http://lod.bco-dmo.org/id/dataset/754354
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
2019-01-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 2014.
2019-02-20
publication
2019-02-20
revision
BCO-DMO Linked Data URI
2019-02-20
creation
http://lod.bco-dmo.org/id/dataset/754354
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Gustavo Ramirez
University of Southern California
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: Orcutt, B. N., Ramirez, G. (2019) 16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-02-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/754354 [access date]
16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs Dataset Description: <p>The DNA data from the Juan de Fuca project are publicly available through NCBI Short Read Archive under BioProject PRJNA472057; BioSample accession numbers: SAMN09228041- SAMN09228055&nbsp;</p>
<p>species: uncultivated marine metagenome</p>
<p>description of the types of sequences: Illumina amplicon sequences of the V1-V3 hypervariable region of the 16S rRNA gene</p>
<p>locations where species were collected: IODP holes U1301A, U1362A, and U1362B on the Juan de Fuca Ridge flank, 47.45N/127.45W</p> Methods and Sampling: <p>Polished mineral chips were prepared and deployed as described in Fisher et al. 2011 (DOI: 10.2204/iodp.proc.327.107.2011). Mineral colonization experiments were recovered during cruise AT26-18 in August 2014 and processed as described in Orcutt et al. 2011 (DOI: 10.1038/ismej.2010.157). Approximately 6g of each substrate underwent total DNA extraction using the MOBIO PowerSoil® DNA Isolation Kit (MOBIO Laboratories, Inc.) with modification from manufacturer instructions to include a phenol:chloroform:isoamyl alcohol (24:25:1) extraction step. Each batch of samples included procedural blanks. Replicate extracts were pooled and concentrated to 100 μl with vacuum centrifugation (SavantTM DNA SpeedVacTM Concentrator). Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq platform.&nbsp; &nbsp;&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260697
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536539 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536539
completed
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 312
60 Bigelow Drive PO Box 380
East Boothbay
Maine
04544
USA
borcutt@bigelow.org
pointOfContact
Gustavo Ramirez
University of Southern California
(401) 874-6220
Graduate School of Oceanography, University of Rhode Island 215 South Ferry Road, Horn 103,
Narragansett
RI
02882
garamirez@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Illumina MiSeq
theme
None, User defined
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
AT26-18
service
Deployment Activity
Eastern Flank of 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
Collaborative Research: Completing single- and cross-hole hydrgeologic and microbial experiments: Juan de Fuca Flank
http://www.darkenergybiosphere.org/research/juandefuca.html
Collaborative Research: Completing single- and cross-hole hydrgeologic and microbial experiments: Juan de Fuca Flank
<p><em>NSF Award Abstract:</em><br />
In 2010, IODP exp. 327 launched series of experiments based on instrumentation placed in 6 boreholes (Holes 1026B, 1027C, 1301A, 1301B, 1362A, and 1362B) on and near the Juan de Fuca Ridge (JDFR). The experiments were designed to examine hydrological and biological processes in basaltic ocean crust. Major issues to be addressed include overall permeability, the magnitudes, velocity and directions of fluid, solute,and heat transport,constraints on the fluid storage properties of crust, determining how fluid reservoirs respond to seismic perturbations, and investigating the variability, diversity, and metabolism of resident microbial populations. This project will recover sensors and samplers in the instrumented boreholes(CORKs),access data and samples, collect biological incubators placed at depth within the boreholes, and seal the CORKs. All of these activities are needed for the completion of the JDFR experiments</p>
<p>Once the data and samples are retrieved, the PI's will develop new numerical models for the hydrology (permeability, thickness and extent of permeable zones, connectivity, direction of flow, and anisotropy) of ocean crust based on the results of flow tests. T sensors will enable thermal structure to be determined in conjunction with flow parameters. DNA will be analyzed via 16S ribosomal RNA (rRNA) genes as well as select full-length Sanger-style sequencing and gene fingerprinting techniques. The PI's will look at diversity, shared species, emergence and disappearance of groups. Metagenomic work will be done on some samples.</p>
<p>Broader Impacts include training of 4 shipboard educators, with an emphasis on recruiting underrepresented groups for these positions, teacher workshops, and special training for undergraduate and graduate students and post-docs. Research team includes grads, undergrads, and post-docs</p>
JdF Flank
largerWorkCitation
project
eng; USA
oceans
Eastern Flank of Juan de Fuca Ridge
-127.45
-127.45
47.45
47.45
2014-08-01
2014-08-31
Eastern flank of Juan de Fuca Ridge: 47 N, 128 W
0
BCO-DMO catalogue of parameters from 16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 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
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://osprey.bco-dmo.org/dataset/754354/data/download
download
onLine
dataset
<p>Polished mineral chips were prepared and deployed as described in Fisher et al. 2011 (DOI: 10.2204/iodp.proc.327.107.2011). Mineral colonization experiments were recovered during cruise AT26-18 in August 2014 and processed as described in Orcutt et al. 2011 (DOI: 10.1038/ismej.2010.157). Approximately 6g of each substrate underwent total DNA extraction using the MOBIO PowerSoil® DNA Isolation Kit (MOBIO Laboratories, Inc.) with modification from manufacturer instructions to include a phenol:chloroform:isoamyl alcohol (24:25:1) extraction step. Each batch of samples included procedural blanks. Replicate extracts were pooled and concentrated to 100 μl with vacuum centrifugation (SavantTM DNA SpeedVacTM Concentrator). Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq platform.&nbsp; &nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- Nothing to report</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
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq platform. 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.
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
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel