http://lod.bco-dmo.org/id/dataset/823131
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
2020-09-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Morphotypes, capsid widths, and tail lengths of viruses 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
2020-09-02
publication
2020-09-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-16
publication
https://doi.org/10.26008/1912/bco-dmo.823131.1
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) Morphotypes, capsid widths, and tail lengths of viruses 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 2020-09-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.823131.1 [access date]
Morphotypes, capsid widths, and tail lengths of viruses from the ETNP Dataset Description: <p>Morphotypes, capsid widths, and tail lengths of viruses in&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. Viruses were deposited onto TEM grids, positively stained, and examined using a transmission electron microscope. Micrographs were collected and characterized by morphotype, as well as measured using ImageJ software.</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>Viruses were deposited onto TEM grids with an air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA) and positively stained by immersion in 2% uranyl acetate (Ted Pella, Redding, CA, USA). Prepared grids were examined using a transmission electron microscope (Phillips CM12, FEI, Hilsboro, OR, USA) with 100 kV accelerating voltage. Micrographs of 100 viruses per sample were collected using a Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA). Viruses were classified as myoviruses, podoviruses, siphoviruses or non-tailed viruses based on their morphology. Viral capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).</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
Station
Depth
Capsid_width
Tail_length
Morphotype
Latitude
Longitude
Date
Macrofire Monochrome CCD camera
Air-driven ultracentrifuge (Beckman)
Phillips CM12 transmission electron microscope
Niskin bottles
theme
None, User defined
station
depth
width
length
sample description
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 Morphotypes, capsid widths, and tail lengths of viruses 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/823283.rdf
Name: Station
Units: unitless
Description: <p>Station where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/823284.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/823285.rdf
Name: Capsid_width
Units: nanometers (nm)
Description: <p>Capsid width</p>
http://lod.bco-dmo.org/id/dataset-parameter/823286.rdf
Name: Tail_length
Units: nanometers (nm)
Description: <p>Tail length (where applicable)</p>
http://lod.bco-dmo.org/id/dataset-parameter/823287.rdf
Name: Morphotype
Units: unitless
Description: <p>Morphotype (siphovirus, myovirus, podovirus, non-tailed)</p>
http://lod.bco-dmo.org/id/dataset-parameter/823288.rdf
Name: Latitude
Units: degrees West
Description: <p>Station latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/823289.rdf
Name: Longitude
Units: degrees East
Description: <p>Station longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/823290.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
76513
https://darchive.mblwhoilibrary.org/bitstream/1912/26179/1/dataset-823131_etnp-viral-morphology__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.823131.1
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>Viruses were deposited onto TEM grids with an air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA) and positively stained by immersion in 2% uranyl acetate (Ted Pella, Redding, CA, USA). Prepared grids were examined using a transmission electron microscope (Phillips CM12, FEI, Hilsboro, OR, USA) with 100 kV accelerating voltage. Micrographs of 100 viruses per sample were collected using a Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA). Viruses were classified as myoviruses, podoviruses, siphoviruses or non-tailed viruses based on their morphology. Viral capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).</p>
Specified by the Principal Investigator(s)
<p>Virus capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).</p>
<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>).</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.
Phillips CM12 transmission electron microscope
Phillips CM12 transmission electron microscope
PI Supplied Instrument Name: Phillips CM12 transmission electron microscope PI Supplied Instrument Description:Epifluorescence microscope (Axio Imager. D2, Zeiss, Jena, Germany) 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