http://lod.bco-dmo.org/id/dataset/969513
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
2025-07-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Incomplete assimilatory nitrate reduction by LLI Prochlorococcus in response to light and temperature stress.
2025-07-31
publication
2025-07-31
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-08-07
publication
https://doi.org/10.26008/1912/bco-dmo.969513.1
Paul Berube
Massachusetts Institute of Technology
principalInvestigator
Sallie W. Chisholm
Massachusetts Institute of Technology
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: Berube, P., Chisholm, S. W. (2025) Incomplete assimilatory nitrate reduction by LLI Prochlorococcus in response to light and temperature stress. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-07-31 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.969513.1 [access date]
Temperature and light perturbations Dataset Description: <p>This dataset is part of a larger study on the impact of different physiological states/responses of Prochlorococcus on nitrite production potential in the presence of nitrate. The different perturbations yielding the different physiological states/responses and the respective analyses are listed below. Links to data for each perturbation can be found in the Related Datasets section.</p>
<p>The analyses include:</p>
<ol>
<li>Cell concentration (Nitrogen limitation dataset, Light perturbation dataset, Temperature perturbation dataset)</li>
<li>Nitrite concentration (Nitrogen limitation dataset, Light perturbation dataset, Temperature perturbation dataset)</li>
<li>Nitrate + nitrite concentration (Nitrogen limitation dataset)</li>
<li>Bead standard normalized forward scatter (Nitrogen limitation dataset)</li>
<li>Bead standard normalized red (chlorophyll) fluorescence (Nitrogen limitation dataset)</li>
<li>FIRe fluorometry (Light perturbation dataset, Temperature perturbation dataset)</li>
</ol>
<p>See Related Datasets section below for links to above mentioned datasets.</p> Methods and Sampling: <p><strong>Cultures: </strong>The strains used in this study included <em>Prochlorococcus</em> MIT0915 and&nbsp;<em>Prochlorococcus&nbsp;</em>MIT0917. Before each experiment, all strains were &nbsp;assayed for heterotrophic contaminants by staining cells with SYBR green and assessing the fluorescence and light scattering properties of both stained and unstained cells using a Guava easyCyte 12HT Flow Cytometer (MilliporeSigma, Burlington, MA, USA) – cultures that did not exhibit the presence of non-photosynthetic cells in the stained samples and had a single cyanobacteria population were presumed axenic and unialgal. Before each experiment, all presumed axenic cultures were &nbsp;assessed for purity by confirming a lack of turbidity after inoculation into a panel of purity test broths as described previously (Berube et al., 2015).</p>
<p><strong>Culture medium: </strong>The cultures&nbsp;were grown using AMP1-Mo-NO3 medium which is a variant of AMP1 artificial medium (Moore et al., 2007)&nbsp;with the following modifications: 400 µM ammonium sulfate was replaced with 800 µM sodium nitrate; the sodium molybdate concentration was increased from 0.3 nM to 100 nM; 1 mM HEPES pH=7.5 was replaced with 5 mM TAPS pH=8.2; and the concentration of sodium bicarbonate was decreased from 6 mM to 2.5 mM. The medium was filter sterilized using a 0.2 µm polyethersulfone (PES) membrane filter instead of using steam sterilization in an autoclave. A nitrogen-free variant (AMP1-Mo) was also prepared by omitting all inorganic nitrogen sources.&nbsp;</p>
<p><strong>Methodology and sampling for light and temperature perturbations: </strong>Batch cultures were grown as triplicates in 35 mL of medium in borosilicate glass culture tubes at a temperature of 24<sup>o</sup>C and a photon flux of 20 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light. Cultures were acclimated for at least 10 generations prior to starting the experiment. Each biological replicate was diluted to 1 x 10<sup>8</sup> cells mL<sup>1</sup> in a total of 50 mL of nitrogen-free AMP1-Mo supplemented with 2.5 mM sodium bicarbonate in duplicate, one to serve as a control and one to be subjected to the perturbation. Shock experiments were conducted in light- and temperature-controlled water baths. In both experiments, the control box was maintained at 23–25<sup>o</sup>C and 21–23 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light. In the light shock experiment, experimental cultures were exposed to 220 µmol photons m<sup>-2</sup> s<sup>-1</sup> of broad spectrum light at 23-25<sup>o</sup>C. In the cold shock experiment, the cultures were exposed to 21–23 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light at 14–16<sup>o</sup>C. Prior to initiating the cold shock, nitrogen-free AMP1-Mo medium was pre-chilled to 15<sup>o</sup>C before inoculation with the harvested biomass. Prior to spiking with nitrate, an initial set of samples were collected for flow cytometry, nitrite concentration determination, and fluorescence induction and relaxation (FIRe) fluorometry. Nitrate was then added to each tube at a final concentration of 80 µM sodium nitrate. Samples for nitrite concentration determination were collected every 30 min for 150 min by syringe filtration of 4 mL of culture through a 0.2 µm PES membrane into a 14 mL polystyrene tube and stored at -20<sup>o</sup>C. Endpoint flow cytometry and FIRe fluormetry samples were also collect at the final time point. Media-only control tubes were prepared using the same batch of nitrogen-free AMP1-Mo medium to facilitate assessment of background signal in nitrite concentration determination; the mean background signal was equivalent to 0.050 µM nitrite (+/- 0.004) for the light shock experiment and 0.076 µM nitrite (+/- 0.012) for the cold shock experiment.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048470 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048470
completed
Paul Berube
Massachusetts Institute of Technology
77 Massachusetts Avenue Bldg 48-424
Cambridge
MA
02139
USA
pmberube@mit.edu
pointOfContact
Sallie W. Chisholm
Massachusetts Institute of Technology
(617) 253 1771
48-419 Department of Civil and Environmental Engineering 15 Vassar Street
Cambridge
MA
02139-4307
USA
chisholm@mit.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment
ExpSampleID
Strain
Rep
ExpCondition
N_source
Light_Intensity
Light_Color
Temperature
Culture_ID
ExpTime
ISOTime
Nitrite_Concentration
Nitrite_Concentration_Notes
Cell_Concentration_FCM
FRRF_filename
FCM_filename
FCM_Beads_Filename
FCM_blank_filename
Guava easyCyte 12HT Flow Cytometer - MilliporeSigma, Burlington, MA, USA
FIRe Fluorometer System - Satlantic, Halifax, NS, Canada
AA3 HR AutoAnalyzer - Seal Analytical Inc, Mequon, WI, USA
theme
None, User defined
experiment type
sample identification
taxon
replicate
treatment
time_elapsed
Date and time
Nitrite
comments
cell_concentration
file_name
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Fluorometer
Nutrient Autoanalyzer
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.
Features and implications of nitrogen assimilation trait variability in populations of Prochlorococcus
https://osprey.bco-dmo.org/project/833527
Features and implications of nitrogen assimilation trait variability in populations of Prochlorococcus
<p><em>NSF Award Abstract:</em><br />
The marine bacterium, <em>Prochlorococcus</em>, is a central part of the food web in the subtropical open ocean, one of the largest biomes on the planet. Like plants on land, <em>Prochlorococcus</em> and other phytoplankton are capable of photosynthesis, harnessing light to convert carbon dioxide into sugars and other organic matter. This matter feeds all the life in the sea. Akin to terrestrial plants, <em>Prochlorococcus</em> requires additional nutrients or "fertilizer" to grow and photosynthesize. Among these nutrients, nitrogen is often scarce across much of the sunlit ocean. Thus, understanding the means through which nitrogen is obtained and used by <em>Prochlorococcus</em> has important consequences for understanding how the nitrogen and carbon cycles are coupled in the ocean. Not all <em>Prochlorococcus</em> cells have the genetic capacity to use all sources of inorganic nitrogen, i.e. nitrate, nitrite, and ammonium. Some can use all three, some the last two, and some only ammonium. Cells that can use nitrate must sequentially transform it to nitrite and then to ammonium before they can make the building blocks for proteins. The genesis of this project derives from the observation that some <em>Prochlorococcus</em> cells release nitrite into the seawater during growth on nitrate. This project examines this feature of the physiology of these cell lines, and asks whether cells that release nitrite can support the growth of other cells than cannot use nitrate, in effect creating a cross-feeding situation that could make the system more robust. Understanding the drivers behind the coexistence of cells with different ways of obtaining nitrogen, a key currency in the ocean, will provide important insights on the flow of nitrogen in marine ecosystems. This project also sheds light on the structure of interactions between microbes and provides the broader scientific community (for instance, those studying diverse microbiomes related to human health and disease or agriculture) a new perspective on how microbes form beneficial partnerships. This project supports immersive laboratory-based research experiences for undergraduate students, who design and execute experiments directly related to the overall project goals. The project further supports the work of the investigators to engage with the general public on topics related to phytoplankton, photosynthesis, and the ecosystem services provided by these marine organisms.</p>
<p>In the low-light adapted LLI clade of <em>Prochlorococcus</em>, the focus of this project, nearly all cells possess the downstream half of the nitrate assimilation pathway (for the assimilation of nitrite). Only a fraction of LLI cells, however, have the complete nitrate assimilation pathway. Incomplete assimilatory nitrate reduction, with concomitant nitrite release, has been observed for LLI cells during growth on nitrate as the sole nitrogen source. Further, the nitrite released by cells growing on nitrate can support the growth of <em>Prochlorococcus</em> that can use nitrite but not the more oxidized nitrate. Overall, within a group of closely-related <em>Prochlorococcus</em>, there is genotypic and phenotypic diversity related to the production and consumption of nitrite, a central intermediate in the nitrogen cycle. The investigators propose to further develop <em>Prochlorococcus</em>as a model system to explore nitrite cycling within populations and provide new insights on how trait variability and the selection of complementary functions facilitates robustness and/or resiliency in microbial populations. The overarching hypothesis is that the population-level assembly of distinct functional types of <em>Prochlorococcus</em> emerges through interactions that are mediated, in part, by cross-feeding of nitrite. To address this broad hypothesis, the investigators are focusing on the following objectives: 1) assessing the physiological underpinnings of incomplete assimilatory nitrate reduction and nitrite release through in-vitro biochemical characterization of nitrite reductase enzymes and transcription profiling of cells subjected to light and temperature stress, 2) examining the nitrite production and consumption rates of <em>Prochlorococcus</em> strains across environmental gradients such as light, temperature, and nutrient availability in order to constrain the environmental parameters that modulate nitrite cycling, and 3) determining the frequencies and activities of nitrogen assimilation genotypes within laboratory and field populations, under varying environmental conditions and perturbations. Outcomes from objectives 1 and 2 help to constrain the tradeoffs associated with incomplete nitrate reduction and the release of nitrite (a valuable commodity to nitrogen limited cells) to facilitate modelling and interpretation of how partnerships between nitrogen assimilation genotypes are structured. These insights help to direct experiments in Objective 3, which aims to examine controlled laboratory co-cultures and field populations in order to produce quantitative data on the emergent features of <em>Prochlorococcus</em> populations where interactions are mediated by the cross-feeding of nitrite. These data are being used to develop an improved understanding of how interactions mediated by a common public good might give rise to emergent properties of populations, including resilience to perturbation and greater population-wide efficiency in nitrogen assimilation.</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>
Prochlorococcus N assimilation
largerWorkCitation
project
eng; USA
oceans
2024-11-26
2024-12-19
Laboratory studies (MIT)
0
BCO-DMO catalogue of parameters from Incomplete assimilatory nitrate reduction by LLI Prochlorococcus in response to light and temperature stress.
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/970383.rdf
Name: Experiment
Units: unitless
Description: <p>Experiment type: Light Perturbations or Temperature Perturbations</p>
http://lod.bco-dmo.org/id/dataset-parameter/970384.rdf
Name: ExpSampleID
Units: unitless
Description: <p>Experiment Sample ID for nitrite analysis and flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/970385.rdf
Name: Strain
Units: unitless
Description: <p>Strain name of pure culture used</p>
http://lod.bco-dmo.org/id/dataset-parameter/970386.rdf
Name: Rep
Units: unitless
Description: <p>Biological Replicate (A/B/C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/970387.rdf
Name: ExpCondition
Units: unitless
Description: <p>Flag for experimental condition (Control/Shock)</p>
http://lod.bco-dmo.org/id/dataset-parameter/970388.rdf
Name: N_source
Units: unitless
Description: <p>Concentration and type of inorganic nitrogen provided as a nitrogen source</p>
http://lod.bco-dmo.org/id/dataset-parameter/970389.rdf
Name: Light_Intensity
Units: micromoles photones per square meter per second (umol photons m-2 s-1)
Description: <p>Photon flux that the cultures were cultivated under</p>
http://lod.bco-dmo.org/id/dataset-parameter/970390.rdf
Name: Light_Color
Units: unitless
Description: <p>Spectra of light that the cultures were cultivated under (W=White or B=Blue)</p>
http://lod.bco-dmo.org/id/dataset-parameter/970391.rdf
Name: Temperature
Units: Degrees Celsius (°C)
Description: <p>Temperature of the waterbath the cultures were kept in over the course of sampling time period</p>
http://lod.bco-dmo.org/id/dataset-parameter/970392.rdf
Name: Culture_ID
Units: unitless
Description: <p>Unique ID for culture tubes in format [A]-[B]-[C]-[DD]-[E]-[F]-[G]. Where A = strain B=ExpCondition; C =Replicate; DD=Light_Color & Light_Intensity; E = N_source;G = temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/970393.rdf
Name: ExpTime
Units: minutes
Description: <p>Time of sample collection measured from the of sodium nitrate addition; -1 min indicates sample collection immediate before the sodium nitrate addition</p>
http://lod.bco-dmo.org/id/dataset-parameter/970394.rdf
Name: ISOTime
Units: unitless
Description: <p>Date and time of sample collection in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/970395.rdf
Name: Nitrite_Concentration
Units: micromoles nitrite per liter (umol nitrite L-1)
Description: <p>Extracellular concentration of dissolved nitrite in the culture determined from an AutoAnalyzer3; BDL = below detection limit of 0.010 micromole per liter (umol/L).</p>
http://lod.bco-dmo.org/id/dataset-parameter/970396.rdf
Name: Nitrite_Concentration_Notes
Units: unitless
Description: <p>Says "BDL" when nitrite concentration is below detection limit of 0.010 micromole per liter (umol/L).</p>
http://lod.bco-dmo.org/id/dataset-parameter/970397.rdf
Name: Cell_Concentration_FCM
Units: cells per milliliter (cells mL-1)
Description: <p>Concentration of total cyanobacteria cells as determined by flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/970398.rdf
Name: FRRF_filename
Units: unitless
Description: <p>Name of FRRF file corresponding to the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/970399.rdf
Name: FCM_filename
Units: unitless
Description: <p>Name of flowcytometry file corresponding to the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/970400.rdf
Name: FCM_Beads_Filename
Units: unitless
Description: <p>Name of flowcytometry file corresponding to the beads normalization well for that flow cytometry run</p>
http://lod.bco-dmo.org/id/dataset-parameter/970401.rdf
Name: FCM_blank_filename
Units: unitless
Description: <p>Name of flowcytometry file corresponding to the blank well for that flow cytometry run</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
32025
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/c1d38e4d-7982-47f4-a68c-b9ee3cd424fc/content
download
https://doi.org/10.26008/1912/bco-dmo.969513.1
download
onLine
dataset
<p><strong>Cultures: </strong>The strains used in this study included <em>Prochlorococcus</em> MIT0915 and&nbsp;<em>Prochlorococcus&nbsp;</em>MIT0917. Before each experiment, all strains were &nbsp;assayed for heterotrophic contaminants by staining cells with SYBR green and assessing the fluorescence and light scattering properties of both stained and unstained cells using a Guava easyCyte 12HT Flow Cytometer (MilliporeSigma, Burlington, MA, USA) – cultures that did not exhibit the presence of non-photosynthetic cells in the stained samples and had a single cyanobacteria population were presumed axenic and unialgal. Before each experiment, all presumed axenic cultures were &nbsp;assessed for purity by confirming a lack of turbidity after inoculation into a panel of purity test broths as described previously (Berube et al., 2015).</p>
<p><strong>Culture medium: </strong>The cultures&nbsp;were grown using AMP1-Mo-NO3 medium which is a variant of AMP1 artificial medium (Moore et al., 2007)&nbsp;with the following modifications: 400 µM ammonium sulfate was replaced with 800 µM sodium nitrate; the sodium molybdate concentration was increased from 0.3 nM to 100 nM; 1 mM HEPES pH=7.5 was replaced with 5 mM TAPS pH=8.2; and the concentration of sodium bicarbonate was decreased from 6 mM to 2.5 mM. The medium was filter sterilized using a 0.2 µm polyethersulfone (PES) membrane filter instead of using steam sterilization in an autoclave. A nitrogen-free variant (AMP1-Mo) was also prepared by omitting all inorganic nitrogen sources.&nbsp;</p>
<p><strong>Methodology and sampling for light and temperature perturbations: </strong>Batch cultures were grown as triplicates in 35 mL of medium in borosilicate glass culture tubes at a temperature of 24<sup>o</sup>C and a photon flux of 20 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light. Cultures were acclimated for at least 10 generations prior to starting the experiment. Each biological replicate was diluted to 1 x 10<sup>8</sup> cells mL<sup>1</sup> in a total of 50 mL of nitrogen-free AMP1-Mo supplemented with 2.5 mM sodium bicarbonate in duplicate, one to serve as a control and one to be subjected to the perturbation. Shock experiments were conducted in light- and temperature-controlled water baths. In both experiments, the control box was maintained at 23–25<sup>o</sup>C and 21–23 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light. In the light shock experiment, experimental cultures were exposed to 220 µmol photons m<sup>-2</sup> s<sup>-1</sup> of broad spectrum light at 23-25<sup>o</sup>C. In the cold shock experiment, the cultures were exposed to 21–23 µmol photons m<sup>-2</sup> s<sup>-1</sup> of blue light at 14–16<sup>o</sup>C. Prior to initiating the cold shock, nitrogen-free AMP1-Mo medium was pre-chilled to 15<sup>o</sup>C before inoculation with the harvested biomass. Prior to spiking with nitrate, an initial set of samples were collected for flow cytometry, nitrite concentration determination, and fluorescence induction and relaxation (FIRe) fluorometry. Nitrate was then added to each tube at a final concentration of 80 µM sodium nitrate. Samples for nitrite concentration determination were collected every 30 min for 150 min by syringe filtration of 4 mL of culture through a 0.2 µm PES membrane into a 14 mL polystyrene tube and stored at -20<sup>o</sup>C. Endpoint flow cytometry and FIRe fluormetry samples were also collect at the final time point. Media-only control tubes were prepared using the same batch of nitrogen-free AMP1-Mo medium to facilitate assessment of background signal in nitrite concentration determination; the mean background signal was equivalent to 0.050 µM nitrite (+/- 0.004) for the light shock experiment and 0.076 µM nitrite (+/- 0.012) for the cold shock experiment.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Nitrate and nitrate + nitrite concentration assay: </strong>Nitrite was analyzed using an AA3 HR Autoanalyzer (Seal Analytical, Milwaukee, WI, USA). In this continuous segmented flow analyzer, nitrite is reacted with sulfanilamide and N-(1-naphthyl)ethylenediamine (NED) to produce a pink diazo dye. For determination of total nitrate and nitrite, any nitrate in the sample was first reduced to nitrite using a copper-cadmium coil. Absorbance was measured in a 1 cm flow cell using a 550 nm bandpass filter (SEAL Analytical method number G-384-08 for a multitest MT19B manifold). For each analysis, sodium nitrite and sodium nitrate standards were freshly prepared and serially diluted in nitrogen-free AMP1 medium to create a calibration curve at the following concentrations: 1.25, 0.5, 0.25, 0.08, 0.04, 0.03, and 0.015 µM. A linear calibration curve was applied to the data and the instrument’s response factor, represented by the slope of the calibration curve, remained consistent and reproducible throughout the nitrite analysis period (r<sup>2</sup> &gt;0.99 in all runs). For samples in nitrogen-free AMP1 medium (AMP1-Mo) as a background matrix, the limit of detection (LOD) for nitrite was 0.010 µM and the limit of blank was 0.003 µM.</p>
<p><strong>Cell concentration determination: </strong>Cell concentrations were obtained by flow cytometry&nbsp;using a Guava easyCyte 12HT Flow Cytometer (MilliporeSigma, Burlington, MA, USA). <em>Prochlorococcus</em> cells were detected based on the fluorescence of cellular pigments excited by a 488 nm laser. Cultures were first diluted to between 50 and 200 cells/µL and data were acquired for up to 6 min at a flow rate of 0.024 µL/s. Bead standards (Guava easyCheck beads;&nbsp;MilliporeSigma, Burlington, MA, USA), were run daily to confirm that the instrument was operating within normal parameters and within predefined tolerances for concentrations, scatter, and emission intensity of the beads. For each flow cytometry run, a diluted sample of Guava easyCheck beads was additionally run using the same parameters as the cultures to serve as a standard for the normalization of forward scatter and fluorescence data.</p>
<p><strong>Fluorescence induction and relaxation fluorometry: </strong>The efficiency for energy conversion at photosystem II (Fv/Fm) for cultures subjected to light or cold shocks was measured using a FIRe Fluorometer System (Satlantic, Halifax, NS, Canada). A sample of each culture was diluted 10 fold in nitrogen-free AMP1 medium, incubated in the dark for 10 minutes in order to allow photosystems to open, and then transferred to a cylindrical quartz cuvette. A total of 10 profiles were collected for each sample. Background profiles for cell-free AMP1-Mo medium at 21 different gain values were collected to facilitate data processing; these files are named in format "AMP1NON.000" where "000" is a 3 digit counter from 000 through 020.</p>
<p>&nbsp;</p>
<p>Flow cytometry data were exported as FSC 3.0 formatted files and analyzed using FlowJo version 10.6.1 (BD Biosciences, Ashland, OR, USA)</p>
<p>Fluorescence data were processed using fireworx version 0.9.1 (https://sourceforge.net/projects/fireworx/)</p>
<p>Continuous segmented flow nutrient autoanalyzer data were analyzed using AACE version 7.12 software (Seal Analytical, Mequon, WI, USA)</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
Guava easyCyte 12HT Flow Cytometer - MilliporeSigma, Burlington, MA, USA
Guava easyCyte 12HT Flow Cytometer - MilliporeSigma, Burlington, MA, USA
PI Supplied Instrument Name: Guava easyCyte 12HT Flow Cytometer - MilliporeSigma, Burlington, MA, USA Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
FIRe Fluorometer System - Satlantic, Halifax, NS, Canada
FIRe Fluorometer System - Satlantic, Halifax, NS, Canada
PI Supplied Instrument Name: FIRe Fluorometer System - Satlantic, Halifax, NS, Canada PI Supplied Instrument Description: FIRe fluorometry exposes cells to µsec scale flashlets of light while collecting data on cell fluorescence over the entire curve of photosystem excitation and relaxation. Data generated using FIRe can be processed to obtain parameters such as the minimum and maximum chlorophyll fluorescence, the maximum quantum yield of photochemistry at photosystem II, and the functional absorption cross section of photosystem II (see: https://datadocs.bco-dmo.org/docs/302/Upwelled_Phytoplankton_Dynamics/data_docs/The%20Satlantic%20Fluorescence%20Induction%20and%20Relaxation%20(FIRe).pdf). 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/
AA3 HR AutoAnalyzer - Seal Analytical Inc, Mequon, WI, USA
AA3 HR AutoAnalyzer - Seal Analytical Inc, Mequon, WI, USA
PI Supplied Instrument Name: AA3 HR AutoAnalyzer - Seal Analytical Inc, Mequon, WI, USA PI Supplied Instrument Description:Nutrient samples were taken according to best practices and were filtered using a 0.2 µm filter and immediately frozen until analysis. Samples were analyzed using methods provided by seal No. G-384-08 Rev 6 (multitest MT19B) which are based off Environmental Protection Agency standard methods for nitrate+nitrite, and nitrite. AA3 HR AutoAnalyzer is a fully automated Segmented Flow Analysis (SFA) system, ideal for water and seawater analysis. It comprises a modular system which integrates an autosampler, peristaltic pump, chemistry manifold and detector. The sample and reagents are pumped continuously through the chemistry manifold, and air bubbles are introduced at regular intervals forming reaction segments which are mixed using glass coils. The AA3 uses segmented flow analysis principles to reduce inter-sample dispersion, and can analyse up to 100 samples per hour using stable LED light sources. Please see http://seal-analytical.com/Products/AA3SFAAnalyzer/tabid/59/Default.aspx for a complete instrument description Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/