http://lod.bco-dmo.org/id/dataset/860652 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 2021-09-13 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Observations of Copepod Reactions to Sinking Aggregates Experiments 2019 2021-09-13 publication 2021-09-13 revision BCO-DMO Linked Data URI 2021-09-13 creation http://lod.bco-dmo.org/id/dataset/860652 Jennifer Prairie University of San Diego 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: Prairie, J. (2021) Observations of Copepod Reactions to Sinking Aggregates Experiments 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/860652 [access date] Observations of Copepod Reactions to Sinking Aggregates Experiments 2019 Dataset Description: Methods and Sampling: &lt;p&gt;During the summer of 2019, two sets of experiments were conducted on July 1 and July 11 to observe reactions of the copepod &lt;em&gt;Calanus pacificus&lt;/em&gt; to sinking aggregates.&lt;/p&gt; &lt;p&gt;&lt;em&gt;C. pacificus&lt;/em&gt; was collected using a small boat near Scripps Canyon in La Jolla, CA (32° 51.720' N, 117° 16.816' W) at least 4 days before each experiment with a 333 µm mesh plankton net (0.5 m diameter mouth). Samples were sorted in the lab to isolate individuals of the species &lt;em&gt;C. pacificus&lt;/em&gt;. Copepods were maintained with regular water changes in an incubator in the dark at 18°C until the experiment and fed &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt;. Copepods were starved for 24 hours prior to each experiment by transferring them into beakers with filtered seawater which were wrapped in aluminum foil to maintain darkness and kept at room temperature. Starved female &lt;em&gt;C. pacificus&lt;/em&gt; were tethered the morning of each experiment and placed in a beaker with filtered seawater at room temperature without food until they were used for the experiment.&lt;/p&gt; &lt;p&gt;Prior to each experiment, phytoplankton cultures of the species &lt;em&gt;T. weissflogii&lt;/em&gt; were started in 2L flasks and were grown in f/2 media at room temperature under 12:12 hour LED light:dark cycle for 3-5 days corresponding to the exponential growth phase. Three days before each experiment, the cultures were diluted to 30,000 cell/mL, using filtered seater that had a density between 0.001-0.002 g/cm3 less than the density of the filtered seawater used in the experimental tank (densities were measured with a handheld density meter). This was done to slow down the sinking velocity of the aggregates. The diluted cultures were then added to cylindrical acrylic tanks (each with a volume of 2.2 L). These cylindrical tanks were allowed to rotate in the dark on roller table for 3 days at a rate of 3.3 rpm to form aggregates.&lt;/p&gt; &lt;p&gt;Individual copepods, tethered to a strand of hair to ensure they stayed in the field of view of the camera, were placed in a 30.5 cm x 16 cm x 8 cm tank filled with filtered seawater. Individual aggregates were then pipetted into a funnel in the top of the tank, and allowed to sink towards the tethered copepod. A Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) was used to image the interactions between the copepods and aggregates, recording at rate of 30 fps. The experiments were filmed completely in the dark with the exception of a near-infrared LED light from below, which was used to ensure there was no effect of light on copepod behavior. In Experiment 1, 4 different copepods were each exposed to 6 different aggregates. In Experiment 2, 10 individual copepods were each exposed to 4 different marine snow aggregates (with the exception of the first copepod which was just exposed to one aggregate). In Experiment 1, some copepod/aggregate interactions were not successfully recorded or the aggregate never entered the field of view of the camera and so these were not included in the data sheet.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1654276 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1654276 onGoing Jennifer Prairie University of San Diego 619-260-8220 Environmental and Ocean Sciences 5998 Alcala Park San Diego CA 92110 USA jcprairie@sandiego.edu pointOfContact asNeeded Dataset Version: 1 Unknown Experiment_Number Copepod Aggregate Reaction AggregateXPosition_cm AggregateYPosition_cm NearestDistance_cm Aggregate_Area_cm2 Agg_Maj_Length_cm Agg_Min_Length_cm Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) hand-held density meter: DMA 35, Anton Paar near-infrared light-emitting diode: M730L4 730 nm, 515 mW Mounted LED, Thorlabs 333 µm mesh plankton net (0.5 m diameter mouth) cylindrical acrylic tanks (each with a volume of 2.2 L) theme None, User defined experiment id sample identification treatment No BCO-DMO term length area_measured featureType BCO-DMO Standard Parameters Camera density meter LED light Plankton Net Roller Tank 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. CAREER: Small-scale plankton-aggregate dynamics and the biological pump: Integrating mathematical biology in research and education https://osprey.bco-dmo.org/project/699441 CAREER: Small-scale plankton-aggregate dynamics and the biological pump: Integrating mathematical biology in research and education <p><em>NSF Award Abstract</em>:<br /> The global carbon cycle is in part modified by marine biological processes, which can impact the amount of carbon that is transported from surface waters to the deep ocean. This project will investigate interactions between planktonic grazers and marine aggregates - sinking particles that form in the surface ocean and have been shown to play an important role in marine food webs. The small scale of these biological processes makes them particularly challenging to study, but modern advances in mathematics and computer science have made direct observations of these interactions feasible. Experiments using high-resolution imaging will provide direct visual observations of zooplankton ingestion and the alteration of marine aggregates. These laboratory studies will guide the development of mathematical models to examine how these interactions affect particulate carbon sinking out of the surface ocean. This project will support an educational initiative focused on training undergraduate biology students in mathematical and computational techniques. This initiative includes the development of new interdisciplinary courses and undergraduate-focused independent research projects to help prepare the next generation of scientists in quantitative techniques that are essential to tackling the most challenging and complex biological problems.</p> <p>Marine snow aggregates are particles that form in the surface ocean from organic and inorganic matter. These aggregates play a fundamental role in the biological pump, as sinking particles are a dominant contributor to the downward transfer of carbon in the ocean. However, much of the small-scale processes governing these particles and their role in the marine carbon cycle are still unknown. The goal of this project is to use mathematical and computational techniques to investigate interactions between aggregates and planktonic grazers, an understudied link in the planktonic food web that has important implications for carbon export. Three-dimensional trajectories of copepods within marine snow thin layers will be obtained to experimentally investigate copepod foraging behavior in response to patchy distributions of marine snow. In addition, high-speed imaging will allow for the direct observation of how copepods manipulate and ingest marine snow aggregates, thus affecting their size and settling velocity. Lastly, a mathematical model will be developed to study the impact of these small-scale interactions on large-scale carbon cycling and export. This project will also support the implementation of a comprehensive education plan focused on teaching undergraduate students how mathematical modeling and computational techniques can be used to address biological questions. This educational objective will be accomplished through the development of new courses in mathematical and computational biology and through the inclusion of undergraduate students in independent research projects.</p> PlanktonAggDyn largerWorkCitation project eng; USA oceans -117.280267 -117.280267 32.862 32.862 2019-07-01 2019-07-11 0 BCO-DMO catalogue of parameters from Observations of Copepod Reactions to Sinking Aggregates Experiments 2019 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/860664.rdf Name: Experiment_Number Units: unitless Description: <p>experiment number. Experiment 1 was conducted on July 1, 2019 and Experiment 2was conducted on July 11, 2019.</p> http://lod.bco-dmo.org/id/dataset-parameter/860665.rdf Name: Copepod Units: unitless Description: <p>copepod number</p> http://lod.bco-dmo.org/id/dataset-parameter/860666.rdf Name: Aggregate Units: unitless Description: <p>aggregate number (each copepod was observed reacting to multiple aggregates, see Acquisition Description for more details)</p> http://lod.bco-dmo.org/id/dataset-parameter/860667.rdf Name: Reaction Units: unitless Description: <p>0 indicates a reaction was not observed. 1 or 2 indicates a reaction was observed (a value of 2 indicates the second distinct reaction by the copepod to the same aggregate, which is presented in a separate row).</p> http://lod.bco-dmo.org/id/dataset-parameter/860668.rdf Name: AggregateXPosition_cm Units: centimeters (cm) Description: <p>the X location in centimeters of the centroid of the aggregate when the copepod reacted. &quot;nd&quot; (no data) means the copepod did not react.</p> http://lod.bco-dmo.org/id/dataset-parameter/860669.rdf Name: AggregateYPosition_cm Units: centimeters (cm) Description: <p>the Y location in centimeters of the centroid of the aggregate when the copepod reacted. &quot;nd&quot; (no data) means the copepod did not react.</p> http://lod.bco-dmo.org/id/dataset-parameter/860670.rdf Name: NearestDistance_cm Units: centimeters (cm) Description: <p>the distance (in cm) from the nearest part of the aggregate to the copepod’s head when the reaction occurred. &quot;nd&quot; (no data) means the copepod did not react.</p> http://lod.bco-dmo.org/id/dataset-parameter/860671.rdf Name: Aggregate_Area_cm2 Units: square centimeters (cm^2) Description: <p>the projected area of the aggregate (in cm squared) measured from the image when the copepod reacted. If the copepod did not react, the aggregate area was measured from an arbitrary image where the aggregate was completely visible.</p> http://lod.bco-dmo.org/id/dataset-parameter/860672.rdf Name: Agg_Maj_Length_cm Units: centimeters (cm) Description: <p>the major axis length (in cm) of the projection of the aggregate from the image when the copepod reacted. If the copepod did not react, the major axis length was measured from an arbitrary image where the aggregate was completely visible.</p> http://lod.bco-dmo.org/id/dataset-parameter/860673.rdf Name: Agg_Min_Length_cm Units: centimeters (cm) Description: <p>the minor axis length (in cm) of the projection of the aggregate from the image when the copepod reacted. If the copepod did not react, the major axis length was measured from an arbitrary image where the aggregate was completely visible.</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/860652/data/download download onLine dataset &lt;p&gt;During the summer of 2019, two sets of experiments were conducted on July 1 and July 11 to observe reactions of the copepod &lt;em&gt;Calanus pacificus&lt;/em&gt; to sinking aggregates.&lt;/p&gt; &lt;p&gt;&lt;em&gt;C. pacificus&lt;/em&gt; was collected using a small boat near Scripps Canyon in La Jolla, CA (32° 51.720' N, 117° 16.816' W) at least 4 days before each experiment with a 333 µm mesh plankton net (0.5 m diameter mouth). Samples were sorted in the lab to isolate individuals of the species &lt;em&gt;C. pacificus&lt;/em&gt;. Copepods were maintained with regular water changes in an incubator in the dark at 18°C until the experiment and fed &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt;. Copepods were starved for 24 hours prior to each experiment by transferring them into beakers with filtered seawater which were wrapped in aluminum foil to maintain darkness and kept at room temperature. Starved female &lt;em&gt;C. pacificus&lt;/em&gt; were tethered the morning of each experiment and placed in a beaker with filtered seawater at room temperature without food until they were used for the experiment.&lt;/p&gt; &lt;p&gt;Prior to each experiment, phytoplankton cultures of the species &lt;em&gt;T. weissflogii&lt;/em&gt; were started in 2L flasks and were grown in f/2 media at room temperature under 12:12 hour LED light:dark cycle for 3-5 days corresponding to the exponential growth phase. Three days before each experiment, the cultures were diluted to 30,000 cell/mL, using filtered seater that had a density between 0.001-0.002 g/cm3 less than the density of the filtered seawater used in the experimental tank (densities were measured with a handheld density meter). This was done to slow down the sinking velocity of the aggregates. The diluted cultures were then added to cylindrical acrylic tanks (each with a volume of 2.2 L). These cylindrical tanks were allowed to rotate in the dark on roller table for 3 days at a rate of 3.3 rpm to form aggregates.&lt;/p&gt; &lt;p&gt;Individual copepods, tethered to a strand of hair to ensure they stayed in the field of view of the camera, were placed in a 30.5 cm x 16 cm x 8 cm tank filled with filtered seawater. Individual aggregates were then pipetted into a funnel in the top of the tank, and allowed to sink towards the tethered copepod. A Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) was used to image the interactions between the copepods and aggregates, recording at rate of 30 fps. The experiments were filmed completely in the dark with the exception of a near-infrared LED light from below, which was used to ensure there was no effect of light on copepod behavior. In Experiment 1, 4 different copepods were each exposed to 6 different aggregates. In Experiment 2, 10 individual copepods were each exposed to 4 different marine snow aggregates (with the exception of the first copepod which was just exposed to one aggregate). In Experiment 1, some copepod/aggregate interactions were not successfully recorded or the aggregate never entered the field of view of the camera and so these were not included in the data sheet.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Data Processing:&lt;/strong&gt;&lt;br /&gt; Image analysis was performed in order to determine characteristics of the aggregates when a reaction occurred. Copepods were usually not moving at all when there was no marine snow present in the tank. Once a marine snow aggregate was inserted into the tank, a &quot;reaction&quot; was then defined as any substantial movement by the copepod that could be detected by the naked eye. MATLAB was used to quantify several different characteristics of the aggregates including: the x and y coordinates of the aggregate's centroid when the copepod reacted, the distance between the nearest part of the aggregate to the copepod's head when the copepod reacted, the projected area of the aggregate in the 2D image when the copepod reacted, and the major and minor axis length of the projection of the aggregate in the 2D image when the copepod reacted. The x and y coordinates of the aggregate are given in centimeters relative to the copepod's head (i.e. with the copepod's head defined as the origin), where positive x values indicate locations in front of the copepod and negative x values indicate locations behind the copepod, and positive y values indicate locations above the copepod and negative y values indicate locations below the copepod. All length scales were converted to centimeters using images of a ruler taken in the tank for each experiment.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - concatenated data from two separate Excel sheets into a single dataset;&lt;br /&gt; - replaced &quot;NaN&quot; with &quot;nd&quot; (no data).&lt;/p&gt; 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 Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) PI Supplied Instrument Name: Point Grey Grasshopper camera (Model GS3-U3-41C6NIR-C) 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/ hand-held density meter: DMA 35, Anton Paar hand-held density meter: DMA 35, Anton Paar PI Supplied Instrument Name: hand-held density meter: DMA 35, Anton Paar Instrument Name: density meter Instrument Short Name:density meter Instrument Description: Portable or bench-top instruments to measure density of liquids. [lab]   near-infrared light-emitting diode: M730L4 730 nm, 515 mW Mounted LED, Thorlabs near-infrared light-emitting diode: M730L4 730 nm, 515 mW Mounted LED, Thorlabs PI Supplied Instrument Name: near-infrared light-emitting diode: M730L4 730 nm, 515 mW Mounted LED, Thorlabs Instrument Name: LED light Instrument Short Name: Instrument Description: A light-emitting diode (LED) is a semiconductor light source that emits light when current flows through it. Electrons in the semiconductor recombine with electron holes, releasing energy in the form of photons. 333 µm mesh plankton net (0.5 m diameter mouth) 333 µm mesh plankton net (0.5 m diameter mouth) PI Supplied Instrument Name: 333 µm mesh plankton net (0.5 m diameter mouth) Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/ cylindrical acrylic tanks (each with a volume of 2.2 L) cylindrical acrylic tanks (each with a volume of 2.2 L) PI Supplied Instrument Name: cylindrical acrylic tanks (each with a volume of 2.2 L) Instrument Name: Roller Tank Instrument Short Name:Roller Tank Instrument Description: Rolling tanks, which keep particles in suspension, thus simulating aggregate formation in situ. Marine snow experiments are conducted in roller tanks, which turn continuously, keeping marine snow in suspension. It is important for marine snow not to touch surfaces. The rolling tanks, which keep particles in suspension, thus simulate aggregate formation in situ. Marine snow formation due to different types of oil was tested. Some treatments are easily identifiable as containing oil by their color (middle). UCSB, CA 2012.