http://lod.bco-dmo.org/id/dataset/939528
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
2024-10-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Oyster shell thickness from study of eastern oysters (Crassostrea virginica) grown in a nursery with or without exposure to chemical cues from blue crabs
2024-10-17
publication
2024-10-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-17
publication
https://doi.org/10.26008/1912/bco-dmo.939528.1
Marc Weissburg
Georgia Institute of Technology
principalInvestigator
Gary H. Dickinson
The College of New Jersey
principalInvestigator
Benjamin A. Belgrad
Dauphin Island Sea Lab
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: Weissburg, M., Dickinson, G. H., Belgrad, B. A. (2024) Oyster shell thickness from study of eastern oysters (Crassostrea virginica) grown in a nursery with or without exposure to chemical cues from blue crabs. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.939528.1 [access date]
Predator Induced and Non-Induced Eastern Oyster Shell Thickness Dataset Description: Methods and Sampling: <p>Eastern oysters were spawned at the Auburn University Shellfish Laboratory in Dauphin Island, AL, USA and juveniles were raised in a nursery system at Dauphin Island Sea Lab, Dauphin Island, AL, USA. Data collection took place at The College of New Jersey, Ewing, NJ, USA. This dataset was collected between March 2023 and December 2023. The oysters were raised in May - July 2019 and preserved in 70% ethanol until the shell mounting and data collection process began.</p>
<p><strong>Oyster Culturing:</strong><br />
The oyster spat used in this experiment were preserved from a previous study on shell strength of predator-induced spat, which confirmed that exposure to predator cues resulted in stronger shells, measured as the amount of force (N) required to break shells standardized to size (Belgrad et al. 2021). Oysters were spawned and cultured at Auburn University Shellfish Laboratory on Dauphin Island, AL, USA, in May 2019. Oyster larvae were settled onto sun-bleached oyster shell where they metamorphosized into spat-on-shell and were housed in four flow-through holding tanks (2.4 meters x 0.9 meters) filled to a water depth of 0.4 meters (m) and flowing at a rate of 36.9 liters per minute (L/min) with natural seawater from Mobile Bay, AL, USA. Oyster spat-on-shell were randomly placed in seven oyster aquaculture baskets (~140 adult shells per basket, 20,000 spat/tank) spaced evenly along the length of the tank and suspended within the tanks to avoid sediment smothering the spat (28 baskets, 80,000 spat total). Two of the holding tanks were kept with only oysters to serve as controls (non-induced), whereas the two treatment tanks also each held four caged live adult blue crabs (<em>Callinectes sapidus</em>, Rathbun) to add predator cues to the tanks (induced). These crabs were fed one adult oyster (~5.0 centimeters in length) daily and were replaced with healthy, fresh-caught crabs at least biweekly. Oyster cages were rotated daily around crab cages to reduce differences in growth due to proximity to cue sources or water intake. A subset of spat-on-shell were removed from each tank after four weeks and eight weeks of culturing under these conditions and stored in 70% ethanol until March 2023 when shell structure analysis began.</p>
<p><strong>Sample Preparation:</strong><br />
Oyster spat-on-shell were removed from ethanol solution in March 2023. A total of 5 left (top) shell valves from each nursery tank per induction state and age group (n = 10 per induction state and age group; 40 valves total) were carefully removed from individual spat and any soft tissue was removed using forceps and scalpel. The separated shell valves sat in 100% ethanol overnight to assist with removal of tissue remains, then were rinsed with DI water, dried at room temperature for 2-3 hours and finished drying in a low-temperature vacuum oven at 45 degrees Celsius (°C) and 25 millimeters of mercury (Hg mm) for 2 hours. The shell valves were then mounted and polished following standard techniques (Prezant et al. 2022). Each valve was placed in a 32-millimeter (mm) mounting cup, with the ventral edge of the shell affixed to the base of the cup using a coil mounting clip that had been glued to the bottom of the cup. This was left to dry overnight, before mounting with Bisphenol A Epichlorohydrin epoxy and hardener mixed in a 10:3 ratio (Allied High Tech). After the epoxy hardened for 24 hours, the mounted valves were removed from their mounting cups and ground to a plane that was visually approximated near the center of the shell running along the longest axis from anterior to posterior end. The shell valves were then polished to 0.04 micrometers (µm) using polycrystalline diamond solution and colloidal silica suspension (Allied High Tech).</p>
<p>Panoramic images of each shell sample were taken under polarized light using a reflected light microscope (Zeiss Axioscope.A1 with a Zeiss, AxioCam 105 color camera), with the analyzer set to 10°. Panoramas were constructed using imaging software (Zeiss Zen 3.8). Four-week-old spat valves were imaged under a 5x objective, and eight-week-old spat valves were imaged under a 2.5x objective.</p>
<p><strong>Determining Shell Thickness:</strong><br />
Measurements of the thickness of the foliated layer, prismatic layer, and total shell thickness took place in ImageJ - FIJI 1.54f (Schindelin et al. 2012) for both four-week and eight-week-old oysters of both induction states. Panoramic images had a grid placed over them (100 µm² for four-week-old, and 200 µm² for eight-week old) and images were divided approximately into thirds. All thickness measurements were taken from the middle third of the shell valve, with one measurement each for the foliated layer, prismatic layer, and total thickness within each grid square (n = 19-31 per four-week-old shell, and n = 16-22 measurements per eight-week-old shell, depending on overall spat size). Grid measurements were averaged to yield a single thickness value for each layer of each shell sample.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948423 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948423
completed
Marc Weissburg
Georgia Institute of Technology
404-894-8433
School of Biological Sciences Georgia Institute of Technology
Atlanta
GA
30332-0230
USA
marc.weissburg@biology.gatech.edu
pointOfContact
Gary H. Dickinson
The College of New Jersey
NJ
USA
dickinga@tcnj.edu
pointOfContact
Benjamin A. Belgrad
Dauphin Island Sea Lab
babelgra@eckerd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Age_group
ID
Measurement_Num
Grid_Num
Overall_Angle
Overall_Length
Foliated_Angle
Foliated_Length
Prismatic_Angle
Prismatic_Length
Zeiss AxioCam 105 color camera
Zeiss Axioscope
theme
None, User defined
sample description
sample identification
number of replicates
angle
length
featureType
BCO-DMO Standard Parameters
Camera
Microscope - Optical
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.
Collaborative Research: Keystone chemicals: Identifying general and universal molecules of fear
https://osprey.bco-dmo.org/project/839801
Collaborative Research: Keystone chemicals: Identifying general and universal molecules of fear
<p><em>NSF Award Abstract:</em><br />
Many prey species use chemicals released in predator urine to detect imminent danger and respond appropriately, but the identity of these ‘molecules of fear’ remains largely unknown. This proposal examines whether prey detect different estuarine predators using the same chemical or whether the identity of the chemical signals varies. Experiments focus on common and important estuarine prey, mud crabs and oysters, and their predators including fishes, crustaceans and marine snails. Bioactive molecules are being collected from predators and prey and characterized. The goal is to determine if there are predictive relationships between either the composition of prey flesh or the predator taxon and the signal molecule. Understanding the molecular nature of these cues can determine if there are general rules governing likely signal molecules. Once identified, investigators will have the ability to precisely manipulate or control these molecules in ecological or other types of studies. Oysters are critical to estuarine health, and they are important social, cultural and economic resources. Broader impacts of the project include training of undergraduate and graduate students from diverse backgrounds and working with aquaculture facilities and conservation managers to improve growth and survival of oysters. One response to predator cues involves creating stronger shells to deter predation. Determining the identity of cues used by oysters to detect predators can provide management options to produce oysters that either grow faster or are more resistant to predators. Project personnel is working with oystermen to increase yields of farmed oysters by managing chemical cues.</p>
<p>For marine prey, waterborne chemical cues are important sources of information regarding the threat of predation, thus, modulating non-consumptive effects of predation in many systems. Often such cues are produced when the predators consume the flesh of that prey. In nearly all cases, the specific bioactive molecules responsible for modulating these interactions are unknown, raising the question whether there is a universal molecule of fear that prey respond to. Thus, the focus of the project is to determine the generality of fear-inducing metabolites released by predators and prey in estuarine food webs. The project combines metabolomics analysis of diet-derived urinary metabolites with bioassays to identify the bioactive molecules producing responses in two prey species from different taxonomic groups and trophic levels (oysters, mud crabs). Metabolites are sampled from three types of predators, fish, gastropods or crustaceans. This project aims to: 1) identify bioactive molecules produced by several common estuarine predators from different taxa; 2) compare cues from predators that induce defenses in prey vs. changes in prey behavior; and 3) contrast the identities and effects of predator-released cues with fear-inducing molecules from injured conspecifics. By identifying and contrasting the effects of waterborne molecules that induce prey responses from six predators and injured prey, this project is yielding insights into the mechanisms that mediate non-lethal predator effects, while addressing long-standing questions related to predator-prey interactions. In addition to the search of a universal molecule of fear, the experiments are exploring the role of complementary and distinct chemical information on the specificity of prey responses to different types of predators.</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>
Identifying molecules of fear
largerWorkCitation
project
eng; USA
oceans
2023-03-01
2023-12-31
Wassaw Sound, GA, US and Dauphin Island, AL
0
BCO-DMO catalogue of parameters from Oyster shell thickness from study of eastern oysters (Crassostrea virginica) grown in a nursery with or without exposure to chemical cues from blue crabs
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/939644.rdf
Name: Age_group
Units: unitless
Description: <p>age group of oysters (8 weeks or 4 weeks)</p>
http://lod.bco-dmo.org/id/dataset-parameter/939645.rdf
Name: ID
Units: unitless
Description: <p>identification number of each shell replicate. Identification number was given based on Treatment - Age - Shell Number - Sample Number, where BC = induced and N = non-induced</p>
http://lod.bco-dmo.org/id/dataset-parameter/939646.rdf
Name: Measurement_Num
Units: unitless
Description: <p>number of technical replicate measurements taken per shell sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/939647.rdf
Name: Grid_Num
Units: unitless
Description: <p>total number of squares in a grid overlaid on each shell sample image</p>
http://lod.bco-dmo.org/id/dataset-parameter/939648.rdf
Name: Overall_Angle
Units: degrees
Description: <p>angle of the line measuring overall shell length per measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/939649.rdf
Name: Overall_Length
Units: micrometers
Description: <p>length of the line measuring overall shell length per measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/939650.rdf
Name: Foliated_Angle
Units: degrees
Description: <p>angle of the line measuring foliated shell length per measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/939651.rdf
Name: Foliated_Length
Units: micrometers
Description: <p>length of the line measuring foliated shell length per measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/939652.rdf
Name: Prismatic_Angle
Units: degrees
Description: <p>angle of the line measuring prismatic shell length per measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/939653.rdf
Name: Prismatic_Length
Units: micrometers
Description: <p>length of the line measuring prismatic shell length per measurement</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
57537
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f8197bed-8f03-4114-b03b-e91299c786d5/content
download
https://doi.org/10.26008/1912/bco-dmo.939528.1
download
onLine
dataset
<p>Eastern oysters were spawned at the Auburn University Shellfish Laboratory in Dauphin Island, AL, USA and juveniles were raised in a nursery system at Dauphin Island Sea Lab, Dauphin Island, AL, USA. Data collection took place at The College of New Jersey, Ewing, NJ, USA. This dataset was collected between March 2023 and December 2023. The oysters were raised in May - July 2019 and preserved in 70% ethanol until the shell mounting and data collection process began.</p>
<p><strong>Oyster Culturing:</strong><br />
The oyster spat used in this experiment were preserved from a previous study on shell strength of predator-induced spat, which confirmed that exposure to predator cues resulted in stronger shells, measured as the amount of force (N) required to break shells standardized to size (Belgrad et al. 2021). Oysters were spawned and cultured at Auburn University Shellfish Laboratory on Dauphin Island, AL, USA, in May 2019. Oyster larvae were settled onto sun-bleached oyster shell where they metamorphosized into spat-on-shell and were housed in four flow-through holding tanks (2.4 meters x 0.9 meters) filled to a water depth of 0.4 meters (m) and flowing at a rate of 36.9 liters per minute (L/min) with natural seawater from Mobile Bay, AL, USA. Oyster spat-on-shell were randomly placed in seven oyster aquaculture baskets (~140 adult shells per basket, 20,000 spat/tank) spaced evenly along the length of the tank and suspended within the tanks to avoid sediment smothering the spat (28 baskets, 80,000 spat total). Two of the holding tanks were kept with only oysters to serve as controls (non-induced), whereas the two treatment tanks also each held four caged live adult blue crabs (<em>Callinectes sapidus</em>, Rathbun) to add predator cues to the tanks (induced). These crabs were fed one adult oyster (~5.0 centimeters in length) daily and were replaced with healthy, fresh-caught crabs at least biweekly. Oyster cages were rotated daily around crab cages to reduce differences in growth due to proximity to cue sources or water intake. A subset of spat-on-shell were removed from each tank after four weeks and eight weeks of culturing under these conditions and stored in 70% ethanol until March 2023 when shell structure analysis began.</p>
<p><strong>Sample Preparation:</strong><br />
Oyster spat-on-shell were removed from ethanol solution in March 2023. A total of 5 left (top) shell valves from each nursery tank per induction state and age group (n = 10 per induction state and age group; 40 valves total) were carefully removed from individual spat and any soft tissue was removed using forceps and scalpel. The separated shell valves sat in 100% ethanol overnight to assist with removal of tissue remains, then were rinsed with DI water, dried at room temperature for 2-3 hours and finished drying in a low-temperature vacuum oven at 45 degrees Celsius (°C) and 25 millimeters of mercury (Hg mm) for 2 hours. The shell valves were then mounted and polished following standard techniques (Prezant et al. 2022). Each valve was placed in a 32-millimeter (mm) mounting cup, with the ventral edge of the shell affixed to the base of the cup using a coil mounting clip that had been glued to the bottom of the cup. This was left to dry overnight, before mounting with Bisphenol A Epichlorohydrin epoxy and hardener mixed in a 10:3 ratio (Allied High Tech). After the epoxy hardened for 24 hours, the mounted valves were removed from their mounting cups and ground to a plane that was visually approximated near the center of the shell running along the longest axis from anterior to posterior end. The shell valves were then polished to 0.04 micrometers (µm) using polycrystalline diamond solution and colloidal silica suspension (Allied High Tech).</p>
<p>Panoramic images of each shell sample were taken under polarized light using a reflected light microscope (Zeiss Axioscope.A1 with a Zeiss, AxioCam 105 color camera), with the analyzer set to 10°. Panoramas were constructed using imaging software (Zeiss Zen 3.8). Four-week-old spat valves were imaged under a 5x objective, and eight-week-old spat valves were imaged under a 2.5x objective.</p>
<p><strong>Determining Shell Thickness:</strong><br />
Measurements of the thickness of the foliated layer, prismatic layer, and total shell thickness took place in ImageJ - FIJI 1.54f (Schindelin et al. 2012) for both four-week and eight-week-old oysters of both induction states. Panoramic images had a grid placed over them (100 µm² for four-week-old, and 200 µm² for eight-week old) and images were divided approximately into thirds. All thickness measurements were taken from the middle third of the shell valve, with one measurement each for the foliated layer, prismatic layer, and total thickness within each grid square (n = 19-31 per four-week-old shell, and n = 16-22 measurements per eight-week-old shell, depending on overall spat size). Grid measurements were averaged to yield a single thickness value for each layer of each shell sample.</p>
Specified by the Principal Investigator(s)
<p>Images panoramas were created in Zeiss Zen 3.8 and shell thickness measurements were collected using Fiji Is Just ImageJ (FIJI) 1.54f. Data were recorded in Microsoft Excel.</p>
Specified by the Principal Investigator(s)
- Imported both data sheets (8 weeks and 4 weeks) from the original file "Raw Shell Thickness Measurements.xlsx" into the BCO-DMO system.
- Concatenated data sheets into a single data file, adding column for Age_Group.
- Filled in empty rows in the "Grid_Num" column.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "939528_v1_oyster_shell_thickness.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
Zeiss AxioCam 105 color camera
Zeiss AxioCam 105 color camera
PI Supplied Instrument Name: Zeiss AxioCam 105 color camera 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/
Zeiss Axioscope
Zeiss Axioscope
PI Supplied Instrument Name: Zeiss Axioscope 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/