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 fluorescence and bacterial enzyme activity during CDOM Coscinodiscus monoculture experiments. Growth stages were initial and exponential.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2018-10-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.748445.1	2019-04-01

Description

The data include fluorescence and bacterial enzyme activity during CDOM Coscinodiscus monoculture experiments. Growth stages were initial and exponential.

Methods & Sampling

Hydrolytic enzyme activities were determined using L-leucine-4-methylcoumarinyl-7-amide (MCA) hydrochloride, 4-methylumbelliferyl α-D-glucopyranoside, and 4-methylumbelliferone (MUF) β-D-glucopyranoside (Sigma-Aldrich) as substrate proxies for leucine-aminopeptidase, α-glucosidase, and β-glucosidase activities, respectively. For each bottle and substrate proxy, 196 µL of unfiltered experimental or control water was added in duplicate to a pure-grade black 96-well plate (Brand Life Sciences) containing a single substrate proxy at saturation levels (final concentration 200 µM). Fluorescence (excitation 370 nm, emission 440 nm) was measured in a Tecan Infinite 200 Pro microplate reader immediately following the addition of the substrate and several more times over 7-20 h. The well plates were incubated in the dark at in situ temperature. MUF and MCA standard solutions prepared in seawater were used to determine hydrolysis rates. Killed controls (boiled sample water) and ultrapure water samples showed little change over the incubations.

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
- converted Excel file tables to a flat file and combined a-glu, b-glu, and leu substrate treatments.

Data Files

File
coscinodiscus_enzyme.csv (Comma Separated Values (.csv), 6.61 KB) MD5:ef6801a2e176a2e2030245bdd79518c7 Primary data file for dataset ID 748445

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)

plate reader

Supplied Name: Tecan Infinite 200 Pro microplate reader

Supplied Description:

Used to measure fluorescence from which hydrolysis rates were calculated.

Instrument Type

Generic Name: plate reader

Generic Description:

Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
substrate	substrate for measuring enzyme activity: a-glu = 4-methylumbelliferyl a-D-glucopyranoside; b-glu = 4-methylumbelliferone (MUF) ß-D-glucopyranoside; leu = L-leucine-4-methylcoumarinyl-7-amide	unitless	no_bcodmo_term
sample	sample identifier denoted as growth stage (days from start) replicate id	unitless	sample
fluor_t0	fluorescence intensity at time 0	relative fluorescence units	fluor
fluor_t1	fluorescence intensity at time 1	relative fluorescence units	fluor
fluor_t2	fluorescence intensity at time 2	relative fluorescence units	fluor
fluor_t3	fluorescence intensity at time 3	relative fluorescence units	fluor
time_t0	time since start of experiment; time point 0	hours	time_elapsed
time_t1	time elapsed from start of experiment; time point 1	hours	time_elapsed
time_t2	time elapsed from start of experiment; time point 2	hours	time_elapsed
time_t3	time elapsed from start of experiment; time point 3	hours	time_elapsed
enz_activity_t0	enzymatic activity at time 0	nanoMol/hour	no_bcodmo_term
enz_activity_t1	enzymatic activity at time 1	nanoMol/hour	no_bcodmo_term
enz_activity_t2	enzymatic activity at time 2	nanoMol/hour	no_bcodmo_term
enz_activity_t3	enzymatic activity at time 3	nanoMol/hour	no_bcodmo_term
SLOPE	the slope of the graph of fluorescence intensity vs substrate concentration	unitless	no_bcodmo_term
RSQR	the square of the correlation coefficient of fluorescence intensity vs substrate concentration	unitless	no_bcodmo_term