http://lod.bco-dmo.org/id/dataset/719487
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
2017-11-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (Patterns of activities project)
2017-11-16
publication
2017-11-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-05-13
publication
https://doi.org/10.26008/1912/bco-dmo.719487.1
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) Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (Patterns of activities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-11-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.719487.1 [access date]
Bulk polysaccharide hydrolysis rates - EN556 Dataset Description: <p>This dataset includes polysaccharide hydrolysis rates to measure microbial enzyme activities and bacterial productivity.</p>
<p>See Niskin Bottle and Cast List EN556 to link specific casts and bottles to each experiment: <a href="https://www.bco-dmo.org/dataset/717427" target="_blank">https://www.bco-dmo.org/dataset/717427</a>.</p> Methods and Sampling: <p>Seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle, using silicone tubing that had been acid washed then rinsed with distilled water prior to use. From each carboy, water was dispensed into smaller glass containers that were cleaned and pre-rinsed three times with water from the carboy prior to dispensing. This water was used to measure cell counts, bacterial productivity, and the activities of polysaccharide hydrolases, peptidases, and glucosidases. A separate glass Duran bottle was filled with seawater from the carboy and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</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; <em>Obayashi and Suzuki</em>, 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 [<em>Hoarfrost</em>, 2017].</p>
<p>The potential of the seawater microbial community to hydrolyze six high-molecular-weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan) was investigated in surface and bottom water. For each substrate, three 50 mL falcon tubes were filled with seawater and one 50 mL falcon tube was filled with autoclaved seawater to serve as a killed control. Substrate was added at 3.5 μM monomer-equivalent concentrations, except for fucoidan, which was added at 5 μM concentrations (a higher concentration was necessary for sufficient fluorescence signal). Two 50 mL falcon tubes – one with seawater and one with autoclaved seawater – with no added substrate served as blank controls. Incubations were stored in the dark at as close to <em>in situ </em>temperature as possible. Subsamples of the incubations were collected at time zero, and at six subsequent time points (t1-t6): 2 days, 5 days, 10 days, 17 days, 30 days, and 42 days. At each time point, 2 mL of seawater was collected from the 50 mL falcon tube using a sterile syringe, filtered through a 0.2 μm pore size syringe filter, and stored frozen until processing.</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
cruise_id
cast
station
depth_no
depth_m
substrate
rep1_rate
rep2_rate
rep3_rate
average
std_dev
30 liter Niskin bottles
TECAN spectrafluor plus
theme
None, User defined
Cruise identfier
cast
station
depth_comment
depth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Fluorometer
Niskin bottle
plate reader
instrument
BCO-DMO Standard Instruments
EN556
service
Deployment Activity
North Atlantic, shelf waters off Rhode Island, then a transect along Line W (farthest stn: ca 37 N, 68W, approximately at ID #9020)
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
North Atlantic, shelf waters off Rhode Island, then a transect along Line W (farthest stn: ca 37 N, 68W, approximately at ID #9020)
-71.0086
-68.4078
37.6675
40.0725
2015-04-27
2015-05-02
Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
0
BCO-DMO catalogue of parameters from Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (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/719499.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/719500.rdf
Name: cast
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/719501.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/719502.rdf
Name: depth_no
Units: unitless
Description: <p>depth description: sequence of depths sampled with 1 is surface and higher numbers at greater depths</p>
http://lod.bco-dmo.org/id/dataset-parameter/719503.rdf
Name: depth_m
Units: meters
Description: <p>actual depth at which water collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/719504.rdf
Name: substrate
Units: unitless
Description: <p>substrates for measurement of enzymatic activities: a-glu = alpha glucosidase: 4-methylumbelliferyl-a-D-glucopyranoside; b-glu = beta glucosidase: 4-methylumbelliferyl-beta-D-glucopyranoside; L = leucine aminopeptidase (L-leucine-7-amido-4 MCA); AAF = chymotrypsin activity: ala-ala-phe-MCA; AAPF = chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA; QAR = trypsin activity: Boc-gln-ala-arg-MCA; FSR = trypsin activity: N-t-boc-phe-ser-arg-MCA</p>
http://lod.bco-dmo.org/id/dataset-parameter/719505.rdf
Name: rep1_rate
Units: nanomol monosaccharide/liter/hour
Description: <p>replicate 1 of enzymatic hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/719506.rdf
Name: rep2_rate
Units: nanomol monosaccharide/liter/hour
Description: <p>replicate 2 of enzymatic hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/719507.rdf
Name: rep3_rate
Units: nanomol monosaccharide/liter/hour
Description: <p>replicate 3 of enzymatic hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/719508.rdf
Name: average
Units: nanomol monosaccharide/liter/hour
Description: <p>average of the 3 hydrolysis rates</p>
http://lod.bco-dmo.org/id/dataset-parameter/719509.rdf
Name: std_dev
Units: nanomol monosaccharide/liter/hour
Description: <p>standard deviation of the 3 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
8525
https://darchive.mblwhoilibrary.org/bitstream/1912/25766/1/dataset-719487_en556-bulk-polysaccharide-hydrolysis-rates-plate-reader__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.719487.1
download
onLine
dataset
<p>Seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle, using silicone tubing that had been acid washed then rinsed with distilled water prior to use. From each carboy, water was dispensed into smaller glass containers that were cleaned and pre-rinsed three times with water from the carboy prior to dispensing. This water was used to measure cell counts, bacterial productivity, and the activities of polysaccharide hydrolases, peptidases, and glucosidases. A separate glass Duran bottle was filled with seawater from the carboy and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</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; <em>Obayashi and Suzuki</em>, 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 [<em>Hoarfrost</em>, 2017].</p>
<p>The potential of the seawater microbial community to hydrolyze six high-molecular-weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan) was investigated in surface and bottom water. For each substrate, three 50 mL falcon tubes were filled with seawater and one 50 mL falcon tube was filled with autoclaved seawater to serve as a killed control. Substrate was added at 3.5 μM monomer-equivalent concentrations, except for fucoidan, which was added at 5 μM concentrations (a higher concentration was necessary for sufficient fluorescence signal). Two 50 mL falcon tubes – one with seawater and one with autoclaved seawater – with no added substrate served as blank controls. Incubations were stored in the dark at as close to <em>in situ </em>temperature as possible. Subsamples of the incubations were collected at time zero, and at six subsequent time points (t1-t6): 2 days, 5 days, 10 days, 17 days, 30 days, and 42 days. At each time point, 2 mL of seawater was collected from the 50 mL falcon tube using a sterile syringe, filtered through a 0.2 μm pore size syringe filter, and stored frozen until processing.</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 />
- removed 'cast00' and 'stn0' from data records for the cast and station columns</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: 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/
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 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.
Cruise: EN556
EN556
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN556
Carol Arnosti
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel