http://lod.bco-dmo.org/id/dataset/963382
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
2025-05-31
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Polysaccharide Hydrolase activities in Danish coastal seawater and sediments under varying hydrostatic pressures on samples collected in September 2023
2025-06-10
publication
2025-06-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-10
publication
https://doi.org/10.26008/1912/bco-dmo.963382.1
Carol Arnosti
University of North Carolina at Chapel Hill
principalInvestigator
Chad Lloyd
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., Ghobrial, S., Arnosti, C. (2025) Polysaccharide Hydrolase activities in Danish coastal seawater and sediments under varying hydrostatic pressures on samples collected in September 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.963382.1 [access date]
Polysaccharide Hydrolase Activities under Varying Hydrostatic Pressures near Helsingor in 2023 Dataset Description: Methods and Sampling: <div>Sample water for incubation and filtration was collected via Niskin bottles mounted on a rosette, equipped with a CTD,&nbsp;as part of a routine collection at a coastal station off the coast of Helsingor, Denmark in September, 2023, aboard the R/V Ophelia.</div>
<div>&nbsp;</div>
<div>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.</div>
<div>&nbsp;</div>
<div>For some of the samples (i.e., amended samples), they were amended with high-molecular-weight organic matter extracted from freeze-dried <em>Thalassiosira weisflogii</em> (following Balmonte et al., 2019) to enhance enzymatic activity. Some of these samples were either immediately pressurized after polysaccharide addition, or incubated for 7 days prior to adding polysaccharide and pressurizing. A subset of this 7-day amended seawater was filtered (0.2 µm) to obtain the dissolved enzyme fraction, and incubated with polysaccharides and pressurized to different pressures.&nbsp;</div>
<div>&nbsp;</div>
<div>Incubations were sub-sampled at different timepoints.&nbsp;&nbsp;</div>
<div>&nbsp;</div>
<div>The hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products was measured using gel permeation chromatography with fluorescence detection, after the method of Arnosti [1996, 2003]. 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. The fluorescence of the column effluent was measured at excitation and emission wavelengths of 490 and 530 nm, respectively.</div>
<div>&nbsp;</div>
<div>Subsamples were run on a gel permeation chromatography instrument to separate out size classes of fluorescently-labeled polysaccharides. Hydrolysis is calculated as a change in the size distribution of polysaccharide with time.</div>
<div>&nbsp;</div>
<div>
<p>Polysaccharide used for incubation:</p>
<ul>
<li>ara = arabinogalactan</li>
<li>chn = chondroitin sulfate</li>
<li>fuc = fucoidan</li>
<li>lam = laminarin</li>
<li>man = mannan</li>
<li>pul = pullulan</li>
<li>xyl = xylan</li>
</ul>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2241720 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2241720
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
Chad Lloyd
University of North Carolina at Chapel Hill
cclloyd@unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
latitude
longitude
ISO_DateTime_UTC
date
time_local_CEST
depth_actual
sample_type
in_situ_T
in_situ_S
incubation_T
unamended_amended
pressure
substrate
timepoint_number
timepoint_days
rate_x_kc
rate_1_kc
rate_2_kc
rate_3_kc
rate_mean_kc
rate_sd_kc
CTD
Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
High-Performance Liquid Chromatograph
Niskin bottle
theme
None, User defined
latitude
longitude
ISO_DateTime_UTC
date
time_local
depth
sample description
temperature of sample or a generic measurement (not in-situ water temp)
salinity from CTD
water pressure
time_point
time_elapsed
hydrolase activity
featureType
BCO-DMO Standard Parameters
CTD - profiler
Fluorometer
Gel Permeation Chromatograph
Niskin bottle
instrument
BCO-DMO Standard Instruments
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.
Collaborative Research: Pressure effects on microbially-catalyzed organic matter degradation in the deep ocean
https://osprey.bco-dmo.org/project/896812
Collaborative Research: Pressure effects on microbially-catalyzed organic matter degradation in the deep ocean
<p><em>NSF Award Abstract:</em><br />
Microbes are important players in the carbon cycle in the ocean. These organisms consume organic carbon and produce carbon dioxide in marine systems. Because the average depth of the ocean is 4000 m, microbes must work at high pressures typical of the deep ocean (>1000 m). Although high pressure is known to affect marine microbes, their carbon cycling activities have mostly been measured at surface ocean pressures. As a result, it remains unknown how closely these measurements reflect the activities of deep-sea microbes at high pressures. As a result of collaborations with scientists in Denmark and Germany, this project will be able to use special equipment to investigate the effects of high pressures on marine microbes and their carbon cycling activities. This work is necessary to quantify rates of carbon cycling and identify the microbes involved, especially in deep waters. The project will provide training for diverse undergraduate and graduate students, and a postdoc who will conduct novel research in the U.S., Denmark, and Germany, both at sea and in the lab. The scientists will also teach middle school students about the role of microbes in the carbon cycle and pressure effects on life in the ocean. The project will provide internships for high school students, focusing on first-generation students who would like to go to college. This work may aid in future efforts to identify enzymes that function well under high pressure.</p>
<p>Heterotrophic microbes (e.g., bacteria and archaea) are found throughout the ocean. Their biogeochemical functions help determine the rates and locations at which carbon and nutrients are regenerated, as well as the extent to which organic matter is preserved. Although research has shown that pressure profoundly affects the activities of marine microbes, most investigations of microbial communities of the deep sea are conducted at atmospheric pressure, due to the limited availability of specialized equipment. In collaboration with the Danish Center for Hadal Research at the University of Southern Denmark, this study will identify the effects of pressure on microbial communities and their extracellular enzymes of pressures characteristic of bathy- and abyssopelagic depths. At sea and in the lab, the scientific team will compare the effects of depressurization on the activities of enzymes produced by microbial communities of the deep ocean, as well as the effects of high pressure on surface-water derived enzymes and communities. Fieldwork will take place in Danish coastal waters, well as in the open North Atlantic and Pacific Oceans. Using pressurization systems and in situ incubations, this study will measure hydrolysis rates of peptides and polysaccharides, two of the major classes of marine organic matter. Project activities will also focus on developing the means to measure enzyme activities in situ in the deep ocean. In collaboration with colleagues from the Max Planck Institute for Marine Microbiology in Germany, this proect will additionally investigate whether pressure affects the selfish uptake of polysaccharides. These studies will provide new insight into understudied but key factors that help determine the fate of organic matter in the deep ocean.</p>
<p>This project is funded by the Biological and Chemical Oceanography Programs.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Pressure effects on microbes
largerWorkCitation
project
eng; USA
biota
oceans
12.685
12.685
55.975
55.975
2023-09-26
2023-09-26
Western North Atlantic, hadal depths of the Pacific
0
BCO-DMO catalogue of parameters from Polysaccharide Hydrolase activities in Danish coastal seawater and sediments under varying hydrostatic pressures on samples collected in September 2023
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/963473.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of sampling site, Positve is North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963474.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sampling site, Positive is East.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963475.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Datetime of collection in ISO format, UTC.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963476.rdf
Name: date
Units: unitless
Description: <p>Date of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963477.rdf
Name: time_local_CEST
Units: unitless
Description: <p>Time of sample collection in Central European Summer Time (CEST).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963478.rdf
Name: depth_actual
Units: m
Description: <p>Depth where sample was collected. Depth of water column was 26 m.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963479.rdf
Name: sample_type
Units: unitless
Description: <p>The type of sample, whether it was incubated using water from the bulk water column, sediments, amended with Thallasiosira weissflogii for 0 days (LV_day0), amended with Thallasiosira weissflogii for 7 days (LV_day7), or dissolved enzymes (<0.2 µm) after 7 days amended with Thallasiosira weissflogii.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963480.rdf
Name: in_situ_T
Units: degrees Celsius
Description: <p>Temperature of the samples in-situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963481.rdf
Name: in_situ_S
Units: psu
Description: <p>CTD salinity measurements of the samples in-situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963482.rdf
Name: incubation_T
Units: degrees Celsius
Description: <p>Temperature the samples were incubated at for enzyme activity measurements.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963483.rdf
Name: unamended_amended
Units: unitless
Description: <p>Whether the sample was amended with <em>Thalassiosira weisflogii</em> or not.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963484.rdf
Name: pressure
Units: MPa
Description: <p>What pressure the incubation was pressurized to.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963485.rdf
Name: substrate
Units: unitless
Description: <p>Polysaccharide used for incubation: ara = arabinogalactan, chn = chondroitin sulfate, fuc = fucoidan, lam = laminarin, man = mannan, pul = pullulan, xyl = xylan</p>
http://lod.bco-dmo.org/id/dataset-parameter/963486.rdf
Name: timepoint_number
Units: unitless
Description: <p>The timepoint number sampled for each incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963487.rdf
Name: timepoint_days
Units: days
Description: <p>The amount of time that has elapsed at each timepoint.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963488.rdf
Name: rate_x_kc
Units: nmol L-1 hr-1
Description: <p>The kill-corrected hydrolysis rate for the kill-control (i.e., ratekc - ratekc).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963489.rdf
Name: rate_1_kc
Units: nmol L-1 hr-1
Description: <p>The kill-corrected hydrolysis rate for the first replicate (i.e., raterep1 - ratekc).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963490.rdf
Name: rate_2_kc
Units: nmol L-1 hr-1
Description: <p>The kill-corrected hydrolysis rate for the second replicate (i.e., raterep2 - ratekc).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963491.rdf
Name: rate_3_kc
Units: nmol L-1 hr-1
Description: <p>The kill-corrected hydrolysis rate for the third replicate (i.e., raterep3 - ratekc).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963492.rdf
Name: rate_mean_kc
Units: nmol L-1 hr-1
Description: <p>The average kill-corrected hydrolysis rate for all replicates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963493.rdf
Name: rate_sd_kc
Units: nmol L-1 hr-1
Description: <p>The standard deviation of the kill-corrected hydrolysis rates for all 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
28089
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/3a76d3ab-faa7-4571-9c87-25c454c841af/content
download
https://doi.org/10.26008/1912/bco-dmo.963382.1
download
onLine
dataset
<div>Sample water for incubation and filtration was collected via Niskin bottles mounted on a rosette, equipped with a CTD,&nbsp;as part of a routine collection at a coastal station off the coast of Helsingor, Denmark in September, 2023, aboard the R/V Ophelia.</div>
<div>&nbsp;</div>
<div>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.</div>
<div>&nbsp;</div>
<div>For some of the samples (i.e., amended samples), they were amended with high-molecular-weight organic matter extracted from freeze-dried <em>Thalassiosira weisflogii</em> (following Balmonte et al., 2019) to enhance enzymatic activity. Some of these samples were either immediately pressurized after polysaccharide addition, or incubated for 7 days prior to adding polysaccharide and pressurizing. A subset of this 7-day amended seawater was filtered (0.2 µm) to obtain the dissolved enzyme fraction, and incubated with polysaccharides and pressurized to different pressures.&nbsp;</div>
<div>&nbsp;</div>
<div>Incubations were sub-sampled at different timepoints.&nbsp;&nbsp;</div>
<div>&nbsp;</div>
<div>The hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products was measured using gel permeation chromatography with fluorescence detection, after the method of Arnosti [1996, 2003]. 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. The fluorescence of the column effluent was measured at excitation and emission wavelengths of 490 and 530 nm, respectively.</div>
<div>&nbsp;</div>
<div>Subsamples were run on a gel permeation chromatography instrument to separate out size classes of fluorescently-labeled polysaccharides. Hydrolysis is calculated as a change in the size distribution of polysaccharide with time.</div>
<div>&nbsp;</div>
<div>
<p>Polysaccharide used for incubation:</p>
<ul>
<li>ara = arabinogalactan</li>
<li>chn = chondroitin sulfate</li>
<li>fuc = fucoidan</li>
<li>lam = laminarin</li>
<li>man = mannan</li>
<li>pul = pullulan</li>
<li>xyl = xylan</li>
</ul>
</div>
Specified by the Principal Investigator(s)
<div>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; Obayashi and Suzuki, 2005].</div>
<div>&nbsp;</div>
<div>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 (ahoarfrost, 2025).</div>
<div>&nbsp;</div>
Specified by the Principal Investigator(s)
- Imported "20250116_FlaRates_HELS_All_FINAL.csv" into the BCO-DMO system
- Replaced ammended with amended in all fields and parameter names
- Replaced all time values at submitter's request from 3:50 to 9:50 local time
- Converted "date" to YYYY-MM-DD format
- Added additional ISO_DateTime_UTC field using local time and date
- Renamed "time" to "time_local_CEST" to indicate timezone
- Exported file as "963382_v1_polysaccharide_hydrolase.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 using a Niskin bottle and salinity values are from the CTD. 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/
Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440)
PI Supplied Instrument Name: Hitachi fluorescence detectors (L-7485, L-2485, Chromaster - 5440) PI Supplied Instrument Description: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; Obayashi and Suzuki, 2005]. 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/
High-Performance Liquid Chromatograph
High-Performance Liquid Chromatograph
PI Supplied Instrument Name: High-Performance Liquid Chromatograph PI Supplied Instrument Description:The hydrolysis of high molecular weight substrate to lower molecular weight hydrolysis products was measured using gel permeation chromatography with fluorescence detection, after the method of Arnosti [1996, 2003]. 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. The fluorescence of the column effluent was measured at excitation and emission wavelengths of 490 and 530 nm, respectively.
Subsamples were run on a gel permeation chromatography instrument to separate out size classes of fluorescently-labeled polysaccharides. Hydrolysis is calculated as a change in the size distribution of polysaccharide with time. Instrument Name: Gel Permeation Chromatograph Instrument Short Name:GPC Instrument Description: Instruments that separate components in aqueous or organic solution based on molecular size generally for molecular weight determination. Gel permeation chromatography (GPC) is a type of size exclusion chromatography (SEC), that separates analytes on the basis of size.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Water was collected using a Niskin bottle and salinity values are from the 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/