Dataset: bacteria

Name: Total bacteria, including Archaea and Prochlorococcus, by flow cytometry from R/V Thomas G. Thompson cruise TN277 in the Eastern North Pacific Ocean in 2012 (POWOW project)
Published: 2013-05-28
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.3900.2

Spatial Extent: N:31.246 E:-120.6976 S:22.75 W:-158

Temporal Extent: 2012-03-01 - 2012-03-10

Project:

Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns (POWOW)

Principal Investigator:

Zackary I. Johnson (Duke University)

BCO-DMO Data Manager:

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

Version:

Version Date:

2013-05-28

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Total bacteria, including Archaea and Prochlorococcus, by flow cytometry from R/V Thomas G. Thompson cruise TN277 in the Eastern North Pacific Ocean in 2012 (POWOW project)

Abstract:

This dataset includes data on total bacteria, including Archaea and Prochlorococcus, by flow cytometry from R/V Thomas G. Thompson cruise TN277 in the Eastern North Pacific Ocean in 2012.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2013-05-28	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.3900.2	2021-12-28

Description

Total bacterioplankton ("bacteria"), including Archaea and Prochlorococcus, determined by flow cytometry from the POWOW1 (TN277) cruise.

Methods & Sampling

Bacterioplankton (i.e. ‘bacteria’) were enumerated using a FACSCalibur flow cytometer (Becton Dickinson) and populations characterized as previously described (Johnson et al., 2010). Briefly, cells were excited with a 488 nm laser (15 mW Ar) and inelastic forward (<15°) scatter, inelastic side (90°) scatter (SSC), green (530 ± 30 nm) fluorescence, orange fluorescence (585 ± 42 nm), and red fluorescence (> 670 nm) emissions were measured. Bacterioplankton were quantified by staining the samples with the nucleic acid stain SYBR Green –I (Molecular Probes Inc.) (Marie et al., 1997).

References:
Johnson, Z.I., Shyam, R., Ritchie, A.E., Lin, Y., Mioni, C., Lance, V.P. et al. (2010) The effects of iron- and light-limitation on phytoplankton communities of deep chlorophyll maxima of the Western Pacific Ocean. Journal of Marine Research 68: 1-26. doi: 10.1357/002224010793721433

Marie, D., Partensky, F., Jacquet, S., and Vaulot, D. (1997) Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I. Applied and Environmental Microbiology 63: 186-193.

Data Processing Description

Cells counts were normalized to volume sampled to determined cells per mL.

BCO-DMO edits made:
- Parameter names have been changed to conform to BCO-DMO conventions.
- month_utc, day_utc, and year were added, based on the original date field.
- Original version of data (dated 22 March 2013) replaced with updated version 28 May 2013.

Data Files

File
bacteria.csv (Comma Separated Values (.csv), 5.48 KB) MD5:409dcd3b993dbabb2ff4361b0195c06a Primary data file for dataset ID 3900

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1031064

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN277	POWOW1	2012-02-29	R/V Thomas G. Thompson	Zackary I. Johnson (Chief Scientist) Erik Zinser (Co-Chief Scientist) Zackary I. Johnson (Contact)	data info

Instruments

Flow Cytometer

Supplied Description:

A FACSCalibur flow cytometer (Becton Dickinson) was used to enumerate bacteria.

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)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	Cruise identifier (POWOW1 = TN277 = R/V Thomas G. Thompson cruise 277).	text	cruise_id
CTD_cast	Number of CTD cast.	unitless	cast
lat	Latitude in decimal degrees. Positive = North.	decimal degrees	lat
lon	Longitude in decimal degrees. Positive = East.	decimal degrees	lon
month_utc	2-digit month of year, UTC.	mm (01 to 12)	month_utc
day_utc	2-digit day of month, UTC.	dd (01 to 31)	day_utc
year	4-digit year.	YYYY	year
depth	Sample depth.	meters	depth
bot	Rosette position of the bottle.	unitless	bot
bacteria	Bacteria (cells/mL) including Archaea and Prochlorococcus.	cells per milliliter	no_bcodmo_term

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Database

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Dataset: bacteria