http://lod.bco-dmo.org/id/dataset/855439
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
2021-07-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019
2021-11-12
publication
2021-11-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-11-15
publication
https://doi.org/10.26008/1912/bco-dmo.855439.1
Ross Cunning
Shedd Aquarium
principalInvestigator
Katie Parker
Shedd Aquarium
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: Parker, K., Cunning, R. (2021) Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.855439.1 [access date]
Symbiont community structure in Orbicella faveolata Dataset Description: Methods and Sampling: <p>Tissue samples from colonies of <em>O. faveolata</em> were collected from Mermaid Reef and sensitive Sandy Cay Reef between 21 and 24 January 2019. Genomic DNA from each coral sample was extracted and assayed using qPCR targeting loci specific to <em>O. faveolata</em> and each of four symbiont genera (<em>Symbiodinium, Breviolum, Cladocopium, and Durusdinium</em>). All reactions were performed on a QuantStudio 3 Real-Time PCR system (Life Technologies, Foster City, CA, USA). The resulting cycle threshold (CT) values at a set threshold of delta Rn = 0.01 were used for data analysis.</p>
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
completed
Ross Cunning
Shedd Aquarium
312-692-2755
1200 South Lake Shore Drive
Chicago
IL
60605-2402
US
rcunning@sheddaquarium.org
pointOfContact
Katie Parker
Shedd Aquarium
312-692-2755
1200 South Lake Shore Drive
Chicago
IL
60605
USA
katep363@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_id
site
Latitude
Longitude
genus
species
colony_tag
colony_depth
date_sampled
A_CT_mean
B_CT_mean
C_CT_mean
D_CT_mean
Orb_CT_mean
A_CT_sd
B_CT_sd
C_CT_sd
D_CT_sd
Orb_CT_sd
A_Orb
B_Orb
C_Orb
D_Orb
theme
None, User defined
sample identification
site
latitude
longitude
genus
species scientific name (binomial)
number
depth
date
mean
standard deviation
ratio
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
-77.0535
-76.989
26.3989
26.5536
2019-01-24
2019-01-24
Coral reefs of the Caribbean and Western Atlantic
0
BCO-DMO catalogue of parameters from Symbiont community structure in Orbicella faveolata from Mermaid Reef and Sandy Cay Reef in Abaco, The Bahamas in January 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/864752.rdf
Name: sample_id
Units: unitless
Description: <p>unique identifier for samples of each coral colony</p>
http://lod.bco-dmo.org/id/dataset-parameter/864753.rdf
Name: site
Units: unitless
Description: <p>reef site location of coral colony</p>
http://lod.bco-dmo.org/id/dataset-parameter/864754.rdf
Name: Latitude
Units: decimal degrees
Description: <p>location of sample site</p>
http://lod.bco-dmo.org/id/dataset-parameter/864755.rdf
Name: Longitude
Units: decimal degrees
Description: <p>location of sample site</p>
http://lod.bco-dmo.org/id/dataset-parameter/864756.rdf
Name: genus
Units: unitless
Description: <p>coral colony genus</p>
http://lod.bco-dmo.org/id/dataset-parameter/864757.rdf
Name: species
Units: unitless
Description: <p>coral colony species</p>
http://lod.bco-dmo.org/id/dataset-parameter/864758.rdf
Name: colony_tag
Units: unitless
Description: <p>number on tag affixed to coral colony in the field</p>
http://lod.bco-dmo.org/id/dataset-parameter/864759.rdf
Name: colony_depth
Units: meters
Description: <p>depth of sampled coral colony on the reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/864760.rdf
Name: date_sampled
Units: unitless
Description: <p>date that the coral sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/864761.rdf
Name: A_CT_mean
Units: cycles
Description: <p>qPCR cycle threshold value for Symbiodinium (clade A) assay, mean of technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864762.rdf
Name: B_CT_mean
Units: cycles
Description: <p>qPCR cycle threshold value for Breviolum (clade B) assay, mean of technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864763.rdf
Name: C_CT_mean
Units: cycles
Description: <p>qPCR cycle threshold value for Cladocopium (clade C) assay, mean of technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864764.rdf
Name: D_CT_mean
Units: cycles
Description: <p>qPCR cycle threshold value for Durusdinium (clade D) assay, mean of technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864765.rdf
Name: Orb_CT_mean
Units: cycles
Description: <p>qPCR cycle threshold value for Orbicella assay, mean of technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864766.rdf
Name: A_CT_sd
Units: cycles
Description: <p>Standard deviation of cycle threshold values for Symbiodinium (clade A) assay technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864767.rdf
Name: B_CT_sd
Units: cycles
Description: <p>Standard deviation of cycle threshold values for Breviolum (clade B) assay technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864768.rdf
Name: C_CT_sd
Units: cycles
Description: <p>Standard deviation of cycle threshold values for Cladocopium (clade C) assay technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864769.rdf
Name: D_CT_sd
Units: cycles
Description: <p>Standard deviation of cycle threshold values for Durusdinium (clade D) assay technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864770.rdf
Name: Orb_CT_sd
Units: cycles
Description: <p>Standard deviation of cycle threshold values for Orbicella assay technical replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/864771.rdf
Name: A_Orb
Units: unitless
Description: <p>Symbiodinium symbiont to host ratio calculated from qPCR assays</p>
http://lod.bco-dmo.org/id/dataset-parameter/864772.rdf
Name: B_Orb
Units: unitless
Description: <p>Breviolum symbiont to host ratio calculated from qPCR assays</p>
http://lod.bco-dmo.org/id/dataset-parameter/864773.rdf
Name: C_Orb
Units: unitless
Description: <p>Cladocopium symbiont to host ratio calculated from qPCR assays</p>
http://lod.bco-dmo.org/id/dataset-parameter/864774.rdf
Name: D_Orb
Units: unitless
Description: <p>Durusdinium symbiont to host ratio calculated from qPCR assays</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
13502
https://darchive.mblwhoilibrary.org/bitstream/1912/27760/1/dataset-855439_symbiont-community-structure-orbicella-faveolata__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.855439.1
download
onLine
dataset
<p>Tissue samples from colonies of <em>O. faveolata</em> were collected from Mermaid Reef and sensitive Sandy Cay Reef between 21 and 24 January 2019. Genomic DNA from each coral sample was extracted and assayed using qPCR targeting loci specific to <em>O. faveolata</em> and each of four symbiont genera (<em>Symbiodinium, Breviolum, Cladocopium, and Durusdinium</em>). All reactions were performed on a QuantStudio 3 Real-Time PCR system (Life Technologies, Foster City, CA, USA). The resulting cycle threshold (CT) values at a set threshold of delta Rn = 0.01 were used for data analysis.</p>
Specified by the Principal Investigator(s)
<p>Cycle threshold (CT) data were imported into R v3.6.0 using the steponeR package (Cunning 2018). Symbiont to host cell ratios for each algal symbiont genus were calculated adjusting for differences in target locus copy number, DNA extraction efficiency, and probe fluorescence intensity following Cunning &amp; Baker (2013) and converted to relative abundance within each sample.</p>
<p>This dataset was generated using code available at Zenodo DOI <a href="http://dx.doi.org/10.5281/zenodo.3827500" target="_blank">10.5281/zenodo.3827500</a>, which contains code for amplicon sequencing data QA/QC, dada2 ASV generation and taxonomic assignment, phyloseq analysis and removal of chloroplast and mitochondrial ASVs, visualization of taxonomic data, and diversity estimates using breakaway and divnet.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;<br />
- Missing data identifiers "NA" and "NAN" replaced with 'nd' (BCO-DMO's default missing data identifier);<br />
- Changed dates incorrectly entered as "2019-01-21" to "2019-01-24";<br />
- Added columns for Latitude and Longitude;<br />
- Added a conventional header with dataset name, PI names, version date.</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
PI Supplied Instrument Name: 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).