http://lod.bco-dmo.org/id/dataset/717532
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-10-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Measurements of peptidase and glucosidase activities in large volume mesocosm incubations on RV/Endeavor EN584, July 2016 (Patterns of activities project)
2022-12-07
publication
2022-12-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-12-07
publication
https://doi.org/10.26008/1912/bco-dmo.717532.1
Carol Arnosti
University of North Carolina at Chapel Hill
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Arnosti, C. (2022) Measurements of peptidase and glucosidase activities in large volume mesocosm incubations on RV/Endeavor EN584, July 2016 (Patterns of activities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.717532.1 [access date]
Large volume incubation, peptidase and glucosidase activities (plate reader), EN584 Dataset Description: <p>Fluorescence was measured over 24-48 hours incubation time with a plate reader (TECAN spectrafluor plus; 360 nm excitation, 460 emission), with time points 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].</p>
<p>See Niskin Bottle and Cast List EN584 to link specific casts and bottles to each experiment: BCO-DMO dataset 717427&nbsp;(see related datasets).</p> Methods and Sampling: <p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), a 30L Niskin bottle rosette was used to collect the water. Separate casts were used to collect surface water, bottom water, and water from the depth at which oxygen showed a minimum, according to the CTD. From each depth, 20L seawater from single Niskin bottles was dispensed using cleaned silicon tubing into a single carboy. Prior to filling, carboys were rinsed 3x with water from the same Niskin bottle used to fill the carboy. Four carboys were filled at each depth. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of HMW Thalassiosira; unamended single carboys were used for controls. All mesocosms were incubated in the dark at near in-situ temperatures. Mesocosms were sub-sampled at the start of incubation (0 days), and then after 2 d, 7d, and 16d for the following assays: bacterial production using 3H-Leucine, dissolved organic carbon (DOC), nutrients, bacterial cell counts,&nbsp;peptidase and glucosidase activity measurements.</p>
<p>Two substrates, a-glucose and b-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 time points 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].</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332881 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332881
completed
Carol Arnosti
University of North Carolina at Chapel Hill
919-962-5754
Dept. of Marine Sciences 3117A Venable/Murray Hall
Chapel Hill
NC
27599-3300
USA
arnosti@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
timepoint
time_elapsed_hr
cruise_id
station
cast
depth_id
depth_m
meso_no
treatment
substrate
subtimepoint
timepoint_average
timepoint_std_dev
subtimepoint_average
subtimepoint_std_dev
30 liter Niskin bottles
TECAN spectrafluor plus
theme
None, User defined
time_point
time_elapsed
cruise_id
station
cast
depth
sample description
treatment
featureType
BCO-DMO Standard Parameters
Niskin bottle
plate reader
Shipboard Incubator
instrument
BCO-DMO Standard Instruments
EN584
service
Deployment Activity
NW Atlantic: Atlantic Ocean, nearshore waters close to Cape Hatteras/Cape Lookout, and a transect along ca 36 N out to ca 58 W.
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
https://osprey.bco-dmo.org/project/712359
Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
<p><em>NSF Award Abstract:</em><br />
Heterotrophic microbial communities are key players in the marine carbon cycle, transforming and respiring organic carbon, regenerating nutrients, and acting as the final filter in sediments through which organic matter passes before long-term burial. Microbially-driven carbon cycling in the ocean profoundly affects the global carbon cycle, but key factors determining rates and locations of organic matter remineralization are unclear. In this study, researchers from the University of North Carolina at Chapel Hill will investigate the ability of pelagic microbial communities to initiate the remineralization of polysaccharides and proteins, which together constitute a major pool of organic matter in the ocean. Results from this study will be predictive on a large scale regarding the nature of the microbial response to organic matter input, and will provide a mechanistic framework for interpreting organic matter reactivity in the ocean.</p>
<p>Broader Impacts: This study will provide scientific training for undergraduate and graduate students from underrepresented groups. The project will also involve German colleagues, thus strengthening international scientific collaboration.</p>
Patterns of activities
largerWorkCitation
project
eng; USA
biota
oceans
NW Atlantic: Atlantic Ocean, nearshore waters close to Cape Hatteras/Cape Lookout, and a transect along ca 36 N out to ca 58 W.
2016-07-01
2016-07-01
Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
0
BCO-DMO catalogue of parameters from Measurements of peptidase and glucosidase activities in large volume mesocosm incubations on RV/Endeavor EN584, July 2016 (Patterns of activities project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/885011.rdf
Name: timepoint
Units: unitless
Description: <p>Sampling point post incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/885012.rdf
Name: time_elapsed_hr
Units: hours (hr)
Description: <p>Elapsed time, incubation time</p>
http://lod.bco-dmo.org/id/dataset-parameter/885013.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/885014.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885015.rdf
Name: cast
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885016.rdf
Name: depth_id
Units: unitless
Description: <p>depth identifier, sequence of depths sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/885017.rdf
Name: depth_m
Units: meters (m)
Description: <p>Actual depth of water collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885018.rdf
Name: meso_no
Units: unitless
Description: <p>Mesocosm number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885019.rdf
Name: treatment
Units: unitless
Description: <p>treatment, amended or unamended</p>
http://lod.bco-dmo.org/id/dataset-parameter/885020.rdf
Name: substrate
Units: unitless
Description: <p>Substrates for measurement of enzymatic activities: a-glu = substrate to measure alpha glucosidase: 4-methylumbelliferyl-a-D-glucopyranoside; b-glu = substrate to measure beta glucosidase: 4-methylumbelliferyl-ß-D-glucopyranoside; 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 </p>
http://lod.bco-dmo.org/id/dataset-parameter/885021.rdf
Name: subtimepoint
Units: unitless
Description: <p>Mesocosm subsampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/885022.rdf
Name: timepoint_average
Units: nmol/L/hr
Description: <p>Average of three plate replicates at an indiviual timepoint for a given Mesocosm subsampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/885023.rdf
Name: timepoint_std_dev
Units: nmol/L/hr
Description: <p>Standard deviation of average enzymatic activity at an indiviual timepoint for a given Mesocosm subsampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/885024.rdf
Name: subtimepoint_average
Units: nmol/L/hr
Description: <p>Average enzymatic activity across timepoints for a given Mesocosm subsampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/885025.rdf
Name: subtimepoint_std_dev
Units: nmol/L/hr
Description: <p>Standard deviation of average enzymatic activity across timepoints for a given Mesocosm subsampling</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
590557
https://darchive.mblwhoilibrary.org/bitstream/1912/29554/1/dataset-717532_en584-lv-incubation-peptidase-and-glucosidase-activities__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.717532.1
download
onLine
dataset
<p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), a 30L Niskin bottle rosette was used to collect the water. Separate casts were used to collect surface water, bottom water, and water from the depth at which oxygen showed a minimum, according to the CTD. From each depth, 20L seawater from single Niskin bottles was dispensed using cleaned silicon tubing into a single carboy. Prior to filling, carboys were rinsed 3x with water from the same Niskin bottle used to fill the carboy. Four carboys were filled at each depth. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of HMW Thalassiosira; unamended single carboys were used for controls. All mesocosms were incubated in the dark at near in-situ temperatures. Mesocosms were sub-sampled at the start of incubation (0 days), and then after 2 d, 7d, and 16d for the following assays: bacterial production using 3H-Leucine, dissolved organic carbon (DOC), nutrients, bacterial cell counts,&nbsp;peptidase and glucosidase activity measurements.</p>
<p>Two substrates, a-glucose and b-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 time points 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].</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added cruise_id column<br />
- replaced 'na'&nbsp;with 'nd' (no data)</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
30 liter Niskin bottles
30 liter Niskin bottles
PI Supplied Instrument Name: 30 liter Niskin bottles PI Supplied Instrument Description:Used to collect water for large volume mesocosm experiments Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
TECAN spectrafluor plus
TECAN spectrafluor plus
PI Supplied Instrument Name: TECAN spectrafluor plus PI Supplied Instrument Description:Used to measure fluorescence of incubated 96-well plate. Settings: 360 nm excitation, 460 emission. Instrument Name: plate reader Instrument Short Name: Instrument 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.
PI Supplied Instrument Name: Instrument Name: Shipboard Incubator Instrument Short Name: Instrument Description: A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Cruise: EN584
EN584
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN584
Carol Arnosti
University of North Carolina at Chapel Hill
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel