http://lod.bco-dmo.org/id/dataset/920837
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
2024-03-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Proportions of healthy, pale, bleached, and dead Orbicella faveolata recruits over time during a heat stress laboratory experiment conducted in 2018 and 2019, corresponding to proportions of different symbiont genera hosted
2024-03-04
publication
2024-03-04
revision
BCO-DMO Linked Data URI
2024-03-04
creation
http://lod.bco-dmo.org/id/dataset/920837
Olivia Williamson
University of Miami Rosenstiel School of Marine and Atmospheric Science
principalInvestigator
Andrew Baker
University of Miami Rosenstiel School of Marine and Atmospheric Science
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: Williamson, O., Baker, A. (2024) Proportions of healthy, pale, bleached, and dead Orbicella faveolata recruits over time during a heat stress laboratory experiment conducted in 2018 and 2019, corresponding to proportions of different symbiont genera hosted. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-03-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/920837 [access date]
Methods and Sampling: <p>This section includes methodology for several related treatments and experiments conducted in the course of research&nbsp;presented in Williamson et al. (2021).&nbsp; &nbsp;Each BCO-DMO page provides access to one of these datasets, see the "Related Datasets" section for access to all related datasets.<br />
<br />
Parents of recruits used in this study were located on Horseshoe Reef in Key Largo, FL at 5 - 8 meters depth.<br />
<br />
<strong>Symbiont uptake experiment</strong>&nbsp;&nbsp;(see related dataset&nbsp;"Recruit survivorship and symbiont acquisition" https://www.bco-dmo.org/dataset/920853)</p>
<p>Throughout symbiont uptake period, a dissecting microscope was used to count the number of: (1) surviving recruits and (2) recruits visibly infected with symbionts. When infection was first observed in all aquaria (day 21) and again after 60&nbsp;days in their treatments, three to five recruits from each aquarium were sacrificed using a razor blade. To standardize sampling, only solitary polyps not clumped with others were sacrificed. Sacrificed recruits were placed in individual 1.5-mL microcentrifuge tubes with 200&nbsp;μL of 1% SDS + DNAB and incubated at 65&nbsp;°C for one hour. Genomic DNA was extracted from SDS archives following modified organic extraction methods (Rowan and Powers&nbsp;1991; Baker and Cunning&nbsp;2016).</p>
<p><strong>Growth and symbiont density&nbsp;</strong>(see related dataset "Recruit area measurements" https://www.bco-dmo.org/dataset/920846)</p>
<p>Five months (150&nbsp;days) after settlement, a random sample of recruits from each of the four original treatments was photographed under a dissecting microscope with QCapture Suite Plus. Only solitary polyps were photographed to maximize accuracy of area measurements. ImageJ was used to calculate recruit skeletal area in mm2. A subset of the photographed recruits was then sacrificed to measure symbiont identity and density at the time of growth measurements.</p>
<p><strong>Heat stress experiment&nbsp;</strong>(data included in this dataset)</p>
<p>A subset of plugs with each symbiont type were placed into new aquaria, where temperature was increased from 22 to 28&nbsp;°C over six days, and then to 32&nbsp;°C over 48&nbsp;h. At this point, all recruits (n = 66) were infected with symbionts. About half the recruits (n = 32) were pre-exposed to mild heat stress (reared at 31&nbsp;°C during Experiment 1), while the other half (n = 34) were naïve to heat stress (reared at 29&nbsp;°C). Temperature was maintained at 32&nbsp;°C for ten days, then raised to 33&nbsp;°C for ten days, then raised to 34&nbsp;°C for 40&nbsp;days. Every two to five days, recruits were scored as “healthy,” “pale,” “bleached,” or “dead” using a fluorescence microscope. After 60&nbsp;days, all remaining living recruits were sacrificed for symbiont community analysis.&nbsp;<br />
<br />
<strong>Recruit PCR (qPCR) data&nbsp;</strong>&nbsp;(see "Recruit qPCR data" https://www.bco-dmo.org/dataset/920860)<br />
<br />
Quantitative PCR (qPCR) assays were used to identify Symbiodiniaceae to genus level and quantify symbiont-to-host (S:H) cell ratios for each recruit sampled. Since O. faveolata commonly hosts members of Symbiodinium, Breviolum, Cladocopium, and Durusdinium (Kemp et al. 2015), assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA). Assays for O. faveolata, Symbiodinium, and Breviolum followed reactions described in Cunning and Baker (2013), whereas Cladocopium and Durusdinium assays were multiplexed as described in Cunning et al. (2015).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851392 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851392
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851305 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851305
onGoing
Olivia Williamson
University of Miami Rosenstiel School of Marine and Atmospheric Science
9782706041
omw10@miami.edu
pointOfContact
Andrew Baker
University of Miami Rosenstiel School of Marine and Atmospheric Science
(305) 421-4642
University of Miami Rosenstiel School of Marine and Atmospheric Science 600 Rickenbacker Cswy.
Miami
FL
33149
USA
abaker@earth.miami.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date
Day
Temp
Tank
Adult
Alive
Symb
Pale
Bleached
Surv
Propsymb
Proppale
Propbleached
D_range
A_range
B_range
QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA)
theme
None, User defined
date
time_elapsed
site description
tank
sample description
count
featureType
BCO-DMO Standard Parameters
qPCR Thermal Cycler
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: Assessing the changing symbiotic milieu on Caribbean coral reefs under climate change: magnitude, tradeoffs, interventions, and implications
https://osprey.bco-dmo.org/project/817973
Collaborative Research: Assessing the changing symbiotic milieu on Caribbean coral reefs under climate change: magnitude, tradeoffs, interventions, and implications
<p><em>NSF Award Abstract:</em><br />
Climate change represents an existential threat to coral reef ecosystems worldwide, with coral bleaching driven by continued ocean warming presenting the most pressing challenge to the persistence of these ecosystems over the next few decades. Given the severity and urgency of this threat it is critical to investigate mechanisms by which some corals might survive warming, assess the degree to which this is happening on reefs, and apply these discoveries to inform conservation interventions that might improve survival trajectories wherever possible. This project aims to fulfill these objectives by testing whether reef corals in the Caribbean are undergoing shifts in their algal symbionts in favor of more heat-tolerant types, what the consequences of these shifts might be for coral reef ecosystems, and the way in which we might use this information to help conserve them. Scientific objectives will be leveraged to improve the effectiveness of reef restoration efforts in the Caribbean by applying findings to ongoing intervention trials which aim to seed outplanted corals (both adult fragments raised in nurseries, and sexually derived coral recruits) with heat tolerant algae that are climate-resistant. It also takes advantage of emerging opportunities at two major public aquariums to highlight the plight of coral reefs to engaged public audiences primed to receive this message and learn about the role of science in both understanding and mitigating the problem. Finally, numerous high school, undergraduate, and graduate students will receive mentorship during this project, helping to train the next generation of marine scientists.</p>
<p>This project tests whether continued climate warming is causing heat-tolerant algal symbionts (such as <em>Durusdinium trenchii</em>) to become increasingly common on coral reefs in the Caribbean. Understanding the changing symbiotic "milieu" in the region, the processes underlying the spread of <em>D. trenchii</em>, and the consequences of this spread, are very timely questions that have the potential to help us understand future reef states. This project will: (1) Manipulate coral symbioses in the laboratory, including a number of Caribbean coral species never before attempted, to assess in a standardized way their relative ability to acquire heat-tolerant symbionts; (2) Outplant corals with manipulated symbiont communities to reefs to assess real-world ecophysiological tradeoffs to heat tolerance, such as reduced growth rate; (3) Introduce heat-tolerant symbionts to coral colonies in the field using tissue implants in order to understand environmental controls on the persistence or loss of introduced symbionts; (4) Evaluate transgenerational feedbacks in the symbiotic milieu by investigating the roles of temperature and <em>D. trenchii</em> availability on the acquisition and establishment of these symbionts in newly settled coral larvae; and (5) Quantify changes in the incidence and relative abundance of heat-tolerant symbionts in the Caribbean over the last ~20 years using unique archived samples dating back to 1995-2002 from Florida, Bahamas, Belize, and Bermuda.</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>
Symbiont Shifts on Reefs
largerWorkCitation
project
eng; USA
oceans
-80.295
-80.295
25.1388
25.1388
2018-08-01
2019-05-01
Coral reefs of the Caribbean and Western Atlantic
0
BCO-DMO catalogue of parameters from Proportions of healthy, pale, bleached, and dead Orbicella faveolata recruits over time during a heat stress laboratory experiment conducted in 2018 and 2019, corresponding to proportions of different symbiont genera hosted
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/921867.rdf
Name: Date
Units: unitless
Description: <p>Date that scoring for health status was done (during Experiment 2), ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/921868.rdf
Name: Day
Units: days
Description: <p>Days under heat stress (number of days in elevated temperature treatment in "Experiment 2")</p>
http://lod.bco-dmo.org/id/dataset-parameter/921869.rdf
Name: Temp
Units: unitless
Description: <p>Temperature at which recruits had been previously reared - same as temperature treatment during symbiont uptake in "Experiment 1" (first ~60 days of life, either elevated [31C] or ambient [29C])</p>
http://lod.bco-dmo.org/id/dataset-parameter/921870.rdf
Name: Tank
Units: unitless
Description: <p>Tank identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/921871.rdf
Name: Adult
Units: unitless
Description: <p>Genus of symbiont that the O.faveolata adult donor colony in this tank hosted ("C" = Cladocopium or "D" = Durusdinium)</p>
http://lod.bco-dmo.org/id/dataset-parameter/921872.rdf
Name: Alive
Units: per recruit
Description: <p>Number of recruits alive on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921873.rdf
Name: Symb
Units: per recruit
Description: <p>Number of recruits in this tank that appeared healthy with full, normal symbiosis on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921874.rdf
Name: Pale
Units: per recruit
Description: <p>Number of recruits in this tank that were paling on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921875.rdf
Name: Bleached
Units: per recruit
Description: <p>Number of recruits in this tank that were bleached on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921876.rdf
Name: Surv
Units: unitless
Description: <p>Survivorship (proportion of recruits in this tank still alive on this day)</p>
http://lod.bco-dmo.org/id/dataset-parameter/921877.rdf
Name: Propsymb
Units: unitless
Description: <p>Proportion of recruits in this tank that appeared healthy with full, normal symbiosis on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921878.rdf
Name: Proppale
Units: unitless
Description: <p>Proportion of recruits in this tank that were paling on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921879.rdf
Name: Propbleached
Units: unitless
Description: <p>Proportion of recruits in this tank that were bleached on this day</p>
http://lod.bco-dmo.org/id/dataset-parameter/921880.rdf
Name: D_range
Units: unitless
Description: <p>Proportion D. trenchii hosted by recruits at the start of Experiment 2 (proportion range)</p>
http://lod.bco-dmo.org/id/dataset-parameter/921881.rdf
Name: A_range
Units: unitless
Description: <p>Proportion Symbiodinium (formerly clade A) hosted by recruits at the start of Experiment 2 (proportion range)</p>
http://lod.bco-dmo.org/id/dataset-parameter/921882.rdf
Name: B_range
Units: unitless
Description: <p>Proportion Breviolum hosted by recruits at the start of Experiment 2 (proportion range)</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/920837/data/download
download
onLine
dataset
<p>This section includes methodology for several related treatments and experiments conducted in the course of research&nbsp;presented in Williamson et al. (2021).&nbsp; &nbsp;Each BCO-DMO page provides access to one of these datasets, see the "Related Datasets" section for access to all related datasets.<br />
<br />
Parents of recruits used in this study were located on Horseshoe Reef in Key Largo, FL at 5 - 8 meters depth.<br />
<br />
<strong>Symbiont uptake experiment</strong>&nbsp;&nbsp;(see related dataset&nbsp;"Recruit survivorship and symbiont acquisition" https://www.bco-dmo.org/dataset/920853)</p>
<p>Throughout symbiont uptake period, a dissecting microscope was used to count the number of: (1) surviving recruits and (2) recruits visibly infected with symbionts. When infection was first observed in all aquaria (day 21) and again after 60&nbsp;days in their treatments, three to five recruits from each aquarium were sacrificed using a razor blade. To standardize sampling, only solitary polyps not clumped with others were sacrificed. Sacrificed recruits were placed in individual 1.5-mL microcentrifuge tubes with 200&nbsp;μL of 1% SDS + DNAB and incubated at 65&nbsp;°C for one hour. Genomic DNA was extracted from SDS archives following modified organic extraction methods (Rowan and Powers&nbsp;1991; Baker and Cunning&nbsp;2016).</p>
<p><strong>Growth and symbiont density&nbsp;</strong>(see related dataset "Recruit area measurements" https://www.bco-dmo.org/dataset/920846)</p>
<p>Five months (150&nbsp;days) after settlement, a random sample of recruits from each of the four original treatments was photographed under a dissecting microscope with QCapture Suite Plus. Only solitary polyps were photographed to maximize accuracy of area measurements. ImageJ was used to calculate recruit skeletal area in mm2. A subset of the photographed recruits was then sacrificed to measure symbiont identity and density at the time of growth measurements.</p>
<p><strong>Heat stress experiment&nbsp;</strong>(data included in this dataset)</p>
<p>A subset of plugs with each symbiont type were placed into new aquaria, where temperature was increased from 22 to 28&nbsp;°C over six days, and then to 32&nbsp;°C over 48&nbsp;h. At this point, all recruits (n = 66) were infected with symbionts. About half the recruits (n = 32) were pre-exposed to mild heat stress (reared at 31&nbsp;°C during Experiment 1), while the other half (n = 34) were naïve to heat stress (reared at 29&nbsp;°C). Temperature was maintained at 32&nbsp;°C for ten days, then raised to 33&nbsp;°C for ten days, then raised to 34&nbsp;°C for 40&nbsp;days. Every two to five days, recruits were scored as “healthy,” “pale,” “bleached,” or “dead” using a fluorescence microscope. After 60&nbsp;days, all remaining living recruits were sacrificed for symbiont community analysis.&nbsp;<br />
<br />
<strong>Recruit PCR (qPCR) data&nbsp;</strong>&nbsp;(see "Recruit qPCR data" https://www.bco-dmo.org/dataset/920860)<br />
<br />
Quantitative PCR (qPCR) assays were used to identify Symbiodiniaceae to genus level and quantify symbiont-to-host (S:H) cell ratios for each recruit sampled. Since O. faveolata commonly hosts members of Symbiodinium, Breviolum, Cladocopium, and Durusdinium (Kemp et al. 2015), assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA). Assays for O. faveolata, Symbiodinium, and Breviolum followed reactions described in Cunning and Baker (2013), whereas Cladocopium and Durusdinium assays were multiplexed as described in Cunning et al. (2015).&nbsp;</p>
Specified by the Principal Investigator(s)
* Submitted file "heat_stress_data.csv" was imported into the BCO-DMO data system for this dataset. "heat_bar_data.csv" was added as a supplemental file.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Date converted to ISO 8601 format
* Taxon ids for names used in metadata were matched on 2024-03-11 using the World Register of Marine Species (WoRMS) taxa match tool. Supplemental file taxon_ids.csv added.
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
QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA)
QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA)
PI Supplied Instrument Name: QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA) PI Supplied Instrument Description:For qPCR data, assays targeting specific actin loci for each genus were performed using a QuantStudio 3 Real-Time PCR Instrument (Applied Biosystems, USA). Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).