http://lod.bco-dmo.org/id/dataset/653698
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
2016-08-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence accession numbers for archaeal and bacterial clone libraries from Guaymas Basin sediments collected from R/V Atlantis cruise AT15-56 in 2009
2016-08-10
publication
2016-08-10
revision
BCO-DMO Linked Data URI
2016-08-10
creation
http://lod.bco-dmo.org/id/dataset/653698
Andreas Teske
University of North Carolina at Chapel Hill
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: Teske, A. (2016) Sequence accession numbers for archaeal and bacterial clone libraries from Guaymas Basin sediments collected from R/V Atlantis cruise AT15-56 in 2009. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 10 Aug 2016) Version Date 2016-08-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/653698 [access date]
Sequence accession numbers for archaeal and bacterial clone libraries from Guaymas Basin sediments Dataset Description: <p>Sequence accession numbers for archaeal and bacterial clone libraries from&nbsp;Guaymas Basin hydrothermal sediments (2000 m depth)&nbsp;collected on R/V Atlantis cruise, AT15-56.</p> Methods and Sampling: <p>Hydrothermal sediments were sampled using HOV Alvin.</p>
<p>For complete acquisition and processing details, refer to:<br />
McKay, L., et al. 2016.&nbsp;Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California. Environmental Microbiology Reports, 8(1), 150-161. doi:<a href="http://dx.doi.org/10.1111/1758-2229.12365" target="_blank">10.1111/1758-2229.12365</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0647633 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0647633
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
Andreas Teske
University of North Carolina at Chapel Hill
508-287-1648
Department of Marine Sciences 3117B Venable Hall, CB 3300
Chapel Hill
NC
27599
USA
teske@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 10 Aug 2016
Unknown
sequence_type
sample_location
method
accession_num
popset_num
closely_related_to
accession_link
popset_link
theme
None, User defined
sample description
site description
sampling_method
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
AT15-56
service
Deployment Activity
Guaymas Basin
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
Constraints on microbial biogeography in hydrothermally active sediments of Guaymas Basin: Energetic limits, physical stressors, and upward compression of metabolic zones
https://osprey.bco-dmo.org/project/637539
Constraints on microbial biogeography in hydrothermally active sediments of Guaymas Basin: Energetic limits, physical stressors, and upward compression of metabolic zones
<p>Project description from <a href="http://www.darkenergybiosphere.org/education/graduatesFunded.html" target="_blank">C-DEBI</a>:<br />
Shallow subsurface temperatures can reach extreme levels in just 40 cm depth in Guaymas Basin sediments, limiting microbial colonization to thermally tolerable surface sediments. At temperatures beyond approximately 80 degrees C and 100 degrees C, respectively, the 13C-isotopic signatures of microbial anaerobic oxidation of methane and organic matter remineralization appear to be thermally restricted. Putative methane consuming archaea dominate the archaeal clone library while sulfur cycling bacteria and<em>Chloroflexi</em>-related sequences dominate the bacterial clone library. Archaeal clone library data suggest that the ANME-1 Guaymas archaea tolerate high in situ temperatures up to approximately 80 degrees C, thereby gaining an advantage in access to the geothermal methane pool in hot Guaymas Basin sediments. Lastly, the results indicate that in situ thermal and/or geochemical gradients structure archaeal community composition and biogeography more than bacterial biogeography.</p>
<p>While the average upper thermal temperature for detectable microbial life by RNA recovery in Guaymas Basin sediments appears to be around 80 degrees C, temperatures may fluctuate by 25 degrees C in as little as a day. Isotopic evidence for microbially mediated methane oxidation is only slight, yet putative methanotrophic archaea are commonly recovered in nearly all samples suggesting they may perform other physiological modes or isotopic signatures are not detectable because of high methane concentrations. High temperature associated archaea appear to be represented by OTUs related to uncultured MCG and ANME-1 Guaymas groups. For bacteria the dominant high temperature associated OTU was phylogenetically associated with the <em>Thermodesulfobacteriaceae</em>.</p>
<p>Two of the four main themes of C-DEBI research are "Extent of Life" and "Limits of Life". Using sediment samples acquired from Guaymas Basin, my C-DEBI research links these two themes by examining how the biogeographical distribution of sedimentary microorganisms is shaped by severe, life-limiting conditions. Although these samples are not from deep sediments, they exemplify deep biogeochemical processes that have been compressed to shallower depths by elevated hydrothermal activity. My research demonstrates how thermal and geochemical regimes interact to control the spatial extent of life by focusing on microbial zonation in an energetically diverse hydrothermal environment. My intention with this research was to accurately describe microbial biogeography and the physicochemical factors controlling it in these unique, compressed sediments, which can be a useful asset in preparation for future IODP sampling procedures and analyses as well as investigations in deep subsurface microbiology around the world.</p>
Microbial Biogeo Guaymas
largerWorkCitation
project
eng; USA
oceans
Guaymas Basin
2016-08-10
Guaymas Basin
0
BCO-DMO catalogue of parameters from Sequence accession numbers for archaeal and bacterial clone libraries from Guaymas Basin sediments collected from R/V Atlantis cruise AT15-56 in 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/653734.rdf
Name: sequence_type
Units: unitless
Description: <p>Description of the type of sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/653735.rdf
Name: sample_location
Units: unitless
Description: <p>Location where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/653736.rdf
Name: method
Units: unitless
Description: <p>Sequencing method used</p>
http://lod.bco-dmo.org/id/dataset-parameter/653737.rdf
Name: accession_num
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/653738.rdf
Name: popset_num
Units: unitless
Description: <p>NCBI Popset number</p>
http://lod.bco-dmo.org/id/dataset-parameter/653739.rdf
Name: closely_related_to
Units: unitless
Description: <p>Description of closely related taxa</p>
http://lod.bco-dmo.org/id/dataset-parameter/653740.rdf
Name: accession_link
Units: unitless
Description: <p>Hyperlink to NCBI for the accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/653741.rdf
Name: popset_link
Units: unitless
Description: <p>Hyperlink to NCBI for the Popset</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
105755
https://datadocs.bco-dmo.org/file/YVVZJoOcNKkvmm/arch_bac_sequences.csv
arch_bac_sequences.csv
Primary data file for dataset ID 653698
download
https://osprey.bco-dmo.org/dataset/653698/data/download
download
onLine
dataset
<p>Hydrothermal sediments were sampled using HOV Alvin.</p>
<p>For complete acquisition and processing details, refer to:<br />
McKay, L., et al. 2016.&nbsp;Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California. Environmental Microbiology Reports, 8(1), 150-161. doi:<a href="http://dx.doi.org/10.1111/1758-2229.12365" target="_blank">10.1111/1758-2229.12365</a></p>
Specified by the Principal Investigator(s)
<p>For complete acquisition and processing details, refer to:<br />
McKay, L., et al. 2016.&nbsp;Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California. Environmental Microbiology Reports, 8(1), 150-161. doi:<a href="http://dx.doi.org/10.1111/1758-2229.12365" target="_blank">10.1111/1758-2229.12365</a></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: AT15-56
AT15-56
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-56
Andreas Teske
University of North Carolina at Chapel Hill
http://www.marine.whoi.edu/at_synop.nsf/9452cb38d8d28f30852568cd004b8077/13f181c7f933dbac052574e4006399a9?OpenDocument
Report describing AT15-56
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel