http://lod.bco-dmo.org/id/dataset/945915
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
2024-12-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014
2024-12-12
publication
2024-12-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-01-02
publication
https://doi.org/10.26008/1912/bco-dmo.945915.1
Stephanie Carr
Hartwick College
principalInvestigator
Olivia Nigro
Hawaii Pacific University
principalInvestigator
Michael S. Rappé
University of Hawaiʻi at Mānoa
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: Rappé, M. S., Nigro, O., Carr, S. (2025) Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-12-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.945915.1 [access date]
Metagenome sequencing samples Dataset Description: Methods and Sampling: <p>Samples were collected from the Northeast Pacific Ocean along the Juan de Fuca ridge flank, off of the continent of North America. CORK observatories are on the seafloor at a water column depth of approximately 2660 meters. CORKs are located in the general vicinity of 47.75 lat, -127.76 lon. Samples were collected during the following R/V Atlantis cruises:</p>
<p>2008 cruise: AT15-35, James Cowen (Chief Sci)<br />
2009 cruise: AT15-51, Andrew Fisher (Chief Sci)<br />
2010 cruise: AT15-66, James Cowen (Chief Sci)<br />
2011 cruise: AT18-07, Andrew Fisher (Chief Sci)<br />
2013 cruise: AT26-03, Andrew Fisher (Chief Sci)<br />
2014 cruise: AT26-18, Geoff Wheat (Chief Sci)</p>
<p>Deep subseafloor basement crustal fluids were collected from boreholes fitted with CORKs (subseafloor borehole observatory systems) along the Juan de Fuca Ridge flank, which are located at a water column depth of approximately 2,650 meters (m) and penetrate through sediment and into the igneous basement. The CORKs fitted to these boreholes feature fluid delivery lines that access fluids at different depth horizons. Custom sampling equipment enabled the pumping of borehole fluids directly through 0.22 micrometer (µm) pore-size polyethersulfone filters or filter cartridges at the seafloor. DNA was extracted directly from the filters using either phenol-chloroform or commercially available kits, as specified in the sample log. Genomic DNA was submitted to the Joint Genome Institute for sequencing.</p>
<p>Sampling used custom-designed equipment: the Medium Volume Bag Sampler (MVBS), Large Volume Bag Sampler (LVBS), and In Situ Passive Viral Filter. These have been described in publications previously (Nigro et al., 2017; Cowen et al., 2012).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851045 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851045
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851099 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851099
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851582 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851582
completed
Stephanie Carr
Hartwick College
607-431-4410
1 Hartwick Drive
Oneonta
NY
13820
USA
carrs@hartwick.edu
pointOfContact
Olivia Nigro
Hawaii Pacific University
808-544-9338
41-202 Kalanianaole Hwy
Waimanalo
HI
96795-1898
USA
onigro@hpu.edu
pointOfContact
Michael S. Rappé
University of Hawaiʻi at Mānoa
808-372-2394
University of Hawaii at Manoa - Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rappe@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Type
Sample_Name
DNA_Isolation_Method
Collection_Date
Collection_Year
Collection_Month
Collection_Day
Sample_Source
Fluid_Delivery_Line
Environment
Latitude
Longitude
Depth
Area
Full_Sample_Name_and_Description
IMG_Genome_ID
NCBI_Bioproject_Accession
NCBI_Biosample_Accession
SRA_ID
theme
None, User defined
sample type
sample identification
sampling_method
date
year
month of year
day of month
sample description
latitude
longitude
depth below seafloor
ocean
accession number
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA experiment accession (SRX)
featureType
BCO-DMO Standard Parameters
AT15-51
AT15-66
AT18-07
AT26-18
AT15-35
AT26-03
service
Deployment Activity
Pacific North-West
Eastern Flank of Juan de Fuca Ridge
Cascadia Basin and JdF Ridge
Juan de Fuca Ridge
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.
Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches
https://osprey.bco-dmo.org/project/854575
Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches
<p><em>NSF Award Abstract:</em><br />
Our planet's seafloor consists primarily of sediment layered over a basement of basalt rock. Every 50,000 to 100,000 years, a volume of seawater equivalent to the entire global ocean circulates through cracks and fissures of this basement beneath the seafloor, forming one of the largest reservoirs for microscopic life on Earth. While high temperature fluids discharging at iconic hydrothermal vents at mid-ocean ridges are visually striking, the fluid flowing in and out of the flanks of these ridges is around three orders of magnitude greater and rivals the discharge of all rivers to the ocean. As it travels through the deep subseafloor, this fluid is significantly altered by water and rock interaction and the metabolic activity of microorganisms that are thought to ultimately help shape nutrient and energy budgets of the global ocean. However, our knowledge and understanding of this system suffer greatly from logistical difficulties in accessing it for scientific inquiry. Initial evidence suggests uncharacterized microbes that possess ancient homologs of enzymes involved in key metabolic pathways thought to be important to Earth's early microbial inhabitants populate this biome and are infected by novel viruses. In this study, the investigators are performing an integrated set of observations, experiments, and analyses aimed to advance our understanding of deep subseafloor microbes and their viruses by providing new, fundamental insights into which organisms and metabolisms are active in this environment, their evolutionary history and genetic characteristics, and their interactions. This project contributes to the development of a diverse STEM-educated workforce, and incorporate the training of one postdoctoral scientist, two graduate students, and ~29 undergraduate students in field-based research, wet-lab experimentation, and bioinformatics. This project also fosters a unique collaboration between scientists and the University of Hawaii Academy for Creative Media that supports undergraduate interns from the Academy to work with project personnel and produce creative videos and graphics to communicate aspects of our research to diverse audiences. Finally, this project supports two early career female scientists who started faculty positions in 2017.</p>
<p>This project leverages existing sampling infrastructure, DNA sequencing by the Department of Energy Joint Genome Institute, and a research expedition to the Juan de Fuca Ridge (JdFR) flank off the coast of Washington, USA, that is already supported by NSF. Here, subseafloor observatories have been previously installed to aid in exploring actively flowing subseafloor crustal fluids. These fluids will be collected from different sampling depths for an integrated set of geochemical, genomic, and cultivation studies. The project's specific objectives are to (i) use genomics to characterize microbial and viral populations inhabiting crustal fluids of the JdFR flank, (ii) use transcriptomics to identify the active metabolic pathways that are performing transformations relevant to elemental cycling within microorganisms of the JdFR flank, as well as identify active viral infections in these microbes, and (iii) generate microbial and viral pure cultures or limited diversity enrichments from crustal fluids of the JdFR flank. It combines bioinformatic analyses, controlled laboratory experiments, and field sampling to pursue both hypothesis-driven and discovery-based cultivation experiments, viral assays, and strain-level ecogenomic and metatranscriptomic analyses. Importantly, the investigators intend to generate new cultivated microbes and viruses to serve as model systems for investigating the characteristics of life in the deep ocean crust.</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>
JdFR Strain level
largerWorkCitation
project
eng; USA
oceans
Pacific North-West; Eastern Flank of Juan de Fuca Ridge; Cascadia Basin and JdF Ridge; Juan de Fuca Ridge
-128.64865
-127.7592
47.75348333
47.88745
2008-08-07
2014-08-21
Boreholes along the eastern flank of Juan de Fuca Ridge (47N, 128 W)
0
BCO-DMO catalogue of parameters from Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014
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/945992.rdf
Name: Sample_Type
Units: unitless
Description: <p>Type of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/945993.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/945994.rdf
Name: DNA_Isolation_Method
Units: unitless
Description: <p>DNA isolation method: MoBio Powersoil, Phenol, Zymobiomics, or mixed.</p>
http://lod.bco-dmo.org/id/dataset-parameter/945995.rdf
Name: Collection_Date
Units: unitless
Description: <p>Collection date</p>
http://lod.bco-dmo.org/id/dataset-parameter/945996.rdf
Name: Collection_Year
Units: unitless
Description: <p>Collection year</p>
http://lod.bco-dmo.org/id/dataset-parameter/945997.rdf
Name: Collection_Month
Units: unitless
Description: <p>Collection month</p>
http://lod.bco-dmo.org/id/dataset-parameter/945998.rdf
Name: Collection_Day
Units: unitless
Description: <p>Day of month of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/945999.rdf
Name: Sample_Source
Units: unitless
Description: <p>Sample source location</p>
http://lod.bco-dmo.org/id/dataset-parameter/946000.rdf
Name: Fluid_Delivery_Line
Units: unitless
Description: <p>Type of fluid delivery line: stainless steel or Tefzel.</p>
http://lod.bco-dmo.org/id/dataset-parameter/946001.rdf
Name: Environment
Units: unitless
Description: <p>Description of sample environment: seawater, sediment, or subseafloor crustal fluid.</p>
http://lod.bco-dmo.org/id/dataset-parameter/946002.rdf
Name: Latitude
Units: decimal degrees North
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/946003.rdf
Name: Longitude
Units: decimal degrees East
Description: <p>Longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/946004.rdf
Name: Depth
Units: msb
Description: <p>Depth of sample collection. "msb" refers to "meters sub-basement", or the depth in meters below the sediment-basement interface.</p>
http://lod.bco-dmo.org/id/dataset-parameter/946005.rdf
Name: Area
Units: unitless
Description: <p>Geographic area of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/946006.rdf
Name: Full_Sample_Name_and_Description
Units: unitless
Description: <p>Sample name and description</p>
http://lod.bco-dmo.org/id/dataset-parameter/946007.rdf
Name: IMG_Genome_ID
Units: unitless
Description: <p>Joint Genome Institute (JGI) IMG ID number (<a href="https://img.jgi.doe.gov/" target="_blank">https://img.jgi.doe.gov/</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/946008.rdf
Name: NCBI_Bioproject_Accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioProject accession number (<a href="https://www.ncbi.nlm.nih.gov/" target="_blank">https://www.ncbi.nlm.nih.gov/</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/946009.rdf
Name: NCBI_Biosample_Accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioSample accession number (<a href="https://www.ncbi.nlm.nih.gov/" target="_blank">https://www.ncbi.nlm.nih.gov/</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/946010.rdf
Name: SRA_ID
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) SRA experiment accession (<a href="https://www.ncbi.nlm.nih.gov/" target="_blank">https://www.ncbi.nlm.nih.gov/</a>)</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
10990
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/17d00c18-1e64-4767-b540-af8be979f86d/content
download
https://doi.org/10.26008/1912/bco-dmo.945915.1
download
onLine
dataset
<p>Samples were collected from the Northeast Pacific Ocean along the Juan de Fuca ridge flank, off of the continent of North America. CORK observatories are on the seafloor at a water column depth of approximately 2660 meters. CORKs are located in the general vicinity of 47.75 lat, -127.76 lon. Samples were collected during the following R/V Atlantis cruises:</p>
<p>2008 cruise: AT15-35, James Cowen (Chief Sci)<br />
2009 cruise: AT15-51, Andrew Fisher (Chief Sci)<br />
2010 cruise: AT15-66, James Cowen (Chief Sci)<br />
2011 cruise: AT18-07, Andrew Fisher (Chief Sci)<br />
2013 cruise: AT26-03, Andrew Fisher (Chief Sci)<br />
2014 cruise: AT26-18, Geoff Wheat (Chief Sci)</p>
<p>Deep subseafloor basement crustal fluids were collected from boreholes fitted with CORKs (subseafloor borehole observatory systems) along the Juan de Fuca Ridge flank, which are located at a water column depth of approximately 2,650 meters (m) and penetrate through sediment and into the igneous basement. The CORKs fitted to these boreholes feature fluid delivery lines that access fluids at different depth horizons. Custom sampling equipment enabled the pumping of borehole fluids directly through 0.22 micrometer (µm) pore-size polyethersulfone filters or filter cartridges at the seafloor. DNA was extracted directly from the filters using either phenol-chloroform or commercially available kits, as specified in the sample log. Genomic DNA was submitted to the Joint Genome Institute for sequencing.</p>
<p>Sampling used custom-designed equipment: the Medium Volume Bag Sampler (MVBS), Large Volume Bag Sampler (LVBS), and In Situ Passive Viral Filter. These have been described in publications previously (Nigro et al., 2017; Cowen et al., 2012).</p>
Specified by the Principal Investigator(s)
- Imported original file "rappe_deepSS_BCODMO.csv" into the BCO-DMO system.
- Created the Creation_Date column in YYYY-MM-DD format.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved final file as "945915_v1_sequencing_samples.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
Cruise: AT15-51
AT15-51
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-51
Andrew Fisher
University of California-Santa Cruz
Cruise: AT15-66
AT15-66
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-66
James Cowen
University of Hawai'i
Cruise: AT18-07
AT18-07
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-07
Andrew Fisher
University of California-Santa Cruz
Cruise: AT26-18
AT26-18
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT26-18
C. Geoffrey Wheat
University of Alaska Fairbanks
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/AT26-18_JFR_Cork_Recovery_Cruise_Report_reduced.pdf
Report describing AT26-18
Cruise: AT15-35
AT15-35
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-35
James Cowen
University of Hawaiʻi at Mānoa
Cruise: AT26-03
AT26-03
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT26-03
Andrew Fisher
University of California-Santa Cruz
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel