http://lod.bco-dmo.org/id/dataset/986522 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 2025-10-10 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Sequence accession numbers for metatranscriptomic sequences from coral microbiomes experimentally exposed to low oxygen in 2022 2025-10-10 publication 2025-10-10 revision Woods Hole Oceanographic Institution (WHOI BCO-DMO) 2026-01-26 publication https://doi.org/10.26008/1912/bco-dmo.986522.1 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. (2026) Sequence accession numbers for metatranscriptomic sequences from coral microbiomes experimentally exposed to low oxygen in 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.986522.1 [access date] Methods and Sampling: &lt;p&gt;Coral colonies were collected in the field from two sites (Cayo Roldan and Hospital Point), fragmented into smaller samples, and acclimated in aquaria for seven days. Ten 40-L aquaria were set up for ex situ manipulation of dissolved oxygen. Five tanks were bubbled with nitrogen gas to induce hypoxic conditions. Five tanks were maintained as normoxic conditions. During the two-week treatment period, corals in hypoxia tanks were exposed to low oxygen conditions (0.3 mg/L dissolved oxygen) for 6 hours each night. Samples were collected after the two-week treatment period and after a two-week recovery period with no induced low oxygen conditions. Whole fragments were preserved in RNAlater and frozen until processing at the University of Florida. RNA extractions were performed with the Qiagen RNeasy Mini Kit with the addition of bashing beads. RNAseq libraries were constructed with the NuGEN Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete kit. Libraries were submitted to the University of Florida Interdisciplinary Center for Biotechnology Research (RRID:SCR_019152) for sequencing on an Illumina NovaSeq6000 with paired 150-bp reads.&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 BioProject BioSample sample SRA_Experiment SRA_Run SRA_Study date sample_descrip host site latitude longitude llumina NovaSeq6000 theme None, User defined NCBI BioProject accession NCBI BioSample accession sample identification NCBI SRA experiment accession (SRX) NCBI SRA run accession (SRR) NCBI SRA study accession (SRP) date sample description taxon site 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 -82.32 -82.22 9.21 9.33 2022-08-08 2022-08-22 Caribbean Coast of Panama 9 N 82 W 0 BCO-DMO catalogue of parameters from Sequence accession numbers for metatranscriptomic sequences from coral microbiomes experimentally exposed to low oxygen in 2022 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/987564.rdf Name: BioProject Units: unitless Description: <p>BioProject accession number in the National Center for Biotechnology Information (NCBI) database</p> http://lod.bco-dmo.org/id/dataset-parameter/987565.rdf Name: BioSample Units: unitless Description: <p>BioSample accession number in the National Center for Biotechnology Information (NCBI) database.</p> http://lod.bco-dmo.org/id/dataset-parameter/987566.rdf Name: sample Units: unitless Description: <p>Sample name used as identifier of microbial community samples</p> http://lod.bco-dmo.org/id/dataset-parameter/987567.rdf Name: SRA_Experiment Units: unitless Description: <p>Sequence Read Archive (SRA) experiment accession number in the National Center for Biotechnology Information (NCBI) database.</p> http://lod.bco-dmo.org/id/dataset-parameter/987568.rdf Name: SRA_Run Units: unitless Description: <p>Sequence Read Archive (SRA) run accession number in the National Center for Biotechnology Information (NCBI) database.</p> http://lod.bco-dmo.org/id/dataset-parameter/987569.rdf Name: SRA_Study Units: unitless Description: <p>Sequence Read Archive (SRA) study accession number in the National Center for Biotechnology Information (NCBI) database.</p> http://lod.bco-dmo.org/id/dataset-parameter/987570.rdf Name: date Units: unitless Description: <p>Date of microbial community sampling in the field</p> http://lod.bco-dmo.org/id/dataset-parameter/987571.rdf Name: sample_descrip Units: unitless Description: <p>Description of the physical type of sample collected</p> http://lod.bco-dmo.org/id/dataset-parameter/987572.rdf Name: host Units: unitless Description: <p>Coral species: Agaricia tenuifolia (LSID urn:lsid:marinespecies.org:taxname:287916), Siderastrea siderea (LSID urn:lsid:marinespecies.org:taxname:207516)</p> http://lod.bco-dmo.org/id/dataset-parameter/987573.rdf Name: site Units: unitless Description: <p>Geographical location Name</p> http://lod.bco-dmo.org/id/dataset-parameter/987574.rdf Name: latitude Units: decimal degrees (DD) Description: <p>Latitude coordinate for the collection site</p> http://lod.bco-dmo.org/id/dataset-parameter/987575.rdf Name: longitude Units: decimal degrees (DD) Description: <p>Longitude coordinate for the collection site</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://doi.org/10.26008/1912/bco-dmo.986522.1 download onLine dataset &lt;p&gt;Coral colonies were collected in the field from two sites (Cayo Roldan and Hospital Point), fragmented into smaller samples, and acclimated in aquaria for seven days. Ten 40-L aquaria were set up for ex situ manipulation of dissolved oxygen. Five tanks were bubbled with nitrogen gas to induce hypoxic conditions. Five tanks were maintained as normoxic conditions. During the two-week treatment period, corals in hypoxia tanks were exposed to low oxygen conditions (0.3 mg/L dissolved oxygen) for 6 hours each night. Samples were collected after the two-week treatment period and after a two-week recovery period with no induced low oxygen conditions. Whole fragments were preserved in RNAlater and frozen until processing at the University of Florida. RNA extractions were performed with the Qiagen RNeasy Mini Kit with the addition of bashing beads. RNAseq libraries were constructed with the NuGEN Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete kit. Libraries were submitted to the University of Florida Interdisciplinary Center for Biotechnology Research (RRID:SCR_019152) for sequencing on an Illumina NovaSeq6000 with paired 150-bp reads.&lt;/p&gt; Specified by the Principal Investigator(s) * Data table within submitted file rnaseq.txt was imported into the BCO-DMO system. It will appear in this dataset as &quot;986522_v1_coral-microbiome-metatranscr-seq.csv&quot; * column &quot;accession number&quot; changed to BioSample for clarity and additional accession columns were added for SRA accessions using information from the NCBI SRA Run selector for the BioProjects PRJNA1041355 (40 SRAs) and PRJNA1098207 (38 SRAs). This indeed has all SRA info corresponding to the 78 BioSamples listed in rnaseq.txt. Extracted from run selector https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%09PRJNA1098207&amp;o=acc_s%3Aa and https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%09PRJNA1041355&amp;o=acc_s%3Aa Missing Data Identifiers: * In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values. * Organism names in this dataset were matched to Life Science Identifiers (LSIDs) using the World Register of Marine Species (WoRMS) on 2025-10-17. LSIDs for &quot;host&quot; were added to the column descriptions in the Parameters section. 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 NovaSeq6000 llumina NovaSeq6000 PI Supplied Instrument Name: llumina NovaSeq6000 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.