http://lod.bco-dmo.org/id/dataset/823295
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
2020-09-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013
2020-09-04
publication
2020-09-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-16
publication
https://doi.org/10.26008/1912/bco-dmo.823295.1
Jennifer R. Brum
University of Arizona
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: Brum, J. (2020) Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.823295.1 [access date]
Accession Numbers of Viral Metagenomes from the ETNP Dataset Description: <p>Accession numbers of viral metagenomes from&nbsp;samples collected in the&nbsp;Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013.</p> Methods and Sampling: <p>Detailed protocols, including suggestions from the scientific community, are published on the lab website at <a href="https://u.osu.edu/viruslab/protocols/" target="_blank">https://u.osu.edu/viruslab/protocols/</a> and maintained on protocols.io at <a href="https://www.protocols.io/workspaces/sullivan-lab" target="_blank">https://www.protocols.io/workspaces/sullivan-lab</a>.</p>
<p>Samples were collected from the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) during the OMZ Microbial Biogeochemistry Expedition cruise (R/V NewHorizon,13-28 June 2013). Seawater was collected from 16 depths spanning the mixed layer, oxycline, OMZ core, and below the OMZ. Collections were made using Niskin bottles on a rosette. Samples were preserved with EM-grade glutaraldehyde (2% final concentration), flash-frozen in liquid nitrogen and stored between -72 °C and -80 °C until analysis.</p>
<p>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-kD cen- trifugal devices (Millipore), treated with DNase I (100 U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted. Viral particle suspensions were treated with Wizard Polymerase Chain Reaction Preps DNA Purification Resin (Promega, Fitchburg, WI, USA) at a ratio of 0.5 ml sample to 1 ml resin, and eluted with TE buffer (10 mM Tris, pH 7.5, 1 mM EDTA) using Wizard Minicolumns. Extracted DNA was Covaris-sheared and size-selected to 160 to 180 bp, followed by amplification and ligation per the standard Illumina protocol. Sequencing was done on a HiSEq 2000 system at the DOE Joint Genome Institute.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658040 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658040
completed
Jennifer R. Brum
University of Arizona
225-578-6364
2201 Energy, Coast and Environment Building
Baton Rouge
LA
70803
USA
jbrum1@lsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SAMPLE
JGI_Project_Id
IMG_Genome_ID
LAT
LONG
Illumina HiSEq 2000
Niskin bottles
theme
None, User defined
sample identification
accession number
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
NH1315
service
Deployment Activity
Eastern Tropical North Pacific (ETNP) oxygen minimum zone off Manzanillo, Mexico; sampling transects run southeast-northwest along the Colima coast (~19-24°N, 106-116°W) and northeast-southwest off the coast (~14-18°N, 106-115°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.
Ecology and biogeochemical impacts of viruses in marine oxygen minimum zones
https://osprey.bco-dmo.org/project/739615
Ecology and biogeochemical impacts of viruses in marine oxygen minimum zones
<p><em>NSF Award Abstract:</em><br />
Marine oxygen minimum zones (OMZs) are regions of the world's oceans that have low or no oxygen. Often referred to as "dead zones" because of their lack of larger organisms, OMZs actually support specific microbial communities adapted to survive in these low-oxygen regions. These microbes perform metabolic processes that produce greenhouse gases such as methane, and significantly alter global nitrogen budgets. In turn, viruses can alter every aspect of microbial communities by causing mortality and altering microbial functions; yet we know little regarding how viruses affect OMZ ecosystems, which is limiting our ability to predict future changes to the Earth system as these OMZs expand over time. This proposed research seeks to fill this knowledge gap by examining the types of viruses that are present in OMZs, as well as how they alter microbial communities and their impact on global processes. In the broader perspective, this proposed work will provide extensive datasets for 7 marine OMZ regions that can be interrogated through publically-available analysis tools, thus enabling environmental science for both research and educational purposes including real-world research experience in undergraduate classes to strengthen scientific education. One postdoc, two graduate students, and undergraduate students will be trained and mentored during this project. Furthermore, the work will facilitate international collaboration with leading microbial oceanographers from across the world.</p>
<p>This project will use recent advances in quantitative environmental viral analysis to rapidly enhance our knowledge of OMZ viral communities through examination of 100s of samples from 7 globally-distributed marine OMZ regions with varying levels of oxygen depletion. The specific aims of the project are to (i) gain a basic understanding of viral abundances, viral-induced microbial mortality, and viral community structure, as well as the environmental conditions that drive differences in these parameters, and (ii) assess the effects of viruses on nutrient and gas cycling in OMZs. These aims will be accomplished through analyzing viral metagenomes to assess how viral communities differ among the 7 diverse OMZ regions, and how they diverge from communities in oxygenated waters. Further, the viral metagenomes will be coupled with microbial metagenomes to assess virus-host dynamics and the effects of viral-induced mortality on microorganisms performing key metabolic functions. Finally, the abundance and expression of viral-encoded metabolic genes will be used to perform gene-based biogeochemical modeling to determine the extent of viral influences in OMZ biogeochemical cycling.</p>
OMZ Viruses
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical North Pacific (ETNP) oxygen minimum zone off Manzanillo, Mexico; sampling transects run southeast-northwest along the Colima coast (~19-24°N, 106-116°W) and northeast-southwest off the coast (~14-18°N, 106-115°W)
-108.79926
-104.88952
18.91944
18.92018
2013-06-19
2013-06-22
0
BCO-DMO catalogue of parameters from Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013
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/823308.rdf
Name: SAMPLE
Units: unitless
Description: <p>unique sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/823309.rdf
Name: JGI_Project_Id
Units: unitless
Description: <p>JGI project ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/823310.rdf
Name: IMG_Genome_ID
Units: unitless
Description: <p>IMG genome ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/823311.rdf
Name: LAT
Units: degrees North
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/823312.rdf
Name: LONG
Units: degrees East
Description: <p>longitude</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
493
https://darchive.mblwhoilibrary.org/bitstream/1912/26180/1/dataset-823295_etnp-viromes__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.823295.1
download
onLine
dataset
<p>Detailed protocols, including suggestions from the scientific community, are published on the lab website at <a href="https://u.osu.edu/viruslab/protocols/" target="_blank">https://u.osu.edu/viruslab/protocols/</a> and maintained on protocols.io at <a href="https://www.protocols.io/workspaces/sullivan-lab" target="_blank">https://www.protocols.io/workspaces/sullivan-lab</a>.</p>
<p>Samples were collected from the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) during the OMZ Microbial Biogeochemistry Expedition cruise (R/V NewHorizon,13-28 June 2013). Seawater was collected from 16 depths spanning the mixed layer, oxycline, OMZ core, and below the OMZ. Collections were made using Niskin bottles on a rosette. Samples were preserved with EM-grade glutaraldehyde (2% final concentration), flash-frozen in liquid nitrogen and stored between -72 °C and -80 °C until analysis.</p>
<p>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-kD cen- trifugal devices (Millipore), treated with DNase I (100 U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted. Viral particle suspensions were treated with Wizard Polymerase Chain Reaction Preps DNA Purification Resin (Promega, Fitchburg, WI, USA) at a ratio of 0.5 ml sample to 1 ml resin, and eluted with TE buffer (10 mM Tris, pH 7.5, 1 mM EDTA) using Wizard Minicolumns. Extracted DNA was Covaris-sheared and size-selected to 160 to 180 bp, followed by amplification and ligation per the standard Illumina protocol. Sequencing was done on a HiSEq 2000 system at the DOE Joint Genome Institute.</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 2000
Illumina HiSEq 2000
PI Supplied Instrument Name: Illumina HiSEq 2000 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.
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles 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/
Cruise: NH1315
NH1315
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
NH1315
Frank James Stewart
Georgia Institute of Technology
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel