Dataset: ETNP Microbial Abundances

Name: Estimated abundances of viruses and bacteria determined in samples collected in the Eastern Tropical North Pacific (ETNP) on R/V New Horizon cruise NH1315 during June 2013
Published: 2020-09-02
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.823094.1

Spatial Extent: N:18.92 E:-104.89 S:18.92 W:-108.799

Temporal Extent: 2013-06-19 - 2013-06-22

Project:

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

Principal Investigator:

Jennifer R. Brum (University of Arizona, UA)

BCO-DMO Data Manager:

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

Version:

Version Date:

2020-09-02

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Estimated abundances of viruses and bacteria determined in samples collected in the Eastern Tropical North Pacific (ETNP) on R/V New Horizon cruise NH1315 during June 2013

Abstract:

Estimated abundances of viruses and bacteria via epifluorescence microscopy of 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.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-09-02	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.823094.1	2020-09-16

Description

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.

Viral and bacterial concentrations were determined based on a previously described method (Noble and Fuhrman, 1998) in which thawed samples were filtered onto 0.02-μm- pore-size filters (Anodisc, Whatman, GE Healthcare Life Sciences, Piscataway, NJ, USA), stained with SYBR Gold nucleic acid stain (Invitrogen, Life Technologies, Carlsbad, CA, USA) and enumerated using an epifluorescence microscope (Axio Imager. D2, Zeiss, Jena, Germany).

Data Processing Description

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

Data Files

File
microbial_abund.csv (Comma Separated Values (.csv), 1.23 KB) MD5:2e7ac141f669eeb62707e3acb47d2af8 Primary data file for dataset ID 823094

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NH1315	OMZoMBiE	2013-06-13	R/V New Horizon	Frank James Stewart (Chief Scientist)	data info

Instruments

Fluorescence Microscope

Supplied Name: Epifluorescence microscope

Supplied Description:

Epifluorescence microscope (Axio Imager. D2, Zeiss, Jena, Germany)

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample	Unique sample identifier	unitless	sample
Viruses	Concentration of viruses (viruses per ml)	per millilter	abundance
v_stdev	Standard deviation of virus concentration	per millilter	abundance
Bacteria	Concentration of bacteria (bacteria per ml)	per millilter	abundance
b_stdev	Standard deviation of bacteria concentration	per millilter	abundance
VBR	Virus to bacteria ratio	unitless	abundance
VBR_stdev	Standard deviation of VBR	unitless	abundance
Station	Station where sample was collected	unitless	station
Depth	Depth of sample	meters (m)	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 Microbial Abundances