http://lod.bco-dmo.org/id/dataset/654298
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
2016-08-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006.
2016-08-16
publication
2016-08-16
revision
BCO-DMO Linked Data URI
2016-08-16
creation
http://lod.bco-dmo.org/id/dataset/654298
Jason B. Sylvan
Texas A&M University
principalInvestigator
Katrina Edwards
University of Southern California
principalInvestigator
Christopher R. German
Woods Hole Oceanographic Institution
principalInvestigator
Benjamin C. Pyenson
Arizona State University
principalInvestigator
Dr Olivier Rouxel
Universite de Brest
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: Sylvan, J. B., Rouxel, O., German, C. R., Pyenson, B. C., Edwards, K. (2016) Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 18 Aug 2016) Version Date 2016-08-16 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/654298 [access date]
Bacterial 16S rRNA sequences from hydrothermal plume particles Dataset Description: <p>Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at&nbsp;9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise&nbsp;AT15-06 in July 2006.</p>
<p><strong>Related references:</strong><br />
Sylvan, JB, BC Pyenson, O. Rouxel, GR German and KJ Edwards. 2012. Time series analysis of two hydrothermal plumes at 9˚50'N East Pacific Rise reveals distinct, heterogeneous bacterial populations. Geobiology, 10: 178-192.&nbsp; doi:<a href="http://dx.doi.org/10.1111/j.1472-4669.2011.00315.x" target="_blank">10.1111/j.1472-4669.2011.00315.x</a></p> Methods and Sampling: <p>The investigators&nbsp;deployed sediment traps adjacent to two active hydrothermal vents at 9°50'N on the East Pacific Rise (EPR) to assess the variability in bacterial community structure associated with plume particles on the timescale of weeks to months, to determine whether an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated that there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (&gt;1 mm) Fe ⁄ (Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (&lt;1 mm) Fe ⁄ (Fe+Mn+Al), Fe, Ca, and Co are reflected in shifts in microbial populations.&nbsp;16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift toward the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle-attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exist on the plume environment that physically and chemically connects them. By employing sediment traps for a time-series approach to sampling, the investigators&nbsp;show that bacterial community composition on plume particles changes on timescales much shorter than previously known.</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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0424953 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0424953
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF1609
completed
Jason B. Sylvan
Texas A&M University
979-845-5105
Department of Oceanography Eller O&M Building, Room 716
College Station
TX
77843-3146
USA
jasonsylvan@tamu.edu
pointOfContact
Katrina Edwards
University of Southern California
pointOfContact
Christopher R. German
Woods Hole Oceanographic Institution
508-289-2853
266 Woods Hole Rd Clark South 276 (MS #24)
Woods Hole
MA
02543
USA
cgerman@whoi.edu
pointOfContact
Benjamin C. Pyenson
Arizona State University
Tempe
AZ
USA
pointOfContact
Dr Olivier Rouxel
Universite de Brest
Universite Europe'enne de Bretagne, Universite de Brest
Plouzane
France
pointOfContact
asNeeded
Dataset Version: 18 Aug 2016
Unknown
cruise_id
location
lat
lon
depth
description
accession_num
accession_link
popset_id
popset_link
Thermo-Electron Element 2
theme
None, User defined
Cruise identfier
site
latitude
longitude
depth
sample description
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Inductively Coupled Plasma Mass Spectrometer
instrument
BCO-DMO Standard Instruments
AT15-06
service
Deployment Activity
9 degrees North, East Pacific Rise
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
EPR 9 North Plume Particles
https://osprey.bco-dmo.org/project/654288
EPR 9 North Plume Particles
<p>The investigators deployed sediment traps adjacent to two active hydrothermal vents at 9°50'N on the East Pacific Rise (EPR) to assess the variability in bacterial community structure associated with plume particles on the timescale of weeks to months, to determine whether an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated that there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (>1 mm) Fe ⁄ (Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (<1 mm) Fe ⁄ (Fe+Mn+Al), Fe, Ca, and Co are reflected in shifts in microbial populations. 16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift toward the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle-attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exist on the plume environment that physically and chemically connects them. By employing sediment traps for a time-series approach to sampling, the investigators show that bacterial community composition on plume particles changes on timescales much shorter than previously known.</p>
RESET06
largerWorkCitation
project
eng; USA
oceans
9 degrees North, East Pacific Rise
2016-08-16
East Pacific Rise, 9 degrees N
0
BCO-DMO catalogue of parameters from Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006.
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/654325.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruie identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/654326.rdf
Name: location
Units: unitless
Description: <p>Sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/654327.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/654328.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/654329.rdf
Name: depth
Units: meters
Description: <p>Depth at which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/654330.rdf
Name: description
Units: unitless
Description: <p>Description of the sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/654331.rdf
Name: accession_num
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/654332.rdf
Name: accession_link
Units: unitless
Description: <p>Link to NCBI for the accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/654333.rdf
Name: popset_id
Units: unitless
Description: <p>NCBI PopSet ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/654334.rdf
Name: popset_link
Units: unitless
Description: <p>Link to NCBI for the PopSet ID</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
146058
https://datadocs.bco-dmo.org/file/0AAMnv4u4gYGqR/EPR_9_North_Plume_Particles.csv
EPR_9_North_Plume_Particles.csv
Primary data file for dataset ID 654298
download
https://osprey.bco-dmo.org/dataset/654298/data/download
download
onLine
dataset
<p>The investigators&nbsp;deployed sediment traps adjacent to two active hydrothermal vents at 9°50'N on the East Pacific Rise (EPR) to assess the variability in bacterial community structure associated with plume particles on the timescale of weeks to months, to determine whether an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated that there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (&gt;1 mm) Fe ⁄ (Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (&lt;1 mm) Fe ⁄ (Fe+Mn+Al), Fe, Ca, and Co are reflected in shifts in microbial populations.&nbsp;16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift toward the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle-attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exist on the plume environment that physically and chemically connects them. By employing sediment traps for a time-series approach to sampling, the investigators&nbsp;show that bacterial community composition on plume particles changes on timescales much shorter than previously known.</p>
Specified by the Principal Investigator(s)
<p>Chimera were checked with Bellerophon.</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Applied Biosystems Automated DNA Sequencer 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.
Thermo-Electron Element 2
Thermo-Electron Element 2
PI Supplied Instrument Name: Thermo-Electron Element 2 PI Supplied Instrument Description:Inductively Coupled Plasma Mass Spectrometer (ICP Mass Spec) - Thermo-Electron Element 2 Instrument Name: Inductively Coupled Plasma Mass Spectrometer Instrument Short Name:ICP Mass Spec Instrument Description: An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/
Cruise: AT15-06
AT15-06
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-06
Karen Von Damm
University of New Hampshire
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel