Dataset: Metagenome sequencing samples

Name: 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
Published: 2024-12-12
Keywords: deep subseafloor, microbiome, metagenome, marine, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.945915.1

Spatial Extent: N:47.88745 E:-127.7592 S:47.75348333 W:-128.64865

Northeast Pacific Ocean along the Juan de Fuca ridge flank

Temporal Extent: 2008-08-07 - 2014-08-21

Project:

Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches (JdFR Strain level)

Principal Investigator:

Stephanie Carr (Hartwick College)

Olivia Nigro (Hawaii Pacific University, HPU)

Michael S. Rappé (University of Hawaiʻi at Mānoa, HIMB)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-12-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

This dataset provides contextual information about samples used for metagenome sequencing. These samples were collected from pristine crustal fluids sampled via CORK observatories along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean off the coast of North America. Also included are metadata for seawater and sediment metagenomes that have been sequenced as controls. All of the data are publicly available via the National Center for Biotechnology Information (NCBI) accession numbers provided in the dataset (BioProject numbers PRJNA655018 to PRJNA655040).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-12-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.945915.1	2025-01-02

Methods & Sampling

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:

2008 cruise: AT15-35, James Cowen (Chief Sci)
2009 cruise: AT15-51, Andrew Fisher (Chief Sci)
2010 cruise: AT15-66, James Cowen (Chief Sci)
2011 cruise: AT18-07, Andrew Fisher (Chief Sci)
2013 cruise: AT26-03, Andrew Fisher (Chief Sci)
2014 cruise: AT26-18, Geoff Wheat (Chief Sci)

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.

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).

BCO-DMO Processing

- 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".

Data Files

File
945915_v1_sequencing_samples.csv (Comma Separated Values (.csv), 10.73 KB) MD5:fec734c132e2520c682759bab62adcef Primary data file for dataset ID 945915, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851582
NSF Division of Ocean Sciences	OCE-1851045
NSF Division of Ocean Sciences	OCE-1851099

Deployments

Deployment	Start Date	Platform	Investigator
AT15-35	2008-07-28	R/V Atlantis	James Cowen (Chief Scientist)	data info
AT15-51	2009-08-20	R/V Atlantis	Andrew Fisher (Chief Scientist)	data info
AT15-66	2010-06-15	R/V Atlantis	James Cowen (Chief Scientist)	data info
AT18-07	2011-06-29	R/V Atlantis	Andrew Fisher (Chief Scientist)	data info
AT26-03	2013-07-13	R/V Atlantis	Andrew Fisher (Chief Scientist)	data info
AT26-18	2014-08-10	R/V Atlantis	C. Geoffrey Wheat (Chief Scientist) Keir Becker (Co-Chief Scientist) Jordan Clark (Co-Chief Scientist) Katrina Edwards (Co-Chief Scientist) Andrew Fisher (Co-Chief Scientist) Michael S. Rappé (Co-Chief Scientist)	data info

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Type	Type of sample	unitless	sample_type
Sample_Name	Sample name	unitless	sample
DNA_Isolation_Method	DNA isolation method: MoBio Powersoil, Phenol, Zymobiomics, or mixed.	unitless	sampling_method
Collection_Date	Collection date Format: %Y-%m-%d	unitless	date
Collection_Year	Collection year	unitless	year
Collection_Month	Collection month	unitless	month
Collection_Day	Day of month of collection	unitless	day
Sample_Source	Sample source location	unitless	sample_descrip
Fluid_Delivery_Line	Type of fluid delivery line: stainless steel or Tefzel.	unitless	sample_descrip
Environment	Description of sample environment: seawater, sediment, or subseafloor crustal fluid.	unitless	sample_descrip
Latitude	Latitude of sample collection	decimal degrees North	lat
Longitude	Longitude of sample collection	decimal degrees East	lon
Depth	Depth of sample collection. "msb" refers to "meters sub-basement", or the depth in meters below the sediment-basement interface.	msb	depth_bsf
Area	Geographic area of sample collection	unitless	ocean
Full_Sample_Name_and_Description	Sample name and description	unitless	sample
IMG_Genome_ID	Joint Genome Institute (JGI) IMG ID number (https://img.jgi.doe.gov/)	unitless	accession_number
NCBI_Bioproject_Accession	National Center for Biotechnology Information (NCBI) BioProject accession number (https://www.ncbi.nlm.nih.gov/)	unitless	BioProject
NCBI_Biosample_Accession	National Center for Biotechnology Information (NCBI) BioSample accession number (https://www.ncbi.nlm.nih.gov/)	unitless	BioSample
SRA_ID	National Center for Biotechnology Information (NCBI) SRA experiment accession (https://www.ncbi.nlm.nih.gov/)	unitless	SRA_experiment