Dataset: SO248: Bulk MCAMUF hydrolysis rates

Name: Microbial enzyme activities: glucosidase and peptidase activities of bulk seawater samples from the RV\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016
Published: 2018-07-31
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.743224.1

Spatial Extent: N:58.9 E:-179 S:-30.0008 W:-180

Temporal Extent: 2016-05-02 - 2016-05-30

Project:

Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean? (Patterns of activities)

Principal Investigator:

Carol Arnosti (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-07-31

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Microbial enzyme activities: glucosidase and peptidase activities of bulk seawater samples from the RV\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016

Abstract:

This dataset includes MCAMUF (glucosidase and peptidase) hydrolysis rates to measure microbial enzyme activities in bulk (not filter-fractionated) seawater. Samples were collected on RV/Sonne cruise SO248 in May 2016. Links to archived CTD data are also provided.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2018-07-31	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.743224.1	2020-04-27

Description

Methods & Sampling

Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.

Two substrates, -glucose and -glucose linked to a 4-methylumbelliferyl (MUF) fluorophore, were used to measure glucosidase activities. Five substrates linked to a 7-amido-4-methyl coumarin (MCA) fluorophore, one amino acid – leucine – and four oligopeptides – the chymotrypsin substrates alanine-alanine-phenylalanine (AAF) and alanine-alanine-proline-phenylalanine (AAPF), and the trypsin substrates glutamine-alanine-arginine (QAR) and phenylalanine-serine-arginine (FSR) – were used to measure exo- and endo-acting peptidase activities, respectively. Hydrolysis rates of the substrates were measured as an increase in fluorescence as the fluorophore was hydrolyzed from the substrate over time [as in Hoppe, 1993; Obayashi and Suzuki, 2005]. Incubations with the seven low molecular weight substrates were set up in a 96-well plate. For each substrate, triplicate wells were filled with a total volume of 200 L seawater for experimental incubations; triplicate wells were filled with 200 L autoclaved seawater for killed control incubations. Substrate was added at saturating concentrations. A saturation curve was determined with surface water from each station to determine saturating concentrations of substrate. The saturating concentration was identified as the lowest tested concentration of substrate at which additional substrate did not yield higher rates of hydrolysis. Fluorescence was measured over 24-48 hours incubation time with a plate reader (TECAN spectrafluor plus; 360 nm excitation, 460 emission), with timepoints taken every 4-6 hours. Hydrolysis rates were calculated from the rate of increase of fluorescence in the incubation over time relative to a set of standards of known concentration of fluorophore. Scripts to calculate hydrolysis rates and produce the figures shown here are available in the associated Github repository [Hoarfrost, 2017].

L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- reduced decimal precision of rate columns from 9 to 6 places; time_elapsed from 7 to 0 places

Data Files

File
SO248_bulk_MCAMUF_joined.csv (Comma Separated Values (.csv), 190.91 KB) MD5:c167b9519194948fd6b8028ff343b72a Primary data file for dataset ID 743224

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1332881

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SO248	BacGeoPac	2016-05-01	R/V Sonne	Meinhard Simon (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Fluorometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Niskin bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
station_no	refers to station number for cruise	unitless	station
depth_no	sequence of depths sampled (1 is surface; higher numbers at greater depths)	unitless	no_bcodmo_term
depth_m	actual depth at which water collected	meters	depth
cast_no	cast number (refers to cast of CTD/Niskin bottles on cruise)	unitless	cast
ISO_DateTime_UTC	date and time in ISO format (yyyy-mm-ddTHH:MM:SS	unitless	ISO_DateTime_UTC
Latitude	latitude; north is positive	decimal degreed	lat
Longitude	longitude; east is postivie	decimal degreed	lon
substrate	Substrates for measurement of enzymatic activities. ara:arabinogalactan: L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA) AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA	unitless	no_bcodmo_term
timepoint	sampling point post-incubation	unitless	time_point
time_elapsed_hr	incubation time	hours	time_elapsed
rep1_rate	replicate 1 hydrolysis rate	nanomoles/liter/hour (nmol L-1 h-1)	no_bcodmo_term
rep2_rate	replicate 2 hydrolysis rate	nanomoles/liter/hour (nmol L-1 h-1)	no_bcodmo_term
rep3_rate	replicate 3 hydrolysis rate	nanomoles/liter/hour (nmol L-1 h-1)	no_bcodmo_term
average	average of hydrolysis rates	nanomoles/liter/hour (nmol L-1 h-1)	no_bcodmo_term
std_dev	std deviation of hydrolysis rates	nanomoles/liter/hour (nmol L-1 h-1)	no_bcodmo_term