http://lod.bco-dmo.org/id/dataset/966488 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 2025-06-25 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Accession numbers for 16S rRNA genes from microbial communities from four stony coral species collected across sites in Bahia Almirante, Panama in summer of 2021 2025-06-25 publication 2025-06-25 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-06-27 publication https://doi.org/10.26008/1912/bco-dmo.966488.1 Julie L. Meyer University of Florida 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: Meyer, J. L. (2025) Accession numbers for 16S rRNA genes from microbial communities from four stony coral species collected across sites in Bahia Almirante, Panama in summer of 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.966488.1 [access date] Field survey coral microbiome composition Dataset Description: Methods and Sampling: &lt;p&gt;For each sampled coral colony, 5 millimeter (mm) circular cores (consisting of tissue and skeleton) were collected by SCUBA using sterile disposable stainless-steel biopsy punches (Integra Miltex). On shore, coral fragments were preserved with RNA Later and frozen until processing at the University of Florida. DNA was extracted with a DNeasy PowerBiofilm kit (Qiagen). The V4 region of the 16S rRNA gene was amplified with the 515F and 806RB Earth Microbiome primers and thermocycler protocol.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048914 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048914 completed Julie L. Meyer University of Florida 352-273-8189 Genetics Institute, Rm 304 Cancer and Genetics Research Complex 2033 Mowry Rd Gainsville FL 32611 USA juliemeyer@ufl.edu pointOfContact asNeeded Dataset Version: 1 Unknown SRA_accession sample_name bioproject_accession organism collection_date env_broad_scale env_local_scale env_medium geo_loc_name host depth Latitude Longitude llumina MiSeq theme None, User defined accession number sample identification NCBI BioProject accession taxon date site description sample description site depth latitude longitude featureType BCO-DMO Standard Parameters Automated DNA Sequencer 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: Biodiversity and resilience of corals and their microbiomes in response to ocean deoxygenation https://osprey.bco-dmo.org/project/838054 Collaborative Research: Biodiversity and resilience of corals and their microbiomes in response to ocean deoxygenation <p><em>NSF Award Abstract:</em><br /> The world's oceans are facing the threat of deoxygenation - events of low dissolved oxygen insufficient for marine life and healthy ecosystems - which is accelerating along with other global crises including climate change and ocean acidification. The pace of these changes can lead to rapid shifts in the structure of marine communities due to changes in the distribution, abundance, and diversity of species. This collaborative project is among the first to examine the consequences of deoxygenation on coral reefs, which are sentinel ecosystems for studying ecological responses to global change because of their importance to human society, sensitivity to stress, and intricate relationships among their inhabitants. Specifically, the research team investigates why and how some coral species are more tolerant than others and the role that bacteria associated with the corals have in such tolerance. This predictive understanding is important to support conservation and management efforts by identifying stress-tolerant coral species and establishing indicators for assessment of hypoxia stress. The project provides training for multiple undergraduate and graduate students and postdoctoral researchers. Findings from this project are disseminated through undergraduate and graduate courses taught at the University of Florida, a teacher training program at the Bocas del Toro Research Station at STRI in Panama, a workshop in Panama to build a community of scientists and informed practitioners, and webinars, toolkits, and other resources communicated through established networks of coral conservation and management practitioners.</p> <p>Understanding the responses of coral reefs to ocean deoxygenation is limited to a few post hoc assessments of how unanticipated hypoxic events have impacted macrofauna. This project employs a predictive approach to examine the resilience of coral reef communities to ocean deoxygenation by examining both corals and their associated microbiomes. Complimentary manipulative laboratory and field experiments and surveys along natural gradients of hypoxic stress are being used to answer the following three fundamental questions about how variation in the tolerance of corals and their microbiomes predicts the resilience of reefs to deoxygenation: (1) How does the physiological response of the coral to hypoxia predict community shifts in the microbiome with deoxygenation? (2) To what degree do corals and their microbiomes show evidence of acclimatization to reduced oxygen, and how do these functional shifts confer increased resistance to subsequent hypoxic stress? (3) How are the feedbacks between coral hosts and their microbiomes apparent in the recovery of coral communities from hypoxia and patterns of community structure at the seascape scale? This project aims at developing a mechanistic and predictive understanding of coral reef community responses to ocean deoxygenation by examining stability and resilience at two levels of ecological organization: the assemblage of coral species at the reef scale, and the assemblage of microbes at the holobiont scale. Moreover, this study examines how those responses are coupled by feedbacks at the colony scale through coral physiological responses and microbial functional shifts.</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 microbiome resilience largerWorkCitation project eng; USA oceans -82.35242 -82.21741 9.21416 9.3484 2021-09-09 2021-09-11 Caribbean Coast of Panama 9 N 82 W 0 BCO-DMO catalogue of parameters from Accession numbers for 16S rRNA genes from microbial communities from four stony coral species collected across sites in Bahia Almirante, Panama in summer of 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/966497.rdf Name: SRA_accession Units: unitless Description: <p>Accession number of sequencing read files in the National Center for Biotechnology Information (NCBI) Sequence Read Archive</p> http://lod.bco-dmo.org/id/dataset-parameter/966498.rdf Name: sample_name Units: unitless Description: <p>Sample name used as identifier of microbial community samples in amplicon analysis</p> http://lod.bco-dmo.org/id/dataset-parameter/966499.rdf Name: bioproject_accession Units: unitless Description: <p>Accession number of the BioProject in the National Center for Biotechnology Information (NCBI) database</p> http://lod.bco-dmo.org/id/dataset-parameter/966500.rdf Name: organism Units: unitless Description: <p>Description of the organism type that was sampled</p> http://lod.bco-dmo.org/id/dataset-parameter/966501.rdf Name: collection_date Units: unitless Description: <p>Date of microbial community sampling in the field</p> http://lod.bco-dmo.org/id/dataset-parameter/966502.rdf Name: env_broad_scale Units: unitless Description: <p>Broad scale environmental type description</p> http://lod.bco-dmo.org/id/dataset-parameter/966503.rdf Name: env_local_scale Units: unitless Description: <p>Local scale environmental type description</p> http://lod.bco-dmo.org/id/dataset-parameter/966504.rdf Name: env_medium Units: unitless Description: <p>Description of the physcial type of sample collected</p> http://lod.bco-dmo.org/id/dataset-parameter/966505.rdf Name: geo_loc_name Units: unitless Description: <p>Geographical Location Name: Panama: Cayo Roldan, Panama: Cayo Hermanas, Panama: Punta STRI, Panama: Hospital Point, Panama: Seagal</p> http://lod.bco-dmo.org/id/dataset-parameter/966506.rdf Name: host Units: unitless Description: <p>Coral species: Agaricia tenuifolia, Stephanocoenia intersepta, Siderastrea siderea, Montastraea cavernosa</p> http://lod.bco-dmo.org/id/dataset-parameter/966507.rdf Name: depth Units: meter (m) Description: <p>Depth of water at sample collection site</p> http://lod.bco-dmo.org/id/dataset-parameter/966508.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude coordinates for the collection site</p> http://lod.bco-dmo.org/id/dataset-parameter/966509.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude coordinates for the collection site (negative values = West)</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 23239 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/60ffbe46-b431-42be-a1a6-634d5d4a1e18/content download https://doi.org/10.26008/1912/bco-dmo.966488.1 download onLine dataset &lt;p&gt;For each sampled coral colony, 5 millimeter (mm) circular cores (consisting of tissue and skeleton) were collected by SCUBA using sterile disposable stainless-steel biopsy punches (Integra Miltex). On shore, coral fragments were preserved with RNA Later and frozen until processing at the University of Florida. DNA was extracted with a DNeasy PowerBiofilm kit (Qiagen). The V4 region of the 16S rRNA gene was amplified with the 515F and 806RB Earth Microbiome primers and thermocycler protocol.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file &quot;SRA_Accession_Numbers_Metadata_FieldSurvey.xlsx&quot; into the BCO-DMO system. - Flagged &quot;not applicable&quot; and &quot;BLANK&quot; as missing data values (missing data are empty/blank in the final CSV file). - Renamed fields to comply with BCO-DMO naming conventions. - Created separate columns for Latitude and Longitude. - Converted dates to YYYY-MM-DD format. - Saved the final file as &quot;966488_v1_accession_numbers.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 llumina MiSeq llumina MiSeq PI Supplied Instrument Name: llumina MiSeq PI Supplied Instrument Description:Illumina MiSeq at the University of Florida Interdisciplinary Center for Biotechnology Research (RRID:SCR_019152) Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.