http://lod.bco-dmo.org/id/dataset/964227
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)
16S rRNA gene amplicon sequences metadata collected from water samples and biofilms on mineral substrates deployed in the Lau Basin (Tonga) during R/V Thompson cruise TN401 from Mar to Apr 2022
2025-06-11
publication
2025-06-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-08-06
publication
https://doi.org/10.26008/1912/bco-dmo.964227.1
Roxanne A. Beinart
University of Rhode Island
principalInvestigator
Corinna Breusing
University of Rhode Island
principalInvestigator
Michelle Hauer
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: Hauer, M., Breusing, C., Beinart, R. A. (2025) 16S rRNA gene amplicon sequences metadata collected from water samples and biofilms on mineral substrates deployed in the Lau Basin (Tonga) during R/V Thompson cruise TN401 from Mar to Apr 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964227.1 [access date]
16S rRNA amplicon sequence metadata from water samples and biofilms Dataset Description: Methods and Sampling: <p>We sequenced the 16S V4 hypervariable region of deep-water samples collected with a Suspended Particulate Rosette Sampler (SuPR) (Mclane Research Laboratories, Inc. Falmouth, MA USA)&nbsp;or Universal Fluid Obtainer (UFO) (National Deep Submergence Facility, Falmouth, MA, USA) using the&nbsp;ROV Jason. At each vent field 15.71–47.51 L of water were pumped through 2–4 0.22 µM Express Plus Membrane filters (MilliporeSigma, MA, USA) both within close proximity to hydrothermal vent animal communities (~10-20 cm above animal assemblages) and away from hydrothermal activity (~10s to 100s of meters distance). A 10 µM custom nylon mesh pre-filter (Sefar Inc., NY, USA) was assembled in front of each sample filter to prevent collection of microbes associated with shed animal cells. Because the SuPR device failed during deployment at Tu’i Malila and during one dive at each ABE and Kilo Moana, 10.5 L deep water samples were additionally taken with the UFO at these localities. To account for cross-contamination using this device, empty filters were deployed but not pumped and used as negative controls.&nbsp;On board ship, filters were preserved in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and frozen at –80°C. DNA from filter samples was extracted with a phenol:chloroform protocol. The 3 Strain Tagged Genomic DNA Even Mix (ATCC, VA, USA) was added as spike-in control and dilutions of the spike-in without DNA extract were prepared to assess cross-contamination during sample processing in the laboratory.&nbsp;</p>
<p>For the collection of microbial biofilms on various mineral and other substrates, we used weighted PVC bait cages containing vertically held open-ended 2-mL polypropylene tubes packed with crushed mineral substrates (andesite, basalt, glass beads or <em>Alviniconcha</em> shells) and contained by window screen mesh on either end for microbial colonization. Three of these cages were deployed during the first dive at each vent field and recovered approximately two weeks later using the ROV Jason. On board ship, water and biofilm samples were preserved in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and frozen at –80°C.&nbsp;DNA from substrate biofilms was extracted with the E.Z.N.A. Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA), including an additional 45 second bead beating step prior to proteinase K digestion.</p>
<p><!--StartFragment-->Samples were sequenced at the&nbsp;Argonne National Laboratory (Lemont, IL, USA) using amplicon library preparation with the 515F/806R primer pairs (Apprill et al. 2015; Parada et al. 2016). All libraries were 2x150 bp paired-end sequenced on a Illumina NextSeq2000 instrument.<!--EndFragment--></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
Michelle Hauer
University of Rhode Island
mhauer@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Bioproject_accession
Biosample_accession
Collection_date
Latitude
Longitude
Depth
Sample_type
Colonizer_No
SRA_Study
SRA_accession
Sequencing_technologies
Illumina NextSeq2000
Suspended Particulate Rosette Sampler (SuPR) or Universal Fluid Obtainer (UFO)
ROV Jason
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
date
latitude
longitude
depth
sample type
sample description
NCBI SRA study accession (SRP)
NCBI SRA run accession (SRR)
seq_descrip
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Discrete water sampler
ROV Jason
instrument
BCO-DMO Standard Instruments
TN401
service
Deployment Activity
Eastern Lau Spreading Center, Valu Fa Ridge, and Mata Tolu Kingdom of Tonga
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
-176.57
-176.13
-21.99
-20.05
2022-03-23
2022-05-08
Eastern Lau Spreading Center, Tonga
0
BCO-DMO catalogue of parameters from 16S rRNA gene amplicon sequences metadata collected from water samples and biofilms on mineral substrates deployed in the Lau Basin (Tonga) during R/V Thompson cruise TN401 from Mar to 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/964643.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID is composed of the ROV Dive #_Vent Field ID (KM = Kilo Moana, TC = Tow Cam, THM = Tahi Moana, ABE = ABE, TM = Tu'i Malila, M = Mariner, MT = Mata Tolu) - Collection InstrumentFilter# (UFO = Universal Fluid Obtainer, SUPR = Suspended Particle Rosette) - Habitat type (C = control filter, SH = shell hash, BG = background, S = Sample)</p>
http://lod.bco-dmo.org/id/dataset-parameter/964644.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/964645.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/964646.rdf
Name: Collection_date
Units: unitless
Description: <p>Date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/964647.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Collection latitude, postive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/964648.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Collection longitude, negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/964649.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of collection in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/964650.rdf
Name: Sample_type
Units: unitless
Description: <p>Type of sample (hydrothermal fluid or seawater), deployment control (sample filter = filter was deployed but not used), mineral or other substrate deployed for this particular sample (Colonizer substrate: Alviniconcha shell, glass beads, andesite, or basalt), or analytical control (PCR water or dilution of the synthetic genomes used spiked into the samples for absolute quantification methods)</p>
http://lod.bco-dmo.org/id/dataset-parameter/964651.rdf
Name: Colonizer_No
Units: unitless
Description: <p>Substrate colonizer number</p>
http://lod.bco-dmo.org/id/dataset-parameter/964652.rdf
Name: SRA_Study
Units: unitless
Description: <p>NCBI Short-Read Archive (SRA) study ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/964653.rdf
Name: SRA_accession
Units: unitless
Description: <p>NCBI Short-Read Archive (SRA) sequence accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/964654.rdf
Name: Sequencing_technologies
Units: unitless
Description: <p>Technology used for sequencing</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
14471
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/06091c40-9d11-4a4a-99f8-c3f5f6455741/content
download
https://doi.org/10.26008/1912/bco-dmo.964227.1
download
onLine
dataset
<p>We sequenced the 16S V4 hypervariable region of deep-water samples collected with a Suspended Particulate Rosette Sampler (SuPR) (Mclane Research Laboratories, Inc. Falmouth, MA USA)&nbsp;or Universal Fluid Obtainer (UFO) (National Deep Submergence Facility, Falmouth, MA, USA) using the&nbsp;ROV Jason. At each vent field 15.71–47.51 L of water were pumped through 2–4 0.22 µM Express Plus Membrane filters (MilliporeSigma, MA, USA) both within close proximity to hydrothermal vent animal communities (~10-20 cm above animal assemblages) and away from hydrothermal activity (~10s to 100s of meters distance). A 10 µM custom nylon mesh pre-filter (Sefar Inc., NY, USA) was assembled in front of each sample filter to prevent collection of microbes associated with shed animal cells. Because the SuPR device failed during deployment at Tu’i Malila and during one dive at each ABE and Kilo Moana, 10.5 L deep water samples were additionally taken with the UFO at these localities. To account for cross-contamination using this device, empty filters were deployed but not pumped and used as negative controls.&nbsp;On board ship, filters were preserved in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and frozen at –80°C. DNA from filter samples was extracted with a phenol:chloroform protocol. The 3 Strain Tagged Genomic DNA Even Mix (ATCC, VA, USA) was added as spike-in control and dilutions of the spike-in without DNA extract were prepared to assess cross-contamination during sample processing in the laboratory.&nbsp;</p>
<p>For the collection of microbial biofilms on various mineral and other substrates, we used weighted PVC bait cages containing vertically held open-ended 2-mL polypropylene tubes packed with crushed mineral substrates (andesite, basalt, glass beads or <em>Alviniconcha</em> shells) and contained by window screen mesh on either end for microbial colonization. Three of these cages were deployed during the first dive at each vent field and recovered approximately two weeks later using the ROV Jason. On board ship, water and biofilm samples were preserved in RNALater™ (Thermo Fisher Scientific, Inc., Waltham, MA, USA) and frozen at –80°C.&nbsp;DNA from substrate biofilms was extracted with the E.Z.N.A. Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA), including an additional 45 second bead beating step prior to proteinase K digestion.</p>
<p><!--StartFragment-->Samples were sequenced at the&nbsp;Argonne National Laboratory (Lemont, IL, USA) using amplicon library preparation with the 515F/806R primer pairs (Apprill et al. 2015; Parada et al. 2016). All libraries were 2x150 bp paired-end sequenced on a Illumina NextSeq2000 instrument.<!--EndFragment--></p>
Specified by the Principal Investigator(s)
- Imported "TN401_16S_Sequencing_NCBI.xlsx" into BCO-DMO system
- Split lat and lon into two fields, with negative and positive decimal degrees
- Removed period from parameter name
- Exported file as "964227_v1_tn401_16s_sequencing_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 NextSeq2000
Illumina NextSeq2000
PI Supplied Instrument Name: Illumina NextSeq2000 PI Supplied Instrument Description:Samples were sequenced at the Argonne National Laboratory (Lemont, IL, USA) using amplicon library preparation with the 515F/806R primer pairs (Apprill et al. 2015; Parada et al. 2016). All libraries were 2x150 bp paired-end sequenced on a Illumina NextSeq2000 instrument 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.
Suspended Particulate Rosette Sampler (SuPR) or Universal Fluid Obtainer (UFO)
Suspended Particulate Rosette Sampler (SuPR) or Universal Fluid Obtainer (UFO)
PI Supplied Instrument Name: Suspended Particulate Rosette Sampler (SuPR) or Universal Fluid Obtainer (UFO) PI Supplied Instrument Description:We sequenced the 16S V4 hypervariable region of deep-water samples collected with a Suspended Particulate Rosette Sampler (SuPR) (Mclane Research Laboratories, Inc. Falmouth, MA USA) or Universal Fluid Obtainer (UFO) (National Deep Submergence Facility, Falmouth, MA, USA). Instrument Name: Discrete water sampler Instrument Short Name: Instrument Description: A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:16S rRNA gene amplicon sequences were generated from seawater or hydrothermal fluid samples collected on to filters via ROV deployed instruments. 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
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel