http://lod.bco-dmo.org/id/dataset/1004883
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
2026-08-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Box Core Macrofauna Species Counts collected Oregon and Washington Shelf 2021-2022
2026-08-12
publication
2026-08-12
revision
BCO-DMO Linked Data URI
2026-08-12
creation
http://lod.bco-dmo.org/id/dataset/1004883
Sarah K. Henkel
Oregon State University
principalInvestigator
Clare E. Reimers
Oregon State University
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: Henkel, S. K., Vaughan, M., Reimers, C. E. (2026) Box Core Macrofauna Species Counts collected Oregon and Washington Shelf 2021-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1004883 [access date]
COP Box Core Macrofauna Species Counts 2021-2022 Dataset Description: Methods and Sampling: <p>At each station, samples were collected with a modified Grey-O’Hara 0.1 m<sup>2</sup> box core. One box core sample was taken at each station. Depth was recorded from the vessels’ echosounder at the time the box corer hit the bottom. Only samples with a penetration depth of at least 5 centimeters (cm) and no slumping or other evidence of disturbance (i.e., by washing) were accepted for processing. Approximately 80 milliliters (mL) of sediment were collected from the undisturbed surface layer for grain size analysis. Any organisms noticed in the sediment subsample at the time of collection were removed and placed in the organism sample jar. The remainder of the collected core was sieved onboard through a 1.0 millimeter (mm) mesh screen, and all organisms (both infauna living in the sediment and small epifauna which may have been on the surface – hereafter collectively called macrofauna) as well as debris retained on the screen were preserved in a mixture of 10% buffered formalin and seawater. Upon return to the Oregon State University (OSU) laboratory, samples were transferred to 70% ethanol. Organisms were then removed from the debris and sorted into major taxonomic groups using a dissecting microscope by trained laboratory staff/students. The residual portion (remaining debris after removal of organisms) of every sample was checked by a second lab personnel, and any found organisms were added to the sorted jars. Crustaceans, polychaetes, other worm-like creatures, and mollusks were then sent to contracted taxonomic experts. OSU staff identified the echinoderms.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2126112 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2126112
onGoing
Sarah K. Henkel
Oregon State University
541-867-0316
2030 SE Marine Science Drive
Newport
OR
USA
sarah.henkel@oregonstate.edu
pointOfContact
Clare E. Reimers
Oregon State University
541-737-2426
Weniger Hall 563 103 SW Memorial Place
Corvallis
OR
97331
USA
creimers@coas.oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
Vessel
CruiseID
Site
Time_PDT
Sample_Date
Date_PDT
ISO_DateTime_PDT
ISO_DateTime_UTC
DecLat
DecLon
Depth_m
Depth_fa
Pen_cm
Organism_Group
Taxon_Name_Identified
Count
Lowest_Identifiable_Taxon_Accepted
AphiaID
LSID
modified Grey-O'Hara 0.1 m² box core built by Halco welding
dissecting microscope
theme
None, User defined
sample identification
ship
Cruise identifier
site
time of day
date_local
ISO_DateTime_Local
ISO_DateTime_UTC
latitude
longitude
depth
depth below seafloor
taxon
count
taxon_code
Life Science Identifier (LSID)
featureType
BCO-DMO Standard Parameters
Box Corer
Microscope - Optical
instrument
BCO-DMO Standard Instruments
COP2021
COP2022A
COP2022B
SP2215
SP2219
COP2022E
service
Deployment Activity
~44.36, -124.22
~45.02, -124.12
44.6545, -124.0265 to 46.9936, -124.5588
44.55, -124.313 to 44.58, -124.213
44.55, -124.031 to 46.45, -124.365
44.569, -124.248 to 46.583, -124.306
place
Locations
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.
Environmental consequences of expanded recruitment of an ecosystem engineer on a hypoxia-influenced continental shelf
https://osprey.bco-dmo.org/project/877543
Environmental consequences of expanded recruitment of an ecosystem engineer on a hypoxia-influenced continental shelf
<p><em>NSF Award Abstract:</em><br />
Highly productive US West Coast fishery species and marine mammals rely on benthic invertebrate communities for food. However, these communities are changing. This project addresses the potential ecological consequences of a new member to these benthic communities, the ghost shrimp Neotrypaea. In estuaries, Neotrypaea continuously rework the sediment via their burrowing activities. The combination of high shrimp abundances and the effects of burrowing mitigate the impacts of nutrient run-off (natural and human-induced) that can exacerbate low oxygen conditions. However, Neotrypaea are also considered threats to the oyster industry because of their sediment-excavating activities. An expansion of their distribution beyond estuaries may have additional unforeseen consequences for the Dungeness crab fishery (regionally valued at $33-74M/y) as Neotrypaea are both competitors with juveniles and prey for larger Dungeness crab. Thus, new data are needed to determine how offshore benthic communities are being altered by the recruitment of Neotrypaea into new habitats. This study is comparing communities with high and low shrimp abundances to understand their impact on offshore benthic communities. The shrimp’s contributions to oxygen and carbon cycling are being estimated through field measurements. Benthic community assessments are quantifying changes to food resources on the seafloor caused by the presence of these relatively large shrimp. The coastal waters along the Oregon-Washington shelf are commercially valuable, yet they are also subject to growing human-related impacts. Sustainable management requires optimizing extractive, cultural, and recreational activities. The broader impacts of this research include key data for managers, commercial fisheries’ stakeholders and oyster growers that inform decisions regarding ocean-use planning and management of burrowing shrimp. This project is providing research training for three graduate students and two summer undergraduate students. Curriculum development for elementary school students is focused on the ecology of soft-bottom benthos. The ocean sandy/muddy benthos are often unknown to K-12 students on the West Coast who are usually more familiar with intertidal and kelp forest systems.</p>
<p>Changing environmental conditions in shelf waters along the Oregon and Washington coasts and elsewhere have included increasingly frequent and severe hypoxia events, ocean acidification, and warming. These changes have affected biological communities and altered species distributions. An abundant mid-shelf population of the burrowing ghost shrimp, Neotrypaea sp. was documented in shelf waters following the Marine Heat Wave of 2015. Neotrypaea are ecosystem engineers that were previously known to be abundant in intertidal estuary mudflats with an insignificant presence in the open ocean. In estuaries Neotrypaea continuously rework the sediment via their burrowing activities. The shrimp can increase oxygen cycling due to burrow irrigation and reduce impacts of nutrient loading such as low-oxygen conditions. However, enhanced benthic oxygen consumption linked to Neotrypaea sp. beds could have the opposite effect on the shelf by intensifying regional hypoxia. This study is characterizing the environmental conditions associated with the expanded distribution of Neotrypaea using a habitat-suitability modeling approach. Model predictions are being validated through extensive field sampling via box coring and video lander observations. In addition, the benthic samples are documenting changes in the benthic invertebrate communities within the Neotrypaea beds and how this is potentially affecting biological interactions. Analyses of aquatic eddy covariance and of core incubations in shelf areas with and without abundant shrimp are providing estimates of the shrimp’s contribution to benthic oxygen fluxes and organic carbon cycling. These data are being used to quantify the shrimp’s and their burrows’ effects on the overall productivity of the mid-shelf benthos relative to reference areas. How Neotrypaea alter seafloor structure and biogeochemistry need to be characterized to predict the impact of these ecosystem engineers on the food supply for higher trophic levels and fisheries.</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>
Neotrypaea COP Effects
largerWorkCitation
project
eng; USA
biota
oceans
~44.36, -124.22; ~45.02, -124.12; 44.6545, -124.0265 to 46.9936, -124.5588; 44.55, -124.313 to 44.58, -124.213; 44.55, -124.031 to 46.45, -124.365; 44.569, -124.248 to 46.583, -124.306
-124.36483
-124.03052
44.33766
46.9936
2021-10-19
2022-09-22
NE Pacific continental shelf
0
BCO-DMO catalogue of parameters from Box Core Macrofauna Species Counts collected Oregon and Washington Shelf 2021-2022
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/1005039.rdf
Name: Sample
Units: unitless
Description: <p>Individual box core sample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005040.rdf
Name: Vessel
Units: unitless
Description: <p>Name of the ship. "Sproul" = R/V Gordon Sproul; "Storm" = R/V Pacific Storm</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005041.rdf
Name: CruiseID
Units: unitless
Description: <p>Internal or UNOLS cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005042.rdf
Name: Site
Units: unitless
Description: <p>Name of sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005043.rdf
Name: Time_PDT
Units: unitless
Description: <p>Local time recorded when box core touched bottom (PDT time zone)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005044.rdf
Name: Sample_Date
Units: unitless
Description: <p>Concatenated field of sample number and month-year of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005045.rdf
Name: Date_PDT
Units: unitless
Description: <p>Sampling date (PDT time zone)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005046.rdf
Name: ISO_DateTime_PDT
Units: unitless
Description: <p>Sampling date and time (PDT) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005047.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Sampling date and time (UTC) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005049.rdf
Name: DecLat
Units: decimal degrees
Description: <p>Latitude of sample collection; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005051.rdf
Name: DecLon
Units: decimal degrees
Description: <p>Longitude of sample collection; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005053.rdf
Name: Depth_m
Units: Meters
Description: <p>Boat echo sounder depth when box corer deployed, in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005055.rdf
Name: Depth_fa
Units: Fathoms
Description: <p>Boat echo sounder depth when box corer deployed, in fathoms</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005056.rdf
Name: Pen_cm
Units: Centimeters
Description: <p>Penetration depth of box corer (depth the box corer penetrated the seafloor sediment) in centimeters</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005057.rdf
Name: Organism_Group
Units: unitless
Description: <p>Major Taxonomic Group of identified taxon</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005058.rdf
Name: Taxon_Name_Identified
Units: unitless
Description: <p>Name of taxon as identified</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005059.rdf
Name: Count
Units: unitless
Description: <p>Number of each taxon in each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005060.rdf
Name: Lowest_Identifiable_Taxon_Accepted
Units: unitless
Description: <p>Name of taxon as currently accepted in WoRMS</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005061.rdf
Name: AphiaID
Units: unitless
Description: <p>ID of currently accepted taxon name in WoRMS</p>
http://lod.bco-dmo.org/id/dataset-parameter/1005062.rdf
Name: LSID
Units: unitless
Description: <p>Life Science Identifier of currently accepted taxon name in WoRMS</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/1004883/data/download
download
onLine
dataset
<p>At each station, samples were collected with a modified Grey-O’Hara 0.1 m<sup>2</sup> box core. One box core sample was taken at each station. Depth was recorded from the vessels’ echosounder at the time the box corer hit the bottom. Only samples with a penetration depth of at least 5 centimeters (cm) and no slumping or other evidence of disturbance (i.e., by washing) were accepted for processing. Approximately 80 milliliters (mL) of sediment were collected from the undisturbed surface layer for grain size analysis. Any organisms noticed in the sediment subsample at the time of collection were removed and placed in the organism sample jar. The remainder of the collected core was sieved onboard through a 1.0 millimeter (mm) mesh screen, and all organisms (both infauna living in the sediment and small epifauna which may have been on the surface – hereafter collectively called macrofauna) as well as debris retained on the screen were preserved in a mixture of 10% buffered formalin and seawater. Upon return to the Oregon State University (OSU) laboratory, samples were transferred to 70% ethanol. Organisms were then removed from the debris and sorted into major taxonomic groups using a dissecting microscope by trained laboratory staff/students. The residual portion (remaining debris after removal of organisms) of every sample was checked by a second lab personnel, and any found organisms were added to the sorted jars. Crustaceans, polychaetes, other worm-like creatures, and mollusks were then sent to contracted taxonomic experts. OSU staff identified the echinoderms.</p>
Specified by the Principal Investigator(s)
<p>The data received from the taxonomic experts have been reviewed to make sure there are no "duplicate" species due to misspellings and all species names have been updated if necessary to the currently accepted names according to WoRMS (World Register of Marine Species).</p>
Specified by the Principal Investigator(s)
This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability.
CURATION ACTIONS PERFORMED ON DATA
- Loaded table COPcomplete_macrofauna_data.csv as table "cop_macrofauna_data", CSV format, header row 1, empty string, "nd", and "NA"
- Converted column Date_PDT from M/D/YY string format (e.g., 10/19/21) to ISO 8601 date format YYYY-MM-DD, overwriting the original column
- Output final table to file 1004883_v1_cop_macrofauna_species_counts.csv
CURATION ACTIONS PERFORMED ON METADATA
- Standard metadata entry and text formatting steps were performed.
- Adjusted the abstract references from 7 cruises to 6, since 6 are referenced the metadata and the dataset.
ISSUES POTENTIALLY IMPACTING REUSE
- Count parameter is a decimal, which could conflict with the definition submitted.
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
modified Grey-O'Hara 0.1 m² box core built by Halco welding
modified Grey-O'Hara 0.1 m² box core built by Halco welding
PI Supplied Instrument Name: modified Grey-O'Hara 0.1 m² box core built by Halco welding PI Supplied Instrument Description:At each station, samples were collected with a modified Grey-O’Hara 0.1 m2 box core. One box core sample was taken at each station. Instrument Name: Box Corer Instrument Short Name:Box Corer Instrument Description: General description of a box corer:
A box corer is a marine geological tool that recovers undisturbed soft surface sediments. It is designed for minimum disturbance of the sediment surface by bow wave effects. Traditionally, it consists of a weighted stem fitted to a square sampling box. The corer is lowered vertically until it impacts with the seabed. At this point the instrument is triggered by a trip as the main coring stem passes through its frame. While pulling the corer out of the sediment a spade swings underneath the sample to prevent loss. When hauled back on board, the spade is under the box. (definition from the SeaVox Device Catalog)
Box corers are one of the simplest and most commonly used types of sediment corers. The stainless steel sampling box can contain a surface sediment block as large as 50cm x 50cm x 75cm with negligible disturbance. Once the sediment is recovered onboard, the sediment box can be detached from the frame and taken to a laboratory for subsampling and further analysis. The core sample size is controlled by the speed at which the corer is lowered into the ocean bottom. When the bottom is firm, a higher speed is required to obtain a complete sample. A depth pinger or other depth indicator is generally used to determine when the box is completely filled with sediment. Once the core box is filled with sediment, the sample is secured by moving the spade-closing lever arm to lower the cutting edge of the spade into the sediment, until the spade completely covers the bottom of the sediment box. (definition from Woods Hole Oceanographic Institution). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
dissecting microscope
dissecting microscope
PI Supplied Instrument Name: dissecting microscope PI Supplied Instrument Description:Organisms were then removed from the debris and sorted into major taxonomic groups using a dissecting microscope by trained laboratory staff/students. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: COP2021
COP2021
R/V Pacific Storm
R/V Pacific Storm
vessel
COP2021
Sarah K. Henkel
Oregon State University
Cruise: COP2022A
COP2022A
R/V Pacific Storm
R/V Pacific Storm
vessel
COP2022A
Sarah K. Henkel
Oregon State University
Cruise: COP2022B
COP2022B
R/V Pacific Storm
R/V Pacific Storm
vessel
COP2022B
Sarah K. Henkel
Oregon State University
Cruise: SP2215
SP2215
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP2215
Clare E. Reimers
Oregon State University
Cruise: SP2219
SP2219
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP2219
Clare E. Reimers
Oregon State University
Cruise: COP2022E
COP2022E
R/V Pacific Storm
R/V Pacific Storm
vessel
COP2022E
Sarah K. Henkel
Oklahoma State University
R/V Pacific Storm
R/V Pacific Storm
vessel
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel