http://lod.bco-dmo.org/id/dataset/994284
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
2026-03-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results of imaging flow cytobot (IFCB) analysis of biovolumes of key phytoplankton taxa from waters collected near study sites along the rocky intertidal on the Oregon coast in 2023 and 2024
2026-04-02
publication
2026-04-02
revision
BCO-DMO Linked Data URI
2026-04-02
creation
http://lod.bco-dmo.org/id/dataset/994284
Bruce A. Menge
Oregon State University
principalInvestigator
Brenna Rothman
Oregon State University
principalInvestigator
Audrey Vinton
University of Washington
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: Menge, B. A., Rothman, B., Vinton, A. (2026) Results of imaging flow cytobot (IFCB) analysis of biovolumes of key phytoplankton taxa from waters collected near study sites along the rocky intertidal on the Oregon coast in 2023 and 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/994284 [access date]
IFCB analysis of biovolumes of key phytoplankton taxa Dataset Description: Methods and Sampling: <p>Collection and analysis of "live" (unprocessed) water samples and separate preserved water samples for assessment of potential toxin-producing phytoplankton was done monthly. Samples were processed by Dr. Eli Meyer of Aquabiomics Inc. (Junction City, OR), by Dr. Ralph Elston of Aquatechnics (Carlsborg, WA), by Dr. Maria Kavanaugh of OSU's College of Earth, Ocean, and Atmospheric Sciences (Seascape Ecology Lab), and Dr. Manuel Garcia-Jaramillo in the Department of Environmental and Molecular Toxicology at OSU.</p>
<p>IFCB sampling following Dr. Kavanaugh's protocol: replicate (n = 3) bottle samples were collected at each site in September and November 2023, and in January, February, and June 2024. Dataset rows are from replicate bottle samples. Live samples are allowed to settle, then processed using Image FlowCytoBot (IFCB) sampling for the presence and abundance of preservation-sensitive phytoplankton (e.g., "naked" flagellates). Hardier plankters can be examined in both live and preserved samples.</p>
<p>Dataset rows: Each row corresponds to an instrument run. Generally, that would be one per sample bottle, but on occasion, samples would be run in duplicate (e.g., if the instrument had an issue with the first run), in which case a single sample might be accounted for in more than one row. The date is embedded in the File ID.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2346837 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2346837
onGoing
Bruce A. Menge
Oregon State University
541-737-5358
Department of Integrative Biology 4575 SW Research Way
Corvallis
OR
97333
USA
mengeb@oregonstate.edu
pointOfContact
Brenna Rothman
Oregon State University
brenroth@uw.edu
pointOfContact
Audrey Vinton
University of Washington
audrey.vinton@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Preserved_Live
site
site_name
site_lat
site_lon
date
File_Comment
Date_Run_on_IFCB
File_ID
Volume_Processed_by_Instrument_ml
Diatom_microns3_ml
Dinoflagellate_microns3_ml
Coccolithophore_microns3_ml
Ciliate_microns3_ml
OtherPhyto_microns3_ml
OtherMixoHet_microns3_ml
Detritus_microns3_ml
Prymnesiophyte_microns3_ml
TOTAL_BIOVOLUME
pcnt_Diatoms
pcnt_Dinoflagellates
pcnt_Detritus
pcnt_Prymnesiophytes
pcntCoccolithophores
pcnt_Ciliates
pcnt_other
Imaging FlowCytoBot, McLane Scientific
theme
None, User defined
sample description
site
latitude
longitude
date
comments
file_name
sample_volume
biovolume
featureType
BCO-DMO Standard Parameters
Imaging FlowCytobot
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.
Partnership for Interdisciplinary Studies of Coastal Oceans
http://www.piscoweb.org/
Partnership for Interdisciplinary Studies of Coastal Oceans
The Partnership for Interdisciplinary Studies of Coastal Oceans is a long-term ecosystem research and monitoring program established with the goals of:
understanding dynamics of the coastal ocean ecosystem along the U.S. west coast
sharing that knowledge so ocean managers and policy makers can make science based decisions regarding coastal and marine stewardship
producing a new generation of scientists trained in interdisciplinary collaborative approaches
Over the last 10 years, PISCO has successfully built a unique research program that combines complementary disciplines to answer critical environmental questions and inform management and policy. Activities are conducted at the latitudinal scale of the California Current Large Marine Ecosystem along the west coast of North America, but anchored around the dynamics of coastal, hardbottom habitats and the oceanography of the nearshore ocean – among the most productive and diverse components of this ecosystem. The program integrates studies of changes in the ocean environment through ecological monitoring and experiments. Scientists examine the causes and consequences of ecosystem changes over spatial scales that are the most relevant to marine species and management, but largely unstudied elsewhere.
Findings are linked to solutions through a growing portfolio of tools for policy and management decisions. The time from scientific discovery to policy change is greatly reduced by coordinated, efficient links between scientists and key decision makers.
Core elements of PISCO are:
Interdisciplinary ecosystem science
Data archiving and sharing
Outreach to public and decision-making user groups
Interdisciplinary training
Coordination of distributed research team
Established in 1999 with funding from The David and Lucile Packard Foundation, PISCO is led by scientists from core campuses Oregon State University (OSU); Stanford University’s Hopkins Marine Station; University of California, Santa Cruz (UCSC); and University of California, Santa Barbara (UCSB). Collaborators from other institutions also contribute to leadership and development of PISCO programs. As of 2005, core PISCO activities are funded by collaborative grants from The David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation. Core support, along with additional funding from diverse public and private sources, make this unique partnership possible.
PISCO
largerWorkCitation
program
RAPID: A subtle epidemic: unique mortality of Mytilus californianus on the Oregon coast
https://osprey.bco-dmo.org/project/910806
RAPID: A subtle epidemic: unique mortality of Mytilus californianus on the Oregon coast
<p><em>NSF Award Abstract:</em><br />
On temperate rocky shores, mussels are a 'foundation' species, serving as prey for multiple predators, able to filter particles out of huge volumes of water, and harboring hundreds of other species, thereby serving a central role in community function. Hence, threats to their abundance and persistence are of significant ecological and societal concern. Past research has shown that mussels are highly resilient and well-adapted to acute, short-lived stresses such as disturbance from winter storms or short-term warming. In summer 2023, a novel pattern of mortality was discovered during routine field research: high numbers of dead mussels, many with tissue remaining in the shell were observed in a scattered pattern. That is, rather than a mass mortality (i.e., all mussels in a large area are killed), single dead mussels surrounded by live and apparently healthy mussels occurred, with multiple dead individuals per square meter. This project investigates the cause of the mortality event, which preliminary data suggests may be a harmful algal bloom. The project also builds capacity by supporting research training for several undergraduate students and informs the public and resource managers about an emerging threat to the stability of rocky intertidal ecosystems.</p>
<p>The hypothesis under investigation is that the 2023 'scattered' mortality event at 8 study sites along the Oregon and northern California coasts affecting the rocky intertidal dominant, <em>Mytilus californianus</em>, may be an unusual consequence of a harmful algal bloom. During this event, densities of dead mussels have ranged from 0.7 to 10.6/m2. This novel pattern contrasts with typical mass mortalities of organisms where all individuals within a specific site or area die due to (e.g.) thermal stress or severe storms. The scattered mortality pattern persisted through late September 2023. Preliminary histological evidence suggests the ability of mussels to digest food is being suppressed, most likely by a water-borne toxin. To investigate the cause of the mortality event, the team is (1) collecting monthly (a) water samples for identification of dinoflagellate species and (b) mussel tissue samples for histological investigation of digestive and kidney tissues and high performance liquid chromatography and mass spectrometry analyses for the presence of algal-derived toxins; (2) continuing mussel bed surveys to determine the seasonality of the mortality event; and (3) quantifying mussel bed persistence through winter storms at sites with higher or lower rates of mortality. This research advances understanding of community responses to intense environmental stresses and how these might influence the future of rocky intertidal ecosystems.</p>
Scattered mussel mortality
largerWorkCitation
project
eng; USA
oceans
-124.12
-124.0718
44.2525
44.8444
2023-09-13
2024-06-06
Rocky intertidal shores of Oregon and northern California
0
BCO-DMO catalogue of parameters from Results of imaging flow cytobot (IFCB) analysis of biovolumes of key phytoplankton taxa from waters collected near study sites along the rocky intertidal on the Oregon coast in 2023 and 2024
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/995868.rdf
Name: Preserved_Live
Units: unitless
Description: <p>Indicates live or preserved samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/995869.rdf
Name: site
Units: unitless
Description: <p>Sampling site code</p>
http://lod.bco-dmo.org/id/dataset-parameter/995870.rdf
Name: site_name
Units: unitless
Description: <p>Sampling site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/995871.rdf
Name: site_lat
Units: decimal degrees
Description: <p>Sampling site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/995872.rdf
Name: site_lon
Units: decimal degrees
Description: <p>Sampling site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/995873.rdf
Name: date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/995874.rdf
Name: File_Comment
Units: unitless
Description: <p>TBD?</p>
http://lod.bco-dmo.org/id/dataset-parameter/995875.rdf
Name: Date_Run_on_IFCB
Units: unitless
Description: <p>Date run on IFCB</p>
http://lod.bco-dmo.org/id/dataset-parameter/995876.rdf
Name: File_ID
Units: unitless
Description: <p>IFCB file name?</p>
http://lod.bco-dmo.org/id/dataset-parameter/995877.rdf
Name: Volume_Processed_by_Instrument_ml
Units: milliliters (mL)
Description: <p>Volume processed by the IFCB</p>
http://lod.bco-dmo.org/id/dataset-parameter/995878.rdf
Name: Diatom_microns3_ml
Units: cubic microns per milliliter
Description: <p>Diatom biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995879.rdf
Name: Dinoflagellate_microns3_ml
Units: cubic microns per milliliter
Description: <p>Dinoflagellate biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995880.rdf
Name: Coccolithophore_microns3_ml
Units: cubic microns per milliliter
Description: <p>Coccolithophore biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995881.rdf
Name: Ciliate_microns3_ml
Units: cubic microns per milliliter
Description: <p>Ciliate biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995882.rdf
Name: OtherPhyto_microns3_ml
Units: cubic microns per milliliter
Description: <p>OtherPhyto the IFCB</p>
http://lod.bco-dmo.org/id/dataset-parameter/995883.rdf
Name: OtherMixoHet_microns3_ml
Units: cubic microns per milliliter
Description: <p>OtherMixoHet the IFCB</p>
http://lod.bco-dmo.org/id/dataset-parameter/995884.rdf
Name: Detritus_microns3_ml
Units: cubic microns per milliliter
Description: <p>Detritus biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995885.rdf
Name: Prymnesiophyte_microns3_ml
Units: cubic microns per milliliter
Description: <p>Prymnesiophyte biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995886.rdf
Name: TOTAL_BIOVOLUME
Units: cubic microns per milliliter
Description: <p>Total biovolume</p>
http://lod.bco-dmo.org/id/dataset-parameter/995887.rdf
Name: pcnt_Diatoms
Units: percent
Description: <p>Percent diatoms</p>
http://lod.bco-dmo.org/id/dataset-parameter/995888.rdf
Name: pcnt_Dinoflagellates
Units: percent
Description: <p>Percent dinoflagellates</p>
http://lod.bco-dmo.org/id/dataset-parameter/995889.rdf
Name: pcnt_Detritus
Units: percent
Description: <p>Percent detritus</p>
http://lod.bco-dmo.org/id/dataset-parameter/995890.rdf
Name: pcnt_Prymnesiophytes
Units: percent
Description: <p>Percent prymnesiophytes</p>
http://lod.bco-dmo.org/id/dataset-parameter/995891.rdf
Name: pcntCoccolithophores
Units: percent
Description: <p>Percent pcntcoccolithophores</p>
http://lod.bco-dmo.org/id/dataset-parameter/995892.rdf
Name: pcnt_Ciliates
Units: percent
Description: <p>Percent ciliates</p>
http://lod.bco-dmo.org/id/dataset-parameter/995893.rdf
Name: pcnt_other
Units: percent
Description: <p>Percent other</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/994284/data/download
download
onLine
dataset
<p>Collection and analysis of "live" (unprocessed) water samples and separate preserved water samples for assessment of potential toxin-producing phytoplankton was done monthly. Samples were processed by Dr. Eli Meyer of Aquabiomics Inc. (Junction City, OR), by Dr. Ralph Elston of Aquatechnics (Carlsborg, WA), by Dr. Maria Kavanaugh of OSU's College of Earth, Ocean, and Atmospheric Sciences (Seascape Ecology Lab), and Dr. Manuel Garcia-Jaramillo in the Department of Environmental and Molecular Toxicology at OSU.</p>
<p>IFCB sampling following Dr. Kavanaugh's protocol: replicate (n = 3) bottle samples were collected at each site in September and November 2023, and in January, February, and June 2024. Dataset rows are from replicate bottle samples. Live samples are allowed to settle, then processed using Image FlowCytoBot (IFCB) sampling for the presence and abundance of preservation-sensitive phytoplankton (e.g., "naked" flagellates). Hardier plankters can be examined in both live and preserved samples.</p>
<p>Dataset rows: Each row corresponds to an instrument run. Generally, that would be one per sample bottle, but on occasion, samples would be run in duplicate (e.g., if the instrument had an issue with the first run), in which case a single sample might be accounted for in more than one row. The date is embedded in the File ID.</p>
Specified by the Principal Investigator(s)
- Imported site metadata from "Copy of 6590_menge_site_descrip.xlsx" (sheet 1) into the BCO-DMO system.
- Imported IFCB biovolume data from "IFCB analysis of biovolumes of key taxa_10_17_24.xlsx" (sheet 1) into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions.
- Joined the site list to the IFCB biovolume data matching on site code, adding fields: "site_lat", "site_lon", and "site_name".
- Converted "date" field from format "%m-%d-%y" to ISO date format "%Y-%m-%d".
- Converted "Date_Run_on_IFCB" from format "%m/%d/%Y" to ISO date format "%Y-%m-%d".
- Saved the final data file as "994284_v1_ifcb_biovolumes_key_taxa.csv".
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
Imaging FlowCytoBot, McLane Scientific
Imaging FlowCytoBot, McLane Scientific
PI Supplied Instrument Name: Imaging FlowCytoBot, McLane Scientific PI Supplied Instrument Description:Gain settings: PMT A: 0.65, PMT B: 0.55. PMT thresholds: PMTA: 0.15, PMTB: 0.14. Flow rate of 5 ml/20 min per sample. Subset of samples were live seawater samples with no preservative, most were fixed in parformaldehyde (0.4% final concentration). Instrument Name: Imaging FlowCytobot Instrument Short Name:IFCB Instrument Description: The Imaging FlowCytobot (IFCB) is an in-situ automated submersible imaging flow cytometer that generates images of particles in-flow taken from the aquatic environment. https://mclanelabs.com/imaging-flowcytobot/