This dataset is from a laboratory experiment. Four phytoplankton cultures and their associated bacterial communities were incubated in replicate roller bottles (1.9 L) over 3-6 weeks under laboratory conditions. Bacterial dynamics in the culture bottles were measured and correlated with geochemical parameters to determine the role of bacterial activities on the formation of CDOM in the cultures (Kinsey et al., 2018, see below). The data include bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2018-10-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.748415.1	2019-04-01

Description

The data include bacterial cell counts during CDOM monoculture experiment. The phytoplankton cultures were Skeletonema sp., Leptocylindrus sp., Phaeocystis sp. and Coscinodiscus sp. Growth stages were initial, exponential, stationary, and degradation.

Methods & Sampling

Bacterial cells were enumerated by flow cytometry. At each sampling point 1 mL of experimental or control water was fixed with 0.1% glutaraldehyde (final concentration) for 10 min at room temperature in the dark, and stored frozen at -80 °C. Prior to analysis, thawed samples were pipetted through a cell strainer (Flowmi, 70 µm porosity) and stained with SYBR Green I for 15 min on ice in the dark. Counts were performed with a FACSCalibur flow cytometer (Becton-Dickson) using fluorescent microspheres (Molecular Probes) of 1 µm in diameter as internal size standard. Cells were enumerated according to their right angle scatter and green fluorescence using the FloJo 7.6.1 software.

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- repeated data in 'taxa' and 'time_point_day' columns to create a flat file

Data Files

File
cell_counts.csv (Comma Separated Values (.csv), 5.31 KB) MD5:dd199f77fb797e523cc4d642847e5685 Primary data file for dataset ID 748415

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1459406

Deployments

None available yet

Instruments

Flow Cytometer

Supplied Name: FACSCalibur flow cytometer (Becton-Dickson)

Supplied Description:

Used to make cell counts.

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
taxon	phytoplankton	unitless	taxon
time_point_day	growth phase (initial/exponential/stationary/degradation) and the number of days since the start of the experiment	days	time_point
time_start	time at start of experiment	unitless	time_start
time_end	time at end of experiment	unitless	time_end
cell_count	bacterial cell count as determined by flow cytometry	cells	count
flow_rate	flow rate of the sample	microliters/minute	flow_rate
time_elapsed_min	flow count duration	minutes	duration
volume	volume of sample	microliters	volume
concentration_uL	bacterial cell concentration	cells/microliter	cell_concentration
concentration_mL	bacterial cell concentration	cells/milliliter	cell_concentration