http://lod.bco-dmo.org/id/dataset/962251
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
2025-05-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Processed aquatic eddy covariance measurements collected under hypoxic conditions from seven eddy covariance lander deployments made during summer cruises on the Oregon and Washington mid-shelf in 2018 and 2022
2025-05-30
publication
2025-05-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-31
publication
https://doi.org/10.26008/1912/bco-dmo.962251.1
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: Reimers, C. E., Henkel, S. K. (2025) Processed aquatic eddy covariance measurements collected under hypoxic conditions from seven eddy covariance lander deployments made during summer cruises on the Oregon and Washington mid-shelf in 2018 and 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.962251.1 [access date]
Aquatic Eddy Covariance Processed Measurements Dataset Description: Methods and Sampling: <p>Seven eddy covariance lander deployments were made on the Oregon or Washington continental shelf at mean water depths ranging from 68-84 m in 2018 during R/V Oceanus cruises OC1807A and OC1808A and in 2022 during&nbsp;R/V Robert Gordon Sproul&nbsp;cruises SP2215 and SP2219.</p>
<p>Data collected in 2018 (Deployments 1-3) were collected under NSF award OCE-1634319 to C. Reimers as part of a seasonal biogeochemical study of stations on the Newport Hydrographic line. Data collected in 2022 (Deployments 4-7) were from research under NSF award OCE-2126112 to S. Henkel and C. Reimers.&nbsp;These collections were combined with invertebrate infauna sampling at each station.</p>
<p>Aluminum lander frames, moored to floats at the sea surface, were the deployment and recovery platforms for the eddy covariance velocity, pressure and dissolved oxygen sensors. The eddy covariance sensors on the landers operated autonomously producing continuous datasets at 32 or 64 Hz that were reduced by averaging to 8 Hz and were 18.5-31.5 hours in&nbsp;duration. A Nortek Vector Acoustic Doppler Velocimeter (ADV)&nbsp;was mounted vertically with the probe pointing down. Sampling&nbsp;heights were measured&nbsp;from a bottom echo at the start of each ADV record and ranged from 27-31 cm above the seafloor.&nbsp;The ADV also recorded its heading, pitch and roll angles at 1 Hz and averages of these essentially constant measurements are reported, and in the results publication were used to transform velocity time series to ENU coordinates. Oxygen sensor tips were positioned approximately 2 cm outside of the ADV sampling volume.</p>
<p>Oxygen concentrations were derived after assembling&nbsp;calibration configuration files for each OXB430 sensor based on both “pre-” and “post-” deployment, in-laboratory, 0% and 100% air-saturation, sensor dphi recordings (i.e., values that represent the phase shift of the sensor’s NIR-emission relative to the red-light excitation) at a known temperature and atmospheric pressure. Next, these files were called by a Matlab function (provided by Rockland Scientific) to convert the sensor’s deployment record into physical units. The function inputs were data vectors of the sensor’s dphi readings, temperature, salinity, and water depth, in addition to the configuration files.</p>
<p><!--StartFragment-->Temperature was either based on temperature measurements made by an onboard Seabird 16plus V2 CTD, an internal sensor in the ADV, interpolated records between independent near-bottom measurements during casts of the ship's CTD, or temperature measurements from the Ocean Observatories Initiative benthic node (for deployment 3).&nbsp;Salinity was based on the same CTD sources.<!--EndFragment--></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634319 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634319
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
completed
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
Elapsed_time
Velocity_x
Velocity_y
Velocity_z
Dissolved_oxygen
Pressure
Matlab_Datenumber_Local
Burst
ISO_DateTime_UTC
Cruise
St_ID
Deployment
Oxy_sensor
Lat
Lon
Heading
Pitch
Roll
Height
Acoustic Doppler Velocimeter (ADV)
Pyroscience fiber-optic oxygen sensors
Seabird 16plusV2CTD
theme
None, User defined
time_elapsed
horizontal velocity towed
vertical velocity towed
dissolved Oxygen
water pressure
Date and time
No BCO-DMO term
ISO_DateTime_UTC
Cruise identfier
station id
deployment number
Sensor/Instrument identifier
latitude
longitude
heading
pitch
roll
altitude
featureType
BCO-DMO Standard Parameters
Acoustic Doppler Velocimeter
Oxygen Sensor
Sea-Bird SBE 16Plus V2 SEACAT
instrument
BCO-DMO Standard Instruments
OC1807A
OC1808A
SP2215
SP2219
service
Deployment Activity
Oregon Shelf
44.55, -124.313 to 44.58, -124.213
44.55, -124.031 to 46.45, -124.365
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
oceans
Oregon Shelf; 44.55, -124.313 to 44.58, -124.213; 44.55, -124.031 to 46.45, -124.365
-124.313
-124.067
44.571
46.45
2018-07-03
2022-09-17
NE Pacific continental shelf
0
BCO-DMO catalogue of parameters from Processed aquatic eddy covariance measurements collected under hypoxic conditions from seven eddy covariance lander deployments made during summer cruises on the Oregon and Washington mid-shelf in 2018 and 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/962341.rdf
Name: Elapsed_time
Units: seconds
Description: <p>Time in seconds since start of data record</p>
http://lod.bco-dmo.org/id/dataset-parameter/962342.rdf
Name: Velocity_x
Units: cm/s
Description: <p>Velocity in X direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/962343.rdf
Name: Velocity_y
Units: cm/s
Description: <p>Velocity in Y direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/962344.rdf
Name: Velocity_z
Units: cm/s
Description: <p>Velocity in Z direction</p>
http://lod.bco-dmo.org/id/dataset-parameter/962345.rdf
Name: Dissolved_oxygen
Units: micromoles/L
Description: <p>Dissolved oxygen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/962346.rdf
Name: Pressure
Units: db
Description: <p>Pressure measured by Vector sensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/962347.rdf
Name: Matlab_Datenumber_Local
Units: unitless
Description: <p>Date/Time of measurement in local time (U.S. Pacific); resolution 8 Hz. Matlab DateNumber.</p>
http://lod.bco-dmo.org/id/dataset-parameter/962348.rdf
Name: Burst
Units: unitless
Description: <p>15-min data segment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/962350.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time (UTC) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/962351.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/962352.rdf
Name: St_ID
Units: unitless
Description: <p>ID of target station</p>
http://lod.bco-dmo.org/id/dataset-parameter/962353.rdf
Name: Deployment
Units: unitless
Description: <p>Deployment number (1-7)</p>
http://lod.bco-dmo.org/id/dataset-parameter/962354.rdf
Name: Oxy_sensor
Units: unitless
Description: <p>Oxygen sensor used (Oxy1 or Oxy2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/962355.rdf
Name: Lat
Units: decimal degrees
Description: <p>Deployment latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/962356.rdf
Name: Lon
Units: decimal degrees
Description: <p>Deployment longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/962357.rdf
Name: Heading
Units: degrees
Description: <p>ADV Heading</p>
http://lod.bco-dmo.org/id/dataset-parameter/962358.rdf
Name: Pitch
Units: degrees
Description: <p>ADV Pitch</p>
http://lod.bco-dmo.org/id/dataset-parameter/962359.rdf
Name: Roll
Units: degrees
Description: <p>ADV Roll</p>
http://lod.bco-dmo.org/id/dataset-parameter/962360.rdf
Name: Height
Units: cm
Description: <p>ADV sampling volume height above bottom</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
936562305
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/7c83082b-b24f-45ed-9ab9-08918dc47848/content
download
https://doi.org/10.26008/1912/bco-dmo.962251.1
download
onLine
dataset
<p>Seven eddy covariance lander deployments were made on the Oregon or Washington continental shelf at mean water depths ranging from 68-84 m in 2018 during R/V Oceanus cruises OC1807A and OC1808A and in 2022 during&nbsp;R/V Robert Gordon Sproul&nbsp;cruises SP2215 and SP2219.</p>
<p>Data collected in 2018 (Deployments 1-3) were collected under NSF award OCE-1634319 to C. Reimers as part of a seasonal biogeochemical study of stations on the Newport Hydrographic line. Data collected in 2022 (Deployments 4-7) were from research under NSF award OCE-2126112 to S. Henkel and C. Reimers.&nbsp;These collections were combined with invertebrate infauna sampling at each station.</p>
<p>Aluminum lander frames, moored to floats at the sea surface, were the deployment and recovery platforms for the eddy covariance velocity, pressure and dissolved oxygen sensors. The eddy covariance sensors on the landers operated autonomously producing continuous datasets at 32 or 64 Hz that were reduced by averaging to 8 Hz and were 18.5-31.5 hours in&nbsp;duration. A Nortek Vector Acoustic Doppler Velocimeter (ADV)&nbsp;was mounted vertically with the probe pointing down. Sampling&nbsp;heights were measured&nbsp;from a bottom echo at the start of each ADV record and ranged from 27-31 cm above the seafloor.&nbsp;The ADV also recorded its heading, pitch and roll angles at 1 Hz and averages of these essentially constant measurements are reported, and in the results publication were used to transform velocity time series to ENU coordinates. Oxygen sensor tips were positioned approximately 2 cm outside of the ADV sampling volume.</p>
<p>Oxygen concentrations were derived after assembling&nbsp;calibration configuration files for each OXB430 sensor based on both “pre-” and “post-” deployment, in-laboratory, 0% and 100% air-saturation, sensor dphi recordings (i.e., values that represent the phase shift of the sensor’s NIR-emission relative to the red-light excitation) at a known temperature and atmospheric pressure. Next, these files were called by a Matlab function (provided by Rockland Scientific) to convert the sensor’s deployment record into physical units. The function inputs were data vectors of the sensor’s dphi readings, temperature, salinity, and water depth, in addition to the configuration files.</p>
<p><!--StartFragment-->Temperature was either based on temperature measurements made by an onboard Seabird 16plus V2 CTD, an internal sensor in the ADV, interpolated records between independent near-bottom measurements during casts of the ship's CTD, or temperature measurements from the Ocean Observatories Initiative benthic node (for deployment 3).&nbsp;Salinity was based on the same CTD sources.<!--EndFragment--></p>
Specified by the Principal Investigator(s)
<p>Calibration configuration files for each OXB430 sensor were based on both “pre-” and “post-” deployment, in-laboratory, 0% and 100% air-saturation, sensor dphi recordings (i.e.,&nbsp;values that represent the phase shift of the sensor’s NIR-emission relative to the red-light excitation)&nbsp;at a known temperature and atmospheric pressure. These files were called by a Matlab function (provided by Rockland Scientific) to convert the sensor’s deployment record into physical units. The function inputs were data vectors of the sensor’s dphi readings, temperature, salinity, and water depth, in addition to the configuration files.&nbsp;</p>
Specified by the Principal Investigator(s)
- Imported "D6NEH2_metadata.xlsx", "D7WLP1_metadata.xlsx", "D5NKW1_metadata.xlsx", "D2NH80_metadata.xlsx", "D3NH80_metadata.xlsx", "D4PWS2_metadata.xlsx", "D1NH80_metadata.xlsx" into the BCO-DMO system
- Concatenated data sources
- Split the filename into deployment and station strings
- Imported "D4PWS2JUL2022.dat", "D1NH80JUL2018.dat", "D3NH80AUG2018.dat", "D2NH80JUL2018.dat", "D7WLP1SEP2022.dat", "D5NKW1SEP2022.dat", "D6NEH2SEP2022ox2.dat", "D6NEH2SEP2022ox1.dat" into the BCO-DMO system
- Concatenated data sources
- Split the filename into deployment and station strings
- Joined metadata files and data files on the station and deployment identifiers
- Renamed fields for clarity and to comply with system requirements
- Removed Temp based on request from submitter
- Rounded Elapsed_time, Velocity_x, Velocity_y, Velocity_z, Dissolved_oxygen, Pressure, and Burst to 5 digits
- Exported file as "962251_v1_aquatic_eddy_covariance.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
Acoustic Doppler Velocimeter (ADV)
Acoustic Doppler Velocimeter (ADV)
PI Supplied Instrument Name: Acoustic Doppler Velocimeter (ADV) PI Supplied Instrument Description:A Nortek Vector Acoustic Doppler Velocimeter (ADV) was used to measure velocities in xyz coordinates and to measure pressure as well as compass heading, pitch and roll. Instrument Name: Acoustic Doppler Velocimeter Instrument Short Name:ADV Instrument Description: ADV is the acronym for acoustic doppler velocimeter. The ADV is a remote-sensing, three-dimensional velocity sensor. Its operation is based on the Doppler shift effect. The sensor can be deployed either as a moored instrument or attached to a still structure near the seabed.
Reference:
G. Voulgaris and J. H. Trowbridge, 1998. Evaluation of the Acoustic Doppler Velocimeter (ADV) for Turbulence Measurements. J. Atmos. Oceanic Technol., 15, 272–289. doi: http://dx.doi.org/10.1175/1520-0426(1998)0152.0.CO;2 Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/384/
Pyroscience fiber-optic oxygen sensors
Pyroscience fiber-optic oxygen sensors
PI Supplied Instrument Name: Pyroscience fiber-optic oxygen sensors PI Supplied Instrument Description:Dissolved oxygen was measured with Pyroscience fiber-optic oxygen sensors activated through PyroScience FireStingO2-Subport modules enclosed in Delrin housings and interfaced with electronics provided by Rockland Scientific (Victoria, BC, Canada) so that digital data was sent to and logged by the Vector. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
Seabird 16plusV2CTD
Seabird 16plusV2CTD
PI Supplied Instrument Name: Seabird 16plusV2CTD PI Supplied Instrument Description:On some deployments temperature and salinity were measured at 0.1 Hz with a Seabird 16plusV2CTD attached to the lander frame and these measurements were extrapolated to 8 Hz to coincide with the eddy covariance records. Instrument Name: Sea-Bird SBE 16Plus V2 SEACAT Instrument Short Name:SBE 16plus V2 SEACAT Instrument Description: The SBE 16plus V2 is a high accuracy conductivity and temperature recorder (pressure optional) with RS232 or RS485 interfaces. It is designed for moorings and other long-duration, fixed-site deployments. It has 6 amplified A/D input channels and conditioned power of 500 ma is available for auxiliary sensors, dissolved oxygen, turbidity, fluorescence, PAR etc. Compared to the previous 16plus, the V2 incorporates an electronics upgrade and additional features, with six differentially amplified A/D input channels, one RS-232 data input channel, and 64 MB FLASH memory. Data can be output in XML as well as ASCII and HEX formats. Firmware upgrades can be downloaded through the communications port, without opening the instrument.
Cruise: OC1807A
OC1807A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1807A
Clare E. Reimers
Oregon State University
Cruise: OC1808A
OC1808A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1808A
Clare E. Reimers
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
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel