http://lod.bco-dmo.org/id/dataset/633015
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
2016-01-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Seep sediment metagenome ANM1 from the R/V Atlantis AT15-53 cruise in the Santa Monica Basin during 2009 (Viruses in Methanotrophic Marine Ecosystems project)
2016-01-19
publication
2016-01-19
revision
BCO-DMO Linked Data URI
2016-01-19
creation
http://lod.bco-dmo.org/id/dataset/633015
David L. Valentine
University of California-Santa Barbara
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: Valentine, D. L. (2016) Seep sediment metagenome ANM1 from the R/V Atlantis AT15-53 cruise in the Santa Monica Basin during 2009 (Viruses in Methanotrophic Marine Ecosystems project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 19 January 2016) Version Date 2016-01-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/633015 [access date]
Seep Sediment Metagenome ANM1 Dataset Description: <p>Metagenomic sequence reads representing viruses from marine sediments at a methane seep — part of the Gordon and Betty Moore Marine Phage Metagenome Initiative</p>
<p><strong>Location:</strong><br />
Pacific Ocean: Santa Monica Basin, offshore California; Depth 820m; Lat. 33.799N, Long. 118.646W</p>
<p><strong>Related files and references:</strong><br />
Henn, M. R., Sullivan, M. B., Stange-Thomann, N., Osburne, M. S., Berlin, A. M., Kelly, L., … Chisholm, S. W. (2010). Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes. PLoS ONE, 5(2), e9083. doi:10.1371/journal.pone.0009083</p>
<p>Paul, B. G., Bagby, S. C., Czornyj, E., Arambula, D., Handa, S., Sczyrba, A., … Valentine, D. L. (2015). Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications, 6(1). doi:10.1038/ncomms7585</p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology:</strong><br />
Metagenomic sequencing was performed at the Broad Institute on 454-FLX plates, as part of the Gordon and Betty Moore Marine Phage Metagenome Initiative (Henn et al. 2010). Detailed methods on processing of metagenomic sequences, assembly, and genome annotation are described in Paul et al. (2015).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046144 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046144
completed
David L. Valentine
University of California-Santa Barbara
805-893-2973
Department of Earth Science 1006 Webb Hall
Santa Barbara
CA
93106
USA
valentine@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 19 January 2016
Unknown
CruiseId
Site
Site_Description
Collection_Date
Latitude
Longitude
Depth
Description
Accession
Submission
Link
theme
None, User defined
cruise_id
site
site description
date
latitude
longitude
depth
sample description
accession number
dataset_id
external_link
featureType
BCO-DMO Standard Parameters
AT15-53
service
Deployment Activity
Santa Monica Basin; Depth 820m; Lat. 33.799N, Long. 118.646W
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems
https://osprey.bco-dmo.org/project/2158
Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems
<p>Marine methanotrophic ecosystems are responsible for consuming around 75 Tg of methane annually, preventing this potent greenhouse gas from entering the atmosphere. These microbial ecosystems thus play a vital role in the global climate system. The nature of these communities depends on the presence or absence of oxygen: methanotrophy is a bacterial lifestyle in aerobic shallow sediments, but in deeper anaerobic sediments it is the exclusive province of archaea, in syntrophy with sulfate-reducing bacteria. It is known which phyla are most commonly found in methanotrophic environments. However, because of these environments' physical inaccessibility and because nearly all microbes from these systems have resisted cultivation, understanding of these communities lags far behind their importance. The cultivation-resistance of microbial hosts from these systems has additionally prevented the use of classical methods to study the viral community. Thus, to date science is largely unable to fill in the broad outlines of marine methanotrophic biodiversity, to fully describe the microbial communities or determine what shapes them.</p>
<p>This project seeks to define the importance of viruses in structuring functional, genetic, and taxonomic diversity in methanotrophic marine ecosystems. The underlying assertion is that viruses structure the diversity of archaeal and bacterial communities in these ecosystems by causing both mortality and horizontal gene transfer. To establish viral contributions to biodiversity of aerobic and anaerobic marine methanotrophic ecosystems, this project combines biogeochemical, genomic, and metagenomic approaches, in both field and laboratory settings.</p>
<p>The project first seeks to assess viral activity in situ by extending established stable isotope probing techniques to quantify rates of viral production at sea floor methane seeps. The same techniques will be used to track the flow of carbon from methane to microbes to viruses and to isolate genetic material from just those organisms that actively cycle methane-derived carbon, enabling the production of microbial and viral metagenomes that are anchored in ecosystem function. Comparisons among these metagenomes will reveal any functional sequences in transit between organisms, providing the basis for an evaluation of the relationships between functional and genetic diversity. At the same time, single-cell whole-genome amplification will pinpoint individual cells for comparison with the microbial and viral assemblages, permitting assessment of the relationships between taxonomic and genetic diversity. Last, the comparison of genomic and metagenomic data both within and across distinctive marine methanotrophic ecosystems will enable analysis of the relationship between functional and taxonomic diversity.</p>
Viruses in Methanotrophic Marine Ecosystems
largerWorkCitation
project
eng; USA
oceans
Santa Monica Basin; Depth 820m; Lat. 33.799N, Long. 118.646W
2016-01-19
0
BCO-DMO catalogue of parameters from Seep sediment metagenome ANM1 from the R/V Atlantis AT15-53 cruise in the Santa Monica Basin during 2009 (Viruses in Methanotrophic Marine Ecosystems 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/633192.rdf
Name: CruiseId
Units: text
Description: <p>Official UNOLS Cruise Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/633193.rdf
Name: Site
Units: text
Description: <p>Site Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/633194.rdf
Name: Site_Description
Units: text
Description: <p>Site Description</p>
http://lod.bco-dmo.org/id/dataset-parameter/633195.rdf
Name: Collection_Date
Units: DD-Mon-YYYY
Description: <p>Collection Date</p>
http://lod.bco-dmo.org/id/dataset-parameter/633196.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude (South is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/633197.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude (West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/633198.rdf
Name: Depth
Units: meters
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/633199.rdf
Name: Description
Units: text
Description: <p>Sample Description</p>
http://lod.bco-dmo.org/id/dataset-parameter/633200.rdf
Name: Accession
Units: text
Description: <p>Accession Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/633201.rdf
Name: Submission
Units: text
Description: <p>Submission Id</p>
http://lod.bco-dmo.org/id/dataset-parameter/633202.rdf
Name: Link
Units: text
Description: <p>Link to Accession in Genbank</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
427
https://datadocs.bco-dmo.org/file/A88rLyvUEExZ6V/ANM1.csv
ANM1.csv
Primary data file for dataset ID 633015
download
https://osprey.bco-dmo.org/dataset/633015/data/download
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology:</strong><br />
Metagenomic sequencing was performed at the Broad Institute on 454-FLX plates, as part of the Gordon and Betty Moore Marine Phage Metagenome Initiative (Henn et al. 2010). Detailed methods on processing of metagenomic sequences, assembly, and genome annotation are described in Paul et al. (2015).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Sediment metagenome ANM1 consists of raw reads from 454-FLX sequencing. To procure the ANMV-1 genome, metagenomic reads were first preprocessed, then assembled as described in Paul et al. (2015).</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
Cruise: AT15-53
AT15-53
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-53
David L. Valentine
University of California-Santa Barbara
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel