http://lod.bco-dmo.org/id/dataset/985574 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 2025-09-30 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) GenBank accessions for 18S rRNA gene amplicons from swab specimens collected in the Caribbean and Réunion (France) from May 2022 to Dec 2024 2025-10-07 publication 2025-10-07 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-10-07 publication https://doi.org/10.26008/1912/bco-dmo.985574.1 Ian Hewson Cornell University principalInvestigator Marilyn Brandt University of the Virgin Islands Center for Marine and Environmental Studies principalInvestigator Mya Breitbart University of South Florida principalInvestigator Michael Henson Northern Illinois University principalInvestigator Alwin Hylkema Van Hall Larenstein University of Applied Sciences 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: Hewson, I., Brandt, M., Budd, K., Breitbart, M., DeRito, C., Gittens, S., Henson, M., Hylkema, A., Sevier, M., Souza, M., Vilanova-Cuevas, B., Von Hoene, S. (2025) GenBank accessions for 18S rRNA gene amplicons from swab specimens collected in the Caribbean and Réunion (France) from May 2022 to Dec 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.985574.1 [access date] 18S rRNA Gene Amplicons from Swabs Dataset Description: Methods and Sampling: &lt;p&gt;Surface swab specimens were collected between May 2022 and December 2024. Samples were collected from sites affected (i.e. sites which bore DaSc-affected urchins) at the time of sampling or those which were previously affected; sites that were never affected (i.e. reference sites); and ports/marinas. Swab specimens were collected by snorkelers at depths of ~1–4 m. Polyester swabs (Dry Transport Systems, Puritan Medical Products) were transported to the survey site sealed in an air-filled transport tube and withdrawn into the water immediately adjacent to the swabbed surface. The swab was gently rubbed for 10 s across a ~2 cm2 surface before retrieval into the air-filled transport tube. Live swabbed surfaces, chosen haphazardly, were photographed to confirm the identity of invertebrate or plant species (seagrass and macroalgae). &amp;nbsp;At some sites, identity of swabbed surfaces could not be determined (i.e. unidentifiable surface swabs), and in some cases, the taxonomy of swabbed specimens was unclear (e.g. macroalgae; n = 11), so they were assigned to higher taxonomy. Swabs were transported at ambient temperature to shore, where the swab tips were cut off with clean scissors into cryovials containing RNAlater Solution (Invitrogen).&lt;/p&gt; &lt;p&gt;DNA was extracted from swab tips were extracted using the Quick-DNA Insect/Tissue kit (Zymo Research). The manufacturer’s extraction protocol (v.2.21) was followed with these exceptions: we did not add beta-mercaptoethanol to the lysis buffer, bead bashing was shortened to 2 min, and DNA was eluted into nuclease-free sterile water instead of elution buffer. Specimens were subjected to PCR employing pan-Ciliophora 18S rRNA gene primers 384F (5’-YTB GAT GGT AGT GTA TTG GA-3’) and 1147R (5’-GAC GGT ATC TRA TCG TCT TT-3’) (Dopheide et al. 2008). PCR was performed in 50 μl reactions comprising 1× PCR buffer, 2.5 mM MgCl2, 0.2 mM deoxynucleoside triphosphates (Promega PCR Nucleotide Mix), 200 pmol forward and reverse primers, 1 μl of 2 ng ml–1 BSA (Sigma), 5U Taq DNA polymerase (Invitrogen), and 2 μl of pooled DNA extracts. Thermal cycling was preceded by an initial heating step for 3 min at 95°C, followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 30 s, followed by a final extension at 72°C for 5 min in a BioRad MyCycler.&lt;/p&gt; &lt;p&gt;The PCR amplicons (5 μl) were then visualized on a 1 % agarose gel in 1× Tris-borate-EDTA after electrophoresis at 85 V for 45 min and staining with SYBR Gold. PCR products were cleaned up using the Zymo Clean &amp;amp; Concentrator-5 kit and subject to dye terminator (Sanger) sequencing at the Biotechnology Resource Center at Cornell University.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049225 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049225 completed Ian Hewson Cornell University 1-607-255-0151 Department of Microbiology Wing Hall 403 Ithaca NY 14853 USA hewson@cornell.edu pointOfContact Marilyn Brandt University of the Virgin Islands Center for Marine and Environmental Studies 340-693-1379 2 John Brewers Bay St. Thomas, USVI 00802 mbrandt@uvi.edu pointOfContact Mya Breitbart University of South Florida (727) 553-3520 USF College of Marine Sciences 140 7th Avenue South St Petersburg FL 33701 USA mya@marine.usf.edu pointOfContact Michael Henson Northern Illinois University mhenson@niu.edu pointOfContact Alwin Hylkema Van Hall Larenstein University of Applied Sciences alwin.hylkema@hvhl.nl pointOfContact asNeeded Dataset Version: 1 Unknown Genbank_Accession Sequence_ID Sample_Location Sample_Type Sample_Month Latitude Longitude ABI 3730xl genetic analyzer Photographed Snorkeler BioRad MyCycler theme None, User defined NCBI Genbank nucleotide accession sample identification region sample type month of year latitude longitude featureType BCO-DMO Standard Parameters Automated DNA Sequencer Camera Diving Mask and Snorkel 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. Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics https://osprey.bco-dmo.org/project/863960 Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics <p>NSF Award Abstract:</p> <p>Marine diseases pose considerable risks to invertebrates, such as sea cucumbers, in the face of changing ocean conditions. While many invertebrate diseases are driven by pathogens, the interplay between animal biology and environmental conditions often mediates the outcome of the pathogen-host relationship. Sea cucumbers are ecologically and economically important animals that occur in a wide range of marine habitats. This project aims to decipher how the interaction between the biology of sea cucumbers, environmental conditions, and a newly-discovered type of virus, seemingly innocuous under typical conditions, may lead to lethal disease in giant Pacific sea cucumbers in the U.S. West Coast. The study includes surveys in coastal regions in southeast Alaska, Washington, and California as well as laboratory experiments manipulating seawater oxygen concentrations, temperature, and simulated microalgal blooms. The project engages community scientists, fishers, high school students, and indigenous groups, and supports training of one graduate and several undergraduate students. A workshop that brings together scientists across marine ecology, disease, and veterinary disciplines is planned to prepare a handbook of best practices in marine disease investigation.</p> <p>Metagenomic and community-level sequencing efforts have revealed an astonishing diversity of viruses associated with grossly normal marine invertebrates. The vast majority of detected viruses likely represents asymptomatic infections under typical conditions but may generate pathology in hosts under changing environmental conditions. This project investigates the ecology of a group of enveloped positive sense single-stranded RNA viruses (flaviviruses) that this research team has recently discovered in the giant California sea cucumber Apostichopus californicus by addressing three hypotheses: 1) Aquatic insect-only Flaviviruses (aiFVs) do not cause gross pathology under typical conditions; 2) aiFVs proliferate and generate clinical and gross pathology under suboxic stress; and 3) Periodic increases in primary production and mean temperature excursions cause aiFV proliferation and subsequently exacerbate holothurian disease process. The study comprises a restricted survey of aiFV diversity via amplicon sequencing and their prevalence within and between populations, development of an antibody-based approach for aiFV detection, and examination of aiFV behavior in concert with host transcription and veterinary pathology. The study includes field surveys and in laboratory manipulative experiments.</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> Holothurian Flaviviruses largerWorkCitation project eng; USA biota oceans -80.9669 55.3294 -21.2705 24.9521 2022-05-01 2024-12-31 Northeastern Pacific Ocean 0 BCO-DMO catalogue of parameters from GenBank accessions for 18S rRNA gene amplicons from swab specimens collected in the Caribbean and Réunion (France) from May 2022 to Dec 2024 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/985745.rdf Name: Genbank_Accession Units: unitless Description: <p>Genbank Accession Number</p> http://lod.bco-dmo.org/id/dataset-parameter/985746.rdf Name: Sequence_ID Units: unitless Description: <p>Sequence identification code</p> http://lod.bco-dmo.org/id/dataset-parameter/985747.rdf Name: Sample_Location Units: unitless Description: <p>Geographic location of specimen collection</p> http://lod.bco-dmo.org/id/dataset-parameter/985748.rdf Name: Sample_Type Units: unitless Description: <p>Sample type: Swab</p> http://lod.bco-dmo.org/id/dataset-parameter/985749.rdf Name: Sample_Month Units: unitless Description: <p>Month of Swab Collection</p> http://lod.bco-dmo.org/id/dataset-parameter/985750.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude of specimen collection, positive is North, negative is South</p> http://lod.bco-dmo.org/id/dataset-parameter/985752.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude of specimen collection, positive is East, negative is 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 9147 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/d367fdb3-fc56-41ab-8d04-344fed263bcf/content download https://doi.org/10.26008/1912/bco-dmo.985574.1 download onLine dataset &lt;p&gt;Surface swab specimens were collected between May 2022 and December 2024. Samples were collected from sites affected (i.e. sites which bore DaSc-affected urchins) at the time of sampling or those which were previously affected; sites that were never affected (i.e. reference sites); and ports/marinas. Swab specimens were collected by snorkelers at depths of ~1–4 m. Polyester swabs (Dry Transport Systems, Puritan Medical Products) were transported to the survey site sealed in an air-filled transport tube and withdrawn into the water immediately adjacent to the swabbed surface. The swab was gently rubbed for 10 s across a ~2 cm2 surface before retrieval into the air-filled transport tube. Live swabbed surfaces, chosen haphazardly, were photographed to confirm the identity of invertebrate or plant species (seagrass and macroalgae). &amp;nbsp;At some sites, identity of swabbed surfaces could not be determined (i.e. unidentifiable surface swabs), and in some cases, the taxonomy of swabbed specimens was unclear (e.g. macroalgae; n = 11), so they were assigned to higher taxonomy. Swabs were transported at ambient temperature to shore, where the swab tips were cut off with clean scissors into cryovials containing RNAlater Solution (Invitrogen).&lt;/p&gt; &lt;p&gt;DNA was extracted from swab tips were extracted using the Quick-DNA Insect/Tissue kit (Zymo Research). The manufacturer’s extraction protocol (v.2.21) was followed with these exceptions: we did not add beta-mercaptoethanol to the lysis buffer, bead bashing was shortened to 2 min, and DNA was eluted into nuclease-free sterile water instead of elution buffer. Specimens were subjected to PCR employing pan-Ciliophora 18S rRNA gene primers 384F (5’-YTB GAT GGT AGT GTA TTG GA-3’) and 1147R (5’-GAC GGT ATC TRA TCG TCT TT-3’) (Dopheide et al. 2008). PCR was performed in 50 μl reactions comprising 1× PCR buffer, 2.5 mM MgCl2, 0.2 mM deoxynucleoside triphosphates (Promega PCR Nucleotide Mix), 200 pmol forward and reverse primers, 1 μl of 2 ng ml–1 BSA (Sigma), 5U Taq DNA polymerase (Invitrogen), and 2 μl of pooled DNA extracts. Thermal cycling was preceded by an initial heating step for 3 min at 95°C, followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 30 s, followed by a final extension at 72°C for 5 min in a BioRad MyCycler.&lt;/p&gt; &lt;p&gt;The PCR amplicons (5 μl) were then visualized on a 1 % agarose gel in 1× Tris-borate-EDTA after electrophoresis at 85 V for 45 min and staining with SYBR Gold. PCR products were cleaned up using the Zymo Clean &amp;amp; Concentrator-5 kit and subject to dye terminator (Sanger) sequencing at the Biotechnology Resource Center at Cornell University.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported &quot;Metadata_GenBankAccessions.txt&quot; into the BCO-DMO system - Adjusted values in &quot;Latitude&quot; and &quot;Longitude&quot; fields to BCO-DMO style, removing cardinal indicators and making West and South values negative - Converted &quot;Sample_Month&quot; to ISO 8601 format YYYY-MM - Removed &quot;object_status&quot; from dataset, upon consultation with submitter - Removed all rows where &quot;Sample_Type&quot; contains &quot;Tissue&quot;, upon request from the submitter - Exported file as &quot;985574_v1_18s_r_rna_gene_amplicons.csv&quot; Scientific names in the data were checked using World Register of Marine Species (WoRMS) Taxon Match. All scientific names in the data are valid and accepted names as of 2025-10-01. 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 ABI 3730xl genetic analyzer ABI 3730xl genetic analyzer PI Supplied Instrument Name: ABI 3730xl genetic analyzer PI Supplied Instrument Description:PCR products were cleaned up using the Zymo Clean & Concentrator-5 kit and subject to dye terminator (Sanger) sequencing at the Biotechnology Resource Center at Cornell University. 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. Photographed Photographed PI Supplied Instrument Name: Photographed PI Supplied Instrument Description:Live swabbed surfaces, chosen haphazardly, were photographed to confirm the identity of invertebrate or plant species (seagrass and macroalgae).  Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/ Snorkeler Snorkeler PI Supplied Instrument Name: Snorkeler PI Supplied Instrument Description:Swab specimens were collected by snorkelers at depths of ~1–4 m. Instrument Name: Diving Mask and Snorkel Instrument Short Name: Instrument Description: A diving mask (also half mask, dive mask or scuba mask) is an item of diving equipment that allows underwater divers, including, scuba divers, free-divers, and snorkelers to see clearly underwater. Snorkel: A breathing apparatus for swimmers and surface divers that allows swimming or continuous use of a face mask without lifting the head to breathe, consisting of a tube that curves out of the mouth and extends above the surface of the water. BioRad MyCycler BioRad MyCycler PI Supplied Instrument Name: BioRad MyCycler PI Supplied Instrument Description:Thermal cycling was preceded by an initial heating step for 3 min at 95°C, followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 30 s, followed by a final extension at 72°C for 5 min in a BioRad MyCycler. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)