http://lod.bco-dmo.org/id/dataset/781137
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
2019-11-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenomic data from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010
2019-11-05
publication
2019-11-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-11-22
publication
https://doi.org/10.1575/1912/bco-dmo.781137.1
Christopher House
Pennsylvania State University
principalInvestigator
Leah Brandt
Pennsylvania 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: House, C., Brandt, L. (2019) Metagenomic data from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-11-05 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.781137.1 [access date]
Metagenomic data Dataset Description: <p>Next-generation sequencing data across a hydrothermal gradient; Okinawa Backarc Basin IODP 331 – subvent biosphere.&nbsp;The purpose these metagenomic data was to capture a distinct changeover of microbial assemblages between the mesophilic horizons above 10 mbsf and the hottest (55C) hydrothermal clay horizon. In this section of the dynamic Iheya North Hydrothermal system, the temperature gradient was estimated to be ~3C/m. These metagenomes provide functional evidence to this model, demonstrating that molecular signals represent a responsive microbial community to the increasingly demanding environmental conditions.</p> Methods and Sampling: <p>Sampling of cores was done in accordance with IODP protocols.</p>
<p>All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic piston coring system).<br />
All C0015 samples were cored on 18 September 2010 via HPCS.<br />
All C0017 samples were cored on 27 September 2010 via HPCS.</p>
<p>Core sections were kept frozen (-80°C) until DNA extractions. A MoBio® Power Soil kit was used to extract environmental DNA. Metagenomic data was produced from whole genome amplified environmental DNA (REPLI-g Mini Kit, Qiagen).</p>
<p>Sequencing was performed at the Penn State Genomics Core Facility – University Park, PA using the Illumina® HiSeq 2500 (NSF-MRI award DBI-1229046 (Axtell et al., 2012)). The sequencing facility prepared DNA libraries using Nextera XT Library Preparation Kits prior to sequencing. Together, the samples were run on one-half of a sequencing plate. This sequencing run was run using rapid-run model that averages up to 300 million single reads, or 600 million paired reads of ~150 nucleotides per rapid-run.</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
Christopher House
Pennsylvania State University
814-865-8801
218 Earth and Engineering Sciences Building
University Park
PA
16802
USA
chrishouse@psu.edu
pointOfContact
Leah Brandt
Pennsylvania State University
ldb163@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise_ID
Sample_Name
Latitude
Longitude
Water_depth
Top_Depth
Bottom_Depth
Sediment_type
Estimated_Temp
MGRAST_Name
MGRAST_ID
Notes
Illumina HiSeq 2500
hydraulic piston coring system (HPCS)
theme
None, User defined
Cruise identfier
sample identification
latitude
longitude
depth_w
depth below seafloor
sample description
water temperature at measurement depth
accession number
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Piston Corer
instrument
BCO-DMO Standard Instruments
Chikyu-331
service
Deployment Activity
Okinawa Trough, Japan
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
International Ocean Discovery Program
http://www.iodp.org/index.php
International Ocean Discovery Program
The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.
IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards.
IODP's three platform providers include:
The U.S. National Science Foundation (NSF)
Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT)
The European Consortium for Ocean Research Drilling (ECORD)
More information on IODP, including the Science Plan and Policies/Procedures, can be found on their website at http://www.iodp.org/program-documents.
A summary table with links to IODP datasets currently hosted on Zenodo (https://zenodo.org/communities/iodp) can be accessed using the following link: https://iodp.tamu.edu/database/zenodo.html
IODP
largerWorkCitation
program
An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments
https://osprey.bco-dmo.org/project/714230
An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments
<p>The Iheya North Hydrothermal Field in the Okinawa Backarc Basin represents an ideal environment in which to investigate the biotic temperature fringe of microbial life at depth because of its subsurface hydrothermal activity within its continental margin-type sediment profile. Geographically, the Okinawa Backarc Basin is situated along a continental margin, which is a sediment profile type commonly sampled and studied across the seafloor (e.g. Peru Margin, Costa Rica Margin, Cascadia Margin). The hydrothermal network within the subsurface here supplies an additional temperature obstacle to microbial life existing in the sediments. In particular, the sediment profile at Site C0014 exhibits a transition from hemipelagic ooze with pumiceous volcaniclastic sediments and low temperature (4°C) to a hydrothermally altered sequence of clays within the top ~10 mbsf of sediment. Temperature measurements indicate a gradient of approximately 3°C/m, which is roughly an order of magnitude greater than continental margin sites (e.g. Cascadia Margin, IODP 311 and Costa Rica Margin, IODP 344), but is more gradual than intense, centimeter-scale gradients from other hot, surface sediments. We have focused on the application of culture-independent, molecular methods to understand taxonomic and functional characteristics through this hydrothermal gradient. Confidence in DNA recovery suggests a microbial biosphere extent of approximately 15 mbsf (55°C).</p>
<p>Results from both 16S rRNA gene surveys and metagenomics analyses suggest a temperature-dependent stratigraphy of taxonomic and functional adaptations between the shallowest and deepest sample horizons. Cosmopolitan marine subsurface bacterial and archaeal taxa are present throughout the top 10 mbsf, whereas, hyperthermophilic heterotrophic as well as thermophilic anaerobic methanotrophic archaea appear in varying local abundances in deeper, hydrothermal clay horizons. "An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments" encompasses datasets funded through C-DEBI to investigate the microbial communities in IODP 331 Iheya North Hydrothermal Field sediments. Site C0014 at this field site is 500 m away from the active vent and experiences a 3C/m temperature gradient with depth. In the research grant "Investigating the active microbial populations in near hydrothermal vent sediments" and the Research Exchange grant "Learning new RNA extraction techniques", we used an RNA-based approach to explore the active microbial community. Upon analysis, the RNA dataset does not appear to reflect the same information as the phylogenetic signals coming from both the 16S rRNA gene as well as the metagenomes. The data indicate significant background noise from the RNA extraction process rather than from an indigenous representation of the subsurface biosphere.</p>
<p>The graduate fellowship "An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field" provided an opportunity to bring together metagenomic, 16S rRNA gene amplicon (DNA), and 16S rRNA amplicon datasets from IODP 331 Iheya North Hydrothermal Field sediments to understand the biogeography of this subvent biosphere.</p>
<p>For more information, refer to the following C-DEBI grants/projects.<br />
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field:<br />
<a href="https://www.darkenergybiosphere.org/award/an-in-depth-analysis-of-the-subvent-biosphere-within-the-okinawa-backarc-basin-iheya-north-hydrothermal-field/" target="_blank">https://www.darkenergybiosphere.org/award/an-in-depth-analysis-of-the-subvent-biosphere-within-the-okinawa-backarc-basin-iheya-north-hydrothermal-field/</a></p>
<p>Investigating the active microbial populations in near hydrothermal vent sediments: <a href="https://www.darkenergybiosphere.org/award/investigating-the-active-microbial-populations-in-near-hydrothermal-vent-sediments/" target="_blank">https://www.darkenergybiosphere.org/award/investigating-the-active-microbial-populations-in-near-hydrothermal-vent-sediments/</a></p>
<p>Learn new RNA extraction techniques: <a href="https://www.darkenergybiosphere.org/award/learn-new-rna-extraction-techniques/" target="_blank">https://www.darkenergybiosphere.org/award/learn-new-rna-extraction-techniques/</a><br />
</p>
Subvent_Biosphere_Sediments
largerWorkCitation
project
eng; USA
oceans
Okinawa Trough, Japan
126.900833
126.900833
27.790278
27.790278
2010-09-16
2010-09-27
Iheya North Hydrothermal Field, Pacific Ocean
0
BCO-DMO catalogue of parameters from Metagenomic data from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010
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/781145.rdf
Name: Cruise_ID
Units: unitless
Description: <p>Cruise ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/781146.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/781147.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/781148.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude; positive values = East</p>
http://lod.bco-dmo.org/id/dataset-parameter/781149.rdf
Name: Water_depth
Units: meters
Description: <p>Water depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/781150.rdf
Name: Top_Depth
Units: meters below seafloor
Description: <p>Top depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/781151.rdf
Name: Bottom_Depth
Units: meters below seafloor
Description: <p>Bottom depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/781152.rdf
Name: Sediment_type
Units: unitless
Description: <p>Sediment type</p>
http://lod.bco-dmo.org/id/dataset-parameter/781153.rdf
Name: Estimated_Temp
Units: degrees Celsius
Description: <p>Estimated temperature; based on 3 degrees C/m</p>
http://lod.bco-dmo.org/id/dataset-parameter/781154.rdf
Name: MGRAST_Name
Units: unitless
Description: <p>MGRAST name</p>
http://lod.bco-dmo.org/id/dataset-parameter/781155.rdf
Name: MGRAST_ID
Units: unitless
Description: <p>MGRAST ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/781156.rdf
Name: Notes
Units: unitless
Description: <p>Notes</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
1367
https://darchive.mblwhoilibrary.org/bitstream/1912/24889/1/dataset-781137_metagenome__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.781137.1
download
onLine
dataset
<p>Sampling of cores was done in accordance with IODP protocols.</p>
<p>All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic piston coring system).<br />
All C0015 samples were cored on 18 September 2010 via HPCS.<br />
All C0017 samples were cored on 27 September 2010 via HPCS.</p>
<p>Core sections were kept frozen (-80°C) until DNA extractions. A MoBio® Power Soil kit was used to extract environmental DNA. Metagenomic data was produced from whole genome amplified environmental DNA (REPLI-g Mini Kit, Qiagen).</p>
<p>Sequencing was performed at the Penn State Genomics Core Facility – University Park, PA using the Illumina® HiSeq 2500 (NSF-MRI award DBI-1229046 (Axtell et al., 2012)). The sequencing facility prepared DNA libraries using Nextera XT Library Preparation Kits prior to sequencing. Together, the samples were run on one-half of a sequencing plate. This sequencing run was run using rapid-run model that averages up to 300 million single reads, or 600 million paired reads of ~150 nucleotides per rapid-run.</p>
Specified by the Principal Investigator(s)
<p>Data Processing: Data assembly was performed with Ray Meta de novo assembly program using a k-mer of 65 for all samples.</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
Illumina HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
hydraulic piston coring system (HPCS)
hydraulic piston coring system (HPCS)
PI Supplied Instrument Name: hydraulic piston coring system (HPCS) 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/
Cruise: Chikyu-331
Chikyu-331
Chikyu
Community Standard Description
International Council for the Exploration of the Sea
Chikyu
vessel
Chikyu-331
Michael Mottl
University of Hawaiʻi at Mānoa
Chikyu
Community Standard Description
International Council for the Exploration of the Sea
Chikyu
vessel