http://lod.bco-dmo.org/id/dataset/717763
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
2017-10-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 2011
2022-05-23
publication
2022-05-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-05-24
publication
https://doi.org/10.26008/1912/bco-dmo.717763.2
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
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: Martínez Martínez, J. (2022) Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2022-05-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.717763.2 [access date]
Single Amplified Virus Genome sequence accessions at NCBI Dataset Description: <p>This dataset contains information related to Single Amplified Virus Genomes originated from hydrothermal fluids collected at a deep-sea subsurface observatory.&nbsp;&nbsp;The accession numbers included in the dataset correspond to genetic sequences at the National Center for Biotechnology Information (NCBI,&nbsp;<a href="https://www.ncbi.nlm.nih.gov/" target="_blank">https://www.ncbi.nlm.nih.gov/</a>). Genetic accessions are available at NCBI under BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA398661">PRJNA398661</a>.</p>
<p>The sampling location was the Integrated Ocean Drilling Program (IODP) Hole U1362B subseafloor borehole&nbsp;("CORK") observatory located at the Juan de Fuca Ridge Flank (47.75833, -127.76219) at a depth of&nbsp;2658 m (280 m below seafloor).&nbsp; The samples were collected during ROV Jason dives conducted from the R/V Atlantis cruise AT18-07 on July 8th, 2011.</p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology:&nbsp;&nbsp;</strong></p>
<p>Deep-sea hydrothermal fluid samples were collected from the IODP Hole U1362B CORK observatory using a custom syringe sampler fired in the 'shimmering' effluent of a free-flow chimney connected to the ball valve of the CORK well-head. Upon recovery, fluids for this project were fixed with a glycerol Tris-EDTA buffer for subsequent single virus sorting and genomic analysis. Single virus-like particles were sorted separately by fluorescence activated sorting. DNA was amplified by Multiple Displacement Amplification.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
410-221-1819
2020 Horns Point Road AREL 239
Cambridge
MD
21613
USA
jmartinez@umces.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Species_Name
Sample_Name
BioSample
SRA
NCBI_BioProject
Types_of_Sequences
Location_collected
Lat
Lon
Date_Collected
Sequencing_method
Analysis_method
Organism
Description
theme
None, User defined
sample description
sample identification
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
NCBI BioProject accession
site
latitude
date
featureType
BCO-DMO Standard Parameters
AT18-07
service
Deployment Activity
Pacific North-West
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Viral genetic richness and functions that shape the microbial community at the Juan de Fuca Ridge
https://osprey.bco-dmo.org/project/712820
Viral genetic richness and functions that shape the microbial community at the Juan de Fuca Ridge
<p><em>Project abstract from <a href="http://www.darkenergybiosphere.org/award/viral-genetic-richness-and-functions-that-shape-the-microbial-community-at-the-juan-de-fuca-ridge/" target="_blank">C-DEBI</a>:</em><br />
Deep-sea subsurface habitats support novel and abundant microbial life. Recently, several studies have explored the phylogenetic diversity of microorganisms, mostly bacteria and archaea, in those environments. Viruses are key components of microbial assemblages, hence, the need to investigate them to better understand the deep biosphere’s ecology. In this study, we performed genomic analysis of 27 targeted flow cytometry-sorted viruses and 3 microbial cells from a one-milliliter hydrothermal fluid sample collected from IODP Hole U1362B CORK observatory at the Juan de Fuca Ridge (JFR) eastern flank. Preliminary results revealed a diverse viral community, as no two sorted viruses were identical to each other. The majority of predicted genes within the partially-sequenced viral genomes had no homology in databases. Phylogenetic analysis of the identified viral genes indicated that the viruses were most similar to large inducible lysogenic myoviruses. Additionally, the discovery of a cell from benthic group E (<em>Euryarchaeota</em>), a key member of the microbial community, containing a prophage in its genome supports the hypothesis that lysogeny is likely more pervasive than lytic infections in the deep biosphere. However, these results might reflect inherited flow cytometry and nucleic acids multiple displacement amplification biases toward large dsDNA viruses (e.g. myoviruses). On the other hand this approach allows investigating larger viruses typically removed by filtration in traditional metagenomics studies, and thus aids in providing a more complete picture of viral assemblages. This exploratory proposal is in line with two of the four C-DEBI research themes: Extent of Life, and Evolution and Survival.</p>
<p>This project was funded by a <a href="http://www.darkenergybiosphere.org/research-activities/research-support/research-grants/" target="_blank">C-DEBI Research Grant</a>.</p>
Juan de Fuca Viruses
largerWorkCitation
project
eng; USA
oceans
Pacific North-West
-127.76219
-127.76219
47.75833
47.75833
2016-03-11
2016-03-11
IODP Hole U1362B CORK observatory at the Juan de Fuca Ridge (JFR) eastern flank
0
BCO-DMO catalogue of parameters from Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 2011
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/874786.rdf
Name: Species_Name
Units: unitless
Description: <p>Species Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/874787.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/874788.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/874789.rdf
Name: SRA
Units: unitless
Description: <p>NCBI Sequence Read Archive Sample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/874790.rdf
Name: NCBI_BioProject
Units: unitless
Description: <p>NCBI BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/874791.rdf
Name: Types_of_Sequences
Units: unitless
Description: <p>Sequence type (e.g. dsDNA genome)</p>
http://lod.bco-dmo.org/id/dataset-parameter/874792.rdf
Name: Location_collected
Units: unitless
Description: <p>Geolocation of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/874793.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitute of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/874794.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/874795.rdf
Name: Date_Collected
Units: unitless
Description: <p>Collection date in ISO 8601 format YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/874796.rdf
Name: Sequencing_method
Units: unitless
Description: <p>Sequencing method</p>
http://lod.bco-dmo.org/id/dataset-parameter/874797.rdf
Name: Analysis_method
Units: unitless
Description: <p>Analysis method</p>
http://lod.bco-dmo.org/id/dataset-parameter/874798.rdf
Name: Organism
Units: unitless
Description: <p>Organism (e.g. viral metagenome)</p>
http://lod.bco-dmo.org/id/dataset-parameter/874799.rdf
Name: Description
Units: unitless
Description: <p>Description</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
2923
https://darchive.mblwhoilibrary.org/bitstream/1912/28909/1/dataset-717763_juan-de-fuca-viruses__v2.tsv
download
https://doi.org/10.26008/1912/bco-dmo.717763.2
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology:&nbsp;&nbsp;</strong></p>
<p>Deep-sea hydrothermal fluid samples were collected from the IODP Hole U1362B CORK observatory using a custom syringe sampler fired in the 'shimmering' effluent of a free-flow chimney connected to the ball valve of the CORK well-head. Upon recovery, fluids for this project were fixed with a glycerol Tris-EDTA buffer for subsequent single virus sorting and genomic analysis. Single virus-like particles were sorted separately by fluorescence activated sorting. DNA was amplified by Multiple Displacement Amplification.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* Since data are now public at NCBI, added columns&nbsp;Sample_Name,BioSample,SRA,Organism and remove Submission identifier.<br />
* Added columns Lat,Lon to data table from metadata information.</p>
Specified by the Principal Investigator(s)
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: 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
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel