http://lod.bco-dmo.org/id/dataset/939332
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
2024-10-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Oyster shell hardness from study of eastern oysters (Crassostrea virginica) grown in a nursery with or without exposure to chemical cues from blue crabs
2024-10-22
publication
2024-10-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-22
publication
https://doi.org/10.26008/1912/bco-dmo.939332.1
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: Roney, S. H., Dickinson, G. H., Belgrad, B. A., Weissburg, M. (2024) Oyster shell hardness 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 2024-10-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.939332.1 [access date]
Predator Induced and Non-Induced Eastern Oyster Shell Hardness 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.</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 Microhardness:</strong><br />
Microhardness testing was performed with a Mitutoyo HM-200 microhardness testing machine. Hardness was measured as an average of 10 indents per shell layer conducted on each shell sample, spaced approximately evenly across the middle third region of the shell (200 to 700 µm apart, depending on the size of each shell). All indents were performed with a 5 g load with a 5-second approach time, 5-second dwelling time, and 5-second unload time. An image of each indent was taken using a Zeiss Axiocam 305 color microscope and the diagonals of each indent (µm) were measured using Zeiss Zen 3.6 Blue edition software. The Vickers Microhardness Number (VHN) was determined as 1.8543 F/d2, where F is force (kilograms (kg)) and d is diagonal length (mm), as described by the American Society for Testing and Materials (ASTM Designation C1327-15R19, 2019). During image analysis, we also recorded the number of cracks and the length of the longest crack emanating from each Vickers microhardness indentation. Crack length (µm) was measured by placing a circle at the centermost point of the Vickers microhardness indentation and measuring circle radius to the end of the longest crack whose source could be traced back to the indentation (Anstis et al. 1981; Baldassarri et al. 2008).</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
Layer
ID
Test_Num
Before_Image
After_Image
Width
D1
D2
Avg
avgD
Force
HV
Crack_Length
Num_cracks
Zeiss AxioCam 105 color camera
Zeiss Axioscope
theme
None, User defined
sample description
sample identification
number of replicates
width
length
mass
shell hardness
number
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
biota
oceans
2023-03-01
2023-12-31
Wassaw Sound, GA, US and Dauphin Island, AL
0
BCO-DMO catalogue of parameters from Oyster shell hardness 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/940714.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/940715.rdf
Name: Layer
Units: unitless
Description: <p>shell layer (foliated or prismatic)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940716.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 is induced and N is non-induced</p>
http://lod.bco-dmo.org/id/dataset-parameter/940717.rdf
Name: Test_Num
Units: unitless
Description: <p>the number of technical replicates per shell sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940718.rdf
Name: Before_Image
Units: unitless
Description: <p>image number of pre-test location picture on shell</p>
http://lod.bco-dmo.org/id/dataset-parameter/940719.rdf
Name: After_Image
Units: unitless
Description: <p>image number of post-test location picture of shell</p>
http://lod.bco-dmo.org/id/dataset-parameter/940720.rdf
Name: Width
Units: millimeters (mm)
Description: <p>overall width (hinge to growing edge) of shell sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940721.rdf
Name: D1
Units: micrometers (um)
Description: <p>measured length in micrometers of first diagonal on microhardness indent</p>
http://lod.bco-dmo.org/id/dataset-parameter/940722.rdf
Name: D2
Units: micrometers (um)
Description: <p>measured length in micrometers of second diagonal on microhardness indent</p>
http://lod.bco-dmo.org/id/dataset-parameter/940723.rdf
Name: Avg
Units: micrometers (um)
Description: <p>average of two diagonal measurements in micrometers</p>
http://lod.bco-dmo.org/id/dataset-parameter/940724.rdf
Name: avgD
Units: millimeters (mm)
Description: <p>conversion of average diagonal measurement to millimeters</p>
http://lod.bco-dmo.org/id/dataset-parameter/940725.rdf
Name: Force
Units: kilograms (kg)
Description: <p>force of the testing load applied to shell sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940726.rdf
Name: HV
Units: ?
Description: <p>Vickers Hardness Value calculated as 1.854*(load force/average diagonal measurements^2) according to ASTM Designation C1327–15R19 2019</p>
http://lod.bco-dmo.org/id/dataset-parameter/940727.rdf
Name: Crack_Length
Units: ?
Description: <p>length of cracks emanating from each indentation</p>
http://lod.bco-dmo.org/id/dataset-parameter/940728.rdf
Name: Num_cracks
Units: unitless
Description: <p>number of cracks emanating from each indentation</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
79395
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/ed089707-ed37-4062-a6fa-d2260dca96b3/content
download
https://doi.org/10.26008/1912/bco-dmo.939332.1
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.</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 Microhardness:</strong><br />
Microhardness testing was performed with a Mitutoyo HM-200 microhardness testing machine. Hardness was measured as an average of 10 indents per shell layer conducted on each shell sample, spaced approximately evenly across the middle third region of the shell (200 to 700 µm apart, depending on the size of each shell). All indents were performed with a 5 g load with a 5-second approach time, 5-second dwelling time, and 5-second unload time. An image of each indent was taken using a Zeiss Axiocam 305 color microscope and the diagonals of each indent (µm) were measured using Zeiss Zen 3.6 Blue edition software. The Vickers Microhardness Number (VHN) was determined as 1.8543 F/d2, where F is force (kilograms (kg)) and d is diagonal length (mm), as described by the American Society for Testing and Materials (ASTM Designation C1327-15R19, 2019). During image analysis, we also recorded the number of cracks and the length of the longest crack emanating from each Vickers microhardness indentation. Crack length (µm) was measured by placing a circle at the centermost point of the Vickers microhardness indentation and measuring circle radius to the end of the longest crack whose source could be traced back to the indentation (Anstis et al. 1981; Baldassarri et al. 2008).</p>
Specified by the Principal Investigator(s)
<p>Shell images and crack measurements were collected in Zeiss Zen 3.6 Blue edition software and data was recorded in Microsoft Excel. As outlined in the ASTM standard (ASTM Designation C1327–15R19 2019), microhardness tests were removed from the analysis if the indent was kite-shaped, with one diagonal more than 10% larger than the other, or were indented into an unreliable position on the shell, such as between prisms or within an unacceptable range (less than 1x the average diagonal length) from the edge.</p>
Specified by the Principal Investigator(s)
Primary data file:
- Imported 4 data sheets ("cleaned data") from original file "Raw Microhardness Measurements.xlsx" into the BCO-DMO system.
- Marked "-" and "#VALUE!" as a missing data values (missing data are empty/blank in the final csv file).
- Concatenated data sheets into a single data file, adding columns for Age and Layer.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved final file as "939332_v1_oyster_shell_hardness.csv".
Supplemental data file:
- Imported 4 data sheets ("raw data") from original file "Raw Microhardness Measurements.xlsx" into the BCO-DMO system.
- Marked "-" and "NA" as missing data values (missing data are empty/blank in the final csv file).
- Concatenated data sheets into a single data file, adding columns for Age and Layer.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved final supplemental file as "939332_v1_oyster_shell_hardness_raw_data.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/