Dataset: Line P virus sample log
Deployment: JPT_2009-03

Pacific Ocean Viral Line P metagenomes with depth, temperature and oxygen

Principal Investigator:

Matthew Sullivan (University of Arizona, UA)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Targeted and comparative viral community genomics of the Eastern North Pacific (ENP viral community)

Current State:

Final no updates expected

Version:

2014-10-06

Deployment Synonyms:

18DD20090127

Version Date:

2014-10-06

Data URL:

https://www.bco-dmo.org/dataset-deployment/529647/data

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Description

This dataset includes metadata for virus metagenome samples from the Line P transect, an Eastern North Pacific Ocean transect from Vancouver to Ocean Station Papa sampling at 10 to 2000 meters at stations P4 (48 N, 126W), P12 (48N, 130W), and P26 (50N, 144W).

All metagenomic sequences used in the analysis are available at CAMERA under the project accessions: CAM_P_0000915. http://camera.crbs.ucsd.edu/projects/details.php?id=CAM_P_0000915 "Pacific Ocean Virus (POV) Protein Clusters.

Relevant References:

Hurwitz, B.L., & Sullivan, M.B. (2013). The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8(2), e57355. doi:10.1371/journal.pone.0057355.

Hurwitz, B.L., Hallam, S.J., & Sullivan, M.B. (2013). Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 14:R123. doi:10.1186/gb-2013-14-11-r123.

Hurwitz, B.L., Brum, J.R., & Sullivan, M.B. (2014). Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISME J. doi:10.1038/ismej.2014.143.

Hurwitz, B.L., Westveld, A.H., Brum, J.R., & Sullivan, M.B. (2014). Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. PNAS. doi:10.1073/pnas.1319778111.

Methods & Sampling

Dataset acquisition description

See "Chemical Precipitation Method for Obtaining Viruses from Seawater" (pdf)

Deployment-specific acquisition description

The data url links to the whole dataset, not just the data for this cruise.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

added conventional header with dataset name, PI name, version date, reference information
renamed parameters to BCO-DMO standard
reformated date from m/d/yyyy to yyyy-mm-dd
removed spaces and special characters
sorted by date and depth
removed columns that were all the same: country (Canada), habitat type (marine), region (eastern N. Pacific (ENP):nr. Vancouver Is.,British Columbia), sample type (virus), protocol (FeCl-Dnase-CsCl), min. filter size (0.2 um)

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0961947	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird SBE 911plus

Supplied Name: CTD SBE 911plus

Supplied Description:

Mounted in a rosette

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

Sea-Bird SBE 43 Dissolved Oxygen Sensor

Supplied Name: SBE-43 DO

Supplied Description:

Instrument Type

Generic Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor

Acronym: SBE-43 DO

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/

Generic Description:

The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
library	CAMERA repository library name	unitless	no_bcodmo_term
site	collection site name	unitless	site
temp	temperature	degrees Celsius	temp
depth	depth	meters	depth
O2	oxygen concentration	milliliters/liter	O2
date_coll	date of collection	yyyy-mm-dd	date
lon	latitude; north is positive	decimal degrees	lon
lat	longitude; east is positive	decimal degrees	lat
site_descrip	description of collection site	unitless	site_descrip

Database

Contribute Data

Dataset: Line P virus sample log
Deployment: JPT_2009-03

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Line P virus sample logDeployment: JPT_2009-03

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Dataset: Line P virus sample log
Deployment: JPT_2009-03