http://lod.bco-dmo.org/id/dataset/918220 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 2024-01-22 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests 2024-01-22 publication 2024-01-22 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2024-01-24 publication https://doi.org/10.26008/1912/bco-dmo.918220.1 Andrew Baker University of Miami Rosenstiel School of Marine and Atmospheric Science principalInvestigator Ross Cunning 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: Buzzoni, D., Cunning, R., Baker, A. (2024) Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-01-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.918220.1 [access date] qPCR assays Dataset Description: Methods and Sampling: &lt;p&gt;Coral cores of 2.5-centimeter (cm) diameter were collected from tagged colonies of three coral species in either April 2019 or October 2019 from Emerald Reef in Southeast Florida, USA. Cores were then maintained in 300-liter (L) indoor flow-through aquaria (in the Marine Technology and Life Science Seawater complex at the University of Miami's Rosenstiel School of Marine, Atmospheric, and Earth Science) and subjected to experimental heat stress. Before, during, and following the heat stress, 2-millimeter (mm) tissue samples were collected from cores and genomic DNA was subsequently extracted from these samples as per Cunning &amp;amp; Baker (2016). Quantitative PCR was performed using Taqman Environmental Master Mix and symbiont genus-specific and coral species-specific primers and probes targeting the actin gene (Cunning &amp;amp; Baker, 2013; Cunning et al., 2015). In addition to collecting tissue samples, the photochemical efficiency of symbionts within coral cores was also assayed before, during, and after heat stress using an imaging-PAM fluorometer.&lt;/p&gt; &lt;p&gt;Full methodology described in Buzzoni, et al. (2023) (DOI: &lt;a href=&quot;http://dx.doi.org/10.1007/s00338-023-02428-x&quot; target=&quot;_blank&quot;&gt;10.1007/s00338-023-02428-x&lt;/a&gt;)&lt;/p&gt; 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 completed 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 Ross Cunning Shedd Aquarium 312-692-2755 1200 South Lake Shore Drive Chicago IL 60605-2402 US rcunning@sheddaquarium.org pointOfContact asNeeded Dataset Version: 1 Unknown Species Treatment Core Collection_Latitude Collection_Longitude Timepoint Sym_Host Y2 PropD Batch Date Colony submersible drill imaging pulse amplitude modulated (PAM) fluorometer QuantStudio3 real-time PCR system theme None, User defined species scientific name (binomial) treatment sample identification latitude longitude time_point ratio quantum yield sample description date featureType BCO-DMO Standard Parameters Drill Fluorometer 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 -80.1005 -80.0974 25.6773 25.6788 2019-05-22 2020-03-05 Coral reefs of the Caribbean and Western Atlantic 0 BCO-DMO catalogue of parameters from Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests 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/918238.rdf Name: Species Units: unitless Description: <p>Coral host species (M. cavernosa, O. faveolata or S. siderea)</p> http://lod.bco-dmo.org/id/dataset-parameter/918239.rdf Name: Treatment Units: unitless Description: <p>Experimental heat stress treatment that core was assigned to (Bleached or Control)</p> http://lod.bco-dmo.org/id/dataset-parameter/918240.rdf Name: Core Units: unitless Description: <p>Unique identifier of each 2.5 cm coral core (&#039;coral species&#039;-&#039;colony tag&#039;-&#039;core tag&#039;)</p> http://lod.bco-dmo.org/id/dataset-parameter/918241.rdf Name: Collection_Latitude Units: decimal degrees Description: <p>Latitude of parent collection from which cores were collected; positive values = North</p> http://lod.bco-dmo.org/id/dataset-parameter/918242.rdf Name: Collection_Longitude Units: decimal degrees Description: <p>Longitude of parent collection from which cores were collected; negative values = West</p> http://lod.bco-dmo.org/id/dataset-parameter/918243.rdf Name: Timepoint Units: unitless Description: <p>Context of the time tissue sample or IPAM measurement was taken with respect to the experimental heat stress (Pre-bleach, Post-bleach, Recovery, or Pre-outplant)</p> http://lod.bco-dmo.org/id/dataset-parameter/918244.rdf Name: Sym_Host Units: unitless Description: <p>In each tissue sample, the ratio of symbiont (the sum of Breviolum, Cladocopium and Durusdinium) cells to host coral cells, calculated using the StepOneR package (see methods for details) from technical replicates of qPCR target-specific Ct values (to 9 decimal places)</p> http://lod.bco-dmo.org/id/dataset-parameter/918245.rdf Name: Y2 Units: unitless Description: <p>Maximum quantum yield of symbionts&#039; PSII of a coral core, as detected by I-PAM fluorometer (to 3 decimal places)</p> http://lod.bco-dmo.org/id/dataset-parameter/918246.rdf Name: PropD Units: unitless Description: <p>In each tissue sample, the ratio of Durusdinium to total symbiont (the sum of Breviolum, Cladocopium and Durusdinium) cells, calculated using the StepOneR package (see methods for details) from technical replicates of qPCR target-specific Ct values (to 9 decimal places)</p> http://lod.bco-dmo.org/id/dataset-parameter/918247.rdf Name: Batch Units: unitless Description: <p>Denotes whether core was collected and heat stressed in either April 2019 (1) or October 2019 (2)</p> http://lod.bco-dmo.org/id/dataset-parameter/918248.rdf Name: Date Units: unitless Description: <p>Date tissue sample/ IPAM measurement was taken in the format YYYY-MM-DD (Eastern Standard Time)</p> http://lod.bco-dmo.org/id/dataset-parameter/918249.rdf Name: Colony Units: unitless Description: <p>Tag number of field colony from which cores were extracted (2, 3, 4, 13, 16, 18, 19, 21, 22, 23, 26, 27, 28, 34, 35, 36, 39, 41, 48, 62, 64, 65, 66, 67, 68, 71, 72, 81, 87, 100)</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 43066 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/02db39c1-4a1b-4c18-aff4-6fa1a97a405d/content download https://doi.org/10.26008/1912/bco-dmo.918220.1 download onLine dataset &lt;p&gt;Coral cores of 2.5-centimeter (cm) diameter were collected from tagged colonies of three coral species in either April 2019 or October 2019 from Emerald Reef in Southeast Florida, USA. Cores were then maintained in 300-liter (L) indoor flow-through aquaria (in the Marine Technology and Life Science Seawater complex at the University of Miami's Rosenstiel School of Marine, Atmospheric, and Earth Science) and subjected to experimental heat stress. Before, during, and following the heat stress, 2-millimeter (mm) tissue samples were collected from cores and genomic DNA was subsequently extracted from these samples as per Cunning &amp;amp; Baker (2016). Quantitative PCR was performed using Taqman Environmental Master Mix and symbiont genus-specific and coral species-specific primers and probes targeting the actin gene (Cunning &amp;amp; Baker, 2013; Cunning et al., 2015). In addition to collecting tissue samples, the photochemical efficiency of symbionts within coral cores was also assayed before, during, and after heat stress using an imaging-PAM fluorometer.&lt;/p&gt; &lt;p&gt;Full methodology described in Buzzoni, et al. (2023) (DOI: &lt;a href=&quot;http://dx.doi.org/10.1007/s00338-023-02428-x&quot; target=&quot;_blank&quot;&gt;10.1007/s00338-023-02428-x&lt;/a&gt;)&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;All imaging-PAM and qPCR data were analysed in RStudio V4.2.1 (R Core Team, 2022). qPCR data were filtered to exclude samples lacking two technical replicates which amplified with Ct values under 40. Ct data were used to calculate the relative abundances of symbiont genera in tissue samples (relative to all Symbiodiniaceae present and relative to coral host cells) using the stepOneR package (Cunning, 2018). Ct data were also adjusted for differences between symbiont genera and coral species in target locus copy number, DNA extraction efficiency, and probe fluorescence intensity.&lt;/p&gt; &lt;p&gt;The Supplemental File &quot;Ct_corrections_table.pdf&quot; contains correction coefficients fed into StepOneR software along with qPCR Ct data. These correct for differences in host and symbiont DNA extraction efficiency and gene copy number, and for differences in fluorescence of target-specific probes.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file &quot;qPCR_IPAM.csv&quot; into the BCO-DMO system. - Flagged &quot;NA&quot; as a missing data identifier (missing data are empty/blank in the final CSV file). - Converted latitude and longitude values to decimal degrees and rounded to 4 decimal places. - Converted the date column to YYYY-MM-DD format. - Replaced the abbreviated species name with the full genus + species name. - Renamed fields/columns to comply with BCO-DMO naming conventions. - Saved the final file as &quot;918220_v1_qpcr_ipam.csv&quot;. 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 submersible drill submersible drill PI Supplied Instrument Name: submersible drill PI Supplied Instrument Description:Coral cores were extracted from reef colonies using a submersible drill (Nemo Power Tools Ltd.) fitted with a diamond core drill bit (Montana Brand Tools). Instrument Name: Drill Instrument Short Name: Instrument Description: A drill is a tool used for making round holes or driving fasteners. There are many types of drills: some are powered manually, and others use electricity (electric drill) or compressed air as the motive power. Drills with a percussive action (hammer drills) are mostly used in hard materials such as masonry (brick, concrete, and stone) or rock. Some types of hand-held drills are also used to drive screws and other fasteners. imaging pulse amplitude modulated (PAM) fluorometer imaging pulse amplitude modulated (PAM) fluorometer PI Supplied Instrument Name: imaging pulse amplitude modulated (PAM) fluorometer PI Supplied Instrument Description:Photochemical efficiency was calculated using measurements from an imaging pulse amplitude modulated fluorometer (MAXI Version IMAGING-PAM M-Series, Walz, Effeltrich, Germany). 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/ QuantStudio3 real-time PCR system QuantStudio3 real-time PCR system PI Supplied Instrument Name: QuantStudio3 real-time PCR system PI Supplied Instrument Description:qPCR was performed using a QuantStudio3 real-time PCR system (Applied Biosystems). 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).