http://lod.bco-dmo.org/id/dataset/853945
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-06-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Quantification of photosynthetic capacity of cells using a laser induction of chlorophyll autofluorescence
2021-06-30
publication
2021-06-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-06-30
publication
https://doi.org/10.26008/1912/bco-dmo.853945.1
Holly V. Moeller
University of California-Santa Barbara
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Moeller, H. (2021) Quantification of photosynthetic capacity of cells using a laser induction of chlorophyll autofluorescence. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.853945.1 [access date]
Photosynthesis-Irradiance Curves Dataset Description: Methods and Sampling: <p>Six independent lineages of each Ochromonas strain were grown in batch cultures in three light- and temperature-controlled incubators (18°C, 24°C, and 30°C), and 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 were conducted every three months for two years. This involved placing subsamples of each evolving lineage into all three temperatures, and comparing their performance in characteristic tests (growth rate, photosynthetic efficiency etc.). Evolved lineages performing equally at all "acclimation temperatures" is evidence of plasticity, while differences in performance indicates adaptation. Using growth rate and photosynthetic rate to compute the relative contributions of autotrophy versus heterotrophy for each evolved lineage.</p>
<p><strong>Procedures for Photosynthesis-Irradiance curves</strong>:<br />
Dark-acclimate cells to be sampled for at least 15 minutes. This operation requires the actinic light source (ALS). In the DOS prompt Type 'fview'. Press enter. The data acquisition program will open. Adjust the number of samples and PAR steps to 20. Adjust the max PAR to 1001. MTF and MTRP stay set to 0. Adjust the acclimation time between each sample to 15 seconds. Homogenize sample before reading. Insert your test tube with dark-acclimated sample. Press 's' (for 'start/stop'). Adjust the 'Gain:' so that the fluorescence trace is as close to, but not greater than, 100%.</p>
<p><strong>Missing Data:</strong><br />
Occasionally, at high light levels and especially high temperatures, the signal to noise ratio of the fluorescence signal is very low. This causes noisy instrument output, which fails at the analysis (fprope.exe) stage. These data are missing from the dataset, and can be identified when a run (unique combination of week, light level, food level, strain, evolutionary temperature, acclimation temperature, and replicate) has fewer than twenty rows of data.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851194 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851194
completed
Holly V. Moeller
University of California-Santa Barbara
805-893-3216
1120 Noble Hall Ecology, Evolution, and Marine Biology
Santa Barbara
CA
93106
USA
hvmoeller@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Week
Light
Food
Strain
Evol
Acc
Rep
File
DATE
PAR
Fo_or_F
Fm
FmDec
Fv
FvDEC
Fv_Fm
FvD_FmD
Sigma
p
Fm_PAM
Fv_Fm_PAM
GAIN
Fo_prime
qp_coeff
baseFvFm
baseSigma
ETR
file_name
mini-FIRe
theme
None, User defined
time_elapsed
No BCO-DMO term
taxon
temperature of sample or a generic measurement (not in-situ water temp)
replicate
file_name
date
PAR
fluorescence
Fv to Fm ratio
featureType
BCO-DMO Standard Parameters
Fluorometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
BEE: Testing the evolutionary responses of mixotrophs to future ocean conditions
https://osprey.bco-dmo.org/project/819827
BEE: Testing the evolutionary responses of mixotrophs to future ocean conditions
<p><em>NSF Award Abstract:</em><br />
Aquatic ecosystems host a wide variety of single-celled, microscopic organisms. Many of these species live near the surface of the water, where they grow and reproduce using different metabolic strategies that shape their place in the marine food web. For example, biologists have traditionally grouped planktonic microbes into either primary producers (which use photosynthesis to create new organic matter) or heterotrophs (which eat organic matter - such as the bodies - produced by other organisms). However, a large number of species are actually mixotrophic: they "mix" these two forms of metabolism by simultaneously conducting photosynthesis and eating smaller cells, including bacteria. Furthermore, many mixotrophs are metabolically flexible: they may rely more or less on each source of metabolism depending on environmental conditions. Because photosynthesis (which takes carbon out of the atmosphere and locks it into organic matter) and heterotrophy (which respires organic matter back into carbon dioxide) control whether or not oceanic food webs act as carbon sinks (having a net removal of carbon dioxide from the atmosphere), understanding mixotroph metabolism is critical to predicting the effects of marine plankton on atmospheric carbon. This project advances understanding of mixotroph metabolism by quantifying the extent to which mixotrophs can alter their reliance on photosynthesis over short and long timescales. The project tests how quickly mixotrophs can adapt to both warmer and colder water conditions, and how these adaptations alter their role in the carbon cycle. Researchers - including graduate students, a postdoctoral researcher, and undergraduate trainees - will measure the physiological responses of experimentally evolved mixotrophs and use mathematical models to connect these changes to global oceanic carbon cycling. As data are collected, they are shared with the public through outreach seminars, annual open house events, and weekly scientific presentations at the local Santa Barbara Museum of Natural History.</p>
<p>In order to predict biologically mediated feedbacks in the climate system, we must understand how marine plankton will respond to future ocean conditions. While a number of studies have sought to quantify the potential evolutionary response of phytoplankton, much less is known about the impacts of shifting conditions (e.g., increased temperature) on mixotrophs. What data are available suggest that mixotrophs may modulate a positive climate feedback loop: when warmed, mixotrophs become more heterotrophic, thus reducing their contribution to the biological pump and enhancing local respiration of organic carbon. Warming may also result in reductions in cell size, reducing sinking fluxes and carbon export from the upper ocean. Furthermore, because the predicted increase in oceanic stratification is expected to favor mixotrophs, their metabolic responses may be increasingly significant to understanding the global carbon cycle. The PI of this project is experimentally evolving mixotrophs under a range of temperature conditions in a fully factorial design that also manipulates the availability of light (photosynthesis) and prey (heterotrophy). She quantifies the carbon budget, grazing activity, nutrient content, and grazer palatability of evolved lineages in order to estimate the impact of any observed adaptations on carbon cycling. Specifically, the investigator asks how evolved lineages compare to ancestral lineages in their ability to tolerate altered thermal conditions, and connects differences in fitness to shifts in reliance on photosynthesis versus heterotrophy. Simultaneously, she incorporates a mixotrophy module into a global ocean biogeochemistry model, allowing the quantification of the impact of mixotrophs with either contemporary or evolved physiological traits. This work will provide some of the first known data on mixotroph plastic and evolutionary responses, and allow the scaling of these responses to their potential impacts on upper ocean biogeochemistry.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
MixoEvo
largerWorkCitation
project
eng; USA
oceans
2018-05-18
2020-05-17
0
BCO-DMO catalogue of parameters from Quantification of photosynthetic capacity of cells using a laser induction of chlorophyll autofluorescence
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/853977.rdf
Name: Week
Units: unitless
Description: <p>Week of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/853978.rdf
Name: Light
Units: microEinsteins (uE)
Description: <p>Light intensity</p>
http://lod.bco-dmo.org/id/dataset-parameter/853979.rdf
Name: Food
Units: unitless
Description: <p>Xenic vs Axenic</p>
http://lod.bco-dmo.org/id/dataset-parameter/853980.rdf
Name: Strain
Units: unitless
Description: <p>The strain of Ochromonoas</p>
http://lod.bco-dmo.org/id/dataset-parameter/853981.rdf
Name: Evol
Units: degrees Celsius (°C)
Description: <p>Temperature that the strain was evolved at</p>
http://lod.bco-dmo.org/id/dataset-parameter/853982.rdf
Name: Acc
Units: degrees Celsius (°C)
Description: <p>Temperature that the strain was acclimated to</p>
http://lod.bco-dmo.org/id/dataset-parameter/853983.rdf
Name: Rep
Units: unitless
Description: <p>Replicate; Which of 6 replicates the data were collected from</p>
http://lod.bco-dmo.org/id/dataset-parameter/853984.rdf
Name: File
Units: unitless
Description: <p>The output file number from the FIRe</p>
http://lod.bco-dmo.org/id/dataset-parameter/853985.rdf
Name: DATE
Units: unitless
Description: <p>Date of sampling; format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/853987.rdf
Name: PAR
Units: microEinsteins per square meter per second (uE/m2/s)
Description: <p>Photosynthetically active radiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/853988.rdf
Name: Fo_or_F
Units: a.u.
Description: <p>Minimum fluorescence yield</p>
http://lod.bco-dmo.org/id/dataset-parameter/853989.rdf
Name: Fm
Units: a.u.
Description: <p>Maximum fluorescence yield</p>
http://lod.bco-dmo.org/id/dataset-parameter/853990.rdf
Name: FmDec
Units: a.u.
Description: <p>Minimum fluorescence yield retrieved from the relaxation phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/853991.rdf
Name: Fv
Units: a.u.
Description: <p>Variable fluorescence yield (=Fm-Fo)</p>
http://lod.bco-dmo.org/id/dataset-parameter/853992.rdf
Name: FvDEC
Units: a.u.
Description: <p>Variable fluorescence yield (=FmDec-Fo) retrieved from the relaxation phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/853993.rdf
Name: Fv_Fm
Units: dimensionless
Description: <p>Fv/Fm. Maximum quantum yield of photochemistry in PSII(dimensionless). This parameter characterizes the efficiency of primary photosynthetic reactions.</p>
http://lod.bco-dmo.org/id/dataset-parameter/853994.rdf
Name: FvD_FmD
Units: dimensionless
Description: <p>FvD/FmD. Quantum yield of photochemistry in PSII retrieved from the relaxation phase</p>
http://lod.bco-dmo.org/id/dataset-parameter/853995.rdf
Name: Sigma
Units: Relative units (see description)
Description: <p>The functional absorption cross-section of PSII. Reported in relative units. Must be multiplied by a calibration coefficient to be converted into absolute units (Angstrom^2). This calibration coefficient is determined for each instrument.</p>
http://lod.bco-dmo.org/id/dataset-parameter/853996.rdf
Name: p
Units: dimensionless
Description: <p>"Connectivity parameter" that determines the probability of excitation energy transfer between individual photosynthetic units</p>
http://lod.bco-dmo.org/id/dataset-parameter/853997.rdf
Name: Fm_PAM
Units: a.u.
Description: <p>Fm(PAM). Maximum fluorescence yield recorded at the end of MTF flash when the plastoquinone (PQ) pool is fully reduced</p>
http://lod.bco-dmo.org/id/dataset-parameter/853998.rdf
Name: Fv_Fm_PAM
Units: unitless
Description: <p>Fv/Fm(PAM). Maximum quantum yield of photochemistry in PSII estimated from the MTF protocol</p>
http://lod.bco-dmo.org/id/dataset-parameter/853999.rdf
Name: GAIN
Units: unitless
Description: <p>Gain of the detector</p>
http://lod.bco-dmo.org/id/dataset-parameter/854000.rdf
Name: Fo_prime
Units: a.u.
Description: <p>Minimum fluorescence yield</p>
http://lod.bco-dmo.org/id/dataset-parameter/854001.rdf
Name: qp_coeff
Units: dimensionless
Description: <p>Coefficient of photochemical quenching, defined as a fraction of open PSII RCs</p>
http://lod.bco-dmo.org/id/dataset-parameter/854002.rdf
Name: baseFvFm
Units: dimensionless
Description: <p>Maximum quantum yield of photochemistry in PSII, measured in a dark-adapted state (PAR=0).</p>
http://lod.bco-dmo.org/id/dataset-parameter/854003.rdf
Name: baseSigma
Units: Relative units (see description)
Description: <p>The functional absorption cross-section of PSII, measured in a dark-adapted state (PAR=0). Reported in relative units. Must be multiplied by a calibration coefficient to be converted into absolute units (Angstrom^2). This calibration coefficient is determined for each instrument.</p>
http://lod.bco-dmo.org/id/dataset-parameter/854004.rdf
Name: ETR
Units: Electrons per second per reaction center
Description: <p>Electron Transport Rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/854005.rdf
Name: file_name
Units: unitless
Description: <p>Name of the original csv file</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
6655589
https://darchive.mblwhoilibrary.org/bitstream/1912/27298/1/dataset-853945_photosynthesis-irradiance-curves__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.853945.1
download
onLine
dataset
<p>Six independent lineages of each Ochromonas strain were grown in batch cultures in three light- and temperature-controlled incubators (18°C, 24°C, and 30°C), and 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 were conducted every three months for two years. This involved placing subsamples of each evolving lineage into all three temperatures, and comparing their performance in characteristic tests (growth rate, photosynthetic efficiency etc.). Evolved lineages performing equally at all "acclimation temperatures" is evidence of plasticity, while differences in performance indicates adaptation. Using growth rate and photosynthetic rate to compute the relative contributions of autotrophy versus heterotrophy for each evolved lineage.</p>
<p><strong>Procedures for Photosynthesis-Irradiance curves</strong>:<br />
Dark-acclimate cells to be sampled for at least 15 minutes. This operation requires the actinic light source (ALS). In the DOS prompt Type 'fview'. Press enter. The data acquisition program will open. Adjust the number of samples and PAR steps to 20. Adjust the max PAR to 1001. MTF and MTRP stay set to 0. Adjust the acclimation time between each sample to 15 seconds. Homogenize sample before reading. Insert your test tube with dark-acclimated sample. Press 's' (for 'start/stop'). Adjust the 'Gain:' so that the fluorescence trace is as close to, but not greater than, 100%.</p>
<p><strong>Missing Data:</strong><br />
Occasionally, at high light levels and especially high temperatures, the signal to noise ratio of the fluorescence signal is very low. This causes noisy instrument output, which fails at the analysis (fprope.exe) stage. These data are missing from the dataset, and can be identified when a run (unique combination of week, light level, food level, strain, evolutionary temperature, acclimation temperature, and replicate) has fewer than twenty rows of data.</p>
Specified by the Principal Investigator(s)
<p><strong>Data processing procedures:</strong><br />
fprope.exe, EGAVGA.bgi (graphic driver), DOSBox emulator</p>
<p><strong>FIRe Analysis:</strong> To run the analysis program on a separate PC, copy the program (fprope.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 fprope.exe.</p>
<p><strong>Calculating ETR data from .RES file</strong>: Copy the .RES file into the ETR template excel sheet. This sheet has prepopulated equations for base FvFm, base Sigma, and ETR. The base FvFm equation is =IF(Par=0, Fv/Fm, base FvFm) The equation for base Sigma is =IF(par=0, Sigma, base sigma) The equation for ETR is =(+par * sigma * 2.04 * (FvFm/(FvFm)) * .00602). Export this completed excel sheet as a CSV file to be used in the R script.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- concatenated separate .csv files into one dataset;<br />
- re-named fields to comply with BCO-DMO naming conventions (replaced special characters with underscores);<br />
- converted date format to YYYY-MM-DD.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
mini-FIRe
mini-FIRe
PI Supplied Instrument Name: mini-FIRe PI Supplied Instrument Description:mini-FIRe (Fluorescence Induction and Relaxation System) custom built by M. Gorbunov, Rutgers University. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/