http://lod.bco-dmo.org/id/dataset/559235
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
2015-05-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE project)
2015-05-22
publication
2015-05-22
revision
BCO-DMO Linked Data URI
2015-05-22
creation
http://lod.bco-dmo.org/id/dataset/559235
Edward DeLong
Massachusetts Institute of Technology
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: DeLong, E. (2015) Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 22 May 2015) Version Date 2015-05-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/559235 [access date]
Marine sediment trap metagenomes Dataset Description: <p>Marine sediment trap metagenomes</p>
<p>This study explores the taxonomic and metabolic diversity of microbes associated with sinking particles in the North Pacific Subtropical Gyre. Marine particles are hotspots of microbial activity, yet the microbial taxa and biochemical processes involved in carbon and energy cycling on sinking particles are poorly understood. Metagenomes generated in this study revealed new insights into the important taxa and metabolisms involved in microbial processing of marine particles.<strong>&nbsp;</strong></p>
<p>NCBI BioProject PRJNA270248</p>
<pre>
# C-MORE sediment trap metagenomes
# DeLong Lab - MIT
# Ed DeLong
# CMORE/HOEDYLAN
# date ingested into BCO-DMO: May 22 2015</pre> Methods and Sampling: <p>A HOE-DYLAN 5 sediment trap filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012. It was filtered onto a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.</p>
<p>Seawater at station ALOHA in the North Pacific Subtropical Gyre was collected by CTD during the HOE-DYLAN 9 expedition on 08/26/2012. Seawater was prefiltered with a 5 micron filter and microbial communities were collected on a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-5 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.</p>
<p><a href="http://bcodata.whoi.edu/C-MORE/CMORE_DNA_Sampling_protocol.pdf" target="_blank">C-MORE DNA Sampling Protocol</a></p>
Funding provided by US Department of Energy (DOE) Award Number: unknown C-MORE DOE
Funding provided by NSF Division of Biological Infrastructure (NSF DBI) Award Number: DBI-0424599 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0424599
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: unknown C-MORE Moore
Funding provided by NSF Division of Biological Infrastructure (NSF DBI) Award Number: DBI-1202684 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1202684
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF3777 Award URL: https://www.moore.org/grant-detail?grantId=GBMF3777
Funding provided by Agouron Institute (AI) Award Number: AI-MO9.12.1
completed
Edward DeLong
Massachusetts Institute of Technology
CMORE 114
Honolulu
HI
96822
USA
edelong@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 22 May 2015
Unknown
lat
lon
sample
depth
date
BioProject
SRX
BioSample
MiSeq instrument
MOBIO Powerwater
Illumina Nextera XT
HOE-DYLAN 5 sediment trap
theme
None, User defined
latitude
longitude
sample identification
depth
date
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Automated DNA Sequencer
CTD Sea-Bird SBE 911plus
Niskin bottle
Sediment Trap
instrument
BCO-DMO Standard Instruments
KM1215
KM1219
service
Deployment Activity
Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii (22.75 N, 158 W)
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 Microbial Oceanography: Research and Education
http://cmore.soest.hawaii.edu/
Center for Microbial Oceanography: Research and Education
<h3>Project summary</h3>
<p>The <strong>Center for Microbial Oceanography: Research and Education</strong> (C-MORE) is a recently established (August 2006; NSF award: EF-0424599) NSF-sponsored Science and Technology Center designed to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements and energy in the marine environment. Stated holistically, C-MORE's primary mission is: <em>Linking Genomes to Biomes</em>.</p>
<p>We believe that the time is right to address several major, long-standing questions in microbial oceanography. Recent advances in the application of molecular techniques have provided an unprecedented view of the structure, diversity and possible function of sea microbes. By combining these and other novel approaches with more well-established techniques in microbiology, oceanography and ecology, it may be possible to develop a meaningful predictive understanding of the ocean with respect to energy transduction, carbon sequestration, bioelement cycling and the probable response of marine ecosystems to global environmental variability and climate change. The strength of C-MORE resides in the synergy created by bringing together experts who traditionally have not worked together and this, in turn, will facilitate the creation and dissemination of new knowledge on the role of marine microbes in global habitability.</p>
<p>The new Center will design and conduct novel research, broker partnerships, increase diversity of human resources, implement education and outreach programs, and utilize comprehensive information about microbial life in the sea. The Center will bring together teams of scientists, educators and community members who otherwise do not have an opportunity to communicate, collaborate or design creative solutions to long-term ecosystem scale problems. The Center's research will be organized around four interconnected themes:</p>
<ul>
<li>(Theme I) microbial biodiversity,</li>
<li>(Theme II) metabolism and C-N-P-energy flow,</li>
<li>(Theme III) remote and continuous sensing and links to climate variability, and</li>
<li>(Theme IV) ecosystem modeling, simulation and prediction.</li>
</ul>
<p> Each theme will have a leader to help coordinate the research programs and to facilitate interactions among the other related themes. The education programs will focus on pre-college curriculum enhancements, in service teacher training and formal undergraduate/graduate and post-doctoral programs to prepare the next generation of microbial oceanographers. The Center will establish and maintain creative outreach programs to help diffuse the new knowledge gained into society at large including policymakers. The Center's activities will be dispersed among five partner institutions:</p>
<ul>
<li>Massachusetts Institute of Technology,</li>
<li>Woods Hole Oceanographic Institution,</li>
<li>Monterey Bay Aquarium Research Institute,</li>
<li>University of California at Santa Cruz and</li>
<li>Oregon State University</li>
</ul>
<p>and will be coordinated at the University of Hawaii at Manoa.</p>
<h4>Related Files:</h4>
<p><a href="http://bcodata.whoi.edu/C-MORE/C-MORE_SIP_ver_09-01-2008.pdf">Strategic plan (PDF file)</a></p>
C-MORE
largerWorkCitation
project
eng; USA
oceans
Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii (22.75 N, 158 W)
2015-05-22
North Pacific Subtropical Gyre (large region around 22 45 N, 158 W)
0
BCO-DMO catalogue of parameters from Marine sediment trap metagenomes from R/V Kilo Moana KM1215, KM1219 in the Station ALOHA, an oligotrophic station 100 miles north of Oahu, Hawaii, July to September 2012 (C-MORE 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
http://lod.bco-dmo.org/id/dataset-parameter/559244.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude (positive north)</p>
http://lod.bco-dmo.org/id/dataset-parameter/559245.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude (positive east)</p>
http://lod.bco-dmo.org/id/dataset-parameter/559246.rdf
Name: sample
Units: dimensionless
Description: <p>sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/559247.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/559248.rdf
Name: date
Units: YYYYMMDD
Description: <p>date</p>
http://lod.bco-dmo.org/id/dataset-parameter/559249.rdf
Name: BioProject
Units: dimensionless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/559250.rdf
Name: SRX
Units: dimensionless
Description: <p>NCBI SRX accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/559251.rdf
Name: BioSample
Units: dimensionless
Description: <p>NCBI BioSample accession number</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
3327
https://datadocs.bco-dmo.org/file/933jzlASqwmW5/sedtrap_metagenomes.csv
sedtrap_metagenomes.csv
Primary data file for dataset ID 559235
download
https://osprey.bco-dmo.org/dataset/559235/data/download
download
onLine
dataset
<p>A HOE-DYLAN 5 sediment trap filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012. It was filtered onto a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.</p>
<p>Seawater at station ALOHA in the North Pacific Subtropical Gyre was collected by CTD during the HOE-DYLAN 9 expedition on 08/26/2012. Seawater was prefiltered with a 5 micron filter and microbial communities were collected on a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-5 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.</p>
<p><a href="http://bcodata.whoi.edu/C-MORE/CMORE_DNA_Sampling_protocol.pdf" target="_blank">C-MORE DNA Sampling Protocol</a></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
MiSeq instrument
MiSeq instrument
PI Supplied Instrument Name: MiSeq instrument PI Supplied Instrument Description:MiSeq instrument
This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3. 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.
MOBIO Powerwater
MOBIO Powerwater
PI Supplied Instrument Name: MOBIO Powerwater PI Supplied Instrument Description:MOBIO Powerwater
Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. 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.
Illumina Nextera XT
Illumina Nextera XT
PI Supplied Instrument Name: Illumina Nextera XT PI Supplied Instrument Description:Illumina Nextera XT
Illumina Nextera XT Data Sheet
Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. 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.
PI Supplied Instrument Name: Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
HOE-DYLAN 5 sediment trap
HOE-DYLAN 5 sediment trap
PI Supplied Instrument Name: HOE-DYLAN 5 sediment trap PI Supplied Instrument Description:A HOE-DYLAN 5 sediment trap filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012.
filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012. Instrument Name: Sediment Trap Instrument Short Name:Sediment Trap Instrument Description: Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/33/
Cruise: KM1215
KM1215
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1215
Samuel T. Wilson
University of Hawai'i
Cruise: KM1219
KM1219
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1219
Samuel T. Wilson
University of Hawai'i
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel