates the data were collected from	unitless	replicate
Week	Weeks since start of experiment	unitless	time_elapsed
D1Pop	Day one population size	cells per milliliter (Cells/mL)	abundance
D2Pop	Day two population size	cells per milliliter (Cells/mL)	abundance
D3Pop	Day three population size	cells per milliliter (Cells/mL)	abundance
D4Pop	Day four population size	cells per milliliter (Cells/mL)	abundance
D1FSC	Day one forward scatter	relative fluorescence units	no_bcodmo_term
D2FSC	Day two forward scatter	relative fluorescence units	no_bcodmo_term
D3FSC	Day three forward scatter	relative fluorescence units	no_bcodmo_term
D4FSC	Day four forward scatter	relative fluorescence units	no_bcodmo_term
Growth_Rate	Rate of growth of cell cultures	per day (d^(-1))	growth
PE_Count	Cell density at the time of the PE measurement	cells per milliliter (Cells/mL)	density
Chl_a_read	Amount of chlorophyll in the sample	nanograms chl-a per milliliter (ng chl-a mL-1)	chl_a
Chl_a_per_cell	Amount of chlorophyll a per cell	picograms chl-a per cell (pg chl-a cell-1)	chl_a
FvFm_0	Day 0 Maximum quantum yield of photochemistry in PSII, measured in a dark-adapted state (dimensionless). This parameter characterizes the efficiency of primary photosynthetic reactions.	dimensionless	Fv_Fm
file_name	Name of the original csv file	unitless	file_name

Database

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Dataset: Cell abundance and chlorophyll content