http://lod.bco-dmo.org/id/dataset/964236
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
2025-06-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI Metagenomic metadata for Lau Basin (Tonga) mollusc gill tissue collected on R/V Thompson cruises TN235 and TN401 and R/V Falkor cruise FK160407 between May 2009 and Apr 2022
2025-08-06
publication
2025-08-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-08-06
publication
https://doi.org/10.26008/1912/bco-dmo.964236.1
Roxanne A. Beinart
University of Rhode Island
principalInvestigator
Corinna Breusing
University of Rhode Island
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: Breusing, C., Beinart, R. A. (2025) NCBI Metagenomic metadata for Lau Basin (Tonga) mollusc gill tissue collected on R/V Thompson cruises TN235 and TN401 and R/V Falkor cruise FK160407 between May 2009 and Apr 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964236.1 [access date]
Metagenomic sequence metadata Dataset Description: Methods and Sampling: <p>Samples were collected between May 2009 to April 2022 aboard R/V Thompson cruises TN235 (May-June 2009) and TN401 (April 2016) and R/V Falkor cruise FK160407 (April 2022) using the&nbsp;ROV Jason.</p>
<p>Mollusc samples were collected with remotely operated vehicles from hydrothermal vent fields along the Eastern Lau Spreading Center-Valu Fa Ridge and Tonga Volcanic Arc.&nbsp;On board the ship, the symbiont-containing gill tissue of each animal was excised and either flash-frozen or stored in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) at –80°C. DNA was extracted with the E.Z.N.A Mollusc DNA Kit (Omega Bio-tek, Norcross, GA) at the University of Rhode Island and sent to Psomagen, Inc. (Rockville, MD, USA) for metagenomic library preparation and sequencing. Libraries were prepared with the plexWell384 and Twist 96-Plex kits and 150 bp paired-end sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736932 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736932
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737145 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737145
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737382 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737382
completed
Roxanne A. Beinart
University of Rhode Island
401-874-6492
215 South Ferry Road
Narragansett
RI
02882
USA
rbeinart@uri.edu
pointOfContact
Corinna Breusing
University of Rhode Island
cbreusing@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Bioproject_accession
Biosample_accession
Host_species
Tissue_type
Latitude
Longitude
Collection_date
Cruise
Depth
MAG_biosample_accession
Sequencing_technologies
SRA_Study
SRA_accession
Assembly_methods
Symbiont_MAG_ID
MAG_acc
MAG_organism
Host_AphiaID_accepted
Host_LSID
Illumina NovaSeq 6000
NovaSeq X Plus
ROV Jason
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
species scientific name (binomial)
sample description
latitude
longitude
date
Cruise identfier
depth
seq_descrip
NCBI SRA study accession (SRP)
NCBI SRA run accession (SRR)
NCBI Genbank nucleotide accession
taxon
taxon_code
Life Science Identifier (LSID)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
ROV Jason
instrument
BCO-DMO Standard Instruments
TN401
TN235
FK160407
service
Deployment Activity
Eastern Lau Spreading Center, Valu Fa Ridge, and Mata Tolu Kingdom of Tonga
Eastern Lau Spreading Center
Tonga and Fiji
place
Locations
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.
RUI: Collaborative Research: The impact of symbiont-larval interactions on species distributions across southwestern Pacific hydrothermal vents
https://osprey.bco-dmo.org/project/775985
RUI: Collaborative Research: The impact of symbiont-larval interactions on species distributions across southwestern Pacific hydrothermal vents
<p>NSF Abstract:</p>
<p>Symbiosis with microbes is ubiquitous and critical to fundamental biological functions such as development and nutrition. Thus, the success of a host animal may depend on its ability to find and associate with its microbial partner(s). While some hosts directly transmit their symbionts from parent to offspring in order to guarantee this, acquisition of microbial symbionts from the environment is vital for the survival of many obligately-symbiotic animals. An understanding of the free-living symbiont population and how the host acquires those symbionts is fundamental to our comprehension of ecological processes in all ecosystems, yet almost nothing is known about either. Hydrothermal vent ecosystems provide important opportunities to investigate the role of microbial symbionts in host-, community-, and ecosystem-level ecology, since these ecosystems are dominated by animals whose survival is clearly linked to the acquisition of one or a few specific symbionts. This project begins to fill a gap in our understanding of the factors driving community structure at hydrothermal vents by addressing the potential for free-living symbiont populations to affect host animal establishment, while also expanding our general knowledge regarding the impact of host-associated microbes on fundamental ecological processes that apply across ecosystems. The results of this project will be shared via educational videos and live-broadcasts to the Smithsonian Institution's National Museum of Natural History and University-run museums. The investigators will also design and implement an educational program about symbiosis and hydrothermal vent biology suitable for middle and high school classes. Finally, the investigators will train a diverse group of undergraduate and graduate students in both research and the development of science educational programs.</p>
<p>This project will focus on two sister genera of snails, Alviniconcha and Ifremeria, which predominate at vents in the southwestern Pacific. At vents in the Lau Basin (Tonga), three species of Alviniconcha and one species of Ifremeria coexist. These four species all host distinct lineages of chemoautotrophic proteobacteria in their gill tissue as adults that provide the bulk of their nutrition. Previous work in this region showed a structured snail species distribution that corresponds to the concentrations of key chemical substrates for symbiont chemoautotrophic metabolism, suggesting that snail species are sorting into geochemical habitats based on symbiont physiology. It is not clear if this sorting is occurring among established snail-bacteria symbioses, or whether environmental effects on the availability of specific symbionts are influencing the recruitment of host species, since arriving and developing snail larvae must obtain their symbionts from the environment. This study aims to 1) assess the larval supply and population structure of symbiotic vent snails via collections of larval, juvenile, and adult snails, 2) investigate the developmental timing of symbiont acquisition through microscopy and marker gene sequencing of gametes, larvae, and juveniles, and 3) use metagenomic sequencing to quantify the availability of free-living symbionts in the environment to arriving larvae. Altogether, this series of interlinked efforts will allow for an improved understanding of free-living bacterial symbiont populations, the timing of symbiont acquisition, and host snail life history, as well as how these things interact to shape vent communities.</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>
symbiont-larval interactions
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Lau Spreading Center, Valu Fa Ridge, and Mata Tolu Kingdom of Tonga; Eastern Lau Spreading Center; Tonga and Fiji
-176.6
-173.79
-22.18
-15
2009-05-22
2022-04-30
Eastern Lau Spreading Center, Tonga
0
BCO-DMO catalogue of parameters from NCBI Metagenomic metadata for Lau Basin (Tonga) mollusc gill tissue collected on R/V Thompson cruises TN235 and TN401 and R/V Falkor cruise FK160407 between May 2009 and Apr 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/966335.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID is composed of the ROV Dive #_collection container ID - specimen #</p>
http://lod.bco-dmo.org/id/dataset-parameter/966336.rdf
Name: Bioproject_accession
Units: unitless
Description: <p>NCBI Bioproject accession number associated with this data</p>
http://lod.bco-dmo.org/id/dataset-parameter/966337.rdf
Name: Biosample_accession
Units: unitless
Description: <p>NCBI Specimen Biosample accession number associated with this data</p>
http://lod.bco-dmo.org/id/dataset-parameter/966338.rdf
Name: Host_species
Units: unitless
Description: <p>Molluscan host species</p>
http://lod.bco-dmo.org/id/dataset-parameter/966339.rdf
Name: Tissue_type
Units: unitless
Description: <p>Tissue type that sample originated from</p>
http://lod.bco-dmo.org/id/dataset-parameter/966340.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection, negative is South</p>
http://lod.bco-dmo.org/id/dataset-parameter/966341.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection, negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/966342.rdf
Name: Collection_date
Units: unitless
Description: <p>Date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/966343.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/966344.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of collection in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/966345.rdf
Name: MAG_biosample_accession
Units: unitless
Description: <p>NCBI Biosample accession for metagenome-assembled genomes (MAGs)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966346.rdf
Name: Sequencing_technologies
Units: unitless
Description: <p>Technology used for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/966347.rdf
Name: SRA_Study
Units: unitless
Description: <p>NCBI Short-Read Archive (SRA) study ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/966348.rdf
Name: SRA_accession
Units: unitless
Description: <p>NCBI Short-Read Archive (SRA) sequence accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/966349.rdf
Name: Assembly_methods
Units: unitless
Description: <p>Method used to assemble metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/966350.rdf
Name: Symbiont_MAG_ID
Units: unitless
Description: <p>ID for the symbiont metagenome-assembled genome (MAG)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966351.rdf
Name: MAG_acc
Units: unitless
Description: <p>NCBI Accession for metagenome-assembled genomes (MAGs)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966352.rdf
Name: MAG_organism
Units: unitless
Description: <p>Taxonomic assignment for the symbiont metageome-assembled genome (MAG)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966353.rdf
Name: Host_AphiaID_accepted
Units: unitless
Description: <p>AphiaID of Molluscan host species</p>
http://lod.bco-dmo.org/id/dataset-parameter/966354.rdf
Name: Host_LSID
Units: unitless
Description: <p>LSID of Molluscan host species</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
150615
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6e97c948-63b0-462b-9a93-0b9ae207f630/content
download
https://doi.org/10.26008/1912/bco-dmo.964236.1
download
onLine
dataset
<p>Samples were collected between May 2009 to April 2022 aboard R/V Thompson cruises TN235 (May-June 2009) and TN401 (April 2016) and R/V Falkor cruise FK160407 (April 2022) using the&nbsp;ROV Jason.</p>
<p>Mollusc samples were collected with remotely operated vehicles from hydrothermal vent fields along the Eastern Lau Spreading Center-Valu Fa Ridge and Tonga Volcanic Arc.&nbsp;On board the ship, the symbiont-containing gill tissue of each animal was excised and either flash-frozen or stored in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) at –80°C. DNA was extracted with the E.Z.N.A Mollusc DNA Kit (Omega Bio-tek, Norcross, GA) at the University of Rhode Island and sent to Psomagen, Inc. (Rockville, MD, USA) for metagenomic library preparation and sequencing. Libraries were prepared with the plexWell384 and Twist 96-Plex kits and 150 bp paired-end sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.</p>
Specified by the Principal Investigator(s)
- Imported "TN401_Metagenomic_Sequencing_NCBI.xlsx" into the BCO-DMO system
- Split "Lat_lon" column into Latitude and Longitude in decimal degrees
- Converted date to ISO YYYY-MM-DD format
- Added accepted AphiaID and LSID for host species in "Host_AphiaID_accepted" and "Host_LSID"
- Exported file as "964236_v1_metagenomic_seq_ncbi.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 NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:These samples were sequenced with Illumina NovaSeq 6000 and NovaSeq X Plus instruments. 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.
NovaSeq X Plus
NovaSeq X Plus
PI Supplied Instrument Name: NovaSeq X Plus PI Supplied Instrument Description:These samples were sequenced with Illumina NovaSeq 6000 and NovaSeq X Plus instruments. 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.
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:Samples were collected between May 2009 to April 2022 aboard R/V Thompson cruises TN235 (May-June 2009) and TN401 (April 2016) and R/V Falkor cruise FK160407 (April 2022) using the ROV Jason. Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument Description: The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/
Cruise: TN401
TN401
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN401
Roxanne A. Beinart
University of Rhode Island
https://doi.org/10.23860/TN401report
Report describing TN401
Cruise: TN235
TN235
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN235
Charles Fisher
Pennsylvania State University
Cruise: FK160407
FK160407
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK160407
Charles Fisher
Pennsylvania State University
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel