http://lod.bco-dmo.org/id/dataset/636479
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
2016-01-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses project)
2016-01-26
publication
2016-01-26
revision
BCO-DMO Linked Data URI
2016-01-26
creation
http://lod.bco-dmo.org/id/dataset/636479
Grieg Steward
University of Hawaiʻi at Mānoa
principalInvestigator
Dr Alexander Culley
University of Hawaiʻi at Mānoa
principalInvestigator
Dr Guylaine Poisson
University of Hawaiʻi at Mānoa
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: Steward, G., Culley, A., Poisson, G. (2016) Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2016-01-26) Version Date 2016-01-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636479 [access date]
Pyrosequencing reads (454) of marine RNA virus metagenomes Dataset Description: <p>This datasest links to accessions at the iMicrobe data repository containing fasta formatted nucleic acid sequences. Samples are from Surface waters of Kaneohe Bay, a tropical embayment on eastern shore of Oahu, HI, 21° 25’ 46.80” N, 157° 47’ 31.51” W.</p>
<p>Sample Name: CAM_SMPL_000815 (collected Aug 1, 2009)<br />
Link: <a href="http://data.imicrobe.us/sample/view/333" target="_blank">http://data.imicrobe.us/sample/view/333</a></p>
<p>Sample Name: CAM_SMPL_000824 (collected Jun 3, 2010)<br />
Link: <a href="http://data.imicrobe.us/sample/view/324" target="_blank">http://data.imicrobe.us/sample/view/324</a></p>
<p><strong>Related References:</strong></p>
<p>Culley AI, JA Mueller, M Belcaid, EM Wood-Charlson, G Poisson, GF Steward (2104). The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics. <em>mBio</em> 5(3):e01210-14. doi:10.1128/mBio.01210-14.</p>
<p>Steward GF, AI Culley, JA Mueller, EM Wood-Charlson, M Belcaid, G Poisson (2013). Are we missing half the viruses in the sea? <em>ISME Journal</em> 7(3) 627-679.</p> Methods and Sampling: <p>454 Pyrosequencing on the GS FLX Titanium platform (Roche Diagnostics Corporation) was used to generate the sequence data.&nbsp;</p>
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 NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0826650 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0826650
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF1799 Award URL: https://www.moore.org/grants/list/GBMF1799
Funding provided by National Institutes of Health (NIH) Award Number: NIH-P20GM103516
Funding provided by National Institutes of Health (NIH) Award Number: NIH-P20GM103466
completed
Grieg Steward
University of Hawaiʻi at Mānoa
808-956-6775
Department of Oceanography, CMORE Hale 1950 East-West Rd.
Honolulu
HI
96822
USA
grieg@hawaii.edu
pointOfContact
Dr Alexander Culley
University of Hawaiʻi at Mānoa
418-656-2131 ext. 8502
Dépt de Biochimie, de Microbiologie et de Bio-informatique 2325, rue de l'Université
Québec City
Québec
G1V 0A6
Canada
alexander.culley.1@ulaval.ca
pointOfContact
Dr Guylaine Poisson
University of Hawaiʻi at Mānoa
808-956-3496
Information and Computer Sciences Department 1680 East-West Road
Honolulu
HI
96822
USA
guylaine@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 2016-01-26
Unknown
sample
sample_type
date
lat
lon
temp
iMicrobe_accession
theme
None, User defined
sample identification
sample type
date
latitude
longitude
water temperature at measurement depth
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
KaneoheBay_Steward
service
Deployment Activity
Kaneohe Bay, HI
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.
Diversity and ecology of marine RNA viruses
https://osprey.bco-dmo.org/project/2193
Diversity and ecology of marine RNA viruses
<p>Viruses are an integral component of the marine food web contributing to the disease and mortality of essentially every type of marine life, yet the diversity of marine viral assemblages remains very poorly characterized. This is especially true of the RNA-containing viruses. There are several reports of isolations of RNA-containing viruses that infect marine protists, but the number of isolates and the number of cultivation-independent surveys of RNA viral diversity are still very limited. Previous studies in coastal British Columbia and in coastal Oahu have shown RNA viruses are diverse and persistent in both temperate and tropical waters. Many of these novel gene sequences appear to derive from viruses of marine protists and their high diversity suggests that viral infections are a persistent force shaping protistan community composition in the sea. It is now clear that the few available isolates of marine RNA viruses are just the tip of the iceberg; novel RNA viruses are still being discovered with each new sample analyzed and the cultivated representatives are not adequately representative. Quantifying the abundance, diversity, and dynamics of these viruses, and obtaining additional representative isolates are some of the important first steps we need to take to incorporate the RNA viruses into the ecology of the sea. Our tasks in this project were to 1) determine the diversity of RNA viruses in coastal and offshore seawater 2) determine whether the RNA viruses make a significant numerical contribution to the total virus pool and 3) isolate and characterize new RNA viruses that infect phytoplankton.</p>
<div>We estimated the relative abundance of RNA viruses using RNA and DNA assays of purified and fractionated viral assemblages harvested from seawater and we characterized the genomic diversity of RNA viruses in a subtropical environment using a metagenomics approach. We found that RNA viruses are probably much more abundant than had been assumed. New bioinformatic tools and approaches specifically designed to handle metagenomic data were tested and implemented and should prove useful for characterizing short reads from viral metagenomic studies. We also initiated a cultivation effort and identified a large number of putative phytoplankton viruses. A number of these have now been confirmed to be viral. One of these has been confirmed to be an RNA-containing virus in the Order <em>Picornavirales</em> and its genome has been fully sequenced. This appears to be the first isolation of a virus infecting a pennate diatom. It is expected that the final output from this project will be of interest and value to researchers in a range of disciplines including microbial oceanographers, evolutionary biologists, virologists, and protistan ecologists.</div>
Diversity and ecology of marine RNA viruses
largerWorkCitation
project
eng; USA
biota
oceans
Kaneohe Bay, HI
2016-01-26
0
BCO-DMO catalogue of parameters from Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses 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/636489.rdf
Name: sample
Units: unitless
Description: <p>sample description</p>
http://lod.bco-dmo.org/id/dataset-parameter/636490.rdf
Name: sample_type
Units: unitless
Description: <p>analysis type</p>
http://lod.bco-dmo.org/id/dataset-parameter/636491.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>collection date; local time</p>
http://lod.bco-dmo.org/id/dataset-parameter/636492.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/636493.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/636494.rdf
Name: temp
Units: degrees Celsius
Description: <p>surface temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/636495.rdf
Name: iMicrobe_accession
Units: unitless
Description: <p>iMicrobe accession number with link</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
384
https://datadocs.bco-dmo.org/file/jAABwyGTy0pZWk/virus_metagenome.csv
virus_metagenome.csv
Primary data file for dataset ID 636479
download
https://osprey.bco-dmo.org/dataset/636479/data/download
download
onLine
dataset
<p>454 Pyrosequencing on the GS FLX Titanium platform (Roche Diagnostics Corporation) was used to generate the sequence data.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Sequences were processed though the quality control pipeline of the RAST metagenomics server (http://metagenomics.anl.gov/?page=Home) to remove short and low-quality reads as well as artificial replicates.</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
PI Supplied Instrument Name: PI Supplied Instrument Description:GS FLX Titanium platform (Roche Diagnostics Corporation) 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.
Deployment: KaneoheBay_Steward
KaneoheBay_Steward
lab UHawaii_SOEST
laboratory
KaneoheBay_Steward
Grieg Steward
University of Hawaiʻi at Mānoa
lab UHawaii_SOEST
laboratory