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

Website: https://www.bco-dmo.org/dataset/823131
Data Type: Cruise Results
Version: 1
Version Date: 2020-09-02

Project
» Ecology and biogeochemical impacts of viruses in marine oxygen minimum zones (OMZ Viruses)
ContributorsAffiliationRole
Brum, Jennifer R.University of Arizona (UA)Principal Investigator
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Morphotypes, capsid widths, and tail lengths of viruses in samples collected in the 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.


Coverage

Spatial Extent: N:18.92 E:-104.89 S:18.92 W:-108.799
Temporal Extent: 2013-06-19 - 2013-06-22

Dataset Description

Morphotypes, capsid widths, and tail lengths of viruses in samples collected in the 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.


Methods & Sampling

Detailed protocols, including suggestions from the scientific community, are published on the lab website at https://u.osu.edu/viruslab/protocols/ and maintained on protocols.io at https://www.protocols.io/workspaces/sullivan-lab.

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.

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).


Data Processing Description

Virus capsid diameters and tail lengths were measured using ImageJ software (US National Institutes of Health, Bethesda, MD, USA).

BCO-DMO Processing:
- added station latitude and longitude;
- added date (from related dataset https://www.bco-dmo.org/dataset/629125).


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Data Files

File
viral_morphology.csv
(Comma Separated Values (.csv), 74.72 KB)
MD5:349405c2ccdb1a2e0069edffb1a84966
Primary data file for dataset ID 823131

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Related Publications

Brum, J. (2015). Adsorbing Viruses on TEM Grids v1. Protocols.io. doi:10.17504/protocols.io.dar2d5
Methods
Brum, J. (2015). Analysis of Viral Morphological Characteristics v1. Protocols.io. doi:10.17504/protocols.io.dde23d
Methods
Brum, J. (2015). Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device v1. Protocols.io. doi:10.17504/protocols.io.c54y8v
Methods
Brum, J. (2015). Positive and Negative Staining of Viruses on TEM Grids v1. Protocols.io. doi:10.17504/protocols.io.day2fv
Methods
Brum, J. (2015). Using ImageJ to Measure Viral Dimensions in Micrographs v1. Protocols.io. doi:10.17504/protocols.io.ddf23m
Methods

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Parameters

ParameterDescriptionUnits
StationStation where sample was collected unitless
DepthDepth of sample meters (m)
Capsid_widthCapsid width nanometers (nm)
Tail_lengthTail length (where applicable) nanometers (nm)
MorphotypeMorphotype (siphovirus, myovirus, podovirus, non-tailed) unitless
LatitudeStation latitude degrees West
LongitudeStation longitude degrees East
DateDate; format: YYYY-MM-DD unitless


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Instruments

Dataset-specific Instrument Name
Niskin bottles
Generic Instrument Name
Niskin bottle
Generic 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.

Dataset-specific Instrument Name
Macrofire Monochrome CCD camera
Generic Instrument Name
Camera
Dataset-specific Description
Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA)
Generic Instrument Description
All types of photographic equipment including stills, video, film and digital systems.

Dataset-specific Instrument Name
Phillips CM12 transmission electron microscope
Generic Instrument Name
Electron Microscope
Dataset-specific Description
Epifluorescence microscope (Axio Imager. D2, Zeiss, Jena, Germany)
Generic Instrument Description
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.

Dataset-specific Instrument Name
Air-driven ultracentrifuge (Beckman)
Generic Instrument Name
Centrifuge
Dataset-specific Description
Air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA)
Generic 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.


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Deployments

NH1315

Website
Platform
R/V New Horizon
Start Date
2013-06-13
End Date
2013-06-28
Description
Oxygen Minimum Zone Microbial Biogeochemistry Expedition (OMZoMBiE) Proposed Sampling Stations Cruise information and original data are available from the NSF R2R data catalog.


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Project Information

Ecology and biogeochemical impacts of viruses in marine oxygen minimum zones (OMZ Viruses)


NSF Award Abstract:
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.

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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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