http://lod.bco-dmo.org/id/dataset/985786
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
2025-10-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Carbohydrate microarray (epitope) analyses of POM-derived carbohydrates in the Western North Atlantic Ocean in May 2019
2025-10-03
publication
2025-10-03
revision
BCO-DMO Linked Data URI
2025-10-03
creation
http://lod.bco-dmo.org/id/dataset/985786
Carol Arnosti
University of North Carolina at Chapel Hill
principalInvestigator
Chad Lloyd
University of North Carolina at Chapel Hill
principalInvestigator
Silvia Vidal
Max Planck Institute for Marine Microbiology
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., Vidal, S., Arnosti, C., Ghobrial, S. (2025) Carbohydrate microarray (epitope) analyses of POM-derived carbohydrates in the Western North Atlantic Ocean in May 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/985786 [access date]
Carb microarray analysis Atlantic 2019 Dataset Description: Methods and Sampling: <p><strong>Collection</strong></p>
<p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD in the western North Atlantic Ocean aboard R/V Endeavor (EN638) during May 2019.&nbsp;Seawater was transferred to carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle.</p>
<p>Particulate organic matter (POM) was harvested by filtering between 5-15 liters of seawater through a 47-mm pre-combusted (400℃ for 6 hours) glass fiber filter (GF/F; nominal pore size 0.7 μm; for volumes filtered at each depth and station, see the dataset). Filers were stored at -80C until further analysis. &nbsp;The same filter was used for both particulate organic carbon (POC) measurements and monosaccharide composition analysis. &nbsp;&nbsp;</p>
<p><strong>Analysis</strong></p>
<p><em>Polysaccharide extraction for microarray analyses of POM</em></p>
<p>POM samples were prepared for polysaccharide analysis according to Vidal-Melgosa et al. (2021). Polysaccharides were sequentially extracted from four filter piece punches (11.2 mm diameter) from GF/F filters. The samples were first extracted with autoclaved MilliQ water, followed by 50 mM EDTA, and finally 4 M NaOH with 0.1% NaBH<sub>4</sub>. The supernatant containing extracted polysaccharides was collected from each of the sequential steps and stored at 4 °C.</p>
<p><em>Carbohydrate microarray analysis to determine structural complexity of POM</em></p>
<p>The polysaccharides extracted as described above were analyzed following Vidal-Melgosa et al. (2021). In brief, the polysaccharide extracts were first diluted in printing buffer (55.2% glycerol, 44% water, 0.8% Triton X-100), and then printed on 0.45 µm pore size nitrocellulose membrane (Whatman) using a microarray robot (Sprint, Arrayjet, Roslin, UK) at 20 °C and 50% humidity. The membranes were probed with one of 9 monoclonal antibodies, washed multiple times, and probed with secondary antibodies (anti-rat, anti-mouse, or anti-His tag) conjugated to alkaline phosphatase for 2 hours. The arrays were developed using 5-bromo-4-chloro-3-indolyphosphate and nitro blue tetrazolium in alkaline phosphatase buffer (100 mM NaCl, 5 mM MgCl<sub>2</sub>, 100 mM Tris-HCl, pH 9.5). The microarrays were scanned and signal intensity was acquired using the software Array-Pro Analyzer 6.3 (Media Cybernetics). Signals were normalized among samples; higher signals correspond to a higher abundance of a given polysaccharide epitope. Note that the carbohydrate microarray data are only semiquantitative; while comparisons can be made for the abundance of a given epitope between stations and depths, the signal intensity cannot be used to compare signals of different epitopes.</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
Chad Lloyd
University of North Carolina at Chapel Hill
cclloyd@unc.edu
pointOfContact
Silvia Vidal
Max Planck Institute for Marine Microbiology
svidal@mpi-bremen.de
pointOfContact
asNeeded
Dataset Version: 1
Unknown
deployment
station
latitude
longitude
ISO_DateTime_Local
ISO_DateTime_UTC
cast_number
depth_sequence
depth_actual
POM_L_filtered
epitope
H2O
EDTA
NaOH
CTD
Array-Pro Analyzer 6.3 (Media Cybernetics)
Niskin bottles
theme
None, User defined
Cruise identfier
station
latitude
longitude
ISO_DateTime_Local
ISO_DateTime_UTC
cast
depth
volume of water filtered
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
microarray scanner
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
-75.67819
-53.3949
34.50102
42.83954
2019-05-14
2019-05-25
Northern Atlantic, Southern Indian Ocean, Svalbard
0
BCO-DMO catalogue of parameters from Carbohydrate microarray (epitope) analyses of POM-derived carbohydrates in the Western North Atlantic Ocean 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/988161.rdf
Name: deployment
Units: unitless
Description: <p>Cruise ID on R/V Endeavor</p>
http://lod.bco-dmo.org/id/dataset-parameter/988162.rdf
Name: station
Units: unitless
Description: <p>Cruise station number (17, 18, 19, 20)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988163.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/988165.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/988167.rdf
Name: ISO_DateTime_Local
Units: unitless
Description: <p>Datetime of sample collection in ISO format, US Eastern Time (ET)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988168.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Datetime of sample collection in ISO format, UTC</p>
http://lod.bco-dmo.org/id/dataset-parameter/988170.rdf
Name: cast_number
Units: unitless
Description: <p>Cast number at station (refers to cast of CTD/Niskin bottles on cruise at each station)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988171.rdf
Name: depth_sequence
Units: unitless
Description: <p>Sequence of depths sampled (d1 is surface; higher numbers at greater depths; d2 is DCM = deep chlorophyll maximum as indicated by chlorophyll-a detection via CTD, etc.)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988172.rdf
Name: depth_actual
Units: meters
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/988174.rdf
Name: POM_L_filtered
Units: Liters
Description: <p>The amount of seawater filtered (liters) for carbohydrate microarray (epitope) analyses of POM-derived carbohydrates</p>
http://lod.bco-dmo.org/id/dataset-parameter/988175.rdf
Name: epitope
Units: unitless
Description: <p>The specific polysaccharide epitope detected for each sample. Note these are relative to the specific antibodies; therefore, you can compare signals between stations/depths between an individual epitope, but cannot compare signals between epitopes, as the binding affinity for a specific polysaccharide structure varies between epitopes</p>
http://lod.bco-dmo.org/id/dataset-parameter/988176.rdf
Name: H2O
Units: unitless
Description: <p>The semi-quantiative signal output for each antibody when H2O was used (initially) for extraction of the polysaccharides. Note that this was part of a sequential extraction, so polysaccharides that were fully extracted with H2O may not show up in subsequent extractions</p>
http://lod.bco-dmo.org/id/dataset-parameter/988177.rdf
Name: EDTA
Units: unitless
Description: <p>The semi-quantiative signal output for each antibody when EDTA was used for extraction of the polysaccharides following H2O. Note that this was a sequential extraction, so polysaccharides that were fully extracted may not show up in subsequent extractions</p>
http://lod.bco-dmo.org/id/dataset-parameter/988178.rdf
Name: NaOH
Units: unitless
Description: <p>The semi-quantiative signal output for each antibody when NAOH was used for extraction of the polysaccharides following H2O and EDTA</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/985786/data/download
download
onLine
dataset
<p><strong>Collection</strong></p>
<p>Water was collected via Niskin bottles mounted on a rosette, equipped with a CTD in the western North Atlantic Ocean aboard R/V Endeavor (EN638) during May 2019.&nbsp;Seawater was transferred to carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle.</p>
<p>Particulate organic matter (POM) was harvested by filtering between 5-15 liters of seawater through a 47-mm pre-combusted (400℃ for 6 hours) glass fiber filter (GF/F; nominal pore size 0.7 μm; for volumes filtered at each depth and station, see the dataset). Filers were stored at -80C until further analysis. &nbsp;The same filter was used for both particulate organic carbon (POC) measurements and monosaccharide composition analysis. &nbsp;&nbsp;</p>
<p><strong>Analysis</strong></p>
<p><em>Polysaccharide extraction for microarray analyses of POM</em></p>
<p>POM samples were prepared for polysaccharide analysis according to Vidal-Melgosa et al. (2021). Polysaccharides were sequentially extracted from four filter piece punches (11.2 mm diameter) from GF/F filters. The samples were first extracted with autoclaved MilliQ water, followed by 50 mM EDTA, and finally 4 M NaOH with 0.1% NaBH<sub>4</sub>. The supernatant containing extracted polysaccharides was collected from each of the sequential steps and stored at 4 °C.</p>
<p><em>Carbohydrate microarray analysis to determine structural complexity of POM</em></p>
<p>The polysaccharides extracted as described above were analyzed following Vidal-Melgosa et al. (2021). In brief, the polysaccharide extracts were first diluted in printing buffer (55.2% glycerol, 44% water, 0.8% Triton X-100), and then printed on 0.45 µm pore size nitrocellulose membrane (Whatman) using a microarray robot (Sprint, Arrayjet, Roslin, UK) at 20 °C and 50% humidity. The membranes were probed with one of 9 monoclonal antibodies, washed multiple times, and probed with secondary antibodies (anti-rat, anti-mouse, or anti-His tag) conjugated to alkaline phosphatase for 2 hours. The arrays were developed using 5-bromo-4-chloro-3-indolyphosphate and nitro blue tetrazolium in alkaline phosphatase buffer (100 mM NaCl, 5 mM MgCl<sub>2</sub>, 100 mM Tris-HCl, pH 9.5). The microarrays were scanned and signal intensity was acquired using the software Array-Pro Analyzer 6.3 (Media Cybernetics). Signals were normalized among samples; higher signals correspond to a higher abundance of a given polysaccharide epitope. Note that the carbohydrate microarray data are only semiquantitative; while comparisons can be made for the abundance of a given epitope between stations and depths, the signal intensity cannot be used to compare signals of different epitopes.</p>
Specified by the Principal Investigator(s)
<p>Data processed using Microsoft Excel.</p>
Specified by the Principal Investigator(s)
- Imported "20250724_Carbohydrate Microarray (epitope) Analyses_Data_BCODMO.csv" into the BCO-DMO system
- Converted "date" and "time" to one date time parameter, "ISO_DateTime_EST"
- Created a new datetime parameter in UTC "ISO_DateTime_UTC"
- Removed "date" and "time" as redundant
- Replaced "Stn" string with "stn" string in the "station" field to be consistent with other datasets in this project
- Exported file as "985786_v1_carb_microarray_epitope.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 in the western North Atlantic Ocean aboard R/V Endeavor (EN638) during May 2019. 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/
Array-Pro Analyzer 6.3 (Media Cybernetics)
Array-Pro Analyzer 6.3 (Media Cybernetics)
PI Supplied Instrument Name: Array-Pro Analyzer 6.3 (Media Cybernetics) PI Supplied Instrument Description:The microarrays were scanned and signal intensity was acquired using the software Array-Pro Analyzer 6.3 (Media Cybernetics). Instrument Name: microarray scanner Instrument Short Name: Instrument Description: Microarray scanners are instruments used to detect and quantify the intensity of fluorescence of spots on a microarray slide, by selectively exciting fluorophores with a laser and measuring the fluorescence.
A microarray scanner typically consists of lasers, a special microscope, and a camera. The DNA material in the microarray is labeled with fluorescents which become excited by the lasers in the scanner. The microscope and camera work together to create a digital image of the array.
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 in the western North Atlantic Ocean aboard R/V Endeavor (EN638) during May 2019. 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