http://lod.bco-dmo.org/id/dataset/984835
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
2025-09-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA V4 sequence metadata from surface swabs from Apostichopus californicus-associated flavivirus experiment under suboxic conditions and organic matter amendment
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.984835.1
Ian Hewson
Cornell University
principalInvestigator
Kyle Hebert
Alaska Department of Fish and Game
principalInvestigator
Em G Lim
Simon Fraser University
principalInvestigator
Joel Markis
University of Alaska Southeast
principalInvestigator
Megan Schwartz
University of Washington
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: Crandell, J., Altera, A., DeRito, C., Hebert, K., Lim, E. G., Markis, J., Philipp, K. H., Rede, J., Schwartz, M., Vilanova-Cuevas, B., Wang, E., Hewson, I. (2025) 16S rRNA V4 sequence metadata from surface swabs from Apostichopus californicus-associated flavivirus experiment under suboxic conditions and organic matter amendment. 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.984835.1 [access date]
Apostichopus californicus 16S rRNA V4 Sequences Dataset Description: Methods and Sampling: <p>Forty-two specimens of <em>Apostichopus californicus</em> (urn:lsid:marinespecies.org:taxname:529363) were collected by SCUBA divers in Thimbleberry Bay (57.031861N, 135.250972W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. Two mesocosms served as controls (no amendment), 4 mesocosms were subject to daily organic matter (20 µM) amendment, and 1 mesocosm was continuously sparged with N<sub>2</sub> (Airgas, medical grade; the other 6 mesocosms were bubbled continuously with air). Seawater was subject to 50% volume water change daily and specimens were not fed during captivity. Mesocosms were covered while not sampled (i.e., they were light limited). We selected two organic matter substrates (glucose and peptone) based on their ability to stimulate microbial activity in prior work in addition to two common constituents of dissolved organic matter in coastal environments (N-acetylglucosamine and fucose + rhamnose). We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers.</p>
<p>Surface swabs of each individual were collected daily by rubbing a Puritan polyester sterile swab over a ~ 1 cm<sup>2</sup> area of epidermis. Swabs were cut using clean scissors to remove the polyester tip and placed into 2 mL cryovials containing RNALater. Tube feet samples were collected from each specimen daily using disposable plastic forceps, and feet were placed immediately into cryovials containing RNALater. A 5mm biopsy punch of the dorsal body wall was collected from half of the individuals in each mesocosm at 0, 1, 3, and 6&nbsp;d, which were then preserved in RNALater. All specimens were photographed and weighed daily. All RNALater preserved samples were frozen at -80°C and transported in liquid N<sub>2</sub> to the laboratory at Cornell University. Animal carcasses were frozen at -20°C and transported on blue ice to Cornell.</p>
<p>Surface swabs were collected from 42 animals over the course of 7&nbsp;d (sampled on t = 0&nbsp;d, 1&nbsp;d, 3&nbsp;d, 5&nbsp;d, and 7&nbsp;d) and frozen at -20°C until further processing. DNA was extracted from frozen swabs using Zymo Quick-DNA Fungal/Bacterial kits (Zymo Research) as per the manufacturer’s protocol. Bacterial communities in sample extracts were identified using dual-barcoded PCR (polymerase chain reaction) amplification and sequencing of the V4 region of the 16S rRNA gene. Each 40 µL PCR reaction comprised 1X PCR master mix (One-Taq Quick-Load 2x Master Mix with Standard; New England Biolabs), 0.125 µM of each barcoded primer (515f; 5’-GTG <strong>Y</strong>CA GCM GCC GCG GTA A-3’ and 806r; 5’-GGA CTA C<strong>N</strong>V GGG TWT CTA AT-3’), and 2 uL of template (swab extract). 16S rRNA amplicons were pooled at equimolar concentrations using SequalPrep Normalization Plate kit (Invitrogen) and sequenced on one lane of Illumina MiSeq (2 x 250 paired end) at the Cornell University Biotechnology Research Center. 16S rRNA amplicon sequences were submitted to NCBI (BioProject accession number PRJNA947521, see Related Datasets).</p>
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
Kyle Hebert
Alaska Department of Fish and Game
kyle.hebert@alaska.gov
pointOfContact
Em G Lim
Simon Fraser University
em_lim@sfu.ca
pointOfContact
Joel Markis
University of Alaska Southeast
jamarkis@alaska.edu
pointOfContact
Megan Schwartz
University of Washington
megansc@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
bioproject_accession
biosample
organism
specimen_collection_date
swab_collection_date
Latitude
Longitude
env_broad_scale
env_local_scale
env_medium
geo_loc_name
host
host_subject_id
replicate_ID
host_tissue_sampled
host_NCBI_taxid
AphiaID
LSID
Illumina MiSeq
Photographed
Submersible HOBO logger
Scale
SCUBA
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
sample description
date
latitude
longitude
region
species scientific name (binomial)
replicate
taxon_code
Life Science Identifier (LSID)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Camera
Oxygen Sensor
scale or balance
Self-Contained Underwater Breathing Apparatus
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
-135.250972
-135.250972
57.031861
57.031861
2021-11-11
2021-11-18
Northeastern Pacific Ocean
0
BCO-DMO catalogue of parameters from 16S rRNA V4 sequence metadata from surface swabs from Apostichopus californicus-associated flavivirus experiment under suboxic conditions and organic matter amendment
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/986105.rdf
Name: sample_name
Units: unitless
Description: <p>Sequencing library name</p>
http://lod.bco-dmo.org/id/dataset-parameter/986106.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/986107.rdf
Name: biosample
Units: unitless
Description: <p>NCBI BioSample Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/986108.rdf
Name: organism
Units: unitless
Description: <p>Microorganism name for accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/986109.rdf
Name: specimen_collection_date
Units: unitless
Description: <p>Date of Specimen Collection (Thimbleberry Bay)</p>
http://lod.bco-dmo.org/id/dataset-parameter/986110.rdf
Name: swab_collection_date
Units: unitless
Description: <p>Date of surface swab; Surface swabs were collected from 42 animals over the course of 7 d (sampled on t = 0 d, 1 d, 3 d, 5 d, and 7 d) starting on 2021-11-11</p>
http://lod.bco-dmo.org/id/dataset-parameter/986111.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of specimen collection, positive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/986112.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of specimen collection, negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/986113.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Biome of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/986114.rdf
Name: env_local_scale
Units: unitless
Description: <p>Marine biome</p>
http://lod.bco-dmo.org/id/dataset-parameter/986115.rdf
Name: env_medium
Units: unitless
Description: <p>Intertidal</p>
http://lod.bco-dmo.org/id/dataset-parameter/986116.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic Location</p>
http://lod.bco-dmo.org/id/dataset-parameter/986117.rdf
Name: host
Units: unitless
Description: <p>Host Organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/986118.rdf
Name: host_subject_id
Units: unitless
Description: <p>Unique identifier by which each sequence can be identified</p>
http://lod.bco-dmo.org/id/dataset-parameter/986119.rdf
Name: replicate_ID
Units: unitless
Description: <p>Sample replicate ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/986120.rdf
Name: host_tissue_sampled
Units: unitless
Description: <p>Type of Tissue of original sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/986121.rdf
Name: host_NCBI_taxid
Units: unitless
Description: <p>NCBI Taxonomy of the Host</p>
http://lod.bco-dmo.org/id/dataset-parameter/986122.rdf
Name: AphiaID
Units: unitless
Description: <p>Unique identifier for the listed taxon in the Aphia database</p>
http://lod.bco-dmo.org/id/dataset-parameter/986123.rdf
Name: LSID
Units: unitless
Description: <p>Life Science Identifier (LSID) for the listed taxon</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
164210
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8010c44e-fae9-47bb-89e7-791e16efd66d/content
download
https://doi.org/10.26008/1912/bco-dmo.984835.1
download
onLine
dataset
<p>Forty-two specimens of <em>Apostichopus californicus</em> (urn:lsid:marinespecies.org:taxname:529363) were collected by SCUBA divers in Thimbleberry Bay (57.031861N, 135.250972W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. Two mesocosms served as controls (no amendment), 4 mesocosms were subject to daily organic matter (20 µM) amendment, and 1 mesocosm was continuously sparged with N<sub>2</sub> (Airgas, medical grade; the other 6 mesocosms were bubbled continuously with air). Seawater was subject to 50% volume water change daily and specimens were not fed during captivity. Mesocosms were covered while not sampled (i.e., they were light limited). We selected two organic matter substrates (glucose and peptone) based on their ability to stimulate microbial activity in prior work in addition to two common constituents of dissolved organic matter in coastal environments (N-acetylglucosamine and fucose + rhamnose). We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers.</p>
<p>Surface swabs of each individual were collected daily by rubbing a Puritan polyester sterile swab over a ~ 1 cm<sup>2</sup> area of epidermis. Swabs were cut using clean scissors to remove the polyester tip and placed into 2 mL cryovials containing RNALater. Tube feet samples were collected from each specimen daily using disposable plastic forceps, and feet were placed immediately into cryovials containing RNALater. A 5mm biopsy punch of the dorsal body wall was collected from half of the individuals in each mesocosm at 0, 1, 3, and 6&nbsp;d, which were then preserved in RNALater. All specimens were photographed and weighed daily. All RNALater preserved samples were frozen at -80°C and transported in liquid N<sub>2</sub> to the laboratory at Cornell University. Animal carcasses were frozen at -20°C and transported on blue ice to Cornell.</p>
<p>Surface swabs were collected from 42 animals over the course of 7&nbsp;d (sampled on t = 0&nbsp;d, 1&nbsp;d, 3&nbsp;d, 5&nbsp;d, and 7&nbsp;d) and frozen at -20°C until further processing. DNA was extracted from frozen swabs using Zymo Quick-DNA Fungal/Bacterial kits (Zymo Research) as per the manufacturer’s protocol. Bacterial communities in sample extracts were identified using dual-barcoded PCR (polymerase chain reaction) amplification and sequencing of the V4 region of the 16S rRNA gene. Each 40 µL PCR reaction comprised 1X PCR master mix (One-Taq Quick-Load 2x Master Mix with Standard; New England Biolabs), 0.125 µM of each barcoded primer (515f; 5’-GTG <strong>Y</strong>CA GCM GCC GCG GTA A-3’ and 806r; 5’-GGA CTA C<strong>N</strong>V GGG TWT CTA AT-3’), and 2 uL of template (swab extract). 16S rRNA amplicons were pooled at equimolar concentrations using SequalPrep Normalization Plate kit (Invitrogen) and sequenced on one lane of Illumina MiSeq (2 x 250 paired end) at the Cornell University Biotechnology Research Center. 16S rRNA amplicon sequences were submitted to NCBI (BioProject accession number PRJNA947521, see Related Datasets).</p>
Specified by the Principal Investigator(s)
- Imported "MIMARKS.survey.host-associated.5.0_Sitka_Sea_Cucumber_16S.xlsx" into the BCO-DMO system
- Converted "collection_date" to ISO 8601 format YYYY-MM-DD
- Removed parameters with no values
- Removed special characters from parameter names
- Split "lat_lon" parameter into "Latitude" and "Longitude"
- Replaced lat and lon values with values provided by submitter for collection location
- Renamed "collection_date" to "swab_collection_date"
- Created a new column, "specimen_collection_date" with values of 2021-11-10, the date all specimens were collected
- Filtered out all rows with "host_subject_id" values that included "BLANK", "Blank", or "Basket", upon submitter request
- Added corresponding BioSample identifiers (provided by submitter) to the dataset
- Added corresponding AphiaIDs and LSIDs for relevant species
- Renamed "misc_param" and "host_taxid" to "replicate_ID" and "host_NCBI_taxid"
- Exported file as "984835_v1_swab_sequence_accessions.csv"
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
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:16S rRNA amplicons were pooled at equimolar concentrations using SequalPrep Normalization Plate kit (Invitrogen) and sequenced on one lane of Illumina MiSeq (2 x 250 paired end) at the Cornell University Biotechnology Research Center. 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:Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. 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/
Submersible HOBO logger
Submersible HOBO logger
PI Supplied Instrument Name: Submersible HOBO logger PI Supplied Instrument Description:We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
Scale
Scale
PI Supplied Instrument Name: Scale PI Supplied Instrument Description:Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Forty-two specimens of Apostichopus californicus were collected by SCUBA divers in Thimbleberry Bay (57.0297N, 135.2283W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html