http://lod.bco-dmo.org/id/dataset/717352
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
2017-10-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries collected from CA and MN in 2012.
2017-10-19
publication
2017-10-19
revision
BCO-DMO Linked Data URI
2017-10-19
creation
http://lod.bco-dmo.org/id/dataset/717352
Dr Benjamin Kimball Harrison
Central Michigan University
principalInvestigator
Dr Jake V. Bailey
University of Minnesota Twin Cities
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: Harrison, B. K., Bailey, J. V. (2017) Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries collected from CA and MN in 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version Final) Version Date 2017-10-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/717352 [access date]
Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries. Dataset Description: <p>Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries. Submarine Canyon Sediment Bacteria data are presented in Harrison et al (2018). Lake Surface Sediment Bacteria data are published in Harrison et al (2016).</p> Methods and Sampling: <p><strong>Submarine Canyon Sediment Bacteria:</strong></p>
<p>A ~35cm multicore was collected from La Jolla submarine canyon and sectioned using pre-sterilized tools shipboard at 1cm intervals for preservation at -80 deg C. DNA was extracted from ~2g subsamples using the MoBio PowerSoil DNA kit with an additional heating step applied during lysis. Sequence libraries were assembled for select bulk sediment samples for the v1–v3 region of the 16S rRNA gene using Eubacteria-specific primers (Muyzer et al. 1993) on the Illumina MiSeq platform (Bartram et al. 2011) at the University of Minnesota Genomics Center (UMGC).</p>
<p><strong>Lake Surface Sediment Bacteria</strong> (excerpt from Harrison et al., 2016)<strong>:</strong></p>
<p>A 1.5 m hollow steel wedge was filled with a mixture of dry ice pellets and isopropyl alcohol and then lowered into the sediment. The coring device was held in place for 15 min and then raised back to the surface, where the dry ice slurry was poured off and unfrozen mud scraped off the sides. The device was then filled with lake surface water, and the frozen core slabs levered off the sides. The recovered frozen cores were wrapped in aluminum foil and placed on dry ice for transport. In the laboratory, the cores were placed on cardboard and kept frozen by regular contact with dry ice pellets. The sampling plane (facing away from the coring device) was smoothed down using a hand-held electric wood planer and utility knives until undisturbed laminae were clearly resolved. Core sections were selected by visual inspection on the basis of lamina thickness and continuity across the sampling plane.</p>
<p>Laminae were excised with pre-sterilized utility knife blades from the top 9 cm of the Twin Lake freeze core: five corresponding to white layers deposited during spring/summer blooms and four corresponding to winter deposition of organic matter and terrigenous particles. 0.2 g of material was collected from the sampling plane as described above, beginning at the lamina base and removing material no greater than 1 mm above that level.</p>
<p>From the Lake McCarrons freeze core, five spring/summer laminae were collected from sub-sampled portions of the 16–24 cm depth range by sequentially exposing the z-plane surface of the horizon with sterilized utility knife blades.”</p>
<p>Additional 5 mm frozen sediment wedges cross-cutting sediment laminae were taken at 2 cm intervals between 0 cm and 30 cm depth and 5 cm intervals from 30 cm to 65 cm, using pre-sterilized instruments. Subsamples were stored at -80 deg C for later extraction. An additional ambient-temperature piston core was collected from Lake McCarrons sediment at a position roughly adjacent (within 5 m) to the freeze core site and subsampled on shore within 2 h after removal. The presence and vertical migration of gas bubbles was observed in core sediment. 2 cc sediment aliquots were collected at 10 cm depth intervals starting at 2 cm beneath the sediment-water interface through predrilled windows, excluding the exterior 1 cm of material in contact with the coring tube. Subsamples were stored at -80 deg C.</p>
<p><u><em>DNA extraction, </em></u><u><em>amplification</em></u><u><em> and sequencing</em></u></p>
<p>Depth intervals corresponding to ambient core subsamples and excised laminae were used to select among the high-frequency bulk sediment samples of the McCarrons core. DNA was extracted from all sediment subsamples with a MoBio Soil DNA kit with an additional heating step added to the lysing step of manufacturer protocols (Harrison and Orphan 2012).</p>
<p>Sequence libraries were assembled for select bulk sediment samples for the v1–v3 region of the 16S rRNA gene using Eubacteria-specific primers (Muyzer et al. 1993) on the Illumina MiSeq platform (Bartram et al. 2011).</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
completed
Dr Benjamin Kimball Harrison
Central Michigan University
310 Pilsbury Dr SE
Minneapolis
MN
55455
United States
bkimballh@gmail.com
pointOfContact
Dr Jake V. Bailey
University of Minnesota Twin Cities
310 Pillsbury Dr SE
Minneapolis
MN
55455
United States
baileyj@umn.edu
pointOfContact
asNeeded
Dataset Version: Final
Unknown
accession
NCBI_link
depth
lat
lon
location
deployment
description
theme
None, User defined
accession number
external_link
depth
latitude
longitude
site
deployment number
brief description
featureType
BCO-DMO Standard Parameters
NH1212
service
Deployment Activity
San Diego, CA
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
Buried alive: Microbial responses to sediment flux with implications for the deep biosphere
http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564
Buried alive: Microbial responses to sediment flux with implications for the deep biosphere
<p>Previous investigation of the microbial diversity of unconsolidated marine sediments has not yet constrained the importance of cell transport associated with physical processes of sedimentation and fluid advection. Organisms must migrate in order to maintain position with respect to geochemical gradients, and many marine bacteria exhibit chemotactic behavior to optimize their position. However, certain microorganisms in subsurface environments form persistent attachments to solid particles or are non-motile, leading to the differential burial of a subset of active cells (i.e. what is preserved may differ from what is—or was—active at a given horizon). Deep sedimentary horizons may inherit a microbial community that fails to maintain its optimum position with respect to geochemical profiles, and the deep biosphere ultimately is composed of cells that survive this transition.</p>
<p>We seek to describe the permanence and overprinting of molecular signatures of microbial communities across discrete horizons associated with rapid sedimentation (e.g. turbidite emplacement), changes in bottom-water geochemistry, and depositional unconformities. This work involved the collection and study of sediment cores from 3 lakes in the Minneapolis-St. Paul Metropolitan, an intact turbidite profile from La Jolla Canyon on the California Borderland, and select core samples from a marine transgressive sequence drilled by IODP leg 337 off the Shimokita Peninsula, Japan. These core samples provided a key opportunity to study microbial relationships to sedimentology at high resolution. Preliminary work suggests microbial community signatures retain evidence of cell displacement resulting from sediment disturbance, and distinct patterns in diversity are not overprinted on decadal timescales. </p>
<p>This work was supported through a C-DEBI postdoctoral fellowship.</p>
Buried Alive
largerWorkCitation
project
eng; USA
oceans
San Diego, CA
2017-10-19
California, Japan, and Minnesota
0
BCO-DMO catalogue of parameters from Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries collected from CA and MN in 2012.
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/717363.rdf
Name: accession
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/717364.rdf
Name: NCBI_link
Units: unitless
Description: <p>NCBI accession link</p>
http://lod.bco-dmo.org/id/dataset-parameter/717365.rdf
Name: depth
Units: meters
Description: <p>Water sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/717366.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/717367.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/717368.rdf
Name: location
Units: unitless
Description: <p>Location where sampling occurred</p>
http://lod.bco-dmo.org/id/dataset-parameter/717369.rdf
Name: deployment
Units: unitless
Description: <p>Deployment name and number</p>
http://lod.bco-dmo.org/id/dataset-parameter/717370.rdf
Name: description
Units: unitless
Description: <p>Description of NCBI accession</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
995
https://datadocs.bco-dmo.org/file/vmmwylzUrjjAV1/sediment_bacteria.csv
sediment_bacteria.csv
Primary data file for dataset ID 717352
download
https://osprey.bco-dmo.org/dataset/717352/data/download
download
onLine
dataset
<p><strong>Submarine Canyon Sediment Bacteria:</strong></p>
<p>A ~35cm multicore was collected from La Jolla submarine canyon and sectioned using pre-sterilized tools shipboard at 1cm intervals for preservation at -80 deg C. DNA was extracted from ~2g subsamples using the MoBio PowerSoil DNA kit with an additional heating step applied during lysis. Sequence libraries were assembled for select bulk sediment samples for the v1–v3 region of the 16S rRNA gene using Eubacteria-specific primers (Muyzer et al. 1993) on the Illumina MiSeq platform (Bartram et al. 2011) at the University of Minnesota Genomics Center (UMGC).</p>
<p><strong>Lake Surface Sediment Bacteria</strong> (excerpt from Harrison et al., 2016)<strong>:</strong></p>
<p>A 1.5 m hollow steel wedge was filled with a mixture of dry ice pellets and isopropyl alcohol and then lowered into the sediment. The coring device was held in place for 15 min and then raised back to the surface, where the dry ice slurry was poured off and unfrozen mud scraped off the sides. The device was then filled with lake surface water, and the frozen core slabs levered off the sides. The recovered frozen cores were wrapped in aluminum foil and placed on dry ice for transport. In the laboratory, the cores were placed on cardboard and kept frozen by regular contact with dry ice pellets. The sampling plane (facing away from the coring device) was smoothed down using a hand-held electric wood planer and utility knives until undisturbed laminae were clearly resolved. Core sections were selected by visual inspection on the basis of lamina thickness and continuity across the sampling plane.</p>
<p>Laminae were excised with pre-sterilized utility knife blades from the top 9 cm of the Twin Lake freeze core: five corresponding to white layers deposited during spring/summer blooms and four corresponding to winter deposition of organic matter and terrigenous particles. 0.2 g of material was collected from the sampling plane as described above, beginning at the lamina base and removing material no greater than 1 mm above that level.</p>
<p>From the Lake McCarrons freeze core, five spring/summer laminae were collected from sub-sampled portions of the 16–24 cm depth range by sequentially exposing the z-plane surface of the horizon with sterilized utility knife blades.”</p>
<p>Additional 5 mm frozen sediment wedges cross-cutting sediment laminae were taken at 2 cm intervals between 0 cm and 30 cm depth and 5 cm intervals from 30 cm to 65 cm, using pre-sterilized instruments. Subsamples were stored at -80 deg C for later extraction. An additional ambient-temperature piston core was collected from Lake McCarrons sediment at a position roughly adjacent (within 5 m) to the freeze core site and subsampled on shore within 2 h after removal. The presence and vertical migration of gas bubbles was observed in core sediment. 2 cc sediment aliquots were collected at 10 cm depth intervals starting at 2 cm beneath the sediment-water interface through predrilled windows, excluding the exterior 1 cm of material in contact with the coring tube. Subsamples were stored at -80 deg C.</p>
<p><u><em>DNA extraction, </em></u><u><em>amplification</em></u><u><em> and sequencing</em></u></p>
<p>Depth intervals corresponding to ambient core subsamples and excised laminae were used to select among the high-frequency bulk sediment samples of the McCarrons core. DNA was extracted from all sediment subsamples with a MoBio Soil DNA kit with an additional heating step added to the lysing step of manufacturer protocols (Harrison and Orphan 2012).</p>
<p>Sequence libraries were assembled for select bulk sediment samples for the v1–v3 region of the 16S rRNA gene using Eubacteria-specific primers (Muyzer et al. 1993) on the Illumina MiSeq platform (Bartram et al. 2011).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>- information was compiled from the submitted metadata forms to form this table of data.<br />
- columns that were created for table: accession, NCBI_link, depth, lat, lon, location, deployment, description</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: NH1212
NH1212
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
NH1212
http://gdc.ucsd.edu/index.php?page=22&cruiseid=NH1212&table=cruise_info
Report describing NH1212
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel