http://lod.bco-dmo.org/id/dataset/996093
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
2026-04-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Peptidase and glucosidase activities from bulk water incubations from waters taken aboard the R/V Thomas G. Thompson in the Southern Indian Ocean during the research cruise TN362 in November and December, 2018
2026-04-06
publication
2026-04-06
revision
BCO-DMO Linked Data URI
2026-04-06
creation
http://lod.bco-dmo.org/id/dataset/996093
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: Brown, S. A., Arnosti, C., Ghobrial, S. (2026) Peptidase and glucosidase activities from bulk water incubations from waters taken aboard the R/V Thomas G. Thompson in the Southern Indian Ocean during the research cruise TN362 in November and December, 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-06 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/996093 [access date]
Plate Rates Bulk TN362 Dataset Description: Methods and Sampling: <p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>From the Niskin bottle, water was dispensed into smaller glass containers that were cleaned and pre-rinsed three times with water from the Niskin bottle prior to dispensing. This water was used to measure the activities of peptidases and glucosidases. A separate glass Duran bottle was filled with seawater from the Niskin bottle and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</p>
<p>Two substrates, alpha-glucose and beta-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. 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 uL seawater for experimental incubations; triplicate wells were filled with 200 uL 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 0-72 hours incubation time with a plate reader (TECAN infiniteF200; 360 nm excitation, 460 emission), with timepoints taken every 4-6 hours.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736772 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736772
onGoing
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
deployment
Station
latitude
longitude
date
depth_sequence
depth_actual
sample_type
Incubation_temp
unamended_amended
substrate
t1_rate
t1_sd
t2_rate
t2_sd
t3_rate
t3_sd
t4_rate
t4_sd
t5_rate
t5_sd
t6_rate
t6_sd
t7_rate
t7_sd
max_mean
max_sd
max_timepoint_id
avg_potential_rate
potential_sd
CTD
Niskin bottles
TECAN infiniteF200
theme
None, User defined
Cruise identfier
station
latitude
longitude
date
depth_comment
depth
sample type
incubation temperature
treatment
hydrolase activity
standard deviation
mean
time_point
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Niskin bottle
plate reader
instrument
BCO-DMO Standard Instruments
TN362
service
Deployment Activity
Indian Ocean
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.
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
https://osprey.bco-dmo.org/project/809975
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
<p><em>NSF Award Abstract:</em><br />
Marine dissolved organic matter (DOM) is one of the largest actively-cycling reservoirs of organic carbon on the planet, and thus a major component of the global carbon cycle. The high molecular weight (HMW) fraction of DOM is younger in age and more readily consumed by microbes than lower molecular weight (LMW) fractions of DOM, but the reasons for this difference in reactivity between HMW DOM and LMW DOM are unknown. Two factors may account for the greater reactivity of HMW DOM: (i) targeted uptake of HMW DOM by specific bacteria, a process the PI and her collaborators at the Max Planck Institute for Marine Microbiology (MPI) recently identified in surface ocean waters; and (ii) a greater tendency of HMW DOM to aggregate and form gels and particles, which can be colonized by bacteria that are well-equipped to breakdown organic matter. Scientists and students from the University of North Carolina (UNC) - Chapel Hill will collaborate with researchers at the MPI for Marine Microbiology (Bremen, Germany) to investigate this breakdown of HMW DOM by marine microbial communities. These investigations will include a field expedition in the North Atlantic, during which HMW DOM degradation rates and patterns will be compared in different water masses and under differing conditions of organic matter availability. DOM aggregation potential, and degradation rates of these aggregates, will also be assessed. Specialized microscopy will be used in order to pinpoint HMW DOM uptake mechanisms and rates. The work will be complemented by ongoing studies of specific bacteria that breakdown HMW DOM, their genes, and their proteins. Graduate as well as undergraduate students will participate as integral members of the research team in all aspects of the laboratory and field work; aspects of the project will also be integrated into classes the scientist teaches at UNC.</p>
<p>The existence of a size-reactivity continuum of DOM - observations and measurements showing that HMW DOM tends to be younger and more reactive than lower MW DOM - has been demonstrated in laboratory and field investigations in different parts of the ocean. A mechanistic explanation for the greater reactivity of HMW DOM has been lacking, however. This project will investigate the mechanisms and measure rates of HMW DOM degradation, focusing on identifying the actors and determining the factors that contribute to rapid cycling of HMW DOM. Collaborative work at UNC and MPI-Bremen recently identified a new mechanism of HMW substrate uptake common among pelagic marine bacteria: these bacteria rapidly bind, partially hydrolyze, and transport directly across the outer membrane large fragments of HMW substrates that can then be degraded within the periplasmic space, avoiding production of LMW DOM in the external environment. This mode of substrate processing has been termed selfish, since targeted HMW substrate uptake sequesters resources away from other members of microbial communities. Measurements and models thus must account for three modes of substrate utilization in the ocean: selfish, sharing (external hydrolysis, leading to low molecular weight products), and scavenging (uptake of low molecular weight hydrolysis products without production of extracellular enzymes). Using field studies as well as mesocosm experiments, the research team will investigate the circumstances and locations at which different modes of substrate uptake predominate. A second focal point of the project is to determine the aggregation potential and microbial degradation of aggregated HMW DOM. Preliminary studies have demonstrated that particle-associated microbial communities utilize a broader range of enzymatic capabilities than their free-living counterparts. These capabilities equip particle-associated communities to effectively target a broad range of complex substrates. The project will thus focus on two key aspects of HMW DOM - the abilities of specialized bacteria to selectively sequester HMW substrates, as well as the greater potential of HMW substrates to aggregate ? and will quantify these factors at different locations and depths in the ocean. The project will thereby provide a mechanistic underpinning for observations of the DOC size-reactivity continuum, an essential part of developing an overall mechanistic understanding of organic matter degradation in the ocean.</p>
Microbial DOC Degradation
largerWorkCitation
project
eng; USA
oceans
Indian Ocean
96.55
100.482
-41.646
-31.299
2018-11-09
2018-12-12
Northern Atlantic, Southern Indian Ocean, Svalbard
0
BCO-DMO catalogue of parameters from Peptidase and glucosidase activities from bulk water incubations from waters taken aboard the R/V Thomas G. Thompson in the Southern Indian Ocean during the research cruise TN362 in November and December, 2018
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/996106.rdf
Name: deployment
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/996107.rdf
Name: Station
Units: unitless
Description: <p>Station number 3, 6, 13, 18, or 31</p>
http://lod.bco-dmo.org/id/dataset-parameter/996108.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of sampling site, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/996110.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sampling site, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/996112.rdf
Name: date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/996113.rdf
Name: depth_sequence
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/996114.rdf
Name: depth_actual
Units: m
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/996116.rdf
Name: sample_type
Units: unitless
Description: <p>Sample from bulk water (bulk) or Large Volume incubation (LV)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996117.rdf
Name: Incubation_temp
Units: degrees Celsius
Description: <p>Temperature of incubation. RT = Room Temperature (~20 C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996118.rdf
Name: unamended_amended
Units: unitless
Description: <p>Whether high molecular weight organic matter was added or not; U for unamended.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996119.rdf
Name: substrate
Units: unitless
Description: <p>Substrates for measurement of enzymatic activities:</p>
<ul>
<li>a.glu= substrate to measure alpha glucosidase: 4-methylumbelliferyl-_-D-</li>
<li>b.glu=substrate to measure beta glucosidase: 4-methylumbelliferyl-_-D-</li>
<li>Leu=substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)</li>
<li>AAF= substrate to measure chymotrypsin activity: ala-ala-phe-MCA</li>
<li>AAPF=substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA</li>
<li>QAR=substrate to measure trypsin activity: Boc-gln-ala-arg-MCA</li>
<li>FSR=substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA</li>
</ul>
http://lod.bco-dmo.org/id/dataset-parameter/996120.rdf
Name: t1_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 6 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996121.rdf
Name: t1_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996122.rdf
Name: t2_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 12 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996123.rdf
Name: t2_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996124.rdf
Name: t3_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 18 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996125.rdf
Name: t3_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996126.rdf
Name: t4_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 24 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996127.rdf
Name: t4_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t4</p>
http://lod.bco-dmo.org/id/dataset-parameter/996128.rdf
Name: t5_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 36 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996129.rdf
Name: t5_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t5</p>
http://lod.bco-dmo.org/id/dataset-parameter/996130.rdf
Name: t6_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 48 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996131.rdf
Name: t6_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t6</p>
http://lod.bco-dmo.org/id/dataset-parameter/996132.rdf
Name: t7_rate
Units: nmol L-1 hr-1
Description: <p>Average of three plate replicates taken at ~ 72 hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/996133.rdf
Name: t7_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of hydrolysis rates for t7</p>
http://lod.bco-dmo.org/id/dataset-parameter/996134.rdf
Name: max_mean
Units: nmol L-1 hr-1
Description: <p>Maximum rate calculated from all timepoints</p>
http://lod.bco-dmo.org/id/dataset-parameter/996135.rdf
Name: max_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of maximum rate calculated from timepoints</p>
http://lod.bco-dmo.org/id/dataset-parameter/996136.rdf
Name: max_timepoint_id
Units: unitless
Description: <p>Time point at which maximum rate was calculated</p>
http://lod.bco-dmo.org/id/dataset-parameter/996137.rdf
Name: avg_potential_rate
Units: nmol L-1 hr-1
Description: <p>Average rate from all timepoints</p>
http://lod.bco-dmo.org/id/dataset-parameter/996138.rdf
Name: potential_sd
Units: nmol L-1 hr-1
Description: <p>Standard deviation of average rate from all timepoints</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
https://osprey.bco-dmo.org/dataset/996093/data/download
download
onLine
dataset
<p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>From the Niskin bottle, water was dispensed into smaller glass containers that were cleaned and pre-rinsed three times with water from the Niskin bottle prior to dispensing. This water was used to measure the activities of peptidases and glucosidases. A separate glass Duran bottle was filled with seawater from the Niskin bottle and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</p>
<p>Two substrates, alpha-glucose and beta-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. 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 uL seawater for experimental incubations; triplicate wells were filled with 200 uL 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 0-72 hours incubation time with a plate reader (TECAN infiniteF200; 360 nm excitation, 460 emission), with timepoints taken every 4-6 hours.</p>
Specified by the Principal Investigator(s)
<p>Hydrolysis of the substrates was measured as an increase in fluorescence as the fluorophore was hydrolyzed from the substrate over time as in Hoppe (1983) and Obayashi and Suzuki (2005).</p>
<p>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.&nbsp;Calculations followed the procedure outlined in the tutorial available in the associated GitHub repository (Hoarfrost et al., 2017).</p>
Specified by the Principal Investigator(s)
- Loaded CSV file "20251229_Plate_RatesBulk_Timepoint_TN362_BCO-DMO.csv" with header row 1; treated "", "nd", and "NA" as missing values; resource named by filename
- Converted date field from "%Y.%m.%d" format to ISO "%Y-%m-%d" date type
- Exported file as "996093_v1_plate_rates_bulk_water_tn362.csv"
Specified by BCO-DMO Data Managers
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
CTD
CTD
PI Supplied Instrument Name: CTD PI Supplied Instrument Description:Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD. 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 infiniteF200
TECAN infiniteF200
PI Supplied Instrument Name: TECAN infiniteF200 PI Supplied Instrument Description:Methods Description: Fluorescence was measured over 0-72 hours incubation time with a plate reader (TECAN infiniteF200; 360 nm excitation, 460 emission), with timepoints taken every 4-6 hours.
Instrument Description: TECAN infiniteF200; 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.
Cruise: TN362
TN362
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN362
Elisabeth Sikes
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel