Dataset: MUSiCC OC1504A - Bacteria Virus and Chlorophyll Containing Cell Abundance

Name: Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015
Published: 2016-07-20
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.652223.1

Spatial Extent: N:43.65434 E:-120.81017 S:34.55467 W:-124.48169

Temporal Extent: 2015-04-20 - 2015-05-01

Project:

Linking physiological and molecular aspects of diatom silicification in field populations (Diatom Silicification)

Principal Investigator:

Kimberlee Thamatrakoln (Rutgers University, Rutgers IMCS)

Co-Principal Investigator:

Mark A. Brzezinski (University of California-Santa Barbara, UCSB-LifeSci)

Contact:

Kimberlee Thamatrakoln (Rutgers University, Rutgers IMCS)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2016-07-20

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015

Abstract:

Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2016-07-20	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.652223.1	2019-06-06

Description

Enumeration of Bacteria, viruses, and chlorophyll containing particles using flow cytometry.

For related datasets, click on the project link at the top of the page.

Methods & Sampling

Environmental Sample Collection

Transfer 1 ml of whole seawater to a 2 ml cryovial.
Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%.
Incubate at 4 degrees celsius for 30 min.
Flash freeze in liquid N2 and store at -80 degrees celsius.

Fluorescent DNA staining (for bacterial and viral abundances)

Thaw samples.
To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)
Heat to 80 degrees celsius for 10 min in the dark
Cool at RT for 5 min
Analyze via flow cytometry

Analysis (for bacterial and viral abundances)

Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences).

An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads.
A gating hierarchy is established using both beads and previously determined virus and bacteria populations as reference (Sybr Gold Fluorescence versus SSC cytogram).
Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission.

Analysis (for chlorophyll containing cells)

Samples are analyzed on a BD Accuri C6. Fixed, frozen samples are thawed and analyzed immediately.

An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using various sized fluorescent beads as reference points (1.0, 2.0, 3.0, 6.0 and 10 um).
Gating is established using both beads and previously determined phytoplankton populations as reference (Chlorophyll Fluorescence versus FSC cytogram).
Samples are analyzed using 488nm laser for excitation and the default BD Accuri threshold (80,000 RFU) on FSC is used.

TE buffer with SYBR Gold recipe

1X TE (for 100 mls)

1 ml of 1M Tris, pH 8.0
1 ml of 0.5 mM EDTA
98 mls MQ water
Store 4 degrees celsius

1X TE + SYBR Gold (for 10 mls)

Filter 10 mls 1 TE buffer, 0.22 um filter
1:20,0000 dilution of SYBR Gold (Molecular Probes) stock (0.5 ul stock to 10 mls TE buffer)

Data Processing Description

DMO notes:

-Changed parameter names to meet BCO-DMO naming conventions
-Added ISO_DateTime column
-Removed 4 unnecessary lat/lon columns (2 remain).

Data Files

File
chl_bact_virus.csv (Comma Separated Values (.csv), 5.92 KB) MD5:61526d1904349c31a8b8172467c4b0f4 Primary data file for dataset ID 652223

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1333929
NSF Division of Ocean Sciences	OCE-1334387

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
OC1504A	MUSiCC	2015-04-19	R/V Oceanus	Kimberlee Thamatrakoln (Chief Scientist) Mark A. Brzezinski (Co-Chief Scientist)	data info

Instruments

Flow Cytometer

Supplied Name: Influx Model 209S Mariner Flow Cytometer

Supplied Description:

Samples were analyzed on flow cytometer using BD Software (BD Biosciences). Bacterial and viral abundances were analyzed on this flow cytometer.

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

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)

Flow Cytometer

Supplied Name: BD Accuri C6

Supplied Description:

Chlorophyll containing cells analyzed on this flow cytometer.

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
station	consecutive station number	unitless	station
virus	virus-like particle abundance (VLP)	VLP per milliliter	abundance
time_utc	UTC time of cast; HH:MM	unitless	time_utc
date_utc	UTC date of cast; mm-bbb-yy	unitless	date_utc
cruise_id	The name of the cruise that collected these data.	unitless	cruise_id
lon	longitude	decimal degrees	lon
time_local	local time of cast; HH:MM	unitless	time_local
date_local	local date of cast; mm-bbb-yy	unitless	date_local
lat	latitude	decimal degrees	lat
depth	depth of sample collection	meters	depth
ISO_DateTime_UTC	DateTime (UTC) ISO formatted	unitless	ISO_DateTime_UTC
chl_total	chlorophyll containing cells	cells per milliliter	abundance
cast	cast number	unitless	cast
bacteria	bacteria-like particle abundance	bacteria per milliliter	abundance