http://lod.bco-dmo.org/id/dataset/809862
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
2020-04-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenomic data from site U1382B at North Pond (IODP 336), western flank of the mid-Atlantic Ridge from core samples collected in November of 2011
2020-04-22
publication
2020-04-22
revision
BCO-DMO Linked Data URI
2020-04-22
creation
http://lod.bco-dmo.org/id/dataset/809862
Adina Paytan
University of California-Santa Cruz
principalInvestigator
Dr Delphine Defforey
University of California-Santa Cruz
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: Paytan, A., Defforey, D. (2020) Metagenomic data from site U1382B at North Pond (IODP 336), western flank of the mid-Atlantic Ridge from core samples collected in November of 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-04-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/809862 [access date]
Dataset Description: <p>Metagenomic data from site U1382B at North Pond (IODP 336), western flank of the mid-Atlantic Ridge from core samples collected on 2011-11-08.&nbsp; These data were published in Defforey, D. (2016).<br />
<br />
Metagenomic sequences are available at the National Center for Biotechnology Information SRA database: https://www.ncbi.nlm.nih.gov/sra/?term=SRP096133, BioProject:&nbsp;https://www.ncbi.nlm.nih.gov/bioproject/PRJNA360271.<br />
<br />
Additional award information:</p>
<p>* NSF C-DEBI subaward # 156246 to Adina Paytan<br />
* NSF C-DEBI subaward # 157598 to Delphine Defforey</p> Methods and Sampling: Location: North Atlantic, western flank of the mid-Atlantic Ridge 22.75589 N 46.08125 W
DNA was extracted using the method described in (Mills et al. 2012) as modified by B. K. Reese for nucleic acids in low biomass open ocean sediments. The interior of the whole-round core for sample U1382B 7H-5 was subsampled using sterile techniques and was divided into 25 splits, each weighing ~0.5 g. Initial cell lysis was achieved using five cycles of freeze (liquid nitrogen), thaw (55oC water bath) and vortex steps while stabilizing nucleic acids in a Tris–EDTA–glucose buffer. This step was followed by the addition of lysozyme to the buffer and incubation at 30oC for 10 minutes. Samples were then treated twice with buffered phenol, chloroform and isoamyl alcohol (25:24:1; pH 8.0), and sodium dodecyl sulfate to dissolve the cell membrane and solubilize both high and low molecular weight proteins. Nucleic acids within the aqueous layer above the phenol–chloroform layer were then precipitated in an ethanol and sodium acetate solution. The ethanol solution was decanted following centrifugation of samples at 4°C. Lastly, DNA pellets were resuspended in sterile water, combined into one sample. We quantified the DNA content using a Quibit fluorometer (Thermo Scientific, Waltham, MA, USA) and assessed its quality on a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA) prior to sequencing at the Marine Biological Laboratory Keck facility (Woods Hole, MA, USA). Extraction blanks were included with each sample extraction and yielded no measurable DNA.
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
Adina Paytan
University of California-Santa Cruz
831-459-1437
Earth & Marine Sciences C308 1156 High St
Santa Cruz
CA
95064
USA
apaytan@ucsc.edu
pointOfContact
Dr Delphine Defforey
University of California-Santa Cruz
Department of Earth and Planetary Sciences 1156 High Street
Santa Cruz
CA
95060
USA
ddeffore@ucsc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Quibit fluorometer (Thermo Scientific, Waltham, MA, USA)
NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA)
theme
None, User defined
Fluorometer
Spectrophotometer
instrument
BCO-DMO Standard Instruments
JRES-336
service
Deployment Activity
Mid-Atlantic Ridge
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
Potential phosphorus uptake mechanisms of the deep sedimentary biosphere
https://osprey.bco-dmo.org/project/664073
Potential phosphorus uptake mechanisms of the deep sedimentary biosphere
<p>The goal of this project is to explore potential microbial P uptake mechanisms in marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use a combination of metagenomic analyses and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to investigate (1) the presence of microbial functional genes pertaining to P uptake and metabolism and (2) the possible P substrates for the deep biosphere in these oligotrophic sediments.</p>
<p>NSF C-DEBI Award #156246 to Dr. Adina Paytan</p>
<p>NSF C-DEBI Award #157598 to Dr. Delphine Defforey </p>
Deep sea sediments
largerWorkCitation
project
eng; USA
oceans
Mid-Atlantic Ridge
-46.08125
-46.08125
22.75589
22.75589
2011-11-08
2011-11-08
Mid-Atlantic Ridge flank
0
BCO-DMO catalogue of parameters from Metagenomic data from site U1382B at North Pond (IODP 336), western flank of the mid-Atlantic Ridge from core samples collected in November of 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
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
https://osprey.bco-dmo.org/dataset/809862/data/download
download
onLine
dataset
Location: North Atlantic, western flank of the mid-Atlantic Ridge 22.75589 N 46.08125 W
DNA was extracted using the method described in (Mills et al. 2012) as modified by B. K. Reese for nucleic acids in low biomass open ocean sediments. The interior of the whole-round core for sample U1382B 7H-5 was subsampled using sterile techniques and was divided into 25 splits, each weighing ~0.5 g. Initial cell lysis was achieved using five cycles of freeze (liquid nitrogen), thaw (55oC water bath) and vortex steps while stabilizing nucleic acids in a Tris–EDTA–glucose buffer. This step was followed by the addition of lysozyme to the buffer and incubation at 30oC for 10 minutes. Samples were then treated twice with buffered phenol, chloroform and isoamyl alcohol (25:24:1; pH 8.0), and sodium dodecyl sulfate to dissolve the cell membrane and solubilize both high and low molecular weight proteins. Nucleic acids within the aqueous layer above the phenol–chloroform layer were then precipitated in an ethanol and sodium acetate solution. The ethanol solution was decanted following centrifugation of samples at 4°C. Lastly, DNA pellets were resuspended in sterile water, combined into one sample. We quantified the DNA content using a Quibit fluorometer (Thermo Scientific, Waltham, MA, USA) and assessed its quality on a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA) prior to sequencing at the Marine Biological Laboratory Keck facility (Woods Hole, MA, USA). Extraction blanks were included with each sample extraction and yielded no measurable DNA.
Specified by the Principal Investigator(s)
Raw reads were quality controlled using cutadapt (v1.7.1) and Trimmomatic (v0.33). The QCed sequences were searched for SSU rRNA fragments using Meta-RNA (v.H3). SSU rRNA fragments were assembled using EMIRGE (v.1.3) utilizing SILVA SSU as the reference database using the SINA web portal aligner (Ludwig et al. 2004; Capella-Gutiérrez et al. 2009; Pruesse et al. 2012).
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
Quibit fluorometer (Thermo Scientific, Waltham, MA, USA)
Quibit fluorometer (Thermo Scientific, Waltham, MA, USA)
PI Supplied Instrument Name: Quibit fluorometer (Thermo Scientific, Waltham, MA, USA) Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA)
NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA)
PI Supplied Instrument Name: NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA) Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Cruise: JRES-336
JRES-336
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
JRES-336
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/336PR.pdf
Report describing JRES-336
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel