Dataset: ETNP Frequency of Lytic Viral Infection
Deployment: NH1315

Estimated frequency of lytic viral infection from the ETNP

Principal Investigator:

Jennifer R. Brum (University of Arizona, UA)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

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

Deployment Synonyms:

OMZoMBiE

Data URL:

https://www.bco-dmo.org/dataset-deployment/822920/data

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Description

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 from 13-28 June 2013. 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.

Methods & Sampling

Dataset acquisition description

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.

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).

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:
- added station latitude and longitude;
- added date (from related dataset https://www.bco-dmo.org/dataset/629125);
- replaced spaces with underscores in parameter names.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1658040	NSF Division of Ocean Sciences

Instruments

Camera

Supplied Name: Macrofire Monochrome CCD camera

Supplied Description:

Macrofire Monochrome CCD camera (Optronics, Goleta, CA, USA)

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Centrifuge

Supplied Name: Air-driven ultracentrifuge (Beckman)

Supplied Description:

Air-driven ultracentrifuge (Airfuge CLS, Beckman Coulter, Brea, CA, USA)

Instrument Type

Generic Name: Centrifuge

Generic 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.

Electron Microscope

Supplied Name: Philips CM12 transmission electron microscope (TEM)

Supplied Description:

Instrument Type

Generic Name: Electron Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB07/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.

Niskin bottle

Supplied Name: Niskin bottles

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Number_of_Infected_Cells	Number of infected cells seen	unitless	abundance
Number_of_Cells_Analyzed	Number of cells analyzed	unitless	abundance
FVIC_percent	Calculated frequency of visibly infected cells	unitless	abundance
Lower_90_CI_FVIC	Lower bound of 90% confidence interval for FVIC	unitless	abundance
Upper_90_CI_FVIC	Upper bound of 90% confidence interval for FVIC	unitless	abundance
FIC	Calculated frequency of infected cells	unitless	abundance
Lower_90_CI_FIC	Lower bound of 90% confidence interval for FIC	unitless	abundance
Upper_90_CI_FIC	Upper bound of 90% confidence interval for FIC	unitless	abundance
Station	Station where sample was collected	unitless	station
Depth	Depth of sample	meters	depth
Latitude	Station latitude	degrees North	lat
Longitude	Station longitude	degrees East	lon
Date	Date; format: YYYY-MM-DD	unitless	date

Database

Contribute Data

Dataset: ETNP Frequency of Lytic Viral Infection
Deployment: NH1315

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ETNP Frequency of Lytic Viral InfectionDeployment: NH1315

Dataset acquisition description

Dataset Processing Description

Dataset: ETNP Frequency of Lytic Viral Infection
Deployment: NH1315