Dataset: Series 1B: photophysiology - computed

Name: Series 1B-3: Multiple stressor experiments on T. pseudonana (CCMP1335) – computed data from the LC3 protocol for samples at 4 temperatures, 15-26C
Published: 2020-11-12
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.829009.1

Temporal Extent: 2018-11-17 - 2019-04-16

Project:

Collaborative Research: Effects of multiple stressors on Marine Phytoplankton (Stressors on Marine Phytoplankton)

Principal Investigator:

Uta Passow (University of California-Santa Barbara, UCSB-MSI)

Co-Principal Investigator:

Edward Laws (Louisiana State University , LSU-CC&E [formerly SC&E])

Scientist:

Julia Sweet (University of California-Santa Barbara, UCSB-MSI)

Contact:

Julia Sweet (University of California-Santa Barbara, UCSB-MSI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2020-11-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Series 1B-3: Multiple stressor experiments on T. pseudonana (CCMP1335) – computed data from the LC3 protocol for samples at 4 temperatures, 15-26C

Abstract:

Four follow-up experiments on the combined effect of light and temperature changes on the growth rate (mu) and photophysiology of Thalassiosira pseudonana CCMP 1335 were conducted to supplement / repeat series 1A experiments. This was necessary because doubt existed regarding the growth during 1A experiments. 1A experiments were conducted in artificial seawater. 1B experiments were conducted in artificial seawater supplemented with 5% sterilized seawater. The experiments were designed to test the combined effects of four temperatures, and eight light intensities on the growth and photophysiology of the diatom T. pseudonana CCMP1335 in a multifactorial design. This dataset contains measurements of photophysiology using the Light curve (LC3) protocol of the Aquapen-C AP-C 100 fluorometer.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-11-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.829009.1	2020-11-30

Description

The raw fluorescence data can be found under the Data Files section as an Excel file and as individual .csv files.

Methods & Sampling

Experimental setup:

The experiments were designed to test the combined effects of four temperatures, and eight light intensities on growth and photophysiology of the diatom T. pseudonana CCMP1335 in a multifactorial design. Four temperatures were tested: 15°C, 18°C, 22°C, and 26°C. Within each temperature, eight light levels were tested: 30, 40, 70,90,105,125,140 and 265 µmol photons · m-2 · s-1. All lights were set at a 12 h day: 12 h dark cycle. For logistical reasons, experiments were partially conducted in series.

Experiments were conducted in Multicultivator MC-1000 OD units (Photon Systems Instruments, Drasov, Czech Republic). Each unit consists of eight 85 ml test-tubes immersed in a thermostated water bath, each independently illuminated by an array of cool white LEDs set at specific intensity and timing. A 0.2µm filtered ambient air was bubbled through sterile artificial seawater, and the humidified air was supplied to each tube Each experiment was split into two phases: An acclimation phase spanning 3 days, was used to acclimate cultures to their new environment. Pre-acclimated, exponentially-growing cultures were then inoculated into fresh media and incubated through a 4-day experimental phase during which assessments of growth, photophysiology, and nutrient cycling were carried out daily. All sampling started 6 hours into the daily light cycle to minimize the effects of diurnal cycles.

Experiments were conducted with artificial seawater (ASW) prepared using previously described methods (Kester et. al 1967), and enriched with 50mL per liter of UV sterilized natural seawater and nitrate (NO3), phosphate (PO4), silicic acid (Si[OH]4), at levels ensuring that the cultures would remain nutrient-replete over the course of the experiment. Trace metals and vitamins were added as in f/2 (Guillard 1975). The pH of the growth media was measured spectrophotometrically using the m-cresol purple method (Dickson 1993), and adjusted using 0.1N HCl or 0.1M NaOH.

Photophysiology

Photophysiology was assessed daily using a handheld Pulse Amplitude Modulated (PAM) fluorometer (AquaPen-C AP-C 100, Photon System Instruments, Czech Republic). A sample was collected from each light treatment for each, 5 hours after the start of the daily light cycle, and placed in the dark for a minimum of 30 minutes prior to measurements. The dark-adapted sample was used to generate light curves that provide measurements of in-vivo chlorophyll autofluorescence (F0), the maximum quantum yield (QYmax or Fv/Fm), and relative photosynthesis rates based on PSII quantum yields at varying light intensities - using the instrument’s LC3 protocol. The LC3 protocol involves measurements of baseline and maximal fluorescence over seven 60-second phases, with each phase representing a light intensity from 10 to 1000 μmol photons m-2 · s-1. Blue light (455 nm) was used as actinic light in these experiments, and measurements were made at measuring illumination (f-pulse) intensity of 0.03 μmol photons m-2 · s-1, and saturating (F-pulse) illumination of 2100 μmol photons m-2 · s-1, and actinic illumination (A-pulse) controlled by the instrument’s protocol were set at 10, 20, 50, 100, 300, 500, and 1000 μmol photons m-2 · s-1 (for each 60-second phase).

Data Processing Description

BCO-DMO Processing Notes:
- data submitted in Excel file "BCODMO_Series 1B - 3_photophysiology_4Aug2020.xlsx" sheets "15C COMPUTED", "18C COMPUTED", "22C COMPUTED", and "26C COMPUTED".
- the four tables were concatenated and transformed so rows became columns.
- extracted the table to csv
- added conventional header with dataset name, PI name, version date

Data Files

File
1B_photophys.csv (Comma Separated Values (.csv), 26.57 KB) MD5:895cb8ce9e1c7b75d275fd3175c41f78 Primary data file for dataset ID 829009
Raw Fluorescence Data - parameter descriptions filename: Passow_Series_1B_3_photophys_param_descriptions_RawData.csv (Comma Separated Values (.csv), 2.66 KB) MD5:946696ceb6f1b4414f02692e4172afa4 Descriptions of rows and columns for fluorescence Raw Data.
Raw Fluorescence Data 15C filename: Passow_Series_1B_3_photophys_15C_RawData.csv (Comma Separated Values (.csv), 17.43 KB) MD5:4a42412df5258c87e0539cffa2db9442 Raw data: fluorescence measurements from the LC3 protocol for samples at 15C at eight light levels.
Raw Fluorescence Data 18C filename: Passow_Series_1B_3_photophys_18C_RawData.csv (Comma Separated Values (.csv), 13.75 KB) MD5:6d96efeea568281191e7d108217135bd Raw data: fluorescence measurements from the LC3 protocol for samples at 18C and 8 light levels.
Raw Fluorescence Data 22C filename: Passow_Series_1B_3_photophys_22C_RawData.csv (Comma Separated Values (.csv), 18.05 KB) MD5:fae88908e6a0fa681078ed8ff31646a9 Raw data: fluorescence measurements from the LC3 protocol for samples at 22C and 8 light levels.
Raw Fluorescence Data 26C filename: Passow_Series_1B_3_photophys_26C_RawData.csv (Comma Separated Values (.csv), 20.31 KB) MD5:b1bf46482ceeebf2c68dc3b790dcf25e Raw data: fluorescence measurements from the LC3 protocol for samples at 26C and 8 light levels.
Raw Fluorescence Data filename: Passow_Series_1B_3_photophys_RawData.xlsx (Microsoft Excel, 77.53 KB) MD5:1ab7778f5afc7bfa7edda6db116ea1e2 Raw data: fluorescence measurements from the LC3 protocol for samples at 15C, 18C, 22C, and 26C and 8 light levels.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1538602

Deployments

None available yet

Instruments

Cell Cultivator

Supplied Name: Multicultivator MC-1000 OD (Photon Systems Instruments, Drasov, Czech Republic)

Supplied Description:

Used for incubation of TP1014 cultures.

Instrument Type

Generic Name: Cell Cultivator

Generic Description:

An instrument used for the purpose of culturing small cells such as algae or bacteria. May provide temperature and light control and bubbled gas introduction.

Fluorometer

Supplied Name: Aquapen-C AP-C 100 (Photon Systems Instruments)

Supplied Description:

Used for assessment of photochemistry.

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.

Spectrophotometer

Supplied Name: Spectrophotometer (Genesys 10SVIS)

Supplied Description:

Used for measurement of pH.

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Phase	Indicates whether the sample was collected during the acclimation phase or the experiment phase of the experiment.	unitless	sample_descrip
Temperature	Indicates the temperature at which the samples were incubated.	degrees Celsius	temp
Day	Indicates the timepoint (day) of sampling. D0 = day 0; D1 = day 1; etc.	unitless	days
Replicate	Indicates replication within a treatment. "NA" indicates "not applicable"	unitless	replicate
Irradiance	Irradiance level: SOL = sub-optimum light; OL = optimum light; EL = extreme light	unitless	treatment
Fo	minimum fluorescence in dark-adapted state.	RFU (Relative Fluorscence Units)	fluor
Fm	the maximum fluorescence in dark-adapted state; measured during the first saturation flash after dark adaptation	RFU (Relative Fluorscence Units)	fluor
QY_max	The maximum Quantum yield. A measure of the Photosystem II efficiency. In a dark-adapted sample this is equivalent to Fv/Fm. In a light-adapted sample it is equivalent to Fv’/Fm’.	unitless	Fv_Fm
Fm_L1	The first measurement of the maximum fluorescence following exposure to actinic light at 10 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L2	The second measurement of the maximum fluorescence following exposure to actinic light at 20 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L3	The third measurement of the maximum fluorescence following exposure to actinic light at 50 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L4	The fourth measurement of the maximum fluorescence following exposure to actinic light at 100 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L5	The fifth measurement of the maximum fluorescence following exposure to actinic light at 300 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L6	The sixth measurement of the maximum fluorescence following exposure to actinic light at 500 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Fm_L7	The seventh measurement of the maximum fluorescence following exposure to actinic light at 1000 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L1	The first measurement of the maximum fluorescence following exposure to actinic light at 10 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L2	The second measurement of the maximum fluorescence following exposure to actinic light at 20 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L3	The third measurement of the maximum fluorescence following exposure to actinic light at 50 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L4	The fourth measurement of the maximum fluorescence following exposure to actinic light at 100 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L5	The fifth measurement of the maximum fluorescence following exposure to actinic light at 300 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L6	The sixth measurement of the maximum fluorescence following exposure to actinic light at 500 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
Ft_L7	The seventh measurement of the maximum fluorescence following exposure to actinic light at 1000 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	RFU (Relative Fluorscence Units)	fluor
QY_L1	The first measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 10 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L2	The second measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 20 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L3	The third measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 50 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L4	The fourth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 100 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L5	The fifth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 300 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L6	The sixth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 500 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm
QY_L7	The seventh measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 1000 micro-mol photons·m-2·sec-1 for 60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	Fv_Fm

Status message

Database

Contribute Data

Dataset: Series 1B: photophysiology - computed