Dataset: viral and bacterial counts

Name: Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy, from samples collected on R/V Knorr cruise KN210-04 in the Western Atlantic Ocean in 2013 (Deep Atlantic DOM project)
Published: 2014-08-08
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.528510.1

Spatial Extent: N:9.703869 E:-23.999036 S:-38.0026 W:-55.304343

Temporal Extent: 2013-03-26 - 2013-05-06

Project:

Dissolved Organic Matter Composition in the Deep Atlantic Ocean (Deep Atlantic DOM)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Principal Investigator:

Ian Hewson (Cornell University, Cornell)

Contact:

Erin Eggleston (Cornell University, Cornell)

Ian Hewson (Cornell University, Cornell)

BCO-DMO Data Manager:

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

Version:

Version Date:

2014-08-08

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy, from samples collected on R/V Knorr cruise KN210-04 in the Western Atlantic Ocean in 2013 (Deep Atlantic DOM project)

Abstract:

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2014-08-08	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.528510.1	2021-12-28

Description

Viral and bacterial counts from filtered water, stained with SYBR Green and counted using epifluorescent microscopy. Duplicates were collected at each depth during the KN210-04 cruise.

Methods & Sampling

Samples for viral and bacterial counts were collected in 50 mL Falcon tubes, held at 4 degrees C until processing, and processed within two hours. SYBR slides were prepared according to Noble and Fuhruman (Noble and Fuhrman, 1998). Briefly, samples were fixed in v/v 2% formalin and then filtered over a 25 mm 0.02 um anodisc filter (Whatman). Varying volumes were fixed depending on the depth of sample collection (surface and DCM: 3 ml; mesopelagic: 10 ml; AAIW, NADW and AABW: 20 ml). The filter was stained with 2.5x10-3 SYBR Green 1 dilution in nuclease free water, and mounted on a slide with antifade solution (0.1% p-phenylenediamine in 1:1 PBS:Glycerol) and stored at -20 degrees C until enumeration. Under epifluorescence microscopy 10 fields of view were selected at random and >200 viruses and >200 bacteria were counted. Calculations for total number or viruses and bacteria in a sample account for volume filtered, magnification and size of the grid included while counting.

Samples from station 1 and 2 were fixed with the wrong concentration of antifade and therefore faded before accurate counts could be made.

References:
Noble, R. T., and Fuhrman, J. A. (1998). Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14, 113-118. doi:10.3354/ame014113

Data Processing Description

Any missing values and/or depths indicate that the slide was not countable, either due to fading or cracked filters in transit.

BCO-DMO Processing Notes:
- Parameter names were modified to conform with BCO-DMO naming conventions.
- lat_start and lon_start were added by joining the data to the event log and matching on the unique event number.
- Replaced missing values with 'nd' to indicate 'no data'.
- 22 Nov 2017: made dataset public (was previously restricted).

Data Files

File
viral_bact_counts.csv (Comma Separated Values (.csv), 164.35 KB) MD5:5aee8c0eeab841beb6b8a2fa8a2d9931 Primary data file for dataset ID 528510

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1154320

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KN210-04	DeepDOM	2013-03-25	R/V Knorr	Elizabeth Kujawinski (Chief Scientist)	data info

Instruments

Fluorescence Microscope

Supplied Name: Epifluorescent microscope

Supplied Description:

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cast	Consecutive cast number for the instrument.	dimensionless	cast
station	Identification number of the sampling station.	dimensionless	station
date_start_utc	Date (UTC) given as 4-digit year - 2-digit month - 2-digit day.	YYYYmmdd	date_utc
time_start_utc	Time (UTC) given as hour - minute.	HHMM	time_utc
event_start	The event number from the ELOG maintained during the cruise.	dimensionless	event
lat_start	Latitude at the time the event started (from the cruise event log).	decimal degrees	lat_start
lon_start	Longitude at the time the event started (from the cruise event log).	decimal degrees	lon_start
niskin	Niskin bottle number.	dimensionless	bot_Nis
depth	Depth.	meters (m)	depth
press	Pressure.	decibars (db)	press
lab_sticker	Lab identification number.	dimensionless	no_bcodmo_term
vir_abund	Viral abundance.	viral abundance per milliliter (per mL)	abundance
vir_abund_SE	Standard error associated with viral abundance.	viral abundance per milliliter (per mL)	std_err
bact_abund	Bacterial abundance.	bacterial abundance per milliliter (per mL)	bact_abund
bact_abund_SE	Standard error associated with bacterial abundance.	bacterial abundance per milliliter (per mL)	std_err
VBR	Virus to bacteria ratio (virus:bacteria).	dimensionless	no_bcodmo_term

Status message

Database

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Dataset: viral and bacterial counts