http://lod.bco-dmo.org/id/dataset/662641
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
2016-10-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA gene sequences of cells in marine methane seep sediments from R/V Atlantis and R/V Western Flyer cruises off the Pacific Northwest, USA in 2010 and 2013
2016-10-25
publication
2016-10-25
revision
BCO-DMO Linked Data URI
2016-10-25
creation
http://lod.bco-dmo.org/id/dataset/662641
Roland Hatzenpichler
Montana State University
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: Hatzenpichler, R. (2016) 16S rRNA gene sequences of cells in marine methane seep sediments from R/V Atlantis and R/V Western Flyer cruises off the Pacific Northwest, USA in 2010 and 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/662641 [access date]
16S rRNA gene sequences of cells in marine methane seep sediments Dataset Description: <p>This dataset contains 16S rRNA gene sequences accession numbers&nbsp;from isolated microbial aggregate&nbsp;from marine methane seep sediments.</p>
<p>These data were published in:</p>
<p>Hatzenpichler, Roland, et al. "Visualizing in situ translational activity for identifying and sorting slow-growing archaeal− bacterial consortia."<em>Proceedings of the National Academy of Sciences</em>&nbsp;113.28 (2016): E4069-E4078.&nbsp;<a href="https://dx.doi.org/10.1073/pnas.1603757113">doi:10.1073/pnas.1603757113</a></p> Methods and Sampling: <p><strong>Environmental Sampling and Storage&nbsp;</strong>(extracted from&nbsp;<a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a>)</p>
<p>R/V Atlantis cruise AT-15-68:</p>
<p>Sediment sample #3730 was obtained from Hydrate Ridge South methane seep field (Alvin Dive 4635; push-core 16; 44 deg&nbsp;34.09 N,125 deg 9.14 W; 775 m water depth; sediment horizon 0–6 cm; 4C in-situ temperature) on 7 August 2010. Sediment was stored underargon headspace in a Mylar bag for 5 wk before being transferred toa 1-L glass bottle with a 1.38 bar 100% methane headspace, which was stored at 4C for ~4 years. Seawater and headspace were exchanged at regular intervals to prevent the accumulation of inhibitory compounds.</p>
<p>MBARI Cruise 2013 "Southern California"</p>
<p>Sediment sample #7142 was collected from Santa Monica Basinon 7 May 2013 (R/V Western Flyer MBARI Cruise 2013; dive 459; push-core 74; 33 deg&nbsp;47.34 N, 118 deg&nbsp;40.09 W; 863 m depth; sedimenthorizon 4–6 cm; 4C in situ temperature). The sediment was sealed under argon and stored at 4C. After 40 days of storage, the sediment was suspended in anaerobic natural bottom seawater from the site in an anaerobic chamber (3% H2 in N2) and aliquots were overpressured with 1.5 bar methane. The sediment was kept for 12 months under 1.5 bar 100% methane in natural bottom seawater that was exchanged every 3 mo.</p>
<p><strong>All Sample Handling:</strong></p>
<p>All samples were kept in an ice bath at all times during handling. Artificial seawater (ASW) consisted of 10.9 g of MgCl2·6H2O, 0.2 g of NaHCO3, 0.76 g ofKCl, 25.9 g ofNaCl, 1.47 g of CaCl2·2H2O, 3.98 g of Na2SO4, and 26.73 mg of NH4Cl per liter of ddH2O at pH 7.4. One milliliter of vitamin solution (see medium 141, https://www.dsmz.de) and 1 mL of trace element solution SL- 10 (see https://www.dsmz.de) were also added. Before use, ASW was filtered through a 0.2-μm filter and N2-bubbled for 10 min. ASW was kept on ice during handling. For more information on resuspension and incubation procedures used see <a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a>. &nbsp;</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
Roland Hatzenpichler
Montana State University
406-994-5469
Chemistry & Biochemistry Building 111
Bozeman
MT
59717
USA
roland.hatzenpichler@montana.edu
pointOfContact
asNeeded
Unknown
cruise_id
dive_id
collection_date
accession_number
accession_link
organism
lat
lon
water_depth
sediment_depth
collection_source
theme
None, User defined
Cruise identfier
dive_id
date
accession number
external_link
sample description
latitude
longitude
depth_w
depth below seafloor
featureType
BCO-DMO Standard Parameters
AT15-68
MBARI_Southern_California_2013
service
Deployment Activity
Pacific Ocean, off USA
Pacific North-West
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
Activity-based cell-sorting and enrichment of newly synthesized proteins via amino acid tagging and click chemistry
http://www.darkenergybiosphere.org/outputs-resources/publications/
Activity-based cell-sorting and enrichment of newly synthesized proteins via amino acid tagging and click chemistry
<p>A fundamental problem faced in deep biosphere research is the low rates at which metabolic activity is occurring in the subsurface. Protein-targeted studies have only rarely been the center of attention, most importantly due to the lack of methodology to visualize protein synthesis within cells and the need for radioactively or stable isotopically labeled substrates to study bulk protein turnover. In response to these limitations, I have recently developed a novel click chemistry-based approach that uses a bioorthogonal non-canonical amino acid to fluorescently track protein synthesis within cells. Within the proposed project I will further develop this method with the goal to establish protocols for the separation and characterization of translationally active cells as well as for the enrichment and identification of newly synthesized proteins. After establishing these techniques using representative pure and co-cultures, I will refine them using enrichments from Hydrate Ridge methane seep sediment. Furthermore, I will study the applicability of other, yet uncharacterized bioorthogonal amino acids to seep sediments as well as >1,700 meters-below-seafloor deep sandstone samples obtained during IODP-expedition 337. This project directly addresses C-DEBI research themes 1, 3, and 4 and will support an early career researcher who has not previously been funded by C-DEBI.</p>
Cell-sorting and enrichment
largerWorkCitation
project
eng; USA
oceans
Pacific Ocean, off USA; Pacific North-West
2016-10-25
Hydrate Ridge (Oregon) and Santa Monica basin (California)
0
BCO-DMO catalogue of parameters from 16S rRNA gene sequences of cells in marine methane seep sediments from R/V Atlantis and R/V Western Flyer cruises off the Pacific Northwest, USA in 2010 and 2013
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/662776.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruise Identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/662777.rdf
Name: dive_id
Units: unitless
Description: <p>Dive ID that collected the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/662778.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/662779.rdf
Name: accession_number
Units: unitless
Description: <p>Accesssion number for sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/662780.rdf
Name: accession_link
Units: unitless
Description: <p>Link to accesssion information at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/662781.rdf
Name: organism
Units: unitless
Description: <p>Organism description</p>
http://lod.bco-dmo.org/id/dataset-parameter/662782.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/662783.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/662784.rdf
Name: water_depth
Units: meters
Description: <p>Water depth at sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/662785.rdf
Name: sediment_depth
Units: centimeters
Description: <p>Sample sediment depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/662786.rdf
Name: collection_source
Units: unitless
Description: <p>Description of collection location</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
20303
https://datadocs.bco-dmo.org/file/4WW2jmXfBYvBB6/CellSorting.csv
CellSorting.csv
Primary data file for dataset ID 662641
download
https://osprey.bco-dmo.org/dataset/662641/data/download
download
onLine
dataset
<p><strong>Environmental Sampling and Storage&nbsp;</strong>(extracted from&nbsp;<a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a>)</p>
<p>R/V Atlantis cruise AT-15-68:</p>
<p>Sediment sample #3730 was obtained from Hydrate Ridge South methane seep field (Alvin Dive 4635; push-core 16; 44 deg&nbsp;34.09 N,125 deg 9.14 W; 775 m water depth; sediment horizon 0–6 cm; 4C in-situ temperature) on 7 August 2010. Sediment was stored underargon headspace in a Mylar bag for 5 wk before being transferred toa 1-L glass bottle with a 1.38 bar 100% methane headspace, which was stored at 4C for ~4 years. Seawater and headspace were exchanged at regular intervals to prevent the accumulation of inhibitory compounds.</p>
<p>MBARI Cruise 2013 "Southern California"</p>
<p>Sediment sample #7142 was collected from Santa Monica Basinon 7 May 2013 (R/V Western Flyer MBARI Cruise 2013; dive 459; push-core 74; 33 deg&nbsp;47.34 N, 118 deg&nbsp;40.09 W; 863 m depth; sedimenthorizon 4–6 cm; 4C in situ temperature). The sediment was sealed under argon and stored at 4C. After 40 days of storage, the sediment was suspended in anaerobic natural bottom seawater from the site in an anaerobic chamber (3% H2 in N2) and aliquots were overpressured with 1.5 bar methane. The sediment was kept for 12 months under 1.5 bar 100% methane in natural bottom seawater that was exchanged every 3 mo.</p>
<p><strong>All Sample Handling:</strong></p>
<p>All samples were kept in an ice bath at all times during handling. Artificial seawater (ASW) consisted of 10.9 g of MgCl2·6H2O, 0.2 g of NaHCO3, 0.76 g ofKCl, 25.9 g ofNaCl, 1.47 g of CaCl2·2H2O, 3.98 g of Na2SO4, and 26.73 mg of NH4Cl per liter of ddH2O at pH 7.4. One milliliter of vitamin solution (see medium 141, https://www.dsmz.de) and 1 mL of trace element solution SL- 10 (see https://www.dsmz.de) were also added. Before use, ASW was filtered through a 0.2-μm filter and N2-bubbled for 10 min. ASW was kept on ice during handling. For more information on resuspension and incubation procedures used see <a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a>. &nbsp;</p>
from Cruise: AT15-68 <p>1. Atlantis cruise AT-15-68, Alvin Dive 4635; push-core 16</p>
<p>4. Atlantis cruise AT-18-10, dive J2-593 E4A; push-core 36</p>
from Cruise: MBARI_Southern_California_2013 <p>R/V Western Flyer MBARI Cruise 2013; dive 463; push-core 43</p>
<p>R/V Western Flyer MBARI Cruise 2013; dive 459; push-core 74</p>
Specified by the Principal Investigator(s)
<p><strong>16S rRNA Gene Tag Sequencing&nbsp;&nbsp;</strong>(extracted from&nbsp;<a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a>)</p>
<p>Sediment DNA was extracted using the Power Soil DNA Isolation Kit according to the manufacturer’s protocol (MoBio), and diluted DNA from genomeamplified sorted consortia was used directly. The V4 region of the 16S rRNA gene was amplified from each extract using archaeal and bacterial primers 515F (GTGCCAGCMGCCGCGGTAA) and 806R (GGACTACHVGGGTWTCTAAT) (67, 68). Sediment samples were amplified in duplicate. The nonbarcoded primers were used with Q5 Hot Start High-Fidelity 2× Master Mix (New England Biolabs) according to the manufacturer’s directions, using annealing conditions of 54 °C for 30 cycles and 58 °C for 32 cycles for sediments and MDAs, respectively. Duplicates of sediment sample amplifications were then pooled. The barcoded 806R primer (CAAGCAGAAGACGGCATACGAGAT XXXXXXXXXXXX AGTCAGTCAG CC GGACTACHVGGGTWTCTAAT) was paired with 515F in a reconditioning reaction (same conditions as above except for five cycles of PCR) to barcode the PCR products. Samples were mixed together in equimolar amounts and purified in bulk through a Qiagen PCR purification kit before submission to Laragen for analysis on an Illumnia MiSeq platform. The resulting paired-end sequence data, 2× 250 bp, was demultiplexed, and sequences with &gt;1 bp mismatch on the 12-bp barcode were removed. The resulting sequences were passed through Illumina’s MiSeq Recorder software to assign quality scores to each base call and remove adapter, barcode, and primer sequence.</p>
<p>Information on the fluorescence activiated cell sorted microbial aggregate composed of ANME and SRB, and other probe information can be found in<strong>&nbsp;</strong>&nbsp;<a href="https://dx.doi.org/10.1073/pnas.1603757113">Hatzenpichler et. al., 2016</a></p>
<p><strong>Data Manager Notes:</strong></p>
<ul>
<li>several columns in submitted dataset removed and included in metadata such as publication information.</li>
<li>converted lat/lon from degrees decimal minutes to decimal degrees.</li>
<li>added underscores in some text fields</li>
<li>removed units from data colums. &nbsp;Units can be found in the parameters section.</li>
</ul>
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: AT15-68
AT15-68
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-68
Lisa A. Levin
University of California-San Diego Scripps
Cruise: MBARI_Southern_California_2013
MBARI_Southern_California_2013
R/V Western Flyer
International Council for the Exploration of the Sea
R/V Western Flyer
vessel
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Western Flyer
International Council for the Exploration of the Sea
R/V Western Flyer
vessel