http://lod.bco-dmo.org/id/dataset/715475
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
2017-09-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific (GOV project)
2017-09-21
publication
2017-09-21
revision
BCO-DMO Linked Data URI
2017-09-21
creation
http://lod.bco-dmo.org/id/dataset/715475
Matthew Sullivan
Ohio State University
principalInvestigator
Maureen L. Coleman
University of Chicago
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: Sullivan, M., Coleman, M. L. (2017) ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific (GOV project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-09-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/715475 [access date]
ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific Dataset Description: <p>This dataset includes metadata and links to scripts and data for the analyses of double- and single-stranded DNA from viruses collected in the Great Lakes, off Bermuda (N. Atlantic) and off Peru (S. Pacific) used to provide first estimates of the natural abundance of ssDNA viruses.</p>
<p>These data were published in&nbsp;<br />
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. (2016) Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 4:e2777 DOI:&nbsp;<a href="https://doi.org/10.7717/peerj.2777" target="_blank">10.7717/peerj.2777</a></p> Methods and Sampling: <p>For full methodology, see Roux et al (2016).</p>
<p><strong>Great Lakes methodology:</strong><br />
For each lake, 33 to 45L of water were 0.22 micron m-filtered and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4 degrees C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).</p>
<p><strong>Tara Expedition methodology:</strong><br />
20 L of seawater were 0.22 μ m-filtered, and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4°C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).</p>
<p><strong>Bermuda BATS methodology:</strong><br />
Approximately 180L of seawater were concentrated using a 100kDa tangential flow filter, 0.22 μ m-filtered, PEG precipitated, cesium chloride purified, and DNA was extracted using formamide.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536989 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536989
completed
Matthew Sullivan
Ohio State University
614-247-1616
496 W 12th Ave Riffe Building
Columbus
OH
43210
USA
sullivan.948@osu.edu
pointOfContact
Maureen L. Coleman
University of Chicago
773-702-8352
5734 S. Ellis Ave.
Chicago
IL
60637
USA
mlcoleman@uchicago.edu
pointOfContact
asNeeded
Unknown
sample_type
iVirus_link
iVirus_url
dataset_id
location
lat
lon
depth
Amicon Ultra 100 kDa centrifugal devices (Millipore)
theme
None, User defined
sample type
external_link
dataset_id
No BCO-DMO term
latitude
longitude
depth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Centrifuge
instrument
BCO-DMO Standard Instruments
1311-SV
service
Deployment Activity
Great Lakes
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.
Ecological impacts and drivers of double-stranded DNA viral communities in the global oceans
https://osprey.bco-dmo.org/project/658383
Ecological impacts and drivers of double-stranded DNA viral communities in the global oceans
<p><strong><span style="font-size:12px">NSF abstract:</span></strong></p>
<p>Ocean microbes produce half of the oxygen that humans breathe and drive much of the energy and nutrient transformations that fuel ocean ecosystems. Viruses of microbes alter these microbial impacts through mortality, moving genes from one organism to another, and reprogramming a host cell's metabolism during infection. However, current understanding of ocean viruses is limited to just a few specific model systems or study sites. This project will produce a foundational dataset - the Global Ocean Virome (GOV) - for contextualizing newly discovered viruses, and use this dataset to evaluate the environmental conditions that structure viral communities or how viral communities change over time and space. Additionally, the project will illuminate 'viral dark matter' by experimentally identifying viral structural proteins and generating and investigating single-cell genomic datasets to link novel and abundant viruses to their host cells. The project will train 6 researchers, as well as lead to curriculum, seminars and a public exhibit at The Wellington School and the Columbus Center Of Science and Industry that will together reach approximately 500 students and 250,000 members of the public.</p>
<p>The GOV dataset is comprised of 104 viral metagenomes from around the world's surface and deep oceans. This project seeks to analyze the GOV to identify and quantify viral populations globally, then evaluate these data for ecological patterns to determine the ecological drivers of surface and deep ocean viral community structure. These patterns and drivers will be interpreted in the context of (i) viral metaproteomic experiments to maximally annotate unknown viral proteins that are structural, (ii) paired microbial sequence datasets (metagenomes and metatranscriptomes) that will enable assessment of how biotic factors impact viral community structure and (iii) single-cell amplified genomes and phageFISH experiments that will enable identification of hosts for abundant and novel viruses identified in the GOV. In total, this project will further optimize recently developed genome- and population-based viral ecology methods to establish a first available global map of surface and deep ocean viral populations from both free viromes and infected microbes. These analyses will help evaluate and establish myriad hypotheses about viral roles in marine microbial ecology and biogeochemistry, and the dataset will be a foundational resource for microbial and viral ecologists to contextualize new viruses, identify viruses in microbial datasets, and explore virus-host interactions both phenomenologically and through ecosystem modeling. The GOV will be made publicly available through the NSF-funded iPlant Cyberinfrastructure and metaVIR (<a href="http://metavir-meb.univ-bpclermont.fr/">http://metavir-meb.univ-bpclermont.fr/</a>).</p>
<p>Note: The above NSF abstract references iPlant Cyberinfrastructure which no longer exists. The GOV dataset is publicly available through iVirus at the NSF-funded CyVerse Cyberinfrastructure while contextual data are available through EMBL and PANGEA (see links below).</p>
<p><strong><u>This </u></strong><strong><u>NFS-</u></strong><strong><u>OCE </u></strong><strong><u>projec</u></strong><strong><u>t </u></strong><strong><u>was </u></strong><strong><u>fu</u></strong><strong><u>nded</u></strong><strong><u> t</u></strong><strong><u>o </u></strong><strong><u>ana</u></strong><strong><u>lyze t</u></strong><strong><u>he follow</u></strong><strong><u>ing pre-</u></strong><strong><u>exist</u></strong><strong><u>ing datase</u></strong><strong><u>ts</u></strong></p>
<p><strong>Raw and processed Global Ocean Viromes (GOV) dataset</strong><br />
Data Access at iVirus: <a href="http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV/"><u>http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV/</u></a><br />
Results Paper:<br />
Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., … Sullivan, M. B. (2016). Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 537(7622), 689–693. doi:10.1038/nature19366</p>
<p><strong>GOV associated microbial metagenomic datasets</strong><br />
Data Access at EMBL: <a href="http://www.ebi.ac.uk/ena/data/view/PRJEB7988"><u>http://www.ebi.ac.uk/ena/data/view/PRJEB7988</u></a></p>
<p><strong>GOV associated oceanographic data</strong><br />
Data Access via PANGEA: <a href="https://www.pangaea.de/search?ie=UTF-8&env=All&count=10&q=Tara+Oceans+Expedition"><u>https://www.pangaea.de/search?ie=UTF-8&env=All&count=10&q=Tara+Oceans+Expedition </u></a></p>
<p>Global Ocean Viromes 2 dataset at iVirus: <a href="http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0">http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0</a><br />
Results Paper:<br />
Gregory, A. C., Zayed, A. A., Conceição-Neto, N., Temperton, B., Bolduc, B., Alberti, A., … Cruaud, C. (2019). Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, 177(5), 1109–1123.e14. doi:10.1016/j.cell.2019.03.040</p>
<p><strong><u>Project results in repositories other than BCO-DMO</u></strong></p>
<p>
<strong>Viral metagenomes from the Eastern Tropical North Pacific, and archaeal viruses </strong><br />
Data Access: <a href="http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Vik_et_al_2017_data"><u>http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Vik_et_al_2017_data</u></a><br />
Results Paper:<br />
Vik DR., Roux S., Brum JR., Bolduc B., Emerson JB., Padilla CC., Stewart FJ., Sullivan MB. 2017. Putative archaeal viruses from the mesopelagic ocean. PeerJ 5:e3428. DOI: <a href="https://peerj.com/articles/3428/"><u>10.7717/peerj.3428.</u></a></p>
<p><strong>Viral mock community and metagenomic datasets</strong><br />
Data Access: <a href="http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/DNA_Viromes_library_comparison"><u>http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/DNA_Viromes_library_comparison</u></a>.<br />
Results Paper:<br />
Roux S., Solonenko NE., Dang VT., Poulos BT., Schwenck SM., Goldsmith DB., Coleman ML., Breitbart M., Sullivan MB. 2016. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 4:e2777. DOI: <a href="https://peerj.com/articles/2777/"><u>10.7717/peerj.2777</u></a>.</p>
<p><strong>Virophage sequences extracted from previously published freshwater microbial metagenomes</strong><br />
Data Access: <a href="http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Freshwater_virophages"><u>http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Freshwater_virophages</u></a></p>
<p>Results Paper:</p>
<p>Roux, S., Chan, L.-K., Egan, R., Malmstrom, R. R., McMahon, K. D., & Sullivan, M. B. (2017). Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications, 8(1). doi:<a href="https://doi.org/10.1038/s41467-017-01086-2"><u>10.1038/s41467-017-01086-2</u></a></p>
<p> [ These virophages were identified in microbial metagenome datasets from North Temperate Lakes NSF-LTER sites] </p>
<p>Metagenomic data Access: <a href="file:////home/adyork/Documents\\x/http://%20genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf%3forganism=TroutBogmetagenomicdata"><u>http://</u></a><a href="file:////home/adyork/Documents\\x/http://%20genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf%3forganism=TroutBogmetagenomicdata"><u> genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=TroutBogmetagenomicdata</u></a><br />
Non-metagenomic data Access: <a href="https://genome.jgi.doe.gov/portal/ComAssLakMendota_FD/ComAssLakMendota_FD.info.html"><u>https://genome.jgi.doe.gov/portal/ComAssLakMendota_FD/ComAssLakMendota_FD.info.html</u></a><u> ]</u></p>
<p> </p>
<p><strong><u>Other publications associated with this project</u></strong></p>
<p>Bolduc, B., Jang, H. B., Doulcier, G., You, Z.-Q., Roux, S., & Sullivan, M. B. (2017). vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ, 5, e3243. doi:<a href="https://doi.org/10.7717/peerj.3243">10.7717/peerj.3243</a></p>
<p>Emerson, J. B., Roux, S., Brum, J. R., Bolduc, B., Woodcroft, B. J., Jang, H. B., … Sullivan, M. B. (2018). Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3(8), 870–880. doi:<a href="https://doi.org/10.1038/s41564-018-0190-y"><u>10.1038/s41564-018-0190-y</u></a></p>
<p>Howard-Varona, C., Hargreaves, K. R., Abedon, S. T., & Sullivan, M. B. (2017). Lysogeny in nature: mechanisms, impact and ecology of temperate phages. The ISME Journal, 11(7), 1511–1520. doi:<a href="https://doi.org/10.1038/ismej.2017.16"><u>10.1038/ismej.2017.16</u></a></p>
<p>Pasulka, A. L., Thamatrakoln, K., Kopf, S. H., Guan, Y., Poulos, B., Moradian, A., … Orphan, V. J. (2017). Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environmental Microbiology, 20(2), 671–692. doi:<a href="https://doi.org/10.1111/1462-2920.13996"><u>10.1111/1462-2920.13996</u></a></p>
<p>Roux, S., Adriaenssens, E.M., Dutlith, B.E., Koonin, E.V., Kropinski, A.M., Krupovic, M., ... Eloe-Fadrosh, E.A. (2018). Minimum Information about an Uncultivated Virus Genome (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses. <em>Nature Biotechnology. In press. </em><a href="http://u.osu.edu/viruslab/files/2015/08/JGI-viralStdsPaper-2g6uqiv.pdf"><u>http://u.osu.edu/viruslab/files/2015/08/JGI-viralStdsPaper-2g6uqiv.pdf</u></a></p>
<p>Roux, S., Chan, L.-K., Egan, R., Malmstrom, R.R., McMahon, K.D., Sullivan, M.B. (2017). Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications. 8: 858. doi: <a href="https://doi.org/10.1038/s41467-017-01086-2"><u>10.1038/s41467-017-01086-2</u></a></p>
<p>Roux, S., Emerson, J. B., Eloe-Fadrosh, E. A., & Sullivan, M. B. (2017). Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ, 5, e3817. doi:<a href="https://doi.org/10.7717/peerj.3817"><u>10.7717/peerj.3817</u></a></p>
<p>Stec, K. F., Caputi, L., Buttigieg, P. L., D’Alelio, D., Ibarbalz, F. M., Sullivan, M. B., … Iudicone, D. (2017). Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine Genomics, 32, 1–17. doi:<a href="https://doi.org/10.1016/j.margen.2017.02.006"><u>10.1016/j.margen.2017.02.006</u></a></p>
<p> </p>
GOV
largerWorkCitation
project
eng; USA
biota
oceans
Great Lakes
-87
-64
-5.2529
48
2017-09-21
Global oceans
0
BCO-DMO catalogue of parameters from ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific (GOV 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/715493.rdf
Name: sample_type
Units: unitless
Description: <p>type of analysis performed on the samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/715494.rdf
Name: iVirus_link
Units: unitless
Description: <p>hypertext link to the CyVerse iVirus data archive</p>
http://lod.bco-dmo.org/id/dataset-parameter/715495.rdf
Name: iVirus_url
Units: unitless
Description: <p>url for link to the CyVerse iVirus data archive</p>
http://lod.bco-dmo.org/id/dataset-parameter/715496.rdf
Name: dataset_id
Units: unitless
Description: <p>identifier for dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/715497.rdf
Name: location
Units: unitless
Description: <p>description of sample collection location</p>
http://lod.bco-dmo.org/id/dataset-parameter/715498.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/715499.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/715500.rdf
Name: depth
Units: meters
Description: <p>sample depth</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
1925
https://datadocs.bco-dmo.org/file/oAAmoVvU68AV7j/ssDNA_dsDNA.csv
ssDNA_dsDNA.csv
Primary data file for dataset ID 715475
download
https://osprey.bco-dmo.org/dataset/715475/data/download
download
onLine
dataset
<p>For full methodology, see Roux et al (2016).</p>
<p><strong>Great Lakes methodology:</strong><br />
For each lake, 33 to 45L of water were 0.22 micron m-filtered and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4 degrees C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).</p>
<p><strong>Tara Expedition methodology:</strong><br />
20 L of seawater were 0.22 μ m-filtered, and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4°C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).</p>
<p><strong>Bermuda BATS methodology:</strong><br />
Approximately 180L of seawater were concentrated using a 100kDa tangential flow filter, 0.22 μ m-filtered, PEG precipitated, cesium chloride purified, and DNA was extracted using formamide.</p>
Specified by the Principal Investigator(s)
<p>Trimmed and filtered reads were assembled with Spades 3.6.2 with the "sc" and "careful" options. All contigs &gt;500 bp and with at least one complete gene were run through VirSorter in the "virome decontamination" mode as well as a custom detection pipeline for small genomes (see Roux et al., 2016). Contig affiliation was based on best BLAST hit against RefSeqVirus (thresholds: bit score &gt; 50 and e-value &lt; 10 −3 ).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- created a table with dataset id, description, latitude, longitude, depth and link to the sequence and associated data at iVirus<br />
- added conventional header with dataset name, PI name, version date</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: 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.
Amicon Ultra 100 kDa centrifugal devices (Millipore)
Amicon Ultra 100 kDa centrifugal devices (Millipore)
PI Supplied Instrument Name: Amicon Ultra 100 kDa centrifugal devices (Millipore) PI Supplied Instrument Description:Used to concentrate viral particles Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Cruise: 1311-SV
1311-SV
NERC Vocabulary Server
R/V Lake Guardian
vessel
NERC Vocabulary Server
R/V Lake Guardian
vessel