http://lod.bco-dmo.org/id/dataset/822914
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
2020-09-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Estimated frequency of lytic viral infection 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
2020-09-01
publication
2020-09-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-16
publication
https://doi.org/10.26008/1912/bco-dmo.822914.1
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) Estimated frequency of lytic viral infection 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 2020-09-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.822914.1 [access date]
Estimated frequency of lytic viral infection from the ETNP Dataset Description: <p>Estimated frequency of lytic viral infection from 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.&nbsp;Samples were deposited onto TEM grids, stained, and examined using a transmission electron microscope. Micrographs of cells were collected and characterized as infected or uninfected.</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>&nbsp;and maintained on protocols.io at&nbsp;<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>Samples were centrifuged for 1 h at 55 000 g using an ultracentrifuge (LM-80, Beckman, Brea, CA, USA) onto TEM grids (200 mesh copper grids with carbon- stabilized formvar support; Ted Pella, Redding, CA, USA). Grids were then stained with uranyl acetate and analyzed as previously described (Brum et al., 2005) to determine the frequency of visibly infected cells using a transmission electron microscope (CM12, Philips, Eindhoven, The Netherlands). The frequency of infected cells was then calculated from the frequency of visibly infected cells (Binder, 1999).</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
Number_of_Infected_Cells
Number_of_Cells_Analyzed
FVIC_percent
Lower_90_CI_FVIC
Upper_90_CI_FVIC
FIC
Lower_90_CI_FIC
Upper_90_CI_FIC
Station
Depth
Latitude
Longitude
Date
Macrofire Monochrome CCD camera
Air-driven ultracentrifuge (Beckman)
Philips CM12 transmission electron microscope (TEM)
Niskin bottles
theme
None, User defined
abundance
station
depth
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Camera
Centrifuge
Electron Microscope
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)
-108.799
-104.89
18.92
18.92
2013-06-19
2013-06-22
0
BCO-DMO catalogue of parameters from Estimated frequency of lytic viral infection 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/822972.rdf
Name: Number_of_Infected_Cells
Units: unitless
Description: <p>Number of infected cells seen</p>
http://lod.bco-dmo.org/id/dataset-parameter/822973.rdf
Name: Number_of_Cells_Analyzed
Units: unitless
Description: <p>Number of cells analyzed</p>
http://lod.bco-dmo.org/id/dataset-parameter/822974.rdf
Name: FVIC_percent
Units: unitless
Description: <p>Calculated frequency of visibly infected cells</p>
http://lod.bco-dmo.org/id/dataset-parameter/822975.rdf
Name: Lower_90_CI_FVIC
Units: unitless
Description: <p>Lower bound of 90% confidence interval for FVIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/822976.rdf
Name: Upper_90_CI_FVIC
Units: unitless
Description: <p>Upper bound of 90% confidence interval for FVIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/822977.rdf
Name: FIC
Units: unitless
Description: <p>Calculated frequency of infected cells</p>
http://lod.bco-dmo.org/id/dataset-parameter/822978.rdf
Name: Lower_90_CI_FIC
Units: unitless
Description: <p>Lower bound of 90% confidence interval for FIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/822979.rdf
Name: Upper_90_CI_FIC
Units: unitless
Description: <p>Upper bound of 90% confidence interval for FIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/822980.rdf
Name: Station
Units: unitless
Description: <p>Station where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/822981.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/822982.rdf
Name: Latitude
Units: degrees North
Description: <p>Station latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/822983.rdf
Name: Longitude
Units: degrees East
Description: <p>Station longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/822984.rdf
Name: Date
Units: unitless
Description: <p>Date; format: YYYY-MM-DD</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
1268
https://darchive.mblwhoilibrary.org/bitstream/1912/26178/1/dataset-822914_etnp-frequency-lytic-viral-infection__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.822914.1
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>&nbsp;and maintained on protocols.io at&nbsp;<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>Samples were centrifuged for 1 h at 55 000 g using an ultracentrifuge (LM-80, Beckman, Brea, CA, USA) onto TEM grids (200 mesh copper grids with carbon- stabilized formvar support; Ted Pella, Redding, CA, USA). Grids were then stained with uranyl acetate and analyzed as previously described (Brum et al., 2005) to determine the frequency of visibly infected cells using a transmission electron microscope (CM12, Philips, Eindhoven, The Netherlands). The frequency of infected cells was then calculated from the frequency of visibly infected cells (Binder, 1999).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
- added station latitude and longitude;<br />
- added date (from related dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/629125" target="_blank">https://www.bco-dmo.org/dataset/629125</a>);<br />
- replaced spaces with underscores in parameter names.</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
Macrofire Monochrome CCD camera
Macrofire Monochrome CCD camera
PI Supplied Instrument Name: Macrofire Monochrome CCD camera PI Supplied Instrument Description:Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA) Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Air-driven ultracentrifuge (Beckman)
Air-driven ultracentrifuge (Beckman)
PI Supplied Instrument Name: Air-driven ultracentrifuge (Beckman) PI Supplied Instrument Description:Air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA) 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.
Philips CM12 transmission electron microscope (TEM)
Philips CM12 transmission electron microscope (TEM)
PI Supplied Instrument Name: Philips CM12 transmission electron microscope (TEM) Instrument Name: Electron Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB07/
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