http://lod.bco-dmo.org/id/dataset/986882
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
2025-10-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenome sequences from deep-sea hydrothermal vent microbial and viral communities collected at International District hydrothermal field, Axial Seamount during 2019, 2021, 2022, and 2023
2026-01-08
publication
2026-01-08
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-01-10
publication
https://doi.org/10.26008/1912/bco-dmo.986882.1
Rika Anderson
Carleton College
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: Anderson, R. (2026) Metagenome sequences from deep-sea hydrothermal vent microbial and viral communities collected at International District hydrothermal field, Axial Seamount during 2019, 2021, 2022, and 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-01-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.986882.1 [access date]
Hydrothermal vent microbial and viral metagenomes Dataset Description: Methods and Sampling: <p>For time series collected at Tiny Towers hydrothermal vent with the PPS instrument, hydrothermal fluid samples were collected remotely and filtered through 0.4 micrometer (μm) polycarbonate filters, then preserved in RNALater in the instrument at the seafloor until instrument recovery. Upon recovery, filters were preserved at -80 degrees Celsius (C).</p>
<p>Other samples were collected using the UFO fluid sampler mounted aboard ROV Jason. Hydrothermal fluid samples were pumped through 0.2 μm Sterivex filters or into sterile 10 liter (L) bags mounted to the vehicle. Upon ROV recovery, Sterivex filters were preserved at -80 degrees C. Fluid from bags was filtered through 0.2 μm Sterivex filters, which were later preserved at -80 degrees C, and the filtrate was treated with iron chloride to precipitate viral particles. Precipitated viral particles were filtered through 1.0 μm polycarbonate filters and preserved at 4 degrees C until processing.</p>
<p>DNA was extracted from all filters using the MasterPure Complete DNA and RNA Purification Kit. Sterivex filters were cracked open prior to processing. PPS filters were cut in half prior to processing, and the second half was archived.</p>
<p>For viral metagenomes, viruses were reconstituted through an ascorbic acid buffer and then extracted using the Qiagen UltraSens Virus spin kit.</p>
<p>All samples were sequenced at the Northwest Genomics Center. Library construction was automated in 96-well plate format. At least 25 nanograms (ng) of genomic DNA was subjected to enzymatic fragmentation and a series of library construction steps utilizing the KAPA HyperPlus kit. All library construction steps were automated on the Perkin Elmer Janus platform. Libraries were validated using the Biorad CFX384 Real-Time System and KAPA Library Quantification Kit. Barcoded genome libraries were pooled using liquid handling robotics prior to loading. Massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides was carried out on the NovaSeq sequencer.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2045697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2045697
completed
Rika Anderson
Carleton College
507-222-4382
One North College Street
Northfield
MN
55057
USA
randerson@carleton.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Accession
Sample_Name
SPUID
Organism
Tax_ID
BioProject
sample_name
collection_date
collection_time
depth
env_broad_scale
env_local_scale
env_medium
geo_loc_name
latitude
longitude
collection_method
temp
NovaSeq sequencer
PPS Sampler
Biorad CFX384 Real-Time System
ROV Jason
UFO fluid sampler
theme
None, User defined
NCBI BioSample accession
sample identification
taxon
NCBI BioProject accession
date
time of day
depth
site description
site
latitude
longitude
instrument
temperature of sample or a generic measurement (not in-situ water temp)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
McLane Particle and Phytoplankton Sampler
qPCR Thermal Cycler
ROV Jason
Universal Fluid Obtainer
instrument
BCO-DMO Standard Instruments
AT42-12
TN393
TN407
TN422
service
Deployment Activity
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.
CAREER: Temporal dynamics of microbial and viral function and adaptation in hydrothermal vents
https://osprey.bco-dmo.org/project/852462
CAREER: Temporal dynamics of microbial and viral function and adaptation in hydrothermal vents
<p><em>NSF Award Abstract:</em><br />
Microbes and viruses living near deep-sea hydrothermal vents act as filters for carbon, sulfur, iron, and other essential elements that emerge from the seafloor and flow into the global oceans. However, due to the challenges associated with sampling the deep sea, most studies to date have captured only snapshots of these communities, leaving significant knowledge gaps about how microbes and viruses adapt, evolve, and respond to changes in this environment. The researchers use infrastructure from the Ocean Observatories Initiative to conduct high-resolution monitoring of genetic changes over five years to investigate microbial communities’ function, ecology, and evolution at hydrothermal vents, which are thought to be one of the most ancient habitats on Earth. Data from this project are expected to be a valuable scientific resource for these and other researchers to address future questions. For example, it will inform our understanding about the early evolution of life on Earth and how microbes and their viruses respond to anthropogenic disturbances like deep-sea mining and climate change. This project engages and trains undergraduate students as scientific partners at all stages of the research process, facilitating their entry into scientific networks. Additionally, a new course guides college students in examining science within its cultural, political, and social context. The project also includes a program with a local elementary school to increase science literacy among young students.</p>
<p>The main objective of this project is to understand the ecological and evolutionary forces that mold hydrothermal vent microbial and viral populations over time. This project uses instruments from the Ocean Observatories Initiative Regional Cabled Array (OOI RCA) at Axial Seamount in the Northeast Pacific Ocean to collect hydrothermal fluid and DNA samples at regular intervals, approximately every 10-20 days over five years, to yield a time series of microbial and viral abundances and metagenomes. The specific scientific aims of this project are to: 1) identify environmental drivers of microbial community composition and function through time-series analyses of 16S rRNA amplicon and metagenomic datasets combined with chemistry, pH, and temperature data; 2) use single nucleotide variant and gene content variation over time in metagenome-assembled genomes to investigate evolutionary dynamics of microbial populations; and 3) assess models of viral population dynamics by tracking microdiversity within viral and microbial metagenomes over time. Comparative samples and data collected from other vent sites are used to determine the generalization of the results.</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>
<p>This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2). This project is funded by the Biological Oceanography and the Ocean Education Programs (Division of Ocean Sciences) and the Systematics and Biodiversity Science Cluster (Division of Environmental Biology).</p>
Vent omics time series
largerWorkCitation
project
eng; USA
oceans
-130.013742
-125.3915667
44.53281667
45.943697
2019-06-01
2023-09-16
Axial Seamount, Juan de Fuca Ridge, North Pacific Ocean
0
BCO-DMO catalogue of parameters from Metagenome sequences from deep-sea hydrothermal vent microbial and viral communities collected at International District hydrothermal field, Axial Seamount during 2019, 2021, 2022, and 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/990437.rdf
Name: Accession
Units: unitless
Description: <p>Accession number in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/990438.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/990439.rdf
Name: SPUID
Units: unitless
Description: <p>Submitter Provided Unique ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/990440.rdf
Name: Organism
Units: unitless
Description: <p>NCBI organism. Here all are hydrothermal vent metagenome.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990441.rdf
Name: Tax_ID
Units: unitless
Description: <p>NCBI Tax ID. Here all correspond to hydrothermal vent metagenome.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990442.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990443.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990444.rdf
Name: collection_date
Units: unitless
Description: <p>Corresponds to the date (UTC) when the PPS was remotely triggered to collect the sample. Most of these samples were collected by remote triggering of an instrument deployed at the seafloor throughout the year, and the physical filters were recovered from the instruments during the cruises listed in the metadata.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990445.rdf
Name: collection_time
Units: unitless
Description: <p>Corresponds to when the PPS was remotely triggered to collect sample. Most of these samples were collected by remote triggering of an instrument deployed at the seafloor throughout the year, and the physical filters were recovered from the instruments during the cruises listed in the metadata.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990446.rdf
Name: depth
Units: meters (m)
Description: <p>Depth below sea surface in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/990447.rdf
Name: env_broad_scale
Units: unitless
Description: <p>NCBI enviromental broad scale. Here all are deep ocean.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990448.rdf
Name: env_local_scale
Units: unitless
Description: <p>NCBI environmental local scale. Here all are hydrothermal vent</p>
http://lod.bco-dmo.org/id/dataset-parameter/990449.rdf
Name: env_medium
Units: unitless
Description: <p>NCBI environmental medium scale. Here all are a mixture of hydrothermal vent fluid and seawater.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990450.rdf
Name: geo_loc_name
Units: unitless
Description: <p>NCBI Geographic location name. Here all were Pacific Ocean at Axial Seamount.</p>
http://lod.bco-dmo.org/id/dataset-parameter/990451.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/990452.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/990453.rdf
Name: collection_method
Units: unitless
Description: <p>Collection method</p>
http://lod.bco-dmo.org/id/dataset-parameter/990454.rdf
Name: temp
Units: degrees Celsius
Description: <p>Temperature</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
https://doi.org/10.26008/1912/bco-dmo.986882.1
download
onLine
dataset
<p>For time series collected at Tiny Towers hydrothermal vent with the PPS instrument, hydrothermal fluid samples were collected remotely and filtered through 0.4 micrometer (μm) polycarbonate filters, then preserved in RNALater in the instrument at the seafloor until instrument recovery. Upon recovery, filters were preserved at -80 degrees Celsius (C).</p>
<p>Other samples were collected using the UFO fluid sampler mounted aboard ROV Jason. Hydrothermal fluid samples were pumped through 0.2 μm Sterivex filters or into sterile 10 liter (L) bags mounted to the vehicle. Upon ROV recovery, Sterivex filters were preserved at -80 degrees C. Fluid from bags was filtered through 0.2 μm Sterivex filters, which were later preserved at -80 degrees C, and the filtrate was treated with iron chloride to precipitate viral particles. Precipitated viral particles were filtered through 1.0 μm polycarbonate filters and preserved at 4 degrees C until processing.</p>
<p>DNA was extracted from all filters using the MasterPure Complete DNA and RNA Purification Kit. Sterivex filters were cracked open prior to processing. PPS filters were cut in half prior to processing, and the second half was archived.</p>
<p>For viral metagenomes, viruses were reconstituted through an ascorbic acid buffer and then extracted using the Qiagen UltraSens Virus spin kit.</p>
<p>All samples were sequenced at the Northwest Genomics Center. Library construction was automated in 96-well plate format. At least 25 nanograms (ng) of genomic DNA was subjected to enzymatic fragmentation and a series of library construction steps utilizing the KAPA HyperPlus kit. All library construction steps were automated on the Perkin Elmer Janus platform. Libraries were validated using the Biorad CFX384 Real-Time System and KAPA Library Quantification Kit. Barcoded genome libraries were pooled using liquid handling robotics prior to loading. Massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides was carried out on the NovaSeq sequencer.</p>
Specified by the Principal Investigator(s)
- Imported original file "SRA_metadata_CAREER_2025.txt" into the BCO-DMO system.
- Marked "NA" as a missing data value (missing data are empty/blank in the final CSV file).
- Renamed fields to comply with BCO-DMO naming conventions.
- Split the "lat_lon" column into two separate columns, "latitude" and "longitude".
- Converted all dates in the "collection_date" column to YYYY-MM-DD format.
- Split the original "collection_date" column into two, one for date and one for time.
- Converted negative depth values to positive.
- Saved the final file as "986882_v1_hydrothermal_vent_metagenomes.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
NovaSeq sequencer
NovaSeq sequencer
PI Supplied Instrument Name: NovaSeq sequencer PI Supplied Instrument Description:Massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides was carried out on the NovaSeq sequencer. 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.
PPS Sampler
PPS Sampler
PI Supplied Instrument Name: PPS Sampler PI Supplied Instrument Description:PPS Sampler: Hydrothermal fluid samples were collected using a McLane PPS sampler deployed on the seafloor, with approximately 6L of fluid filtered through eac filter. Instrument Name: McLane Particle and Phytoplankton Sampler Instrument Short Name:PPS Instrument Description: The McLane Particle and Phytoplankton Sampler (PPS) is an autonomous time-series particulate sampler. It consists of a stainless steel frame, aluminium controller housing, 25-port valve, pump and 24-filter holders containing 47mm 0.7 micron GF/F filters. Individual water samples are collected by user-defined time-series events. The 25 port valve physically isolates samples and pumps samples through the selected filter position before passing through the 50, 125, or 250 ml/min pump. The maximum volume per sample is 10 liters. The data recorded during a deployment include flow rates, volume pumped, pump feedback, power, temperature, and event times. These data are offloaded from the PPS after deployment and used for sample analysis. It is depth-rated to 5,500 m.
Biorad CFX384 Real-Time System
Biorad CFX384 Real-Time System
PI Supplied Instrument Name: Biorad CFX384 Real-Time System PI Supplied Instrument Description:Libraries were validated using the Biorad CFX384 Real-Time System and KAPA Library Quantification Kit. Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:Hydrothermal fluid samplers were collected using the UFO fluid sampler mounted to 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/
UFO fluid sampler
UFO fluid sampler
PI Supplied Instrument Name: UFO fluid sampler PI Supplied Instrument Description:Hydrothermal fluid samplers were collected using the UFO fluid sampler mounted to ROV Jason. Instrument Name: Universal Fluid Obtainer Instrument Short Name:UFO Instrument Description: The Universal Fluid Obtainer (UFO) is a specialized, community-developed fluid sampler designed to collect deep-sea fluids (like water and gases) from hydrothermal vents and other seafloor environments. It can be used with vehicles operated by the National Deep Submergence Facility (NDSF), including ROV Jason and HOV Alvin.
The UFO uses positive pumping and in situ filtering and preservation to capture fluids and preserve them for analysis back on the ship or in labs.
Cruise: AT42-12
AT42-12
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT42-12
Deborah Kelley
University of Washington
Cruise: TN393
TN393
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN393
Michael Vardaro
University of Washington
Cruise: TN407
TN407
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN407
Orest Kawka
University of Washington
Cruise: TN422
TN422
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN422
Deborah Kelley
University of Washington
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel