http://lod.bco-dmo.org/id/dataset/985780
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
2025-10-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Measurement of polysaccharide hydrolase activities from mesocosm incubations from water samples taken aboard R/V Endeavor cruise EN638 in the Western North Atlantic in May 2019
2025-10-24
publication
2025-10-24
revision
BCO-DMO Linked Data URI
2025-10-24
creation
http://lod.bco-dmo.org/id/dataset/985780
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: Lloyd, C., Arnosti, C., Brown, S. A., Ghobrial, S. (2025) Measurement of polysaccharide hydrolase activities from mesocosm incubations from water samples taken aboard R/V Endeavor cruise EN638 in the Western North Atlantic in May 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/985780 [access date]
EN638 LV FLA Rates all Dataset Description: Methods and Sampling: <p>Samples were taken from incubation experiments of deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom waters aboard R/V Endeavor (EN638), May 2019 in the Northern Atlantic. Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), 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. Four carboys were filled at each depth from bottom water, water from the depth at which oxygen showed a minimum, and DCM&nbsp;water, according to the CTD. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of High molecular weight (HMW) <em>Thalassiosira</em>; unamended single carboys were used for controls.&nbsp;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 at approximately 3 d, 5 or 7 d, 10 d, 15 d, and 30 d for multiple assays including: bacterial production using 3H-Leucine, dissolved organic carbon (DOC), nutrients, bacterial cell counts, peptidase and glucosidase activity measurements in addition to&nbsp;the potential of the seawater microbial community to hydrolyze six high-molecular-weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan).</p>
<p>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.&nbsp;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.&nbsp;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 in situ temperature as possible.</p>
<p>Subsamples of the incubations were collected at time zero, and at a sequence of subsequent time points. 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 analysis.</p>
<p>Gel permeation chromatography with fluorescence detection was used to measure the hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products after the method of Arnosti (1996, 2003). &nbsp;In short, the subsample was injected onto a series of columns consisting of a 21 cm column of G50 and a 19 cm column of G75 Sephadex gel for adequate molecular size separation. The fluorescence of the column effluent was measured at excitation and emission wavelengths of 490 and 530 nm, respectively.</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
ISO_DateTime_UTC
cast_number
depth_sequence
depth_m
sample_type
unamended_amended
substrate
timepoint_number
time_elapsed
rate_x
rate_1
rate_2
rate_3
mean_rate
sd_rate
kcrate_x
kcrate_1
kcrate_2
kcrate_3
mean_kcrate
sd_kcrate
CTD
HPLC systems with Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
Niskin bottles
theme
None, User defined
Cruise identfier
station
latitude
longitude
Date and time
cast
depth
sample type
treatment
sample description
time_point
time_elapsed
hydrolase activity
mean
standard deviation
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
High-Performance Liquid Chromatograph
Niskin bottle
instrument
BCO-DMO Standard Instruments
EN638
service
Deployment Activity
Northern Atlantic
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
biota
oceans
Northern Atlantic
-72.0021
-53.3949
34.6369
42.83954
2019-05-17
2019-06-26
Northern Atlantic, Southern Indian Ocean, Svalbard
0
BCO-DMO catalogue of parameters from Measurement of polysaccharide hydrolase activities from mesocosm incubations from water samples taken aboard R/V Endeavor cruise EN638 in the Western North Atlantic in May 2019
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/987907.rdf
Name: Deployment
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/987908.rdf
Name: Station
Units: unitless
Description: <p>Station number for cruise 18, 19, 20</p>
http://lod.bco-dmo.org/id/dataset-parameter/987909.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/987911.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/987913.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of sample collection in UTC</p>
http://lod.bco-dmo.org/id/dataset-parameter/987914.rdf
Name: cast_number
Units: unitless
Description: <p>Cast number (refers to cast of CTD/Niskin bottles on cruise)</p>
http://lod.bco-dmo.org/id/dataset-parameter/987915.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/987916.rdf
Name: depth_m
Units: meters
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/987918.rdf
Name: sample_type
Units: unitless
Description: <p>Sample from bulk water (Bulk) or Large Volume (LV) incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/987919.rdf
Name: unamended_amended
Units: unitless
Description: <p>Refers to whether high molecular weight thalassiosira weissflogii extract was added or not; A, B, C refers to incubation depth, and the following number corresponds to incubation replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/987920.rdf
Name: substrate
Units: unitless
Description: <p>Polysaccharide used for incubation: ara = arabinogalactan, chn = chondroitin sulfate, fuc = fucoidan, lam = laminarin, pul = pullulan, xyl = xylan</p>
http://lod.bco-dmo.org/id/dataset-parameter/987921.rdf
Name: timepoint_number
Units: unitless
Description: <p>Timepoint number of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/987922.rdf
Name: time_elapsed
Units: hours
Description: <p>Incubation time elapsed at sample collection in hours</p>
http://lod.bco-dmo.org/id/dataset-parameter/987923.rdf
Name: rate_x
Units: nM*hr-1
Description: <p>Hydrolysis rate of killed control incubation at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987924.rdf
Name: rate_1
Units: nM*hr-1
Description: <p>Hydrolysis rate of incubation replicate #1 at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987925.rdf
Name: rate_2
Units: nM*hr-1
Description: <p>Hydrolysis rate of incubation replicate #2 at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987926.rdf
Name: rate_3
Units: nM*hr-1
Description: <p>Hydrolysis rate of incubation replicate #3 at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987927.rdf
Name: mean_rate
Units: nM*hr-1
Description: <p>Mean hydrolysis rate of incubation replicates at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987928.rdf
Name: sd_rate
Units: nM*hr-1
Description: <p>Standard deviation of mean hydrolysis rates at subsampled timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/987929.rdf
Name: kcrate_x
Units: nM*hr-1
Description: <p>Kill control corrected hydrolysis rate of killed control incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/987930.rdf
Name: kcrate_1
Units: nM*hr-1
Description: <p>Kill control corrected hydrolysis rate of incubation replicate #1</p>
http://lod.bco-dmo.org/id/dataset-parameter/987931.rdf
Name: kcrate_2
Units: nM*hr-1
Description: <p>Kill control corrected hydrolysis rate of incubation replicate #2</p>
http://lod.bco-dmo.org/id/dataset-parameter/987932.rdf
Name: kcrate_3
Units: nM*hr-1
Description: <p>Kill control corrected hydrolysis rate of incubation replicate #3</p>
http://lod.bco-dmo.org/id/dataset-parameter/987933.rdf
Name: mean_kcrate
Units: nM*hr-1
Description: <p>Mean hydrolysis rate of kill control corrected incubation replicates</p>
http://lod.bco-dmo.org/id/dataset-parameter/987934.rdf
Name: sd_kcrate
Units: nM*hr-1
Description: <p>Standard deviation of mean hydrolysis rate of kill control corrected incubation replicates</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/985780/data/download
download
onLine
dataset
<p>Samples were taken from incubation experiments of deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom waters aboard R/V Endeavor (EN638), May 2019 in the Northern Atlantic. Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD.</p>
<p>For mesocosm (large volume) incubation experiments (referred to as “LV” incubations), 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. Four carboys were filled at each depth from bottom water, water from the depth at which oxygen showed a minimum, and DCM&nbsp;water, according to the CTD. Triplicate 20L carboys were amended with ca. 500 mg (exact mass was recorded for each addition) of High molecular weight (HMW) <em>Thalassiosira</em>; unamended single carboys were used for controls.&nbsp;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 at approximately 3 d, 5 or 7 d, 10 d, 15 d, and 30 d for multiple assays including: bacterial production using 3H-Leucine, dissolved organic carbon (DOC), nutrients, bacterial cell counts, peptidase and glucosidase activity measurements in addition to&nbsp;the potential of the seawater microbial community to hydrolyze six high-molecular-weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan).</p>
<p>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.&nbsp;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.&nbsp;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 in situ temperature as possible.</p>
<p>Subsamples of the incubations were collected at time zero, and at a sequence of subsequent time points. 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 analysis.</p>
<p>Gel permeation chromatography with fluorescence detection was used to measure the hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products after the method of Arnosti (1996, 2003). &nbsp;In short, the subsample was injected onto a series of columns consisting of a 21 cm column of G50 and a 19 cm column of G75 Sephadex gel for adequate molecular size separation. The fluorescence of the column effluent was measured at excitation and emission wavelengths of 490 and 530 nm, respectively.</p>
Specified by the Principal Investigator(s)
<p>Hydrolysis rates were calculated from the change in molecular weight distribution of the substrate over time, as described in detail in Arnosti (2003). Scripts to calculate hydrolysis rates are available in the associated Github repository (Hoarfrost, 2017).</p>
Specified by the Principal Investigator(s)
- Imported "20250718_EN638_LV_FLA_Rates_all_csv.csv" into the BCO-DMO system
- Converted "time_sampled" into ISO UTC datetime format
- Removed "time_sampled" as redundant
- Removed units and periods from parameter names
- Exported file as "985780_v1_en638_large_vol_fla_rates_all.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/
HPLC systems with Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
HPLC systems with Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
PI Supplied Instrument Name: HPLC systems with Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440) PI Supplied Instrument Description:HPLC systems with Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
Gel permeation chromatography with fluorescence detection was used to measure the hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products after the method of Arnosti [1996, 2003]. Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
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/
Cruise: EN638
EN638
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN638
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