http://lod.bco-dmo.org/id/dataset/658175
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
2016-09-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) collected on R/V Thomas G. Thompson cruise TN235 in the Eastern Lau Spreading Center from May to June 2009
2016-08-24
publication
2016-08-24
revision
BCO-DMO Linked Data URI
2016-08-24
creation
http://lod.bco-dmo.org/id/dataset/658175
Jason B. Sylvan
Texas A&M University
principalInvestigator
Katrina Edwards
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: Sylvan, J. B., Edwards, K. (2016) Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) collected on R/V Thomas G. Thompson cruise TN235 in the Eastern Lau Spreading Center from May to June 2009. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 24 Aug 2016) Version Date 2016-08-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/658175 [access date]
Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) Dataset Description: <p>Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) sampled on R/V Thomas G. Thompson cruise TN235 in the Lau Basin.</p>
<p><strong>Related references:</strong><br />
Sylvan, JB, Sia, TY, Haddad, AG, Briscoe, LJ, Toner, BM, Girguis, PR and Edwards KJ. 2013. Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin.&nbsp;Frontiers in Microbiology, 4:61. doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00061" target="_blank">10.3389/fmicb.2013.00061&nbsp;</a></p> Methods and Sampling: <p>Samples were taken from the following locations and depths:<br />
Kilo Moana (~2600 m water depth),<br />
ABE (~2100 m water depth),<br />
Tui Malila (~1875 m water depth), and<br />
Mariner (~1900 m water depth) hydrothermal vent fields</p>
<p>The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. The investigators studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. Alphaproteobacteria, Epsilonproteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (&lt;90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing Alphaproteobacteria, Gammaproteobacteria, and Epsilonproteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing Deltaproteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.</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 Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF1609
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0732369 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0732369
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
asNeeded
Dataset Version: 24 Aug 2016
Unknown
cruise_id
description
sample
location
lat
lon
depth
accession_num
accession_link
popset_id
popset_link
Automated DNA Sequencer
Inductively Coupled Plasma mass spectrometer
Inductively Coupled Plasma Optical Emission Spectrophotometer
X-Ray Diffractometer
theme
None, User defined
Cruise identfier
sample description
sample identification
site
latitude
longitude
depth
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Inductively Coupled Plasma Mass Spectrometer
Inductively Coupled Plasma Optical Emission Spectrometer
X-ray diffractometer
instrument
BCO-DMO Standard Instruments
TN235
service
Deployment Activity
Eastern Lau Spreading Center
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
Lau Basin low temperature geomicrobiology
https://osprey.bco-dmo.org/project/655679
Lau Basin low temperature geomicrobiology
<p>The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. The investigators studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. Alphaproteobacteria, Epsilonproteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (<90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing Alphaproteobacteria, Gammaproteobacteria, and Epsilonproteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing Deltaproteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.</p>
<p>Note: This project was supported by NSF award OCE-0732369 as add-on work to the original proposal. The <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=0732369" target="_blank">proposal abstract is available from NSF</a>.</p>
Lau Basin Geomicrobio
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Lau Spreading Center
2016-08-24
Lau Basin hydrothermal vent fields
0
BCO-DMO catalogue of parameters from Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) collected on R/V Thomas G. Thompson cruise TN235 in the Eastern Lau Spreading Center from May to June 2009
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/658186.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruie identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/658187.rdf
Name: description
Units: unitless
Description: <p>Description of the sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/658188.rdf
Name: sample
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/658189.rdf
Name: location
Units: unitless
Description: <p>Sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/658190.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/658191.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/658192.rdf
Name: depth
Units: meters
Description: <p>Depth at which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/658193.rdf
Name: accession_num
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658194.rdf
Name: accession_link
Units: unitless
Description: <p>Link to NCBI for the accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658195.rdf
Name: popset_id
Units: unitless
Description: <p>NCBI PopSet ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658196.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
130813
https://datadocs.bco-dmo.org/file/l880lQOToXrQok/Lau_Basin_sequences.csv
Lau_Basin_sequences.csv
Primary data file for dataset ID 658175
download
https://osprey.bco-dmo.org/dataset/658175/data/download
download
onLine
dataset
<p>Samples were taken from the following locations and depths:<br />
Kilo Moana (~2600 m water depth),<br />
ABE (~2100 m water depth),<br />
Tui Malila (~1875 m water depth), and<br />
Mariner (~1900 m water depth) hydrothermal vent fields</p>
<p>The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. The investigators studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. Alphaproteobacteria, Epsilonproteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (&lt;90% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing Alphaproteobacteria, Gammaproteobacteria, and Epsilonproteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing Deltaproteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.</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
Automated DNA Sequencer
Automated DNA Sequencer
PI Supplied Instrument Name: Automated DNA Sequencer PI Supplied Instrument Description:Applied Biosystems 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.
Inductively Coupled Plasma mass spectrometer
Inductively Coupled Plasma mass spectrometer
PI Supplied Instrument Name: Inductively Coupled Plasma mass spectrometer PI Supplied Instrument Description:Thermo Scientific XSERIES 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/
Inductively Coupled Plasma Optical Emission Spectrophotometer
Inductively Coupled Plasma Optical Emission Spectrophotometer
PI Supplied Instrument Name: Inductively Coupled Plasma Optical Emission Spectrophotometer PI Supplied Instrument Description:Thermo Scientific iCAP 6500 Instrument Name: Inductively Coupled Plasma Optical Emission Spectrometer Instrument Short Name:ICP-OES or ICP-AES Instrument Description: Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
X-Ray Diffractometer
X-Ray Diffractometer
PI Supplied Instrument Name: X-Ray Diffractometer PI Supplied Instrument Description:Siemens D-500 Instrument Name: X-ray diffractometer Instrument Short Name:XRD Instrument Description: Instruments that identify crystalline solids by measuring the characteristic spaces between layers of atoms or molecules in a crystal.
Cruise: TN235
TN235
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN235
Charles Fisher
Pennsylvania State University
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel