http://lod.bco-dmo.org/id/dataset/905469
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
2023-08-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Flow cytometric counts from grazing saturation culture experiment using single prey (Micromonas pusilla) and predator (Ochromonas danica) in October 2019
2023-08-02
publication
2023-08-02
revision
BCO-DMO Linked Data URI
2023-08-02
creation
http://lod.bco-dmo.org/id/dataset/905469
Stephen D. Archer
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Nicole J. Poulton
Bigelow Laboratory for Ocean Sciences
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: Archer, S. D., Poulton, N. J. (2023) Flow cytometric counts from grazing saturation culture experiment using single prey (Micromonas pusilla) and predator (Ochromonas danica) in October 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-08-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/905469 [access date]
Culture experiment (M.pusilla + O.danica) Dataset Description: Methods and Sampling: <p>The experiments used the mixotrophic chrysophyte <em>Ochromonas danica</em>, ~ 6 to 9 µm in diameter, as a predator, and the generally abundant picoeukaryote <em>Micromonas pusilla</em>, ~ 1 to 2 µm in diameter, as prey.</p>
<ul>
<li><u>prey</u>:&nbsp;<em>Micromonas pusilla,&nbsp;</em>CCMP 485; AphiaID=134564</li>
<li><u>predator</u>:&nbsp;<em>Ochromonas danica,&nbsp;</em>CCMP 1391; AphiaID=1305802 (recommended name of&nbsp;<em>Chlorochromonas danica</em>).</li>
</ul>
<p>For detailed methods, refer to Archer et al. (2022) in the section 'Tests Using Single Prey and Predator Combinations'.&nbsp;</p>
<p><strong>Culture experiment</strong><br />
The cultures were maintained in sterile L1 media in a 21˚C incubator with a 14 h light/10 h dark cycle and light levels of ~ 90 µE m<sup>-2</sup> sec<sup>-</sup><sup>1</sup>. Prior to the start of the experiments, <em>O. danica</em> was transitioned from K media and rice to sterile L1 media and then fed every other day on <em>M. pusilla</em>. The prey, <em>M. pusilla</em> was maintained in semi-continuous growth through regular transfers (2 - 3 days). Similar ratios of predator-to-prey were generated in tubes containing a total volume of 40 ml. Fluorescent polystyrene microspheres (beads) of 2 µm in diameter (Fluoresbrite Plain YG microspheres, Polysciences, Inc., Warrington, PA), were used as surrogate prey.&nbsp; To minimize clumping, the beads were blocked in a solution of 1% bovine serum albumin overnight then centrifuged for 5 minutes at 2000 rpm, after which the pellet was resuspended in 0.2 µm filtered seawater. A new solution of beads was prepared at the start of each experiment. During the incubations, the experimental tubes were rotated at 1.2 rpm on a plankton wheel to keep particles in suspension. Two subsamples of 1 ml were removed from each tube at the start (T<sub>0</sub>) and the final time point (T<sub>24</sub>) after ~24 hours, for flow cytometric analysis.</p>
<p><strong>Flow Cytometric Measurements</strong><br />
Particles were excited with a 488 nm blue excitation laser (100 mW). Data acquisition was triggered on forward scatter (FSC). Signals were recorded from detectors with bandpass filters for right angle light scatter and fluorescence emission in red (692 nm/80 nm band pass) indicative of chlorophyll a, orange for phycoerythrin (593/52 nm), and green (525/35 nm). To ensure accurate calibration of the flow cytometer, ZE5 QC beads (Bio-Rad, Hercules, CA, USA) were run daily.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1738061 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1738061
onGoing
Stephen D. Archer
Bigelow Laboratory for Ocean Sciences
207-350-0791
60 Bigelow Drive
East Boothbay
ME
04554
USA
sarcher@bigelow.org
pointOfContact
Nicole J. Poulton
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext. 513
60 Bigelow Drive
npoulton@bigelow.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Latitude
Longitude
Date
Experiment
Duration
Beads_T0
Micromonas_T0
Beads_T24
Micromonas_T24
Bio-Rad ZE5 Cell Analyzer
theme
None, User defined
latitude
longitude
date
experiment id
incubation time or duration
abundance
featureType
BCO-DMO Standard Parameters
Flow Cytometer
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.
EAGER: A Saturation Approach to Microzooplankton Grazing Rate Determination
https://osprey.bco-dmo.org/project/735732
EAGER: A Saturation Approach to Microzooplankton Grazing Rate Determination
<p><span style="background-color:transparent; color:rgb(0, 0, 0); font-family:arial; font-size:11pt">NSF Award Abstract:</span></p>
<p>Heterotrophic protists are the dominant consumers of the 50% of global primary production by phytoplankton in the oceans. Hence, they play a key role in influencing ocean biogeochemistry, the composition of microbial communities, and transfer of energy to higher trophic levels. The aim of the project is to develop a novel saturation approach to quantify the rates of grazing on phytoplankton by phagotrophic protists in the ocean. As a proof-of-concept, this study will focus on determining grazing rates on picophytoplankton. This smallest size-class of phytoplankton often dominates oceanic primary production and can contribute up to 50% of annual primary production in coastal waters. Understanding grazing is of critical importance to understanding how planktonic communities function and respond to environmental change has the important societal benefit of potentially more accurately predicting the future of global fisheries and interactions between ocean and atmosphere that influence our climate. The project incorporates experiential education of undergraduates in the research environment and biological oceanography and will be a feature of an Advanced Aquatic Flow Courses designed for graduate students, faculty members and commercial entities. Public engagement in the science will be through Cafe Scientifique presentations and the series of Open House events that occur at Bigelow Laboratory through the year.</p>
<p>The motivation behind this project is that challenges in performing and interpreting current experimental measurements of herbivory by protists in the ocean constrain our understanding of this key process. The basis of the present approach is saturation of the grazers with a surrogate prey, resulting in release of grazing pressure on the natural prey. Measurement of the resulting increased growth rate of the natural prey provides a value for the rate of grazing. The project involves laboratory experiments using cultures of model predator-prey combinations to select suitable surrogate prey and test the underlying theoretical assumptions of the approach. This information will then be used to inform the design of experiments on natural planktonic communities. The objectives of these experiments are to test the efficacy of the saturation approach and to compare results to traditional experimental approaches run in parallel. This research will introduce a new approach to biological oceanography that will have been thoroughly tested, with recommendations for optimum set-up procedures and an assessment of the factors that influence uncertainty in the results. The saturation approach has potential advantages over previous methods. It lends itself to analysis by flow cytometry allowing high throughput and accurate measurements, avoids manipulation of the natural seawater and microbial communities, and provides growth and grazing information on defined components of the phytoplankton community.</p>
Grazing Saturation
largerWorkCitation
project
eng; USA
biota
oceans
-69.58
-69.58
43.8597
43.8597
2019-10-17
2019-10-25
Gulf of Maine
0
BCO-DMO catalogue of parameters from Flow cytometric counts from grazing saturation culture experiment using single prey (Micromonas pusilla) and predator (Ochromonas danica) in October 2019
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/905544.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of experiment location (Bigelow Lab)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905545.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of experiment location (Bigelow Lab)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905546.rdf
Name: Date
Units: unitless
Description: <p>Start date of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/905547.rdf
Name: Experiment
Units: unitless
Description: <p>Code ID for each experiment (MP1, MP2, MP3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905548.rdf
Name: Duration
Units: day (d)
Description: <p>Duration of the incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/905549.rdf
Name: Beads_T0
Units: beads per milliliter (beads/ml)
Description: <p>Bead abundance at time zero</p>
http://lod.bco-dmo.org/id/dataset-parameter/905550.rdf
Name: Micromonas_T0
Units: cells per milliliter (cells/ml)
Description: <p>Abundance of <em>Micromonas pusilla</em> at time zero</p>
http://lod.bco-dmo.org/id/dataset-parameter/905551.rdf
Name: Beads_T24
Units: beads per milliliter (beads/ml)
Description: <p>Bead abundance at end of incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/905552.rdf
Name: Micromonas_T24
Units: cells per milliliter (cells/ml)
Description: <p>Abundance of <em>Micromonas pusilla</em> at end of incubation</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
https://osprey.bco-dmo.org/dataset/905469/data/download
download
onLine
dataset
<p>The experiments used the mixotrophic chrysophyte <em>Ochromonas danica</em>, ~ 6 to 9 µm in diameter, as a predator, and the generally abundant picoeukaryote <em>Micromonas pusilla</em>, ~ 1 to 2 µm in diameter, as prey.</p>
<ul>
<li><u>prey</u>:&nbsp;<em>Micromonas pusilla,&nbsp;</em>CCMP 485; AphiaID=134564</li>
<li><u>predator</u>:&nbsp;<em>Ochromonas danica,&nbsp;</em>CCMP 1391; AphiaID=1305802 (recommended name of&nbsp;<em>Chlorochromonas danica</em>).</li>
</ul>
<p>For detailed methods, refer to Archer et al. (2022) in the section 'Tests Using Single Prey and Predator Combinations'.&nbsp;</p>
<p><strong>Culture experiment</strong><br />
The cultures were maintained in sterile L1 media in a 21˚C incubator with a 14 h light/10 h dark cycle and light levels of ~ 90 µE m<sup>-2</sup> sec<sup>-</sup><sup>1</sup>. Prior to the start of the experiments, <em>O. danica</em> was transitioned from K media and rice to sterile L1 media and then fed every other day on <em>M. pusilla</em>. The prey, <em>M. pusilla</em> was maintained in semi-continuous growth through regular transfers (2 - 3 days). Similar ratios of predator-to-prey were generated in tubes containing a total volume of 40 ml. Fluorescent polystyrene microspheres (beads) of 2 µm in diameter (Fluoresbrite Plain YG microspheres, Polysciences, Inc., Warrington, PA), were used as surrogate prey.&nbsp; To minimize clumping, the beads were blocked in a solution of 1% bovine serum albumin overnight then centrifuged for 5 minutes at 2000 rpm, after which the pellet was resuspended in 0.2 µm filtered seawater. A new solution of beads was prepared at the start of each experiment. During the incubations, the experimental tubes were rotated at 1.2 rpm on a plankton wheel to keep particles in suspension. Two subsamples of 1 ml were removed from each tube at the start (T<sub>0</sub>) and the final time point (T<sub>24</sub>) after ~24 hours, for flow cytometric analysis.</p>
<p><strong>Flow Cytometric Measurements</strong><br />
Particles were excited with a 488 nm blue excitation laser (100 mW). Data acquisition was triggered on forward scatter (FSC). Signals were recorded from detectors with bandpass filters for right angle light scatter and fluorescence emission in red (692 nm/80 nm band pass) indicative of chlorophyll a, orange for phycoerythrin (593/52 nm), and green (525/35 nm). To ensure accurate calibration of the flow cytometer, ZE5 QC beads (Bio-Rad, Hercules, CA, USA) were run daily.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Flow cytometric data files were analyzed from logarithmic dot plots based on fluorescence and characteristic light scattering properties (DuRand and Olson, 1996) using FlowJo 10.6 Software (Becton Dickinson &amp; Company, San Jose, CA, USA)</p>
<p>Model fitting of the experimental data was carried out using the nonlinear least squares regression function (nls) in R (R Core Team 2021).</p>
<p>These data were published in&nbsp;Figure 1 and Table 1 of Archer et al. (2022).</p>
Specified by the Principal Investigator(s)
- Imported data from source file "Grazing_Saturation_Culture_experiments_1.xlsx"
- Modified field (parameter/column) names to conform to BCO-DMO naming conventions. The only allowed characters are A-Z,a-z,0-9, and underscores. (NO spaces, hyphens, commas, parentheses, or Greek letters.)
- Converted yyyy/mm/dd date format to ISO Date format yyyy-mm-dd
- Added latitude and longitude for Bigelow
- Taxonomic names were checked using the World Register of Marine Species (WoRMS) taxa match tool at http://www.marinespecies.org/
. * Micromonas pusilla (AphiaID=134564)
. * Ochromonas danica is NOT accepted taxon name. Accepted name is Chlorochromonas danica (AphiaID=1305802).
Specified by BCO-DMO Data Managers
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
Bio-Rad ZE5 Cell Analyzer
Bio-Rad ZE5 Cell Analyzer
PI Supplied Instrument Name: Bio-Rad ZE5 Cell Analyzer PI Supplied Instrument Description:A ZE5 Cell Analyzer (Bio-Rad, Hercules, CA, USA) was used to measure optical properties and abundance of single cells from each sample 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/