http://lod.bco-dmo.org/id/dataset/743224
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
2018-08-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2018-07-31
publication
2018-07-31
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-04-27
publication
https://doi.org/10.26008/1912/bco-dmo.743224.1
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. (2020) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-07-31 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.743224.1 [access date]
SO248: Bulk MCAMUF Dataset Description: <p>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.</p> Methods and Sampling: <p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>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].</p>
<p>L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)<br />
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA<br />
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA<br />
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA&nbsp;&nbsp;<br />
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA&nbsp;</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
station_no
depth_no
depth_m
cast_no
ISO_DateTime_UTC
Latitude
Longitude
substrate
timepoint
time_elapsed_hr
rep1_rate
rep2_rate
rep3_rate
average
std_dev
theme
None, User defined
station
No BCO-DMO term
depth
cast
ISO_DateTime_UTC
latitude
longitude
time_point
time_elapsed
featureType
BCO-DMO Standard Parameters
CTD - profiler
Fluorometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
SO248
service
Deployment Activity
South and North Pacific, along 180 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
oceans
South and North Pacific, along 180 W
-180
-179
-30.0008
58.9
2016-05-02
2016-05-30
Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
0
BCO-DMO catalogue of parameters from 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
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/743236.rdf
Name: station_no
Units: unitless
Description: <p>refers to station number for cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/743237.rdf
Name: depth_no
Units: unitless
Description: <p>sequence of depths sampled (1 is surface; higher numbers at greater depths)</p>
http://lod.bco-dmo.org/id/dataset-parameter/743238.rdf
Name: depth_m
Units: meters
Description: <p>actual depth at which water collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/743239.rdf
Name: cast_no
Units: unitless
Description: <p>cast number (refers to cast of CTD/Niskin bottles on cruise)</p>
http://lod.bco-dmo.org/id/dataset-parameter/743240.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>date and time in ISO format (yyyy-mm-ddTHH:MM:SS</p>
http://lod.bco-dmo.org/id/dataset-parameter/743241.rdf
Name: Latitude
Units: decimal degreed
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/743242.rdf
Name: Longitude
Units: decimal degreed
Description: <p>longitude; east is postivie</p>
http://lod.bco-dmo.org/id/dataset-parameter/743243.rdf
Name: substrate
Units: unitless
Description: <p>Substrates for measurement of enzymatic activities. ara:arabinogalactan:<br />
L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)<br />
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA<br />
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA<br />
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA <br />
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA </p>
http://lod.bco-dmo.org/id/dataset-parameter/743244.rdf
Name: timepoint
Units: unitless
Description: <p>sampling point post-incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/743245.rdf
Name: time_elapsed_hr
Units: hours
Description: <p>incubation time</p>
http://lod.bco-dmo.org/id/dataset-parameter/743246.rdf
Name: rep1_rate
Units: nanomoles/liter/hour (nmol L-1 h-1)
Description: <p>replicate 1 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/743247.rdf
Name: rep2_rate
Units: nanomoles/liter/hour (nmol L-1 h-1)
Description: <p>replicate 2 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/743248.rdf
Name: rep3_rate
Units: nanomoles/liter/hour (nmol L-1 h-1)
Description: <p>replicate 3 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/743249.rdf
Name: average
Units: nanomoles/liter/hour (nmol L-1 h-1)
Description: <p>average of hydrolysis rates</p>
http://lod.bco-dmo.org/id/dataset-parameter/743250.rdf
Name: std_dev
Units: nanomoles/liter/hour (nmol L-1 h-1)
Description: <p>std deviation of hydrolysis rates</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
195487
https://darchive.mblwhoilibrary.org/bitstream/1912/25690/1/dataset-743224_so248-bulk-mcamuf-hydrolysis-rates__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.743224.1
download
onLine
dataset
<p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>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].</p>
<p>L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)<br />
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA<br />
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA<br />
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA&nbsp;&nbsp;<br />
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- added conventional header with dataset name, PI name, version date<br />
- reduced decimal precision of rate columns from 9 to 6 places; time_elapsed from 7 to 0 places</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
PI Supplied Instrument Name: Instrument Name: CTD - profiler Instrument Short Name: Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PI Supplied Instrument Name: Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
PI Supplied Instrument Name: 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/
Cruise: SO248
SO248
R/V Sonne
Community Standard Description
R/V Sonne
vessel
SO248
Meinhard Simon
University of Oldenburg
R/V Sonne
Community Standard Description
R/V Sonne
vessel