http://lod.bco-dmo.org/id/dataset/942962 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 2024-11-05 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Micromorphological analyses of Pocillopora damicornis calyxes collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021 2025-03-28 publication 2025-03-28 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-04-14 publication https://doi.org/10.26008/1912/bco-dmo.942962.1 Katie Barott University of Pennsylvania principalInvestigator Kristen Brown University of Queensland principalInvestigator Hollie Putnam University of Rhode Island 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: Brown, K., Dellaert, Z., Putnam, H., Barott, K. (2025) Micromorphological analyses of Pocillopora damicornis calyxes collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-03-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.942962.1 [access date] Pocillopora damicornis skeletal micromorphological analysis: Calyxes Dataset Description: Methods and Sampling: &lt;p&gt;&lt;strong&gt;Sample Collection&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The experiment was performed during the austral summer from mid-January to late March 2021 at Heron Island Research Station (HIRS), southern Great Barrier Reef (23 27°S, 151 55°E). Heron Reef is composed of five distinct geomorphological habitats characterized by diverse benthic communities and biogeochemical conditions. Fragments of the coral&amp;nbsp;P. damicornis&amp;nbsp;were collected from the reef flat and slope locations within the same depth range (1–3 m) on 14 and 15 January 2021.&amp;nbsp;Four fragments were collected from each individual colony (genetic clones), totalling 96 fragments from 24 colonies (n = 12 per habitat). For more information about sample collection methods and treatment, see&amp;nbsp;Brown et al., 2022.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Skeletal micromorphological analysis&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The limited amount of new CaCO3 deposition observed during the 8-week exposure (~15–30% for each fragment; (Brown et al., 2022)) precluded our resolution to detect changes in net calcification or CaCO3 density of newly formed skeleton that were attributable to experimental pCO2 treatment conditions. To better resolve changes in biomineralization resulting from the seawater pCO2 variability treatments, a total of 16 coral fragments (n=4 per origin per treatment) were selected for skeletal micromorphological analyses. All tissue was removed from the skeletons by soaking the fragments in 10% sodium hypochlorite for 24 hr, rinsing with deionized (DI) water, and drying. Areas of CaCO3 deposition that occurred during the experiment were identified by comparing images at the start and end of the 8-week experiment. These deposits of new CaCO3 were carefully chipped off of the experimental fragments using a razor blade and imaged using a scanning electron microscope (SEM; Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company). Using the SEM, fragments were imaged across scales with magnification maintained between samples: an overall view of the skeleton (56x), individual whole calyxes (124x), spine structures between (141x) and inside (164x) the calyxes, and the rapid accretion deposits (RADs) on the spines (1013x). Several features of interest previously used to investigate coral biomineralization (Scucchia et al., 2023; Scucchia, Malik, Zaslansky, et al., 2021) were quantified using ImageJ (v1.53c) (Schneider et al., 2012), including: number of corallites, distance between corallites (i.e., coenosteum width), corallite diameter, circularity of the corallite, number of spines within calyx, spine length and maximum spine width (on spines both between and inside the calyx), number of RADs, and size of RADs.&lt;/p&gt; &lt;p&gt;The significant interaction between treatment and origin was explored on all micromorphological features using linear mixed effects models, with colony as a random effect. The significance of fixed effects and their interactions was determined using an analysis of variance with a type III error structure using the Anova function in car package (Fox et al., 2012). Significant interactive effects were followed by pairwise comparison of estimate marginal means using the emmeans package with Tukey HSD adjusted p values (Lenth et al., 2018). Data were tested for homogeneity of variance and normality of distribution through graphical analyses of residual plots for all models. All statistical analyses were done using R version 4.0.3 software (R Core Team, 2020), and graphical representations were produced using the package ggplot2 (Wickham, 2016).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923743 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923743 completed Katie Barott University of Pennsylvania 215-746-6911 433 South University Avenue Leidy Laboratories 326 Philadelphia PA 19104 USA kbarott@sas.upenn.edu pointOfContact Kristen Brown University of Queensland 433 S University Ave Philadelphia PA 19104-4544 USA ktbrown@sas.upenn.edu pointOfContact Hollie Putnam University of Rhode Island 808-554-1462 120 Flagg Rd. Kingston RI 02881 USA hputnam@uri.edu pointOfContact asNeeded Dataset Version: 1 Unknown Origin Treatment Colony_ID Feature_of_interest Image_magnification Image_name Observer Replicate corallite_diameter corallite_distance Area Perimeter Circularity Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company theme None, User defined site description treatment sample description image_analysis file_name person name replicate diameter length area featureType BCO-DMO Standard Parameters Scanning Electron Microscope 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. Influence of environmental pH variability and thermal sensitivity on the resilience of reef-building corals to acidification stress https://osprey.bco-dmo.org/project/843347 Influence of environmental pH variability and thermal sensitivity on the resilience of reef-building corals to acidification stress <p><strong>NSF Award Abstract:</strong><br /> Coral reefs are incredibly diverse ecosystems that provide food, tourism revenue, and shoreline protection for coastal communities. The ability of coral reefs to continue providing these services to society is currently threatened by climate change, which has led to increasing ocean temperatures and acidity that can lead to the death of corals, the animals that build the reef framework upon which so many species depend. This project examines how temperature and acidification stress work together to influence the future health and survival of corals. The scientists are carrying out the project in Hawaii where they have found individual corals with different sensitivities to temperature stress that are living on reefs with different environmental pH conditions. This project improves understanding of how an individual coral's history influences its response to multiple stressors and helps identify the conditions that are most likely to support resilient coral communities. The project will generate extensive biological and physicochemical data that will be made freely available. Furthermore, this project supports the education and training of undergraduate and high school students and one postdoctoral researcher in marine science and coral reef ecology. Hands-on activities for high school students are being developed into a free online educational resource.</p> <p>This project compares coral responses to acidification stress in populations experiencing distinct pH dynamics (high diel variability vs. low diel variability) and with distinct thermal tolerances (historically bleaching sensitive vs. tolerant) to learn about how coral responses to these two factors differ between coral species and within populations. Experiments focus on the two dominant reef builders found at these stable and variable pH reefs: Montipora capitata and Porites compressa. Individuals of each species exhibiting different thermal sensitivities (i.e., bleached vs. pigmented) were tagged during the 2015 global coral bleaching event. This system tests the hypotheses that 1) corals living on reefs with larger diel pH fluctuations have greater resilience to acidification stress, 2) coral resilience to acidification is a plastic trait that can be promoted via acclimatization, and 3) thermally sensitive corals have reduced capacity to cope with pH stress, which is exacerbated at elevated temperatures. Coral cells isolated from colonies from each environmental and bleaching history are exposed to acute pH stress and examined for their ability to recover intracellular pH in vivo using confocal microscopy, and the expression level of proteins predicted to be involved in this recovery (e.g., proton transporters) is examined via Western blot and immunolocalization. Corals from each pH history are exposed to stable and variable seawater pH in a controlled aquarium setting to determine the level of plasticity of acidification resilience and to test for pH acclimatization in this system. Finally, corals with different levels of thermal sensitivity are exposed to thermal stress and recovery, and their ability to regulate pH is examined over time. The results of these experiments help identify reef conditions that promote coral resilience to ocean acidification against the background of increasingly common thermal stress events, while advancing mechanistic understanding of coral physiology and symbiosis.</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> Coral Resilience largerWorkCitation project eng; USA biota oceans 151.55 151.55 -23.27 -23.27 2021-01-06 2021-04-06 Kaneohe Bay, Oahu, HI; Heron Island, Queensland, Australia 0 BCO-DMO catalogue of parameters from Micromorphological analyses of Pocillopora damicornis calyxes collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021 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/957334.rdf Name: Origin Units: unitless Description: <p>Habitat of origin (flat v. slope)</p> http://lod.bco-dmo.org/id/dataset-parameter/957335.rdf Name: Treatment Units: unitless Description: <p>Treatment (pCO2 variability (stable v. variable))</p> http://lod.bco-dmo.org/id/dataset-parameter/957336.rdf Name: Colony_ID Units: unitless Description: <p>Colony ID</p> http://lod.bco-dmo.org/id/dataset-parameter/957337.rdf Name: Feature_of_interest Units: unitless Description: <p>Feature of interest (Macro (M), polyp (P), Spine in calyx (SC), Spine between calyx (SBC), Spine (S))</p> http://lod.bco-dmo.org/id/dataset-parameter/957338.rdf Name: Image_magnification Units: unitless Description: <p>Image magnification</p> http://lod.bco-dmo.org/id/dataset-parameter/957339.rdf Name: Image_name Units: unitless Description: <p>Image name</p> http://lod.bco-dmo.org/id/dataset-parameter/957340.rdf Name: Observer Units: unitless Description: <p>Observer</p> http://lod.bco-dmo.org/id/dataset-parameter/957341.rdf Name: Replicate Units: unitless Description: <p>Replicate</p> http://lod.bco-dmo.org/id/dataset-parameter/957342.rdf Name: corallite_diameter Units: micrometers (um) Description: <p>Corallite diameter</p> http://lod.bco-dmo.org/id/dataset-parameter/957343.rdf Name: corallite_distance Units: micrometers (um) Description: <p>Distance between corallites</p> http://lod.bco-dmo.org/id/dataset-parameter/957344.rdf Name: Area Units: micrometers (um) Description: <p>Area</p> http://lod.bco-dmo.org/id/dataset-parameter/957345.rdf Name: Perimeter Units: micrometers (um) Description: <p>Perimeter</p> http://lod.bco-dmo.org/id/dataset-parameter/957346.rdf Name: Circularity Units: unitless Description: <p>Circularity</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 30179 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4f557e98-fc62-4d11-a1c4-0fb49cc5d97a/content download https://doi.org/10.26008/1912/bco-dmo.942962.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Sample Collection&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The experiment was performed during the austral summer from mid-January to late March 2021 at Heron Island Research Station (HIRS), southern Great Barrier Reef (23 27°S, 151 55°E). Heron Reef is composed of five distinct geomorphological habitats characterized by diverse benthic communities and biogeochemical conditions. Fragments of the coral&amp;nbsp;P. damicornis&amp;nbsp;were collected from the reef flat and slope locations within the same depth range (1–3 m) on 14 and 15 January 2021.&amp;nbsp;Four fragments were collected from each individual colony (genetic clones), totalling 96 fragments from 24 colonies (n = 12 per habitat). For more information about sample collection methods and treatment, see&amp;nbsp;Brown et al., 2022.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Skeletal micromorphological analysis&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The limited amount of new CaCO3 deposition observed during the 8-week exposure (~15–30% for each fragment; (Brown et al., 2022)) precluded our resolution to detect changes in net calcification or CaCO3 density of newly formed skeleton that were attributable to experimental pCO2 treatment conditions. To better resolve changes in biomineralization resulting from the seawater pCO2 variability treatments, a total of 16 coral fragments (n=4 per origin per treatment) were selected for skeletal micromorphological analyses. All tissue was removed from the skeletons by soaking the fragments in 10% sodium hypochlorite for 24 hr, rinsing with deionized (DI) water, and drying. Areas of CaCO3 deposition that occurred during the experiment were identified by comparing images at the start and end of the 8-week experiment. These deposits of new CaCO3 were carefully chipped off of the experimental fragments using a razor blade and imaged using a scanning electron microscope (SEM; Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company). Using the SEM, fragments were imaged across scales with magnification maintained between samples: an overall view of the skeleton (56x), individual whole calyxes (124x), spine structures between (141x) and inside (164x) the calyxes, and the rapid accretion deposits (RADs) on the spines (1013x). Several features of interest previously used to investigate coral biomineralization (Scucchia et al., 2023; Scucchia, Malik, Zaslansky, et al., 2021) were quantified using ImageJ (v1.53c) (Schneider et al., 2012), including: number of corallites, distance between corallites (i.e., coenosteum width), corallite diameter, circularity of the corallite, number of spines within calyx, spine length and maximum spine width (on spines both between and inside the calyx), number of RADs, and size of RADs.&lt;/p&gt; &lt;p&gt;The significant interaction between treatment and origin was explored on all micromorphological features using linear mixed effects models, with colony as a random effect. The significance of fixed effects and their interactions was determined using an analysis of variance with a type III error structure using the Anova function in car package (Fox et al., 2012). Significant interactive effects were followed by pairwise comparison of estimate marginal means using the emmeans package with Tukey HSD adjusted p values (Lenth et al., 2018). Data were tested for homogeneity of variance and normality of distribution through graphical analyses of residual plots for all models. All statistical analyses were done using R version 4.0.3 software (R Core Team, 2020), and graphical representations were produced using the package ggplot2 (Wickham, 2016).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;See related code package&amp;nbsp;Dellaert et al. (2024)&amp;nbsp;&quot;imkristenbrown/Heron-Pdam-gene-expression: pCO2 variability and biomineralization&quot;, doi: 10.5281/zenodo.14041606.&amp;nbsp;This code package was used for results publication&amp;nbsp;Brown et al. (2024).&lt;/p&gt; Specified by the Principal Investigator(s) All 4 datasets submitted in same ticket were processed in same data pipeline, but steps have been broken out separately in the processing sections. Additionally 4 of 5 data files required implied data to filled into blank values. To do this in the BCO-DMO system, they are imported twice and joined. -Imported &quot;Polyp.csv&quot; into the BCO-DMO system as polyp_metadata, filtered dataset to include only rows with &quot;Circularity&quot; values and removed all other fields -Imported &quot;Polyp.csv&quot; into the BCO-DMO system as Polyp and joined to polyp_metadata on the &quot;Image name&quot; to populate &quot;Circularity&quot; in all fields for the specified image -Changed parameter names to comply with BCO-DMO naming conventions -Exported file as &quot;942939_v1_pocillopora_damicornis_calyxes.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 Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company PI Supplied Instrument Name: Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company PI Supplied Instrument Description:These deposits of new CaCO3 were carefully chipped off of the experimental fragments using a razor blade and imaged using a scanning electron microscope (SEM; Quanta 600 FEG Mark II Environmental Scanning Electron Microscope, Field Electron and Ion Company). Instrument Name: Scanning Electron Microscope Instrument Short Name:SEM Instrument Description: A scanning electron microscope (SEM) scans a focused electron beam over a surface to create an image. The electrons in the beam interact with the sample, producing various signals that can be used to obtain information about the surface topography and composition.