http://lod.bco-dmo.org/id/dataset/858150
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
2021-08-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physiological metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress
2021-08-11
publication
2021-08-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-08-11
publication
https://doi.org/10.26008/1912/bco-dmo.858150.1
Daniel J. Barshis
Old Dominion University
principalInvestigator
Mark E. Warner
University of Delaware
principalInvestigator
Nicolas R. Evensen
Old Dominion University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Evensen, N. R., Warner, M. E., Barshis, D. J. (2021) Physiological metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.858150.1 [access date]
Final Physiology Dataset Description: Methods and Sampling: <p>Multiple ramets of five genets of <em>Acropora hemprichii </em>and five genets of <em>Porites lobata</em> were collected from two sites (protected and exposed) used in two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a two-week prolonged heating experiment using the indoor aquarium system at the King Abdullah University of Science and Technology (KAUST) Coastal and Marine Resources laboratory. Physiological responses of the coral host and associated endosymbionts were measured during (Fv/Fm, and phosynthesis and respiration) and at the end of the experiments (Final: symbiont densities, host protein, and chlorophyll a concentrations per cell and per cm2). Experimental tanks were ramped up from the 32°C control treatment to temperature treatments reaching 35°C, 36.5°C, and 38°C over 3h in the CBASS, and temperature treatments reaching 33.5°C, 35°C, and 36.5°C in the prolonged experiment at rates of 0.5 and 1.5°C per day. Each temperature treatment contained two replicate tanks (A and B).</p>
<p>Corals were subjected to short-term (7h) acute thermal profiles with four peak target temperatures (32°C, 35°C, 36.5°C, and 38°C), versus more prolonged heat exposures lasting 7 to 15 days, where temperatures were raised 0.5 and 1.5°C per day to four target temperatures (32°C, 33.5°C, 35°C, and 36.5°C). Physiological response metrics were recorded during and at the end of the experiments.</p>
<p>This dataset includes the final physiological metrics from both experiments.</p>
<p><strong>Problem report</strong>:<br />
Missing data were samples that were not measured or that are missing due to sample mortality.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1833215 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1833215
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1833201 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1833201
completed
Daniel J. Barshis
Old Dominion University
757-683-3614
Dept of Biological Sciences MGB 110
Norfolk
VA
23529-0266
US
dbarshis@odu.edu
pointOfContact
Mark E. Warner
University of Delaware
302-645-4365
School of Marine Science and Policy 700 Pilottown Rd.
Lewes
DE
19958
USA
mwarner@udel.edu
pointOfContact
Nicolas R. Evensen
Old Dominion University
Department of Biological Sciences
Norfolk
VA
23529
USA
nevensen@odu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Species
Experiment
Ramp
Temperature
Treatment
Tank
Site
Genotype
Replicate
Sym_density
Pro
Chla_cell
Chla
Pulse amplitude-modulated (PAM) fluorometer (MINI-PAM, WALZ)
flow cytometer (BD LSRFortessa, BD Biosciences)
fiberoptic oxygen probes (FireSting O2, Pyroscience)
handheld homogenizer (Diax 900, Heidolph Instruments)
SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices)
3D scanner (HDI 120, LMI Technologies Inc.)
CBASS
theme
None, User defined
species
experiment type
treatment
water temperature
tank
site description
replicate
density
proteins
chlorophyll a
featureType
BCO-DMO Standard Parameters
Fluorometer
Flow Cytometer
Dissolved Oxygen Sensor
Aquarium
Homogenizer
plate reader
3D scanner
Coral Bleaching Automated Stress System
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.
EAGER: Collaborative Research: Bleaching phenotypes of acute vs. chronic coral bleaching susceptibility and resilience: towards a standardized coral resilience diagnostic
https://www.bco-dmo.org/project/776327
EAGER: Collaborative Research: Bleaching phenotypes of acute vs. chronic coral bleaching susceptibility and resilience: towards a standardized coral resilience diagnostic
<p><em>NSF Award Abstract:</em><br />
The past few years have seen an unprecedented amount of coral bleaching across the globe. Global bleaching events in 2015-17, severely impacting iconic coral reefs in places such as the Great Barrier Reef, Micronesia, Hawaiian Islands, and Caribbean, were the worst recorded in recent human history. When ocean temperatures rise, the symbiosis between reef-building corals and their photosynthetic algae deteriorates, many times resulting in widespread coral die-offs as corals can starve without their symbiotic partners to supply food. These widespread events can have drastic impacts on ocean health and biodiversity, as well as the communities that depend on reefs for fishing, tourism, and protection from storms. Importantly, some corals resist or recover from bleaching better than others. Such variability in coral response to ocean warming could be critical to reef survival in the future, yet the scientific community lacks any standardized diagnostics to rapidly assess bleaching tolerance limits. Here, we plan to: 1) develop a standardized, short-term exposure to assess bleaching limits (analogous to cardiac stress tests for humans), 2) design an experimental system capable of delivering a range of thermal treatments as an open-source, low-cost, highly-portable device that can be readily adapted for bleaching tests in a wide variety of coral habitats, and 3) disseminate the results, instructions, and technologies to the reef research and conservation community through a combination of hands-on workshops, online outreach materials, press releases, and open-access research publications. Widespread dissemination of project products will be achieved via hands-on demonstrations and workshops in key geographic areas (Middle East, Caribbean, and Indo-Pacific), with a focus on the assembly of the system and operation of the experimental assay using local corals. This project will train both graduate students and a postdoctoral researcher, and brings together a team of national and global researchers in a collaborative investigation to address the international problem of coral bleaching.</p>
<p>With each passing year, coral bleaching has shifted from an issue of serious sporadic concern to a critical widespread threat to reefs across the globe that is increasing in frequency and severity. However, during widespread bleaching events, some scattered corals and reef sections are able to survive better than others. Whether this is due to acclimatization or adaptation in thermal stress tolerance, this variability in response is critical to coral resilience to climate impacts. Currently, the scientific community lacks a standardized approach to rapidly assess coral thermal limits and identify resilient individuals or populations. Present day approaches range from observational surveys of natural bleaching and mortality, to multiple weeks of controlled chronic thermal exposure, to rapid, single or multi-day acute heat shocks. To what degree bleaching response varies across short-term versus longer-term experiments and how these responses compare to natural bleaching patterns is largely unknown. Using a group of coral species representative of a historical range of bleaching susceptibility (e.g., Acropora hemprichii, Pocillopora meandrina, and Porites lobata), research will address this important knowledge gap by experimental evaluation of the bleaching response to acute (0 - 2 day) versus chronic (>4 week) thermal stress. The overarching questions for this study are: how are the acute and chronic coral bleaching responses related, and can investigators predict ecologically relevant bleaching outcomes from the response to a short-term, acute heat-stress? To answer these questions, the research team will: 1) objectively compare acute versus chronic heat-stress exposures and synthesize a variety of response metrics based on core physiological measurements to develop a standardized, short-term thermal assay and diagnostic approach to rapidly assess bleaching, 2) operationalize an experimental system built around an open-source, cost-effective, easily transportable temperature control technology, and 3) distribute the results, experimental procedures, and temperature controlling technologies to the reef research and conservation communities. This project will produce an affordable experimental system and short-term diagnostic capable of determining coral thermal limits in just a few days in almost any location with reliable access to seawater and electricity or a portable generator. The research fills a critical knowledge gap through the development of a standardized set of diagnostic tools to assess coral thermal vulnerability before widespread bleaching events actually occur, so that proactive conservation and management strategies can be implemented ahead of widespread impacts to reef ecosystems.</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>
EAGER-CBASS
largerWorkCitation
project
eng; USA
oceans
39.113112
39.113112
22.275795
22.275795
2019-07-29
2019-08-11
Red Sea, Thuwal, Saudi Arabia, Eilat Israel
0
BCO-DMO catalogue of parameters from Physiological metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress
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/858166.rdf
Name: Species
Units: unitless
Description: species: Acropora or Porites
http://lod.bco-dmo.org/id/dataset-parameter/858167.rdf
Name: Experiment
Units: unitless
Description: experiment: CBASS = Coral Bleaching Automated Stress System; Prolonged = two-week prolonged heating experiment at the King Abdullah University of Science and Technology (KAUST)
http://lod.bco-dmo.org/id/dataset-parameter/858168.rdf
Name: Ramp
Units: unitless
Description: method of ramping up temperature
http://lod.bco-dmo.org/id/dataset-parameter/858169.rdf
Name: Temperature
Units: degrees Celsius
Description: temperature
http://lod.bco-dmo.org/id/dataset-parameter/858170.rdf
Name: Treatment
Units: unitless
Description: treatment
http://lod.bco-dmo.org/id/dataset-parameter/858171.rdf
Name: Tank
Units: unitless
Description: tank ID
http://lod.bco-dmo.org/id/dataset-parameter/858172.rdf
Name: Site
Units: unitless
Description: description of coral collection site: exposed or protected
http://lod.bco-dmo.org/id/dataset-parameter/858173.rdf
Name: Genotype
Units: unitless
Description: genotype
http://lod.bco-dmo.org/id/dataset-parameter/858174.rdf
Name: Replicate
Units: unitless
Description: replicate: each temperature treatment contained two replicate tanks (A and B)
http://lod.bco-dmo.org/id/dataset-parameter/858175.rdf
Name: Sym_density
Units: cells per square centimeter (cells per cm2)
Description: symbiont densities measured in each ramet, normalised to the surface area of the ramet
http://lod.bco-dmo.org/id/dataset-parameter/858176.rdf
Name: Pro
Units: milligrams per square centimeter (mg per cm2)
Description: animal protein concentrations extracted from each ramet, normalised to the surface area of the ramet
http://lod.bco-dmo.org/id/dataset-parameter/858177.rdf
Name: Chla_cell
Units: picograms per (pg per cell)
Description: chlorophyll a extracted from algal symbionts extracted in each ramet, normalised to number of symbiont cells in each ramet
http://lod.bco-dmo.org/id/dataset-parameter/858178.rdf
Name: Chla
Units: micrograms per square centimeter (ug per cm2)
Description: chlorophyll a extracted from algal symbionts extracted in each ramet, normalised to the surface area of the ramet
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
33477
https://darchive.mblwhoilibrary.org/bitstream/1912/27436/1/dataset-858150_final-physiology__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.858150.1
download
onLine
dataset
<p>Multiple ramets of five genets of <em>Acropora hemprichii </em>and five genets of <em>Porites lobata</em> were collected from two sites (protected and exposed) used in two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a two-week prolonged heating experiment using the indoor aquarium system at the King Abdullah University of Science and Technology (KAUST) Coastal and Marine Resources laboratory. Physiological responses of the coral host and associated endosymbionts were measured during (Fv/Fm, and phosynthesis and respiration) and at the end of the experiments (Final: symbiont densities, host protein, and chlorophyll a concentrations per cell and per cm2). Experimental tanks were ramped up from the 32°C control treatment to temperature treatments reaching 35°C, 36.5°C, and 38°C over 3h in the CBASS, and temperature treatments reaching 33.5°C, 35°C, and 36.5°C in the prolonged experiment at rates of 0.5 and 1.5°C per day. Each temperature treatment contained two replicate tanks (A and B).</p>
<p>Corals were subjected to short-term (7h) acute thermal profiles with four peak target temperatures (32°C, 35°C, 36.5°C, and 38°C), versus more prolonged heat exposures lasting 7 to 15 days, where temperatures were raised 0.5 and 1.5°C per day to four target temperatures (32°C, 33.5°C, 35°C, and 36.5°C). Physiological response metrics were recorded during and at the end of the experiments.</p>
<p>This dataset includes the final physiological metrics from both experiments.</p>
<p><strong>Problem report</strong>:<br />
Missing data were samples that were not measured or that are missing due to sample mortality.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:&nbsp;</strong><br />
Data were organised using R statistical software (version 4.0.3).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to comply with BCO-DMO naming conventions.</p>
<p>The originally submitted GitHub repository&nbsp;<a href="https://github.com/BarshisLab/Heating-Duration-vs-Intensity-vs-RampRate" target="_blank">https://github.com/BarshisLab/Heating-Duration-vs-Intensity-vs-RampRate</a>&nbsp;was forked to&nbsp;<a href="https://github.com/BCODMO/Heating-Duration-vs-Intensity-vs-RampRate" target="_blank">https://github.com/BCODMO/Heating-Duration-vs-Intensity-vs-RampRate</a>&nbsp;and tagged with release 1.0, which corresponds with this dataset submission. The original repository may have continued updates.</p>
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
Pulse amplitude-modulated (PAM) fluorometer (MINI-PAM, WALZ)
Pulse amplitude-modulated (PAM) fluorometer (MINI-PAM, WALZ)
PI Supplied Instrument Name: Pulse amplitude-modulated (PAM) fluorometer (MINI-PAM, WALZ) Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
flow cytometer (BD LSRFortessa, BD Biosciences)
flow cytometer (BD LSRFortessa, BD Biosciences)
PI Supplied Instrument Name: flow cytometer (BD LSRFortessa, BD Biosciences) Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
fiberoptic oxygen probes (FireSting O2, Pyroscience)
fiberoptic oxygen probes (FireSting O2, Pyroscience)
PI Supplied Instrument Name: fiberoptic oxygen probes (FireSting O2, Pyroscience) Instrument Name: Dissolved 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
PI Supplied Instrument Name: Instrument Name: Aquarium Instrument Short Name:Aquarium Instrument Description: Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
handheld homogenizer (Diax 900, Heidolph Instruments)
handheld homogenizer (Diax 900, Heidolph Instruments)
PI Supplied Instrument Name: handheld homogenizer (Diax 900, Heidolph Instruments) Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices)
SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices)
PI Supplied Instrument Name: SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
3D scanner (HDI 120, LMI Technologies Inc.)
3D scanner (HDI 120, LMI Technologies Inc.)
PI Supplied Instrument Name: 3D scanner (HDI 120, LMI Technologies Inc.) Instrument Name: 3D scanner Instrument Short Name: Instrument Description: A 3D scan captures digital information about the shape of an object with equipment that uses a laser or light to measure the distance between the scanner and the object.
CBASS
CBASS
PI Supplied Instrument Name: CBASS Instrument Name: Coral Bleaching Automated Stress System Instrument Short Name:CBASS Instrument Description: CBASS, which stands for "Coral Bleaching Automated Stress System", are portable, field-deployable experimental tanks used to apply rapid, acute heat stress challenges. This system is described in:
Voolstra, C. R., Buitrago‐López, C., Perna, G., Cárdenas, A., Hume, B. C. C., Rädecker, N., & Barshis, D. J. (2020). Standardized short‐term acute heat stress assays resolve historical differences in coral thermotolerance across microhabitat reef sites. Global Change Biology, 26(8), 4328-4343. Portico. https://doi.org/10.1111/gcb.15148