Dataset: Series 3B: bubble expt LC computed

Name: Series 3B: Supplemental experiments on T. pseudonana (CCMP1014) growth under bubbling stress: computed photochemical measurements using LC3 protocol for non-aerated samples and aerated samples
Published: 2018-10-31
Keywords: biota, oceans

Cite This Dataset

Temporal Extent: 2018-07-03 - 2018-07-06

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 College of the Coast and Environment, LSU-CC&E [formerly SC&E])

Scientist:

Nigel D'Souza (University of California-Santa Barbara, UCSB-MSI)

Contact:

Nigel D'Souza (University of California-Santa Barbara, UCSB-MSI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2018-10-31

Restricted:

Release Date:

2019-07-01

Validated:

Yes

Current State:

Final no updates expected

Series 3B: Supplemental experiments on T. pseudonana (CCMP1014) growth under bubbling stress: computed photochemical measurements using LC3 protocol for non-aerated samples and aerated samples

Abstract:

Experiments were conducted to investigate the impact of bubbling on the growth yield of Thalassiosira pseudonana CCMP 1014 grown in 80 ml culture tubes. This dataset includes LC3 protocol computed photochemical measurements for non-aerated samples and aerated samples.

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Description

Methods & Sampling

Experiments were conducted to investigate the impact of bubbling gas through cultures of Thalassiosira pseudonana CCMP 1014 grown in Multicultivator MC-1000 OD culture tubes. TP1014 stock cultures were maintained in artificial seawater (Kester et. al 1967), enriched as with f/2 media (Guillard 1975). For the experiment, 5 ml of the TP1014 stock cultures were inoculated into 75 ml of ASW in eight tubes. The tubes were incubated in a Multicultivator MC-1000 OD unit (Qubit Systems), at 25 deg C and 400 µmol photons * m-2 * sec-1, set at a 12:12 day:night cycle for four days. Three tubes had no aeration (T1, T2, and T3); three tubes were bubbled with air at 60 ml·min-1 through a 0.2 µm stainless steel “carbonating stone” (T4, T5, and T6); and two tubes were bubbled with air at 120 ml·min-1 through a 0.2 µm stainless steel “carbonating stone” (T7 and T8). Samples were collected from each tube at the start of the experiment (day-0), and 5 hours after the start of the light phase each day (i.e. at 24-hour intervals) after that for four days. Samples were always collected 5 hours after the start of the light phase.

Three ml of samples from the non-aerated (T1, T2, and T3) and the 60 ml·min-1 aeration tubes (T4, T5, and T6) were used for assessment of photochemistry using the Aquapen-C AP-C 100 (Photon Systems Instruments). Samples were placed in the dark at 25 deg C for a minimum of 30 minutes prior to measuring photochemistry. The NPQ1 protocol on the instrument was used for assessment of non-photochemical quenching in samples, and the LC3 protocol was used to generate light curves that provide measurements of photosynthesis rates. The NPQ1 protocol administers 5 light pulses over 60 seconds during actinic light exposure, followed by 3 light pulses over 88 seconds during recovery in the dark. The LC3 protocol involves measurements of baseline fluorescence and maximal fluorescence during 7 phases of 60 seconds each, with each phase representing a light intensity from 10 to 1000 μmol * m-2 * s-1. Blue light (455 nm) was used as actinic light in these experiments. Baseline measurements were made at 0.03 μmol * m-2 * s-1, Saturating pulses were set at 2100 μmol * m-2 * s-1, and actinic light pulses (for the NPQ1 protocol only) were set at 1000 μmol * m-2 * s-1.

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- transformed rows and columns to conform to database best practices (each column has single description and units)
- modified parameter names to conform with BCO-DMO naming conventions
- replaced blank cells with 'nd' for 'no data'

Data Files

File
3B_bubble_LC_computed_trans.csv (Comma Separated Values (.csv), 2.07 KB) MD5:1e186bd5abb2ca2d2ead86d37a94185d Primary data file for dataset ID 749239

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 (Qubit Systems)

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.

Flow Cytometer

Supplied Name: Guava easyCyte HT Sampling Flow Cytometer

Supplied Description:

Used to count cells.

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

Supplied Description:

Used to measure fluorescence.

A hand-held cuvette version of the FluorPen fluorometer equipped with a blue and red LED emitter. Blue excitation light (455 nm) is intended for chlorophyll excitation, i.e., for measuring chlorophyll fluorescence in algal cultures. Red-orange excitation light (620 nm) is intended for excitation through phycobilins and is suitable for measuring in cyanobacteria.

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
treatment	Treatment formatted as Tn_Apn: a culture grown at a specific light intensity (as described by T(n)) and each of these samples was tested at different A-pulse settings (described as (AP(n)).	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	no_bcodmo_term
Fm_L1	The first measurement of the maximum fluorescence following exposure to actinic light at 10 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 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 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L2	The second measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 20 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L3	The third measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 50 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L4	The fourth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 100 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L5	The fifth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 300 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L6	The sixth measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 500 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QY_L7	The seventh measurement of the instantenous photosystem II quantum yield following exposure to actinic light at 1000 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L1	The (calculated) relative Electron Transport Rate following exposure to actinic light at 10 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L2	The (calculated) relative Electron Transport Rate following exposure to actinic light at 20 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L3	The (calculated) relative Electron Transport Rate following exposure to actinic light at 50 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L4	The (calculated) relative Electron Transport Rate following exposure to actinic light at 100 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L5	The (calculated) relative Electron Transport Rate following exposure to actinic light at 300 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L6	The (calculated) relative Electron Transport Rate following exposure to actinic light at 500 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
rETR_L7	The (calculated) relative Electron Transport Rate following exposure to actinic light at 1000 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L1	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 10 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L2	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 20 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L3	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 50 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L4	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 100 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L5	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 300 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L6	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 500 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
NPQ_L7	The (calculated) non photochemical chlorophyll fluorscence quenching following exposure to actinic light at 1000 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L1	The (calculated) coefficient of photochemical quenching following exposure to actinic light at 10 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L2	The (calculated) coefficient of photochemical quenching following exposure to actinic light at 20 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L3	The (calculated) coefficient of photochemical quenching following exposure to actinic light at 50 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L4	The (calculated) coefficient of photochemical quenching following exposure to actinic light at 100 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L5	The (calculated) coefficient of photochemical quenching following exposure to actinic light at 300 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L6	The sixth coefficient of photochemical quenching following exposure to actinic light at 500 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term
QP_L7	The seventh coefficient of photochemical quenching following exposure to actinic light at 1000 µmol photons·m-2·sec-1 for60 seconds (L1 indicates the first measurement in the "light" phase)	unitless	no_bcodmo_term

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Dataset: Series 3B: bubble expt LC computed