Dataset: MO - virioplankton abund-FISH probe

Name: Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2003-2005 (Ocean Microbial Observatory project)
Published: 2014-12-16
License: https://creativecommons.org/licenses/by/4.0/
Keywords: biota, oceans

View Data: Data not available yet

Cite This Dataset

Project:

Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory (Ocean Microbial Observatory)

Principal Investigator:

Dr Craig Carlson (University of California-Santa Barbara, UCSB)

Co-Principal Investigator:

Dr Stephen Giovannoni (Oregon State University, OSU)

BCO-DMO Data Manager:

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

Version Date:

2014-12-16

Restricted:

Yes

Validated:

Virioplankton abundance using FISH probe at BATS site in the western Sargasso Sea from 2003-2005 (Ocean Microbial Observatory project)

Expand/Collapse All

Description

Virioplankton abundances were measured from samples collected from January 2000 to December 2009 as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). This dataset reports abundances quantified using FISH (Fluorescence in situ hybridization).

Acquisition Description

The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002).

Relevant References:

Morris R, Rapp M, Connon S, Vergin K, SieboldW, Carlson, CA et al. (2002). SAR11 clade dominates ocean surface
bacterioplankton communities. Nature 420: 806–810. doi:10.1038/nature01240

Parsons, R. J., Breitbart, M., Lomas, M. W., & Carlson, C. A. (2011). Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. The ISME journal, 6(2), 273-284.

Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- added UNOLS cruise id's

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0802004

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
BATS_cruises	Bermuda Atlantic Time-series Study cruises	1988-10-20	Unknown Platform	Nicholas Bates (Principal Investigator) Michael W. Lomas (Co-Principal Investigator) Rodney Johnson (Scientist) Theresa McKee (BCO-DMO Data Manager)	data info

Instruments

CTD profiler

(more info)

Short Name: CTD

Community Standard Description

Generic Description

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.

PI supplied instrument name: CTD

Dataset-specific description

Flow Cytometer

(more info)

Short Name: Flow Cytometer

Community Standard Description

Generic Description

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

PI supplied instrument name: Flow Cytometer

Dataset-specific description

Becton Dickenson (Franklin Lakes, NJ, USA; formerly Cytopeia) high speed jet-in-air InFlux flow cytometer, using a 488 nm blue excitation laser, appropriate Chl-a (692±20 nm) and phycoerythrin (580±15 nm) bandpass filters.

Fluorescence Microscope Image Analysis System

(more info)

Short Name: Fluorescence Microscope

Community Standard Description

Generic Description

A Fluorescence (or Epifluorescence) Microscope Image Analysis System uses semi-automated color image analysis to determine cell abundance, dimensions and biovolumes from an Epifluorescence Microscope. An Epifluorescence Microscope (conventional and inverted) includes a camera system that generates enlarged images of prepared samples. The microscope uses excitation ultraviolet light and the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light.

PI supplied instrument name: Epifluorescence Microscope

Dataset-specific description

Olympus AX70 microscope (Olympus, Tokyo, Japan) equipped with a Toshiba CCD video camera (Irvine, CA, USA)

Niskin bottle

(more info)

Short Name: Niskin bottle

Community Standard Description

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.

PI supplied instrument name: Niskin bottle

Dataset-specific description

12 liter Niskin bottles

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	UNOLS cruise identification	unitless	cruise_id
cruise_id2	BATS cruise during which sample was collected	unitless	cruise_id
date	date of collection	yyyymmdd	date
year_decimal	decimal year date of collection	yyyy.fraction_of_year	year_decimal
lat_nom	nominal latitude of BATS station; north is positive	decimal degrees	lat_n
lon_nom	nominal longitude of BATS station; east is positive	decimal degrees	lon_n
depth_n	bottle target depth	meters	depth_n
abund_SAR11	abundance of SAR11 bacterioplankton	10^8 cells/liter	abundance
abund_Bacter	abundance of Bacteroidetes bacterioplankton	10^7 cells/liter	abundance
abund_Rhodo	abundance of Rhodobacteraceae bacterioplankton	10^7 cells/liter	abundance

Database

Geospatial Access

Contribute Data

Dataset: MO - virioplankton abund-FISH probe