http://lod.bco-dmo.org/id/dataset/717660
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
2017-10-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial enzymatic activities from seawater and from particle-associated seawater communities from Greenland, August 2015 (Patterns of activities project)
2017-10-30
publication
2017-10-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-05-13
publication
https://doi.org/10.26008/1912/bco-dmo.717660.1
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 enzymatic activities from seawater and from particle-associated seawater communities from Greenland, August 2015 (Patterns of activities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-10-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.717660.1 [access date]
hydrolysis rates Dataset Description: <p>Bacterial activity as measured by hydrolysis&nbsp;rates from unfiltered seawater and particle-associated communities collected near shore in northeastern&nbsp;Greenland in August 2015.</p> Methods and Sampling: <p>Using a small boat, samples were collected in 20L carboys in Tylerfjord-Young Sound. Three rivers that feed into Tyrolerfjord-Young Sound (Tyroler River, Lerbugten River and Zackenberg River) were sampled; surface and subsurface water samples were also collected at transition sites where the rivers feed into the fjord (Tyro_01, Zac_30, Ler_30, altogether referred to as ‘river transition sites’). Enzyme activities were measured in unfiltered water. In addition, water was size-fractionated using gravity filtration through a GF/A filter to capture ≥1.6 µm particles.</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]. &nbsp;All substrates were used to measure enzyme activities in unfiltered water, as well as particle-associated (≥1.6 µm) enzymatic activities.</p>
<p>In unfiltered water, enzyme activities were measured by adding 4 mL of water to triplicate cuvettes. One incubation containing autoclaved water served as the killed control. This procedure was applied to each of the 7 substrates and one live blank and autoclave blank (no substrate addition). Each cuvette containing either live or autoclaved water was amended with one substrate to a concentration of 100 µM. Fluroescence was measured using a Promega Quantifluor solid-state single-cuvette fluorimeter; excitation and emission maxima were 365 nm and 410–450 nm, respectively,</p>
<p>To measure particle-associated enzyme assays, 1/12th piece of a GF/A filter through which water had been gravity filtered was put into a cuvette containing 4 mL of cooled, autoclaved water from the same station/depth as the live samples. In addition, killed controls were set up using sterile GF/A filters cut into 1/12th pieces. Bulk water and particle-associated enzyme assays were incubated for up to 24 and 16 hours, respectively; timepoints were taken at specific intervals. Incubations were kept in the dark either at 0°C, 5°C, or 8°C, depending on in situ water temperature at the time of sampling.</p>
<p>Activities of polysaccharide hydrolases were measured using fluorescently labeled polysaccharides (Arnosti 2003). Activities of enzymes that hydrolyze pullulan, laminarin, xylan, fucoidan, arabinogalactan, and chondroitin sulfate were measured in unfiltered water, and using GF/A filters through which water had been gravity-filtered. For these measurements, substrate was added (of 3.5 µM monomer equivalent) to 15 mL of water; autoclaved ambient water served as the killed control. Particle-associated activities were measured by submerging 1/12th of a GF/A filter in 15 ml autoclaved seawater. Samples were incubated in the dark at near in situ temperature (0°C, 5°C, or 8°C), and sub-sampled at specific time intervals—t0 (0h, upon substrate addition), t1 (120 h), t2 (240 h), t3 (360 h) and t4 (600 h). Sub-samples from each timepoint were filtered using 0.2 µM pore size SFCA (surfactant-free cellulose acetate) syringe filters, and the filtrate was collected in tubes and frozen at -20°C until processing in the lab. Sub-samples were processed using gel permeation chromatography (Arnosti, 2003).&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
trip_id
sample_type
fluorophore
cast
station
depth_id
depth_m
substrate
timepoint
time_elapsed_hr
rep1_rate
rep2_rate
rep3_rate
rate_average
rate_std_dev
filter_um
Promega Quantifluor solid-state single-cuvette fluorimeter
20 liter Niskin bottles
theme
None, User defined
cruise name
sample type
No BCO-DMO term
cast
station
depth_comment
depth
time_point
time_elapsed
filter_size
featureType
BCO-DMO Standard Parameters
Fluorometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
zodiac_Arnosti
service
Deployment Activity
Tylerfjord-Young Sound, including the Tyroler River, Lerbugten River and Zackenberg River; coastal East Greenland Sea
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
Tylerfjord-Young Sound, including the Tyroler River, Lerbugten River and Zackenberg River; coastal East Greenland Sea
-20.574
-20.574
74.46
74.46
2015-08-02
2015-08-02
Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
0
BCO-DMO catalogue of parameters from Microbial enzymatic activities from seawater and from particle-associated seawater communities from Greenland, August 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/718071.rdf
Name: trip_id
Units: unitless
Description: <p>sampling trip identifier; YS means Young Sound</p>
http://lod.bco-dmo.org/id/dataset-parameter/718072.rdf
Name: sample_type
Units: unitless
Description: <p>indication of whether sample was filtered (GF) or not (bulk)</p>
http://lod.bco-dmo.org/id/dataset-parameter/718073.rdf
Name: fluorophore
Units: unitless
Description: <p>fluorescent molecules used to measure hydrolysis rates: fluorescently-labeled polysaccharides (FLA) or small substrate proxies tagged with methylcoumarine (MCA) and methylumbelliferone (MUF) fluorophores.</p>
http://lod.bco-dmo.org/id/dataset-parameter/718074.rdf
Name: cast
Units: unitless
Description: <p>cast identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/718075.rdf
Name: station
Units: unitless
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/718076.rdf
Name: depth_id
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/718077.rdf
Name: depth_m
Units: meters
Description: <p>actual depth at which water collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/718078.rdf
Name: substrate
Units: unitless
Description: <p>substrates for measurement of enzymatic activities: ara = arabinogalactan; chn = chondroitin sulfate; fuc = fucoidan; lam = laminarin; pul = pullulan; xyl = xylan</p>
http://lod.bco-dmo.org/id/dataset-parameter/718079.rdf
Name: timepoint
Units: unitless
Description: <p>sampling time point (0; 1; 2; etc.) post-incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/718080.rdf
Name: time_elapsed_hr
Units: hours
Description: <p>hours elapsed to reach a specific timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718532.rdf
Name: rep1_rate
Units: nanomol monomer/liter/hour
Description: <p>replicate 1 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/718533.rdf
Name: rep2_rate
Units: nanomol monomer/liter/hour
Description: <p>replicate 2 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/718534.rdf
Name: rep3_rate
Units: nanomol monomer/liter/hour
Description: <p>replicate 3 hydrolysis rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/718535.rdf
Name: rate_average
Units: nanomol monomer/liter/hour
Description: <p>average of the 3 hydrolysis rates</p>
http://lod.bco-dmo.org/id/dataset-parameter/718536.rdf
Name: rate_std_dev
Units: nanomol monomer/liter/hour
Description: <p>standard deviation of the 3 hydrolysis rates</p>
http://lod.bco-dmo.org/id/dataset-parameter/718537.rdf
Name: filter_um
Units: nanomol monomer/liter/hour
Description: <p>filter size</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
98960
https://darchive.mblwhoilibrary.org/bitstream/1912/25767/1/dataset-717660_greenland-experiment-microbial-enzymatic-activities__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.717660.1
download
onLine
dataset
<p>Using a small boat, samples were collected in 20L carboys in Tylerfjord-Young Sound. Three rivers that feed into Tyrolerfjord-Young Sound (Tyroler River, Lerbugten River and Zackenberg River) were sampled; surface and subsurface water samples were also collected at transition sites where the rivers feed into the fjord (Tyro_01, Zac_30, Ler_30, altogether referred to as ‘river transition sites’). Enzyme activities were measured in unfiltered water. In addition, water was size-fractionated using gravity filtration through a GF/A filter to capture ≥1.6 µm particles.</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]. &nbsp;All substrates were used to measure enzyme activities in unfiltered water, as well as particle-associated (≥1.6 µm) enzymatic activities.</p>
<p>In unfiltered water, enzyme activities were measured by adding 4 mL of water to triplicate cuvettes. One incubation containing autoclaved water served as the killed control. This procedure was applied to each of the 7 substrates and one live blank and autoclave blank (no substrate addition). Each cuvette containing either live or autoclaved water was amended with one substrate to a concentration of 100 µM. Fluroescence was measured using a Promega Quantifluor solid-state single-cuvette fluorimeter; excitation and emission maxima were 365 nm and 410–450 nm, respectively,</p>
<p>To measure particle-associated enzyme assays, 1/12th piece of a GF/A filter through which water had been gravity filtered was put into a cuvette containing 4 mL of cooled, autoclaved water from the same station/depth as the live samples. In addition, killed controls were set up using sterile GF/A filters cut into 1/12th pieces. Bulk water and particle-associated enzyme assays were incubated for up to 24 and 16 hours, respectively; timepoints were taken at specific intervals. Incubations were kept in the dark either at 0°C, 5°C, or 8°C, depending on in situ water temperature at the time of sampling.</p>
<p>Activities of polysaccharide hydrolases were measured using fluorescently labeled polysaccharides (Arnosti 2003). Activities of enzymes that hydrolyze pullulan, laminarin, xylan, fucoidan, arabinogalactan, and chondroitin sulfate were measured in unfiltered water, and using GF/A filters through which water had been gravity-filtered. For these measurements, substrate was added (of 3.5 µM monomer equivalent) to 15 mL of water; autoclaved ambient water served as the killed control. Particle-associated activities were measured by submerging 1/12th of a GF/A filter in 15 ml autoclaved seawater. Samples were incubated in the dark at near in situ temperature (0°C, 5°C, or 8°C), and sub-sampled at specific time intervals—t0 (0h, upon substrate addition), t1 (120 h), t2 (240 h), t3 (360 h) and t4 (600 h). Sub-samples from each timepoint were filtered using 0.2 µM pore size SFCA (surfactant-free cellulose acetate) syringe filters, and the filtrate was collected in tubes and frozen at -20°C until processing in the lab. Sub-samples were processed using gel permeation chromatography (Arnosti, 2003).&nbsp;</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 trip_id, bulk_or_not, FLA_MCAMUF columns<br />
-&nbsp;reduced&nbsp;the decimal&nbsp;precision of time_elapsed_hr and the rates columns to 3.<br />
-&nbsp;sorted by sample_type, fluorophore, station, cast, depth_id</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
Promega Quantifluor solid-state single-cuvette fluorimeter
Promega Quantifluor solid-state single-cuvette fluorimeter
PI Supplied Instrument Name: Promega Quantifluor solid-state single-cuvette fluorimeter 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/
20 liter Niskin bottles
20 liter Niskin bottles
PI Supplied Instrument Name: 20 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/
Cruise: zodiac_Arnosti
zodiac_Arnosti
small boat Zackenber Res. Sta.
vessel
zodiac_Arnosti
Carol Arnosti
University of North Carolina at Chapel Hill
small boat Zackenber Res. Sta.
vessel