http://lod.bco-dmo.org/id/dataset/926332
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
2024-04-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results from Calanus pacificus Hypoxia Laboratory Experiments from 2019-2020 (Zooplankton Swimming project)
2024-04-30
publication
2024-04-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-06-24
publication
https://doi.org/10.26008/1912/bco-dmo.926332.1
Julie E. Keister
University of Washington
principalInvestigator
Daniel Grunbaum
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: Keister, J. E., Grunbaum, D. (2024) Results from Calanus pacificus Hypoxia Laboratory Experiments from 2019-2020 (Zooplankton Swimming project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926332.1 [access date]
Dataset Description: <p>The latitude and longitude coordinates of this dataset represent the collection sites where zooplankton were collected for experiments that later took place in an onshore laboratory at the University of Washington. The time bounds of this dataset represent the dates experiments were conducted (from the Experiment_Date column), not the dates of zooplankton collection (Collection_Date column).</p> Methods and Sampling: <p><strong>Sample Collection</strong></p>
<p>Zooplankton samples were collected using either a 60 cm diameter, 200 μm mesh ring net with a non-filtering cod- end or a 60 cm diameter, 335 μm mesh bongo net with non-filtering codends, lifted vertically from 10 m off the seafloor. Samples were stored in a cooler and air-bubbled for &lt;24 h until actively swimming adult female&nbsp;<em>C. pacificus</em>&nbsp;were manually sorted under a microscope into 1 liter jars filled with 200 μm filtered seawater. The copepods were kept at 14°C and fed a pre-made mixture of five marine microalgae (<em>Isochrysis, Pavlova, Tetraselmis, Thalassiosira weissflogii&nbsp;</em>and&nbsp;<em>T. pseudonana</em>) daily, for no more than 2 wk until they were used in a single laboratory experiment.</p>
<p>&nbsp;</p>
<p><strong>Experiment Details&nbsp;</strong></p>
<p>Water treatments of 2 different salinities (29 and 31) were made using Instant Ocean (~36 and ~39 g l−1) and verified with a YSI Pro 2030 salinity probe. Replicate 2-layer water columns with stable haloclines were created by pumping light (low salinity) water into the bottom of the tanks using a peristaltic pump until the water level was 500 mm from the bottom. Then, heavy (high salinity) water was pumped slowly to avoid mix- ing into the bottom, displacing the light water up- wards until the water columns were 780 mm deep with haloclines located 280 mm above the bottom.</p>
<p>To create the different oxygen conditions, bottom water was split into 2 buckets of equal volume to use in treatment and control tanks. Treatment bottom water was then bubbled with pure N2 gas until dissolved oxygen (DO) was &lt;0.2 mg l−1, as measured by a Pre- Sens oxygen dipping probe. Surface water and control bottom water were not bubbled and were left at ambi- ent oxygen concentrations (~10 mg l−1). At the end of each experiment, oxygen was measured at the surface, upper halocline, lower halocline, and bottom of each tank by lowering the oxygen probe slowly through the water column so as not to disrupt the halocline.</p>
<p><em>C. pacificus&nbsp;</em>behaviors and vertical distributions in response to either hypoxic or acidic bottom waters were observed in an array of 4 replicate 1 × 0.1 × 0.1 m acrylic tanks, installed in an environmental chamber set to 14°C.&nbsp; Stressful water layers (or non-stressful controls) were placed at the bottoms of salinity-stratified tanks, modeled after conditions experienced in the field. To start each experiment, 20 animals were gently introduced to the top of each of the 4 tanks. Swimming behavior was then observed for 90 min using 5-megapixel IR USB cameras. Experiments were run during the day in the dark, with the tanks backlit with IR LED strips behind and around the base of each tank. Two front-facing cameras (‘bottom camera’, ‘surface camera’) recorded swimming in the X (left, right) and Z (up, down) directions, observing true vertical motion and projected horizontal motion. An upwards-facing ‘base camera’ was added to each tank in 2020 to improve tracking and behavioral analysis of copepods near the bottom. Base cameras recorded the bottom 2 cm of each tank in the X and Y (front, back) directions and therefore observed true horizontal motion but not vertical motion.</p>
<p>&nbsp;</p>
<p><strong>Video output details</strong></p>
<p>Videos were processed with the software Fosica (Wallingford Imaging) to distinguish moving copepods from stationary background and noise and to extract copepod pixel coordinates. Pixel coordinates were converted into physical space units and then assembled into individual swimming paths using the Matlab software package Tracker3D (Chan &amp; Grünbaum 2010), neglecting parallax in the camera field of view. A smoothing spline was applied to remove features changing faster than 6 Hz, which were dominated by frame rate noise. X and Z (or, for the base cameras, X and Y) pixel coordinates for each object and the total projected speed and velocities were calculated at every frame for each swimming path. Swimming paths included only animals actively moving in the tank, excluding motionless (moribund) animals at the bottom of the tank. Copepod swimming paths were used to calculate the mean height from the bottom of the tank, mean number of copepod localizations per frame, and mean swimming speeds.</p>
<p>Our video system could not distinguish between individuals that were dead and those that were lying immobilized on the bottom for extended periods (a behavior leading, at least in hypoxia, to a high likelihood of eventual mortality). Therefore, for 2020 experiments, we developed a video-based metric using the base cameras to classify copepods at the bottom of tanks that were ‘moribund.’ Remaining motionless on the bottom of the tank is an uncommon behavior for&nbsp;<em>C. pacificus</em>, and we conservatively estimated that copepods motionless for a 2 minute threshold were in a ‘moribund’ or stressed state. To quantify moribundity, we calculated the mean brightness values for each pixel from frames in each of the last 1 minute sections (89th and 90th minutes). Because the videos were recorded in a dark field with IR back-lighting, copepods appeared as bright spots in the videos. The brightness of pixels representing a copepod in these 1 min means was a direct function of the number of frames in which it remained stationary. We then used a brightness threshold to classify copepods as moribund if pixel brightness indicated they had not moved during the last 2 minute of video observations.</p>
<p>More details on the methodology can be found here: Wyeth, A.C., Grünbaum D., Keister J.E. (2022). Effects of hypoxia and acidification on Calanus pacificus: behavioral changes in response to stressful environments. Marine Ecology Progress Series, 697: 15-29. https://doi.org/10.3354/meps14142.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657992 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657992
completed
Julie E. Keister
University of Washington
206-543-7620
School of Oceanography Box 357940
Seattle
WA
98195
United States
jkeister@uw.edu
pointOfContact
Daniel Grunbaum
University of Washington
206-221-6594
School of Oceanography Box 357940
Seattle
WA
98195
USA
random@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment_Date
Collection_Date
Sort_Date
Collector
Collection_Site
Lifestage
Sex
Collection_Lat
Collection_Long
Experiment_Type
Collection_Notes
Experiment_Notes
IR USB Camera
PreSens Oxygen Dipping Probe
YSI Pro 2030 Salinity Probe
theme
None, User defined
date
person name
site
stage
sex
latitude
longitude
experiment type
comments
featureType
BCO-DMO Standard Parameters
Camera
Oxygen Sensor
Salinity Sensor
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.
Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution.
https://osprey.bco-dmo.org/project/709640
Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution.
<p><em>NSF Award Abstract:</em><br />
Low oxygen (hypoxia) and low pH are known to have profound physiological effects on zooplankton, the microscopic animals of the sea. It is likely that many individual zooplankton change vertical mirgration behaviors to reduce or avoid these stresses. However, avoidance responses and their consequences for zooplankton distributions, and for interactions of zooplankton with their predators and prey, are poorly understood. This study will provide information on small-scale behavioral responses of zooplankton to oxygen and pH using video systems deployed in the field in a seasonally hypoxic estuary. The results will deepen our understanding of how zooplankton respond to low oxygen and pH conditions in ways that could profoundly affect marine ecosystems and fisheries through changes in their populations and distributions. This project will train graduate students and will engage K-12 students and teachers in under-served coastal communities by developing ocean technology-based citizen-scientist activities and curricular materials in plankton ecology, ocean change, construction and use of biological sensors, and quantitative analysis of environmental data.</p>
<p>Individual directional motility is a primary mechanism underlying spatio-temporal patterns in zooplankton population distributions. Motility is used by most zooplankton species to select among water column positions that differ in biotic and abiotic variables such as prey, predators, light, oxygen concentration, and pH. Species-specific movement responses to de-oxygenation and acidification are likely mechanisms through which short-term, localized impacts of these stressful conditions on individual zooplankton will be magnified or suppressed as they propagate up to population, community, and ecosystem-level dynamics. This study will quantify responses by key zooplankton species to oxygen and pH using in situ video systems to measure changes in individual behavior in hypoxic, low- pH versus well-oxygenated, high-pH regions of a seasonally hypoxic estuary. Distributions and movements of zooplankton will be quantified using three approaches: 1) an imaging system deployed in situ on a profiling mooring over two summers in a hypoxic region, 2) imagers deployed on Lagrangian drifters to sample simultaneously throughout the water column, and 3) vertically-stratified pumps and net tows to verify species identification and video-based abundance estimates. These field observations will be combined with laboratory analysis of zooplankton movements in oxygen and pH gradients, and with spatially-explicit models to predict how behavioral mechanisms lead to large-scale impacts of environmental stresses.</p>
<p>The following deployments were conducted in 2017 and 2018:<br />
CB1077: <a href="https://www.bco-dmo.org/deployment/735746" target="_blank">https://www.bco-dmo.org/deployment/735746</a><br />
CB1072: <a href="https://www.bco-dmo.org/deployment/735748" target="_blank">https://www.bco-dmo.org/deployment/735748</a><br />
Zoocam_ORCA_Twanoh_2017: <a href="https://www.bco-dmo.org/deployment/735762" target="_blank">https://www.bco-dmo.org/deployment/735762</a><br />
RC0008: <a href="https://www.bco-dmo.org/deployment/775288" target="_blank">https://www.bco-dmo.org/deployment/775288</a><br />
Mooring ORCA_Hoodsport; NANOOS-APL4: <a href="https://www.bco-dmo.org/deployment/775291" target="_blank">https://www.bco-dmo.org/deployment/775291</a></p>
Zooplankton Swimming
largerWorkCitation
project
eng; USA
oceans
-123.111667
-122.254141
47.27327
47.48022
2019-01-09
2020-01-09
Puget Sound, WA
0
BCO-DMO catalogue of parameters from Results from Calanus pacificus Hypoxia Laboratory Experiments from 2019-2020 (Zooplankton Swimming 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
http://lod.bco-dmo.org/id/dataset-parameter/929624.rdf
Name: Experiment_Date
Units: unitless
Description: <p>Date when the experiment took place.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929625.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date zooplankton were collected from Puget Sound.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929626.rdf
Name: Sort_Date
Units: unitless
Description: <p>Date zooplankton were sorted under the microscope and moved into artificial seawater.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929627.rdf
Name: Collector
Units: unitless
Description: <p>Brief details highlighting who conducted the live zooplankton tow.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929628.rdf
Name: Collection_Site
Units: unitless
Description: <p>Location of zooplankton tow.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929629.rdf
Name: Lifestage
Units: unitless
Description: <p>Lifestage of sorted Calanus pacificus (all are adult).</p>
http://lod.bco-dmo.org/id/dataset-parameter/929630.rdf
Name: Sex
Units: unitless
Description: <p>Sex of sorted Calanus pacificus (all are female).</p>
http://lod.bco-dmo.org/id/dataset-parameter/929631.rdf
Name: Collection_Lat
Units: decimal degrees
Description: <p>Latitude of zooplankton tow in decimal degrees; a positive value indicates a Northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929632.rdf
Name: Collection_Long
Units: decimal degrees
Description: <p>Longitude of zooplankton tow in decimal degrees; a negative value indicates a Western coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929633.rdf
Name: Experiment_Type
Units: unitless
Description: <p>Indicates the experiment type; can be used to determine differences between experiment types if merged with related BCO-DMO dataset Zooplankton Acidification Lab Results (#926368).</p>
http://lod.bco-dmo.org/id/dataset-parameter/929634.rdf
Name: Collection_Notes
Units: unitless
Description: <p>Field notes on zooplankton collection including time of day, tow depth, and net type.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929635.rdf
Name: Experiment_Notes
Units: unitless
Description: <p>Important experimental notes (if applicable).</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
3479
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/eb8fa790-0c05-434b-bd70-00943e98e7e1/content
download
https://doi.org/10.26008/1912/bco-dmo.926332.1
download
onLine
dataset
<p><strong>Sample Collection</strong></p>
<p>Zooplankton samples were collected using either a 60 cm diameter, 200 μm mesh ring net with a non-filtering cod- end or a 60 cm diameter, 335 μm mesh bongo net with non-filtering codends, lifted vertically from 10 m off the seafloor. Samples were stored in a cooler and air-bubbled for &lt;24 h until actively swimming adult female&nbsp;<em>C. pacificus</em>&nbsp;were manually sorted under a microscope into 1 liter jars filled with 200 μm filtered seawater. The copepods were kept at 14°C and fed a pre-made mixture of five marine microalgae (<em>Isochrysis, Pavlova, Tetraselmis, Thalassiosira weissflogii&nbsp;</em>and&nbsp;<em>T. pseudonana</em>) daily, for no more than 2 wk until they were used in a single laboratory experiment.</p>
<p>&nbsp;</p>
<p><strong>Experiment Details&nbsp;</strong></p>
<p>Water treatments of 2 different salinities (29 and 31) were made using Instant Ocean (~36 and ~39 g l−1) and verified with a YSI Pro 2030 salinity probe. Replicate 2-layer water columns with stable haloclines were created by pumping light (low salinity) water into the bottom of the tanks using a peristaltic pump until the water level was 500 mm from the bottom. Then, heavy (high salinity) water was pumped slowly to avoid mix- ing into the bottom, displacing the light water up- wards until the water columns were 780 mm deep with haloclines located 280 mm above the bottom.</p>
<p>To create the different oxygen conditions, bottom water was split into 2 buckets of equal volume to use in treatment and control tanks. Treatment bottom water was then bubbled with pure N2 gas until dissolved oxygen (DO) was &lt;0.2 mg l−1, as measured by a Pre- Sens oxygen dipping probe. Surface water and control bottom water were not bubbled and were left at ambi- ent oxygen concentrations (~10 mg l−1). At the end of each experiment, oxygen was measured at the surface, upper halocline, lower halocline, and bottom of each tank by lowering the oxygen probe slowly through the water column so as not to disrupt the halocline.</p>
<p><em>C. pacificus&nbsp;</em>behaviors and vertical distributions in response to either hypoxic or acidic bottom waters were observed in an array of 4 replicate 1 × 0.1 × 0.1 m acrylic tanks, installed in an environmental chamber set to 14°C.&nbsp; Stressful water layers (or non-stressful controls) were placed at the bottoms of salinity-stratified tanks, modeled after conditions experienced in the field. To start each experiment, 20 animals were gently introduced to the top of each of the 4 tanks. Swimming behavior was then observed for 90 min using 5-megapixel IR USB cameras. Experiments were run during the day in the dark, with the tanks backlit with IR LED strips behind and around the base of each tank. Two front-facing cameras (‘bottom camera’, ‘surface camera’) recorded swimming in the X (left, right) and Z (up, down) directions, observing true vertical motion and projected horizontal motion. An upwards-facing ‘base camera’ was added to each tank in 2020 to improve tracking and behavioral analysis of copepods near the bottom. Base cameras recorded the bottom 2 cm of each tank in the X and Y (front, back) directions and therefore observed true horizontal motion but not vertical motion.</p>
<p>&nbsp;</p>
<p><strong>Video output details</strong></p>
<p>Videos were processed with the software Fosica (Wallingford Imaging) to distinguish moving copepods from stationary background and noise and to extract copepod pixel coordinates. Pixel coordinates were converted into physical space units and then assembled into individual swimming paths using the Matlab software package Tracker3D (Chan &amp; Grünbaum 2010), neglecting parallax in the camera field of view. A smoothing spline was applied to remove features changing faster than 6 Hz, which were dominated by frame rate noise. X and Z (or, for the base cameras, X and Y) pixel coordinates for each object and the total projected speed and velocities were calculated at every frame for each swimming path. Swimming paths included only animals actively moving in the tank, excluding motionless (moribund) animals at the bottom of the tank. Copepod swimming paths were used to calculate the mean height from the bottom of the tank, mean number of copepod localizations per frame, and mean swimming speeds.</p>
<p>Our video system could not distinguish between individuals that were dead and those that were lying immobilized on the bottom for extended periods (a behavior leading, at least in hypoxia, to a high likelihood of eventual mortality). Therefore, for 2020 experiments, we developed a video-based metric using the base cameras to classify copepods at the bottom of tanks that were ‘moribund.’ Remaining motionless on the bottom of the tank is an uncommon behavior for&nbsp;<em>C. pacificus</em>, and we conservatively estimated that copepods motionless for a 2 minute threshold were in a ‘moribund’ or stressed state. To quantify moribundity, we calculated the mean brightness values for each pixel from frames in each of the last 1 minute sections (89th and 90th minutes). Because the videos were recorded in a dark field with IR back-lighting, copepods appeared as bright spots in the videos. The brightness of pixels representing a copepod in these 1 min means was a direct function of the number of frames in which it remained stationary. We then used a brightness threshold to classify copepods as moribund if pixel brightness indicated they had not moved during the last 2 minute of video observations.</p>
<p>More details on the methodology can be found here: Wyeth, A.C., Grünbaum D., Keister J.E. (2022). Effects of hypoxia and acidification on Calanus pacificus: behavioral changes in response to stressful environments. Marine Ecology Progress Series, 697: 15-29. https://doi.org/10.3354/meps14142.</p>
Specified by the Principal Investigator(s)
<p>Videos were processed with the software Fosica (Wallingford Imaging) to distinguish moving copepods from stationary background and noise and to extract copepod pixel coordinates. Pixel coordinates were converted into physical space units and then assembled into individual swimming paths using the Matlab software package Tracker3D (Chan &amp; Grünbaum 2010).</p>
Specified by the Principal Investigator(s)
- Originally, this data and related Zooplankton Acidification Lab Result Data (see related datasets section of this metadata page) were contained in the same .csv file, these data from separate but related experiments were parsed out and served separately through BCO-DMO in order to describe and represent data and experiments more accurately
- Column names across the Supplemental data tables and primary data table were made the same across all files
- Blank spaces in column names replaced with underscores ("_")
- Date columns within the data file (Experiment_Date, Collection_Date, and Sort_Date) were converted from %m%d%y format to %Y-%M-%D format
- Replaced NA missing data values in the dataset with blank values ("")
- Column name weight.avg changed to mean_height
- Column name camera changed to camera_ID
- Special characters in column names changed to underscores ("_")
- Latitude and longitude values rounded to 6 degrees of precision
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
IR USB Camera
IR USB Camera
PI Supplied Instrument Name: IR USB Camera PI Supplied Instrument Description:Copepod Swimming behavior was then observed for 90 min periods using 5-megapixel Infrared (IR) USB cameras with 8 mm wide angle lenses. 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/
PreSens Oxygen Dipping Probe
PreSens Oxygen Dipping Probe
PI Supplied Instrument Name: PreSens Oxygen Dipping Probe PI Supplied Instrument Description:A PreSens oxygen dipping probe was used to measure dissolved oxygen when different oxygen conditions were being created within the experimental tanks, and at the end of each experiment at the surface, upper halocine, lower halocine, and bottom of each tank. 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
YSI Pro 2030 Salinity Probe
YSI Pro 2030 Salinity Probe
PI Supplied Instrument Name: YSI Pro 2030 Salinity Probe PI Supplied Instrument Description:Water treatments of 2 different salinities (29 and 31) were made using Instant Ocean (~36 and ~39 g l−1) and verified with a YSI Pro 2030 salinity probe. Instrument Name: Salinity Sensor Instrument Short Name:Salinity Sensor Instrument Description: Category of instrument that simultaneously measures electrical conductivity and temperature in the water column to provide temperature and salinity data. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/350/