http://lod.bco-dmo.org/id/dataset/985655
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
2025-10-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Viral metagenomic investigation of the Caribbean echinoderm Holothuria floridana collected in Marathon, Florida on 25 Aug 2023
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.985655.1
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) Viral metagenomic investigation of the Caribbean echinoderm Holothuria floridana collected in Marathon, Florida on 25 Aug 2023. 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.985655.1 [access date]
Holothuria floridana viromes Dataset Description: Methods and Sampling: <p>Specimens (<em>n</em>&nbsp;= 4) of grossly normal <em>Holothuria floridana</em> (urn:lsid:marinespecies.org:taxname:210900) were collected offshore of Marathon, Florida (24.7592N, 81.1076W)&nbsp;on 2023-08-25 and immediately subsampled by five mm biopsy punches, which were transferred to sterile cryovials per Crandell et al. (2023). Punches were frozen at −80&nbsp;°C on arrival to the lab at the Florida Fish and Wildlife Commission (within an hour of collection) before shipping to Cornell University. Small subsamples of each specimen were prepared for viral metagenomic sequencing broadly following the approach of Ng et al. (2011). Briefly, tissues were homogenized in sterile, 0.02&nbsp;µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2&nbsp;µm pore size polyethersulfone syringe filters. Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37&nbsp;°C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80&nbsp;°C until further processing.</p>
<p>RNA in viral extracts was amplified using the SeqPlex RNA kit (Sigma Aldrich; part number SEQXE-10RXN, <em>n</em>&nbsp;=&nbsp;11 libraries). Subsequent specimens were amplified using the TransPlex kit (WTA2; Sigma Aldrich; part number WTA2-10RXN, <em>n</em>&nbsp;=&nbsp;3 libraries), which was used in prior RNA viral metagenomic work. Amplification products were purified using the Zymo DNA Clean and Concentrator -5 (part number D4004), quantified by Pico Green fluorescence (Invitrogen; part number P11496), and submitted for sequencing at the Cornell Biotechnology Resource Center. Libraries were prepared for sequencing using the Nextera Flex kit (Illumina; part number 20018704) and sequenced on the Illumina MiSeq platform using the 500 bp Nano kit. Sequences from all libraries were archived at NCBI under Bioproject PRJNA1117494 and SRA accessions SRR29258991-SRR29258993 and SRR29259000.</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
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
SRA_accession
SRA_study
bioproject_accession
biosample_accession
sample_name
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filename2
Latitude
Longitude
Date_specimen_collected
Illumina MiSeq
Centrifuge
Biospec Instruments homogenizer
Incubator
theme
None, User defined
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
NCBI BioProject accession
NCBI BioSample accession
sample identification
seq_descrip
instrument
instrument model
datatype
file_name
latitude
longitude
month of year
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Centrifuge
Homogenizer
Incubator
Manual Biota Sampler
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
-81.1076
-81.1076
24.7592
24.7592
2023-08-25
2023-08-25
Northeastern Pacific Ocean
0
BCO-DMO catalogue of parameters from Viral metagenomic investigation of the Caribbean echinoderm Holothuria floridana collected in Marathon, Florida on 25 Aug 2023
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/985669.rdf
Name: SRA_accession
Units: unitless
Description: <p>NCBI Run accession in the Sequence Read Archive (SRA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/985670.rdf
Name: SRA_study
Units: unitless
Description: <p>NCBI study accession in the Sequence Read Archive (SRA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/985672.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/985673.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/985674.rdf
Name: sample_name
Units: unitless
Description: <p>Sample Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/985675.rdf
Name: library_ID
Units: unitless
Description: <p>Sample Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/985676.rdf
Name: title
Units: unitless
Description: <p>Title of library</p>
http://lod.bco-dmo.org/id/dataset-parameter/985677.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing strategy: RNA-Seq</p>
http://lod.bco-dmo.org/id/dataset-parameter/985678.rdf
Name: library_source
Units: unitless
Description: <p>Source of sequencing library: Metagenomic DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/985679.rdf
Name: library_selection
Units: unitless
Description: <p>Size selection of DNA used</p>
http://lod.bco-dmo.org/id/dataset-parameter/985680.rdf
Name: library_layout
Units: unitless
Description: <p>Description of sequencing reads: paired</p>
http://lod.bco-dmo.org/id/dataset-parameter/985681.rdf
Name: platform
Units: unitless
Description: <p>Platform used for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/985682.rdf
Name: instrument_model
Units: unitless
Description: <p>Model of instrument used for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/985683.rdf
Name: design_description
Units: unitless
Description: <p>Brief description of how libraries were prepared from source material</p>
http://lod.bco-dmo.org/id/dataset-parameter/985684.rdf
Name: filetype
Units: unitless
Description: <p>Format of sequencing file</p>
http://lod.bco-dmo.org/id/dataset-parameter/985685.rdf
Name: filename
Units: unitless
Description: <p>First filename</p>
http://lod.bco-dmo.org/id/dataset-parameter/985686.rdf
Name: filename2
Units: unitless
Description: <p>Second filename</p>
http://lod.bco-dmo.org/id/dataset-parameter/985687.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude the specimens were collected, North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/985689.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude the specimens were collected, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/985691.rdf
Name: Date_specimen_collected
Units: unitless
Description: <p>Date the specimens were collected</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
1842
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/88353a1b-8667-4467-8a9a-6f180049d8ba/content
download
https://doi.org/10.26008/1912/bco-dmo.985655.1
download
onLine
dataset
<p>Specimens (<em>n</em>&nbsp;= 4) of grossly normal <em>Holothuria floridana</em> (urn:lsid:marinespecies.org:taxname:210900) were collected offshore of Marathon, Florida (24.7592N, 81.1076W)&nbsp;on 2023-08-25 and immediately subsampled by five mm biopsy punches, which were transferred to sterile cryovials per Crandell et al. (2023). Punches were frozen at −80&nbsp;°C on arrival to the lab at the Florida Fish and Wildlife Commission (within an hour of collection) before shipping to Cornell University. Small subsamples of each specimen were prepared for viral metagenomic sequencing broadly following the approach of Ng et al. (2011). Briefly, tissues were homogenized in sterile, 0.02&nbsp;µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2&nbsp;µm pore size polyethersulfone syringe filters. Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37&nbsp;°C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80&nbsp;°C until further processing.</p>
<p>RNA in viral extracts was amplified using the SeqPlex RNA kit (Sigma Aldrich; part number SEQXE-10RXN, <em>n</em>&nbsp;=&nbsp;11 libraries). Subsequent specimens were amplified using the TransPlex kit (WTA2; Sigma Aldrich; part number WTA2-10RXN, <em>n</em>&nbsp;=&nbsp;3 libraries), which was used in prior RNA viral metagenomic work. Amplification products were purified using the Zymo DNA Clean and Concentrator -5 (part number D4004), quantified by Pico Green fluorescence (Invitrogen; part number P11496), and submitted for sequencing at the Cornell Biotechnology Resource Center. Libraries were prepared for sequencing using the Nextera Flex kit (Illumina; part number 20018704) and sequenced on the Illumina MiSeq platform using the 500 bp Nano kit. Sequences from all libraries were archived at NCBI under Bioproject PRJNA1117494 and SRA accessions SRR29258991-SRR29258993 and SRR29259000.</p>
Specified by the Principal Investigator(s)
- Imported "Virome_Accession_Metadata.txt" into the BCO-DMO system
- Removed empty fields (fasta_file, assembly, filename3, filename4, filename5, filename6, filename7, filename8)
- Added latitude, longitude, and date of collection from the methods information
- Renamed NCBI identifier fields to include more standard and descriptive titles
- Removed "object_status" upon consultation with the submitter
- Exported file as "985655_v1_virome_accession.csv"
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
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Libraries were prepared for sequencing using the Nextera Flex kit (Illumina; part number 20018704) and sequenced on the Illumina MiSeq platform using the 500 bp Nano kit. 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.
Centrifuge
Centrifuge
PI Supplied Instrument Name: Centrifuge PI Supplied Instrument Description:The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2 µm pore size polyethersulfone syringe filters. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Biospec Instruments homogenizer
Biospec Instruments homogenizer
PI Supplied Instrument Name: Biospec Instruments homogenizer PI Supplied Instrument Description:Briefly, tissues were homogenized in sterile, 0.02 µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Incubator
Incubator
PI Supplied Instrument Name: Incubator PI Supplied Instrument Description:Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37 °C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80 °C until further processing. Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled.
Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).
PI Supplied Instrument Name: PI Supplied Instrument Description:Specimens (n = 4) of grossly normal H. floridana were collected offshore of Marathon, Florida (24.7592N, 81.1076W), on 2023-08-25 and immediately subsampled by five mm biopsy punches, which were transferred to sterile cryovials per Crandell et al. (2023). Instrument Name: Manual Biota Sampler Instrument Short Name:Manual Biota Sampler Instrument Description: "Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/90/