http://lod.bco-dmo.org/id/dataset/626625
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
2015-11-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Assessments of bacterial and archaeal diversity from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge from R/V Atlantis cruise AT15-67 in the Juan de Fuca Ridge in 2010
2015-11-17
publication
2015-11-17
revision
BCO-DMO Linked Data URI
2015-11-17
creation
http://lod.bco-dmo.org/id/dataset/626625
Peter Girguis
Harvard University
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: Girguis, P. (2015) Assessments of bacterial and archaeal diversity from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge from R/V Atlantis cruise AT15-67 in the Juan de Fuca Ridge in 2010. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 17 November 2015) Version Date 2015-11-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626625 [access date]
Assessments of bacterial and archaeal diversity from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge. Dataset Description: <p>Assessments of bacterial and archaeal diversity from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge. Samples were recovered from actively venting sulfide deposits in the Middle Valley vent field along the Juan de Fuca Ridge at Needles (48.45778, -128.709), Dead Dog (48.45603,-128.71), and Chowder Hill (48.455543, -128.709) vents.</p>
<p><em>Analysis and write up of these data can be found at:</em><br />
Frank, K.L., Rogers, D. R., Olins, H. C., Vidoudez, C., &amp; Girguis, P. R. 2013. Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents. The ISME journal, 7, 1391–1401. doi:<a href="http://dx.doi.org/10.1038/ismej.2013.17" target="_blank">10.1038/ismej.2013.17</a></p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology</strong>: Once on board ship, samples were directly transferred to sterile anaerobic seawater and handled/processed using appropriate sterile microbiological techniques. DNA was extracted from this crushed deposit sample with a protocol modified from (Santelli et al. 2008). Subsamples were washed with 0.1 N HCl, followed by two rinses with a sterile solution containing 10 mM Tris (pH 8.0) and 50 mM EDTA. A known mass of material was added to PowerSoil beadbeating tubes(MoBio Laboratories, Carlsbad CA), incubated at 70 degrees C for 10 minutes, and then amended with 200 ng of poly-A. Subsamples were subjected to beadbeating, followed by three cycles of freeze-thaw steps to further lyse cells. Nucleic acids were extracted using hot phenol (60 degrees C for 3 min.), followed by two chloroform:isoamyl separations and precipitated with ethanol. DNA was resuspended in TE (pH 8.0) and quantified using the Qubit™ fluorometer (Life Technologies, Grand Island, NY).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061934 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1061934
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0838107 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0838107
Funding provided by NASA Astrobiology Science & Technology for Exploring Planets (NASA-ASTEP) Award Number: NNX09AB78G
Funding provided by NASA Astrobiology Science & Technology for Exploring Planets (NASA-ASTEP) Award Number: NNX07AV51G
completed
Peter Girguis
Harvard University
617-496-8328
Biological Laboratories, Room 3085 16 Divinity Ave
Cambridge
MA
02138-2020
USA
pgirguis@oeb.harvard.edu
pointOfContact
asNeeded
Dataset Version: 17 November 2015
Unknown
accession_num
sample_name
organism
sample
accession_link
description
theme
None, User defined
No BCO-DMO term
sample identification
featureType
BCO-DMO Standard Parameters
AT15-67
service
Deployment Activity
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.
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
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents
https://osprey.bco-dmo.org/project/626603
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents
<p>This project characterizes rates of microbially mediated sulfate reduction from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. Maximum rates of sulfate reduction occurred at 90°C in all three deposits. Pyrosequencing and functional gene abundance data reveal differences in both biomass and community composition among sites, including differences in the abundance of known sulfate reducing bacteria. The abundance of sequences for Thermodesulfovibro-like organisms and higher sulfate reduction rates at elevated temperatures, suggests that Thermodesulfovibro-like organisms may play a role in sulfate reduction in warmer environments. The rates of sulfate reduction observed suggest that - within anaerobic niches of hydrothermal deposits - heterotrophic sulfate reduction may be quite common and might contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents.</p>
<p>This project was funded, in part, by a C-DEBI Graduate Student Fellowship.</p>
Middle Valley Vents
largerWorkCitation
project
eng; USA
oceans
Juan de Fuca Ridge
2015-11-17
Middle Valley vent field along the Juan de Fuca Ridge
0
BCO-DMO catalogue of parameters from Assessments of bacterial and archaeal diversity from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge from R/V Atlantis cruise AT15-67 in the Juan de Fuca Ridge in 2010
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/626648.rdf
Name: accession_num
Units: dimensionless
Description: <p>NCBI accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626649.rdf
Name: sample_name
Units: dimensionless
Description: <p>GenBank sample number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626650.rdf
Name: organism
Units: dimensionless
Description: <p>Organism name/description.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626651.rdf
Name: sample
Units: dimensionless
Description: <p>Sample (site) name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626652.rdf
Name: accession_link
Units: dimensionless
Description: <p>Hyperlink to NCBI for the accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626653.rdf
Name: description
Units: dimensionless
Description: <p>Description of the sequence.</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
2221
https://datadocs.bco-dmo.org/file/DwwxOBxcj7GGZM/MV_sequences.csv
MV_sequences.csv
Primary data file for dataset ID 626625
download
https://osprey.bco-dmo.org/dataset/626625/data/download
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology</strong>: Once on board ship, samples were directly transferred to sterile anaerobic seawater and handled/processed using appropriate sterile microbiological techniques. DNA was extracted from this crushed deposit sample with a protocol modified from (Santelli et al. 2008). Subsamples were washed with 0.1 N HCl, followed by two rinses with a sterile solution containing 10 mM Tris (pH 8.0) and 50 mM EDTA. A known mass of material was added to PowerSoil beadbeating tubes(MoBio Laboratories, Carlsbad CA), incubated at 70 degrees C for 10 minutes, and then amended with 200 ng of poly-A. Subsamples were subjected to beadbeating, followed by three cycles of freeze-thaw steps to further lyse cells. Nucleic acids were extracted using hot phenol (60 degrees C for 3 min.), followed by two chloroform:isoamyl separations and precipitated with ethanol. DNA was resuspended in TE (pH 8.0) and quantified using the Qubit™ fluorometer (Life Technologies, Grand Island, NY).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing</strong>: DNA samples were sequenced using 454 pyrotag methods similar to those described previously (Dowd et al. 2008). All samples were sequenced at the Research and Testing Laboratory (Lubbock, TX) using a 454FLX instrument (Roche Inc.) with Titanium™ reagents. The resulting bacterial and archaeal 16S rRNA (bacterial V1-V3 and archaeal V3-V4 of the 16S rRNA genes; primers are shown in Table 1) as well as drsB sequences were analyzed via Mothur (Schloss et al. 2009). Sequences were trimmed, quality checked, aligned to the SILVA-compatible alignment database reference alignment (dsrB gene datasets were aligned to a dsrB gene database generated from the Ribosomal Database Project (RDP)), analyzed for chimeras, classified against the Greengenes99 database and clustered in to OTUs. Rarefaction curves were used to examine the number of OTUs as a function of sampling depth. Alpha diversity was assessed by generating values from the Chao1 richness estimators and the inverse Simpson diversity index.</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: AT15-67
AT15-67
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-67
Dr Raymond Lee
Washington State University
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel