http://lod.bco-dmo.org/id/dataset/956298
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
2025-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microsphere counts from incubation chambers of Oikopleura dioica prior to and following feeding incubations for experiment with artificial microspheres with two functionalized surfaces in three sizes
2025-03-18
publication
2025-03-18
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-03
publication
https://doi.org/10.26008/1912/bco-dmo.956298.1
Kelly Rakow Sutherland
University of Oregon
principalInvestigator
Anne W. Thompson
Portland State University
principalInvestigator
Anne E. Aasjord
Sars International Centre for Marine Molecular Biology
principalInvestigator
Daniel M. Chourrout
Sars International Centre for Marine Molecular Biology
principalInvestigator
Terra C. Hiebert
University of Oregon
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: Hiebert, T. C., Aasjord, A. E., Chourrout, D. M., Thompson, A. W., Sutherland, K. R. (2025) Microsphere counts from incubation chambers of Oikopleura dioica prior to and following feeding incubations for experiment with artificial microspheres with two functionalized surfaces in three sizes. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-03-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.956298.1 [access date]
Microsphere counts from incubation chambers of Oikopleura dioica Dataset Description: Methods and Sampling: <p>Experiments with 5-day old <em>O. dioica</em> were conducted at the Michael Sars Centre in Bergen, Norway in October 2022 and 2023. Individual animals (15-24 replicates) were removed from their culture chamber, probed to abandon their house, and placed in a staging beaker containing 0.22 µm filtered seawater (FSW) to build fresh houses. Up to 12 actively pumping animals were then transferred from the staging beaker to an incubation chamber. Feeding incubations were carried out in a 12˚C water table with a motorized stir paddle to maintain suspension for 10 minutes. Following the 10-minute incubation, 3-8 animals were individually pipetted into watch glasses and probed to abandon houses so that the appendicularian and house could be preserved separately. Appendicularians were fixed by pipetting animal in 1 mL FSW into a 1.8 mL cryovial with 5 µl 25% microscopy grade glutaraldehyde (0.125% final concentration) to stop digestion. Houses were pipetted into cryovials in a volume of 100 µl without fixative.</p>
<p>&nbsp;</p>
<p>Laboratory feeding incubations were carried out on two occasions with two experimental designs. One with all particle sizes (1.0 and 2.0 µm) available in equal concentration to appendicularians. The other with particle sizes (0.5, 1.0 and 3.0 µm) simulated environmental conditions with smaller particles available in higher concentration. For each particle size, two different microsphere types were used with different functionalized surfaces (carboxylate- and amine-modified).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2419056 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2419056
completed
Kelly Rakow Sutherland
University of Oregon
541-913-6560
5289 University of Oregon
Eugene
OR
97403-5219
USA
ksuth@uoregon.edu
pointOfContact
Anne W. Thompson
Portland State University
503-725-8052
PO Box 751
Portland
OR
97201
USA
awt@pdx.edu
pointOfContact
Anne E. Aasjord
Sars International Centre for Marine Molecular Biology
anne.aasjord@uib.no
pointOfContact
Daniel M. Chourrout
Sars International Centre for Marine Molecular Biology
Daniel.Chourrout@uib.no
pointOfContact
Terra C. Hiebert
University of Oregon
5289 University of Oregon
Eugene
OR
97403-5219
USA
terrah@uoregon.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Incubation
Sample_Number
Ti_Tf
C_0_5_um_ml
C_1_um_ml
C_2_um_ml
C_3_um_ml
A_0_5_um_ml
A_1_um_ml
A_2_um_ml
A_3_um_ml
Nikon D850
Nikon Eclipse
theme
None, User defined
experiment id
sample identification
sample description
count
featureType
BCO-DMO Standard Parameters
Camera
Fluorescence Microscope
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.
Collaborative Proposal: Are all cell surfaces the same? The effects of particle surface property on predator-prey interactions in the microbial loop
http://www.sutherlandlab.org
Collaborative Proposal: Are all cell surfaces the same? The effects of particle surface property on predator-prey interactions in the microbial loop
<p><em>NSF Award Abstract:</em><br />
Marine microorganisms are among the most abundant life forms on the planet, playing a key role in ocean nutrient cycling. Though predation on these microorganisms is critical to nutrient cycling, little is known about their interactions with predators - specifically the direct interaction between microorganism cell surfaces and predator capture surfaces. This project examines how cell surfaces may influence the predation of marine microorganisms. Cell surface modification is a recognized strategy for predator avoidance among terrestrial microorganisms, but its application in the ocean is largely unexplored. By examining microbial prey with varying surface characteristics and predators with a range of feeding strategies, this research is providing foundational knowledge for future ocean food web models. This project engages public audiences through exhibits and workshops at museums (e.g., Oregon Museum of Science and Industry) and coastal aquariums with a focus on predator-prey interactions in the ocean from small microbial prey to larger predators. A large-scale art installment emphasizes these food web interactions. These 'Eco Murals' focus on ocean ecosystems and involve participation from community members, especially underrepresented minorities. This project is training the next generation of scientists by involving graduate and undergraduate students in research, professional development, and scientific communication. This research includes independent graduate student research as well as capstone projects in Bioinformatics and Genomics. Undergraduate students participate in this research following the previously successful NSF REU Exploration of Marine Biology on the Oregon Coast model. Finally, by leveraging initiatives aimed at promoting the persistence of historically underrepresented and underserved populations in STEM fields, this project recruits, supports, and retains female, first-generation, and underrepresented minority students.</p>
<p>The differential selection and rejection of microbial prey alters our understanding of carbon fate and nutrient cycling in the ocean. This project directly tests the effects of microbial surface properties on particle selection by globally abundant suspension feeders. Cell surface properties are known to be a fundamental aspect of predation avoidance in terrestrial microbes, but the role of microbial surface properties in avoiding or enhancing predation is a research frontier in ocean science. This knowledge gap limits understanding of microbial mortality, microbial loop function, and prediction of ecosystem response to future climate scenarios. This research links specific particle properties with ecologically-relevant trophic interactions through experiments with widespread suspension feeders representing major feeding strategies by copepod nauplii, pteropods, appendicularians, and echinoderm larvae. First, this project quantifies the surface properties of major marine microbial groups to inform feeding incubations with artificial prey. Second, artificial microspheres with varying surface properties are used in controlled laboratory feeding incubations to determine selectivity and third, to quantify particle fate from released fecal pellets and pseudofeces. Finally, the major marine microbial taxa in the guts of wild-caught suspension feeders are quantified using qPCR. This research forms an integrative approach, yet the results of each objective have scientific impact which can be applied to diverse fields beyond the ocean.</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>
Surf Props
largerWorkCitation
project
eng; USA
oceans
5.33145
5.33145
60.38147
60.38147
2022-10-18
2023-10-18
Oregon Institute of Marine Biology, Friday Harbor Labs (FHL), Michael Sars Centre in Bergen, Norway
0
BCO-DMO catalogue of parameters from Microsphere counts from incubation chambers of Oikopleura dioica prior to and following feeding incubations for experiment with artificial microspheres with two functionalized surfaces in three sizes
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/957265.rdf
Name: Incubation
Units: unitless
Description: <p>Incubation name for all incubations was alphabetical. Name is unique to entire project</p>
http://lod.bco-dmo.org/id/dataset-parameter/957266.rdf
Name: Sample_Number
Units: unitless
Description: <p>Sample number in incubation. Cumulative for incubations A-D and 1-4 for incubations E and F</p>
http://lod.bco-dmo.org/id/dataset-parameter/957267.rdf
Name: Ti_Tf
Units: unitless
Description: <p>Sample from incubation start (Ti) or end (Tf), Ti = Time initial, Tf = Time final</p>
http://lod.bco-dmo.org/id/dataset-parameter/957268.rdf
Name: C_0_5_um_ml
Units: Count per grid
Description: <p>Number of 0.5 µm carboxylate-modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957269.rdf
Name: C_1_um_ml
Units: Count per grid
Description: <p>Number of 1.0 µm carboxylate-modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957270.rdf
Name: C_2_um_ml
Units: Count per grid
Description: <p>Number of 2.0 µm carboxylate- modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957271.rdf
Name: C_3_um_ml
Units: Count per grid
Description: <p>Number of 3.0 µm carboxylate-modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957272.rdf
Name: A_0_5_um_ml
Units: Count per grid
Description: <p>Number of 0.5 µm amine-modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957273.rdf
Name: A_1_um_ml
Units: Count per grid
Description: <p>Number of 1.0 µm amine- modified microspheres counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/957274.rdf
Name: A_2_um_ml
Units: Count per grid
Description: <p>Number of 2.0 µm amine-modified microspheres counted per ml</p>
http://lod.bco-dmo.org/id/dataset-parameter/957275.rdf
Name: A_3_um_ml
Units: Count per grid
Description: <p>Number of 3.0 µm amine-modified microspheres counted per ml</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
1443
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a1d412a7-b897-487c-adca-a32a1e174966/content
download
https://doi.org/10.26008/1912/bco-dmo.956298.1
download
onLine
dataset
<p>Experiments with 5-day old <em>O. dioica</em> were conducted at the Michael Sars Centre in Bergen, Norway in October 2022 and 2023. Individual animals (15-24 replicates) were removed from their culture chamber, probed to abandon their house, and placed in a staging beaker containing 0.22 µm filtered seawater (FSW) to build fresh houses. Up to 12 actively pumping animals were then transferred from the staging beaker to an incubation chamber. Feeding incubations were carried out in a 12˚C water table with a motorized stir paddle to maintain suspension for 10 minutes. Following the 10-minute incubation, 3-8 animals were individually pipetted into watch glasses and probed to abandon houses so that the appendicularian and house could be preserved separately. Appendicularians were fixed by pipetting animal in 1 mL FSW into a 1.8 mL cryovial with 5 µl 25% microscopy grade glutaraldehyde (0.125% final concentration) to stop digestion. Houses were pipetted into cryovials in a volume of 100 µl without fixative.</p>
<p>&nbsp;</p>
<p>Laboratory feeding incubations were carried out on two occasions with two experimental designs. One with all particle sizes (1.0 and 2.0 µm) available in equal concentration to appendicularians. The other with particle sizes (0.5, 1.0 and 3.0 µm) simulated environmental conditions with smaller particles available in higher concentration. For each particle size, two different microsphere types were used with different functionalized surfaces (carboxylate- and amine-modified).</p>
Specified by the Principal Investigator(s)
<p>Artificial particles were quantified from incubation suspension samples using a Nikon Eclipse Ei compound microscope with GFP and CY3 filter cubes for fluorescent particles and dark-field condenser for non-fluorescent particles (Abdel-Fattah et al. 2002). Counts were made using a Petroff-Hausser Bacteria Counter (0.2 mm deep, Fisher Scientific) with a 20x or 40x objective. All samples were vortexed for 30 s prior to counting. Nine grids were counted per 10-µl replicate, in duplicate.&nbsp;</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
Nikon D850
Nikon D850
PI Supplied Instrument Name: Nikon D850 Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Nikon Eclipse
Nikon Eclipse
PI Supplied Instrument Name: Nikon Eclipse PI Supplied Instrument Description:Nikon Eclipse Ni epifluorescence microscope Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/