http://lod.bco-dmo.org/id/dataset/988643
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
2025-11-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Detection of polysaccharide enzymatic hydrolysis using a novel detection method from waters taken aboard the R/V Endeavor in the Western North Atlantic (EN683 in May and June, 2022), and from a freshwater lake in North Carolina in 2025
2026-02-04
publication
2026-02-04
revision
BCO-DMO Linked Data URI
2026-02-04
creation
http://lod.bco-dmo.org/id/dataset/988643
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., DeMaesschalck, M., Arnosti, C., Ghobrial, S. (2026) Detection of polysaccharide enzymatic hydrolysis using a novel detection method from waters taken aboard the R/V Endeavor in the Western North Atlantic (EN683 in May and June, 2022), and from a freshwater lake in North Carolina in 2025. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-02-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/988643 [access date]
EN683 FLA-Bead Data and ULake Dataset Description: Methods and Sampling: <p><strong>FLA-laminarin linked beads preparation:</strong><br />
Fluorescently-labeled laminarin (FLA-laminarin) was synthesized using previously described methods (Arnosti 2003). Laminarin was used because it is commonly found throughout the surface water of the ocean (Becker et al. 2020). Subsequently, epoxy-activated beads (MC LAB) were covalently linked to lyophilized FLA-laminarin. One week prior to the cruise, beads were aliquoted into incubation vials to ensure a consistent starting number of beads in each vial. A bead slurry was prepared by mixing 1 volume of beads to 10 volumes of bicarbonate buffer. Then, 100 microliters (µL) of the bead slurry was aliquoted into 1.5-milliliter (mL) GC vials and stored at 4 degrees Celsius (°C) in the dark. Directly prior to the start of each experiment, the bicarbonate was removed, and the beads were washed using seawater or autoclaved seawater.</p>
<p><strong>Collection:</strong><br />
Seawater was collected from 13 stations in the western North Atlantic on R/V Endeavor cruise EN683. Water samples were taken at the depth of the deep chlorophyll maximum (determined via CTD; ca 35 meters (m) and 152m, respectively) and at the bottom, 4092m and 5305 m, respectively.</p>
<p>Twelve experiments used seawater that was collected from the ship's underway intake, located ~3 m below the surface, and one experiment used bottom water collected at 4100 m from a Niskin bottle at station 22-B. At each site, temperature and salinity parameters were recorded. For Sargassum mesocosm experiments, an acid-washed 50 mL Falcon tube was submerged into tanks in which Sargassum was incubating to collect surrounding seawater. For freshwater experiments, University Lake (North Carolina) water was collected on August 8th, 2025 from the University of North Carolina (UNC) rowing dock at 09:55. A separate glass Duran bottle was filled with seawater, Sargassum incubation water, or filtered (0.2-mirometer (μm) pore size) freshwater and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</p>
<p><strong>Incubation and measurement:</strong><br />
For seawater and Sargassum experiments, aliquoted beads were pre-washed, using either live or autoclaved seawater, before the start of each experiment. This pre-washing step was done to remove any leftover bicarbonate and reduce the potential salt shock effect on bacterial communities. After the pre-wash, the supernatant was removed, and 300 µL of fresh seawater was added to the vial and then gently mixed together. Once the beads settled, 70 µL of overlying liquid was measured on a mini-fluorimeter using the micro-cuvette adapter (Fig. 2). After measuring the fluorescence, the liquid was placed back into the corresponding vial it came from. Incubations were stored in the dark at room temperature; note that for Stn. 7B, the incubation was stored in the dark in a 4°C fridge, which was close to the in-situ temperature. The signal of the overlying solution was taken every 24 hours for 96 hours.</p>
<p>For freshwater experiments, beads were washed with bicarbonate buffer and kept suspended to maintain a homogeneous slurry. A 1 mL pipettor and a 1.25 mL pipette tip with approximately 5 millimeters (mm) of the tip cut off was used to maintain a homogeneous slurry and transfer 150 µL of bead slurry to triplicate 3 mL exetainer vials per incubation set. The bead slurry was mixed several times between each transfer. Reverse pipetting technique was used to improve precision. To each exetainer vial, 850 µL of either bicarbonate, bulk, 105 µm screened, or killed control water was added. A fourth vial per set containing only 1 mL of the incubation water was used as a background control. Vials were capped, and an initial (t0) measurement was taken. Additionally, vials were fitted with a 1/2 inch interior diameter (ID) rubber grommet just below the cap to keep vials securely and precisely positioned in the mini-fluorometer. Incubations were stored in the dark at room temperature. Measurements were taken at 0.75, 16.25, and 22.42 hrs, and ~ 2, 3, 4, 7, 10, 15, 20, 25, and 30 days.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2022952 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2022952
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
sample_date
sample_time
ISO_DateTime_Local
source
depth_actual
temperature
salinity
incubation_time
live1
live2
live3
kill1
kill2
kill3
live_avg
live_avg_std
kill_avg
kill_avg_std
Promega QuantiFluor -ST or Turner BioSystems TBS-380 mini-Fluorometers
Niskin bottle
ship's underway intake
theme
None, User defined
deployment number
station
latitude
longitude
date
time of day
ISO_DateTime_Local
sample description
depth
water temperature at measurement depth
salinity
incubation time or duration
fluorescence
featureType
BCO-DMO Standard Parameters
Fluorometer
Niskin bottle
Pump - Surface Underway Ship Intake
instrument
BCO-DMO Standard Instruments
EN683
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.
Substrate structural complexity and abundance control distinct mechanisms of microbially-driven carbon cycling in the ocean
https://osprey.bco-dmo.org/project/896822
Substrate structural complexity and abundance control distinct mechanisms of microbially-driven carbon cycling in the ocean
<p>Substrate Structural Complexity and Abundance Control Distinct Mechanisms of Microbially-Driven Carbon Cycling in the Ocean</p>
<p>Almost half of the organic carbon produced in the ocean is processed by bacteria. Bacteria use extracellular (outside the cell) enzymes to break down large organic molecules to small sizes that can be transported into their cells. It has recently been discovered that bacteria use extracellular enzymes in two ways: ‘selfish uptake’ and ‘external hydrolysis’. External hydrolysis releases low molecular weight products to the environment where they can be used by other organisms. ‘Selfish uptake’ releases little or no products. This research will determine the extent and location of ‘selfish uptake’ in ocean waters. This process affects the distribution of organic carbon in the ocean, the flow of small organic molecules to feed a wider range of bacteria, and the composition and dynamics of the bacterial community. Recent results show that ‘selfish’ bacteria are active in deep ocean waters, where they take up complex polysaccharides (sugars) that are not hydrolyzed externally. These results inspired a new model that links ‘selfish uptake’ and external hydrolysis to the amount and complexity of the organic matter that is used by bacteria. This project will test the model by describing the polysaccharide fraction of marine organic matter, and studying the relationships between organic matter abundance, structural complexity, and extracellular enzyme use. Graduate and undergraduate students will participate in the project as members of the research team in the field and in the laboratory.</p>
<p>This research will test the hypothesis that the mechanism of polysaccharide processing is related to the cost to a cell of producing the enzymes required for its hydrolysis, and the probability that a cell will receive sufficient return on investment for producing the enzymes. The conceptual model that will be tested suggests that external hydrolysis is favored when organic matter is abundant, or when enzyme production costs can be shared (e.g., on particles, in biofilms); selfish uptake would be a better strategy when high molecular weight (HMW) organic matter is scarce, and particularly when the HMW organic matter is very complex. This study will test this model by characterizing the structure of polysaccharide-containing components of dissolved organic matter (DOM) and particulate organic matter (POM) collected from the ocean, by determining the extent of selfish uptake and rates of external hydrolysis of different polysaccharides by natural microbial communities from the surface and the deep ocean, and by incubation experiments that control for the abundance of polysaccharides of different structural complexity. This project will be carried out in collaboration with colleagues at the Max Planck Institute for Marine Microbiology, whose expertise in carbohydrate chemistry and structural analyses, and in advanced microscopy and analysis of complex microbial communities, are central to the project.</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>
Substrate complexity and microbes
largerWorkCitation
project
eng; USA
oceans
Northern Atlantic
-79.0935
-53.8678
33.74341667
42.8701
2022-05-24
2025-08-11
Western North Atlantic
0
BCO-DMO catalogue of parameters from Detection of polysaccharide enzymatic hydrolysis using a novel detection method from waters taken aboard the R/V Endeavor in the Western North Atlantic (EN683 in May and June, 2022), and from a freshwater lake in North Carolina in 2025
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/993842.rdf
Name: deployment
Units: unitless
Description: <p>Cruise ID (EN683), or University Lake water (U.Lake)</p>
http://lod.bco-dmo.org/id/dataset-parameter/993843.rdf
Name: station
Units: unitless
Description: <p>Station number 21, 22, 23, Sargassum incubation, or crew dock at University Lake</p>
http://lod.bco-dmo.org/id/dataset-parameter/993844.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of sampling site, south is negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993845.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sampling site, west is negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993846.rdf
Name: sample_date
Units: unitless
Description: <p>Date of sample collection. </p>
http://lod.bco-dmo.org/id/dataset-parameter/993847.rdf
Name: sample_time
Units: unitless
Description: <p>Time of sample collection (local time), US Eastern Time (UTC-05:00)</p>
http://lod.bco-dmo.org/id/dataset-parameter/993848.rdf
Name: ISO_DateTime_Local
Units: unitless
Description: <p>Date and time of sample collection (local time) in ISO 8601 format</p>
http://lod.bco-dmo.org/id/dataset-parameter/993849.rdf
Name: source
Units: unitless
Description: <p>Source, one fo the following: Underway water from ship's intake ("intake"); cast for deep water ("cast-2"); Sargassum incubation tank-1 ("Tank1"); Bicarbonate, University Lake surface water ("surface"); University Lake surface water filtered ("surface_105um_filtered").</p>
http://lod.bco-dmo.org/id/dataset-parameter/993850.rdf
Name: depth_actual
Units: meters (m)
Description: <p>Actual depth at which water was collected. </p>
http://lod.bco-dmo.org/id/dataset-parameter/993851.rdf
Name: temperature
Units: degrees Celsius
Description: <p>Temperature of water sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993852.rdf
Name: salinity
Units: grams per liter (g/L)
Description: <p>Salinity of water sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993853.rdf
Name: incubation_time
Units: hours
Description: <p>The amount of incubation time that has elapsed at each timepoint in hours.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993854.rdf
Name: live1
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the live-1 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993855.rdf
Name: live2
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the live-2 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993856.rdf
Name: live3
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the live-3 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993857.rdf
Name: kill1
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the kill-1 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993858.rdf
Name: kill2
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the kill-2 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993859.rdf
Name: kill3
Units: fluorescence units
Description: <p>The fluorescence signal at given timepoint of the kill-3 replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993860.rdf
Name: live_avg
Units: fluorescence units
Description: <p>The average corrected fluorescence signal for all live replicates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993861.rdf
Name: live_avg_std
Units: fluorescence units
Description: <p>The standard deviation of the average corrected fluorescence signal for all live replicates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993862.rdf
Name: kill_avg
Units: fluorescence units
Description: <p>The average kill corrected fluorescence signal for all kill replicates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/993863.rdf
Name: kill_avg_std
Units: fluorescence units
Description: <p>The standard deviation of the average kill corrected fluorescence signal for all kill 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/988643/data/download
download
onLine
dataset
<p><strong>FLA-laminarin linked beads preparation:</strong><br />
Fluorescently-labeled laminarin (FLA-laminarin) was synthesized using previously described methods (Arnosti 2003). Laminarin was used because it is commonly found throughout the surface water of the ocean (Becker et al. 2020). Subsequently, epoxy-activated beads (MC LAB) were covalently linked to lyophilized FLA-laminarin. One week prior to the cruise, beads were aliquoted into incubation vials to ensure a consistent starting number of beads in each vial. A bead slurry was prepared by mixing 1 volume of beads to 10 volumes of bicarbonate buffer. Then, 100 microliters (µL) of the bead slurry was aliquoted into 1.5-milliliter (mL) GC vials and stored at 4 degrees Celsius (°C) in the dark. Directly prior to the start of each experiment, the bicarbonate was removed, and the beads were washed using seawater or autoclaved seawater.</p>
<p><strong>Collection:</strong><br />
Seawater was collected from 13 stations in the western North Atlantic on R/V Endeavor cruise EN683. Water samples were taken at the depth of the deep chlorophyll maximum (determined via CTD; ca 35 meters (m) and 152m, respectively) and at the bottom, 4092m and 5305 m, respectively.</p>
<p>Twelve experiments used seawater that was collected from the ship's underway intake, located ~3 m below the surface, and one experiment used bottom water collected at 4100 m from a Niskin bottle at station 22-B. At each site, temperature and salinity parameters were recorded. For Sargassum mesocosm experiments, an acid-washed 50 mL Falcon tube was submerged into tanks in which Sargassum was incubating to collect surrounding seawater. For freshwater experiments, University Lake (North Carolina) water was collected on August 8th, 2025 from the University of North Carolina (UNC) rowing dock at 09:55. A separate glass Duran bottle was filled with seawater, Sargassum incubation water, or filtered (0.2-mirometer (μm) pore size) freshwater and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements.</p>
<p><strong>Incubation and measurement:</strong><br />
For seawater and Sargassum experiments, aliquoted beads were pre-washed, using either live or autoclaved seawater, before the start of each experiment. This pre-washing step was done to remove any leftover bicarbonate and reduce the potential salt shock effect on bacterial communities. After the pre-wash, the supernatant was removed, and 300 µL of fresh seawater was added to the vial and then gently mixed together. Once the beads settled, 70 µL of overlying liquid was measured on a mini-fluorimeter using the micro-cuvette adapter (Fig. 2). After measuring the fluorescence, the liquid was placed back into the corresponding vial it came from. Incubations were stored in the dark at room temperature; note that for Stn. 7B, the incubation was stored in the dark in a 4°C fridge, which was close to the in-situ temperature. The signal of the overlying solution was taken every 24 hours for 96 hours.</p>
<p>For freshwater experiments, beads were washed with bicarbonate buffer and kept suspended to maintain a homogeneous slurry. A 1 mL pipettor and a 1.25 mL pipette tip with approximately 5 millimeters (mm) of the tip cut off was used to maintain a homogeneous slurry and transfer 150 µL of bead slurry to triplicate 3 mL exetainer vials per incubation set. The bead slurry was mixed several times between each transfer. Reverse pipetting technique was used to improve precision. To each exetainer vial, 850 µL of either bicarbonate, bulk, 105 µm screened, or killed control water was added. A fourth vial per set containing only 1 mL of the incubation water was used as a background control. Vials were capped, and an initial (t0) measurement was taken. Additionally, vials were fitted with a 1/2 inch interior diameter (ID) rubber grommet just below the cap to keep vials securely and precisely positioned in the mini-fluorometer. Incubations were stored in the dark at room temperature. Measurements were taken at 0.75, 16.25, and 22.42 hrs, and ~ 2, 3, 4, 7, 10, 15, 20, 25, and 30 days.</p>
Specified by the Principal Investigator(s)
<p>Data were processed using Excel.</p>
Specified by the Principal Investigator(s)
- Imported original file "20251017_EN683_Bead_Data_STN_21_22_23_and_Ulake_BCO-DMO.csv" into the BCO-DMO system.
- Created local date-time column in ISO 8601 format.
- Replaced non-standard character "µ" with "u" in "source" column.
- Saved the final file as "988643_v1_en683_bead_data_ulake.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
Promega QuantiFluor -ST or Turner BioSystems TBS-380 mini-Fluorometers
Promega QuantiFluor -ST or Turner BioSystems TBS-380 mini-Fluorometers
PI Supplied Instrument Name: Promega QuantiFluor -ST or Turner BioSystems TBS-380 mini-Fluorometers 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/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle 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/
ship's underway intake
ship's underway intake
PI Supplied Instrument Name: ship's underway intake Instrument Name: Pump - Surface Underway Ship Intake Instrument Short Name:Pump-Ship Intake Instrument Description: The 'Pump-underway ship intake' system indicates that samples are from the ship's clean water intake pump. This is essentially a surface water sample from a source of uncontaminated near-surface (commonly 3 to 7 m) seawater that can be pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the underway supply that may also be referred to as the non-toxic supply. Ideally the data contributor has specified the depth in the ship's hull at which the pump is mounted. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/31/
Cruise: EN683
EN683
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN683
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