http://lod.bco-dmo.org/id/dataset/746718
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
2018-09-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011
2018-06-14
publication
2018-06-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-20
publication
https://doi.org/10.26008/1912/bco-dmo.746718.1
Brandon Briggs
Oregon State University
principalInvestigator
Frederick Colwell
Oregon 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: Briggs, B., Colwell, F. (2021) Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.746718.1 [access date]
Dataset Description: <p>Presence/ absence of taxa detected with the Phylochip.</p> Methods and Sampling: <p>In summary, sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores. Aboard ship, whole round cores were subcored by paring the outer two cm of sediment with an alcohol and flame sterilized chisel. The sub-cores were placed into sterile Whirl Pak Bags and stored at -80C. DNA was extracted from 10g of sediment using a PowerMax Soil DNA extraction kit. DNA was amplified using 27F and 1492R (bacterial) or 4F and 1492R (archaeal) universal primers. 150ng of bacterial and 50ng of archaeal amplicons were hybridized to the PhyloChip array.</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
Brandon Briggs
Oregon State University
907-786-1538
University of Alaska 3101 Science Cir.
Anchorage
AK
99508
USA
bbriggs6@alaska.edu
pointOfContact
Frederick Colwell
Oregon State University
541-737-5220
519 Weniger Hall, Oregon State University, Corvallis, OR 97331
rcolwell@coas.oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Domain
Phylum
Subphylum
Class
Order
Family
BSR03691
BSR03692
BSR36165_A
HY03682
HY03684
HY03685
HY03687
HY03689
HY03690
HY03672
HY03673
HY03675
HY03676
HY03682_A
HY36145_A
HY36146_A
HY36147_A
HY36148_A
HY36149
HY36150_A
HY36153_A
HY36154_A
HY36151_A
HY36152_A
SMI03648
SMI36123_A
SMI36124_A
SMI03647
SMI36126_A
SMI36127_A
SMI36128_A
SMI03649
SMI03650
lon
lat
Furor Hydraulic Piston Corer
theme
None, User defined
kingdom
phylum
taxonomic class
order
family
flag
longitude
latitude
featureType
BCO-DMO Standard Parameters
Piston Corer
instrument
BCO-DMO Standard Instruments
Ulleung_Basin_Core
service
Deployment Activity
Ulleung 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
The Effect of Methane on Microbial Community Distributions in the Ulleung Basin
https://www.darkenergybiosphere.org/award/the-effect-of-methane-on-microbial-community-distributions-in-the-ulleung-basin/
The Effect of Methane on Microbial Community Distributions in the Ulleung Basin
<p>The DEBI/C-DEBI research exchange gave me the opportunity to travel to Lawrence Berkeley National Laboratory (LBNL) to work with Dr. Eoin Brodie. While at LBNL, I was able to learn and adopt a new microarray technology for subseafloor microbial ecology investigations. The PhyloChip is a microarray that contains probes for Bacterial and Archaeal 16s rRNA genes and uses parallel hybridization to minimizes the influence of dominant organisms; therefore, it is highly sensitive to rare microbes. In addition, to this data the research exchange provided necessary funding for me to finish my dissertation. The research exchange funds allowed two sites in the Ulleung Basin to be fully analyzed and incorporated into my dissertation “Geomicrobiology of sediment containing methane”. This collaboration also introduced me to how research is conducted at a national laboratory. This information is valuable in deciding my future career path. Whatever that path may be the collaboration and techniques that I learned will continue beyond graduate school, as we are planning future studies using the PhyloChip. For more on this method, see Briggs, Pohlman, Torres, Reidel, Brodie and Colwell’s 2011 AEM paper Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane.</p>
Methane_Microbes
largerWorkCitation
project
eng; USA
oceans
Ulleung Basin
131
131
37
37
2011-01-01
2011-12-31
Ulleung Basin 37 N 131 E
0
BCO-DMO catalogue of parameters from Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011
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/746726.rdf
Name: Domain
Units: unitless
Description: <p>Domain level phylogenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746727.rdf
Name: Phylum
Units: unitless
Description: <p>Phylum level phylogenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746728.rdf
Name: Subphylum
Units: unitless
Description: <p>Subphylum level phylogenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746729.rdf
Name: Class
Units: unitless
Description: <p>Class level phylogenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746730.rdf
Name: Order
Units: unitless
Description: <p>Order level phylogenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746731.rdf
Name: Family
Units: unitless
Description: <p>Familty level phylgenetic classification</p>
http://lod.bco-dmo.org/id/dataset-parameter/746732.rdf
Name: BSR03691
Units: unitless
Description: <p>Presence (1) Absence (0) in sample BSR03691</p>
http://lod.bco-dmo.org/id/dataset-parameter/746733.rdf
Name: BSR03692
Units: unitless
Description: <p>Presence (1) Absence (0) in sample BSR03692</p>
http://lod.bco-dmo.org/id/dataset-parameter/746734.rdf
Name: BSR36165_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample BSR36165_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746735.rdf
Name: HY03682
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03682</p>
http://lod.bco-dmo.org/id/dataset-parameter/746736.rdf
Name: HY03684
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03684</p>
http://lod.bco-dmo.org/id/dataset-parameter/746737.rdf
Name: HY03685
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03685</p>
http://lod.bco-dmo.org/id/dataset-parameter/746738.rdf
Name: HY03687
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03687</p>
http://lod.bco-dmo.org/id/dataset-parameter/746739.rdf
Name: HY03689
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03689</p>
http://lod.bco-dmo.org/id/dataset-parameter/746740.rdf
Name: HY03690
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03690</p>
http://lod.bco-dmo.org/id/dataset-parameter/746741.rdf
Name: HY03672
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03672</p>
http://lod.bco-dmo.org/id/dataset-parameter/746742.rdf
Name: HY03673
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03673</p>
http://lod.bco-dmo.org/id/dataset-parameter/746743.rdf
Name: HY03675
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03675</p>
http://lod.bco-dmo.org/id/dataset-parameter/746744.rdf
Name: HY03676
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03676</p>
http://lod.bco-dmo.org/id/dataset-parameter/746745.rdf
Name: HY03682_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY03682_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746746.rdf
Name: HY36145_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36145_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746747.rdf
Name: HY36146_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36146_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746748.rdf
Name: HY36147_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36147_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746749.rdf
Name: HY36148_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36148_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746750.rdf
Name: HY36149
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36149</p>
http://lod.bco-dmo.org/id/dataset-parameter/746751.rdf
Name: HY36150_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36150_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746752.rdf
Name: HY36153_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36153_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746753.rdf
Name: HY36154_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36154_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746754.rdf
Name: HY36151_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36151_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746755.rdf
Name: HY36152_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample HY36152_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746756.rdf
Name: SMI03648
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI03648</p>
http://lod.bco-dmo.org/id/dataset-parameter/746757.rdf
Name: SMI36123_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI36123_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746758.rdf
Name: SMI36124_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI36124_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746759.rdf
Name: SMI03647
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI03647</p>
http://lod.bco-dmo.org/id/dataset-parameter/746760.rdf
Name: SMI36126_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI36126_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746761.rdf
Name: SMI36127_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI36127_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746762.rdf
Name: SMI36128_A
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI36128_A</p>
http://lod.bco-dmo.org/id/dataset-parameter/746763.rdf
Name: SMI03649
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI03649</p>
http://lod.bco-dmo.org/id/dataset-parameter/746764.rdf
Name: SMI03650
Units: unitless
Description: <p>Presence (1) Absence (0) in sample SMI03650</p>
http://lod.bco-dmo.org/id/dataset-parameter/746769.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude in decimal degrees east.</p>
http://lod.bco-dmo.org/id/dataset-parameter/746771.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude in decimal degrees north.</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
161254
https://darchive.mblwhoilibrary.org/bitstream/1912/27148/1/dataset-746718_ulleung-basin-phylochip__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.746718.1
download
onLine
dataset
<p>In summary, sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores. Aboard ship, whole round cores were subcored by paring the outer two cm of sediment with an alcohol and flame sterilized chisel. The sub-cores were placed into sterile Whirl Pak Bags and stored at -80C. DNA was extracted from 10g of sediment using a PowerMax Soil DNA extraction kit. DNA was amplified using 27F and 1492R (bacterial) or 4F and 1492R (archaeal) universal primers. 150ng of bacterial and 50ng of archaeal amplicons were hybridized to the PhyloChip array.</p>
Specified by the Principal Investigator(s)
<p>Data processing can be found in Briggs et al. (2013).&nbsp;</p>
<p><strong>BCO-DMO Processing:</strong></p>
<ul>
<li>added conventional header with dataset name, PI name, version date</li>
<li>modified parameter names to conform with BCO-DMO naming conventions</li>
<li>adjusted the duplicate column header&nbsp;HY03682 to&nbsp;HY03682_A</li>
<li>appended latitude and longitude fields for mapping.</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
Furor Hydraulic Piston Corer
Furor Hydraulic Piston Corer
PI Supplied Instrument Name: Furor Hydraulic Piston Corer PI Supplied Instrument Description:Sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores. Instrument Name: Piston Corer Instrument Short Name:Piston Corer Instrument Description: The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Deployment: Ulleung_Basin_Core
Ulleung_Basin_Core
Unknown Platform
Ulleung_Basin_Core
Brandon Briggs
Oregon State University
Unknown Platform