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Collection

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. 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.

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. The same filter was used for both particulate organic carbon (POC) measurements and monosaccharide composition analysis.

Analysis

Polysaccharide extraction for microarray analyses of POM

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% NaBH₄. The supernatant containing extracted polysaccharides was collected from each of the sequential steps and stored at 4 °C.

Carbohydrate microarray analysis to determine structural complexity of POM

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 MgCl₂, 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.

16:T4e0,This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability. CURATION ACTIONS PERFORMED ON DATA - 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" CURATION ACTIONS PERFORMED ON METADATA - BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits ISSUES POTENTIALLY IMPACTING REUSE - Citations for inline references not provided for: Hansell 2013, Carlson & Hansell 2015, Guo et al. 1996, Walker et al. 2016, Benner & Amon 2015, Benner et al. 1992, and Kaiser & Benner 200917:Tb57,Marine dissolved organic carbon (DOC) is one of the largest actively-cycling carbon reservoirs on earth—comparable in magnitude to atmospheric CO2 (Hansell 2013)—and thus is an essential component of the global carbon cycle. DOC has a multitude of sources, including phytoplankton productivity, grazing, excretion, solubilization from particulate organic matter (POM), viral lysis, and riverine input; the major DOC sink in the ocean is consumption by heterotrophic microbial communities (Carlson & Hansell 2015). Measurement of bulk DOC characteristics such as 14C age and molecular size have demonstrated that the high molecular weight (HMW) DOC fraction is generally younger and more biologically reactive than the low molecular weight (LMW) fraction (e.g. Guo et al. 1996; Walker et al. 2016). We know that a substantial fraction of HMW DOC consists of carbohydrates, including neutral sugars, and that its concentration is lower in the deep ocean than in the upper mesopelagic/surface ocean (Benner & Amon 2015). Characterization of the HMW DOC fraction has primarily used chemical measurements that provide information about monomeric constituents (Benner et al. 1992; Kaiser & Benner 2009), but yield no information on the order in which such constituents are linked together, or about the 3D structure of the intact HMW DOC. Beyond these observations and measurements, however, the specific factors controlling the rate, location, and extent to which DOC is transformed and remineralized by heterotrophic microbial communities in the ocean are still not well understood. A key focus of this project's field work is investigating the potential of marine heterotrophic microbial communities from different water masses and under differing conditions of organic matter availability to hydrolyze six well-characterized high-molecular-weight (HMW) polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan). To better contextualize this hydrolysis, bulk water characterization of the deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom waters used in our mesocosm incubation experiments was performed. This dataset includes the measurement of carbohydrate microarray (epitope) analyses of POM-derived carbohydrates from bulk waters collected in the western North Atlantic Ocean aboard R/V Endeavor (EN638) during May 2019. 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, since the binding affinity for individual epitopes differs between antibodies. Note also that analyses were performed for all sampled depths at all stations. There was, however, no positive signal at depths that are shown as "0" in this dataset. 18:T112b,NSF Award Abstract: 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. 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.6:["$","$L14",null,{"dataset":{"_id":"985786","description":"","problem":"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, since the binding affinity for individual epitopes differs between antibodies. Note also that analyses were performed for all sampled depths at all stations. There was, however, no positive signal at depths that are shown as \"0\" in this dataset.","acquisition":"$15","processing":"

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","type_id":"413","type_name":"Niskin bottle","type_desc":"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.","type_acronym":"Niskin bottle"},{"_id":"988155","name":"CTD","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. ","type_id":"591","type_name":"Sea-Bird SBE 911plus CTD","type_desc":"[tethered, real-time] The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. 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Cruise ID on R/V Endeavor

","units":{"_id":"","name":"unitless"},"type":{"_id":"1102","name":"cruise_id","description":"

cruise designation; name

"}},{"_id":"988162","name":"station","format":"","frictionlessType":"string","description":"

Cruise station number (17, 18, 19, 20)

","units":{"_id":"","name":"unitless"},"type":{"_id":"987","name":"station","description":"

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

"}},{"_id":"988163","name":"latitude","format":"","frictionlessType":"number","description":"

Latitude, south is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"988165","name":"longitude","format":"","frictionlessType":"number","description":"

Longitude, west is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"988167","name":"ISO_DateTime_Local","format":"%Y-%m-%dT%H:%M:%S","frictionlessType":"datetime","description":"

Datetime of sample collection in ISO format, US Eastern Time (ET)

","units":{"_id":"","name":"unitless"},"type":{"_id":"1909","name":"ISO_DateTime_Local","description":"

Date/Time (Local) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\nYYYY-MM-DDTHH:MM:SS[.xx]
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Note the Time Zone (TZ) as +/-HH:MM
\nTime Zone signage is for conversion from local to UTC
\nWest Coast USA in summer is +7 (add 7 hrs to local time for UTC)

"}},{"_id":"988168","name":"ISO_DateTime_UTC","format":"%Y-%m-%dT%H:%M:%SZ","frictionlessType":"datetime","description":"

Datetime of sample collection in ISO format, UTC

","units":{"_id":"","name":"unitless"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Date/Time (UTC) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}},{"_id":"988170","name":"cast_number","format":"","frictionlessType":"string","description":"

Cast number at station (refers to cast of CTD/Niskin bottles on cruise at each station)

","units":{"_id":"","name":"unitless"},"type":{"_id":"761","name":"cast","description":"

cast or profile number

"}},{"_id":"988171","name":"depth_sequence","format":"","frictionlessType":"string","description":"

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.)

","units":{"_id":"","name":"unitless"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"988172","name":"depth_actual","format":"","frictionlessType":"number","description":"

Actual depth at which water was collected

","units":{"_id":"","name":"meters"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

"}},{"_id":"988174","name":"POM_L_filtered","format":"","frictionlessType":"number","description":"

The amount of seawater filtered (liters) for carbohydrate microarray (epitope) analyses of POM-derived carbohydrates

","units":{"_id":"","name":"Liters"},"type":{"_id":"1040","name":"vol_filt","description":"

volume of water filtered; in this form generally applies to the volume of water filtered during plankton tows; however; this parameter name is also used for a variety of non plankton sampling and the units can vary, e.g. US JGOFS EqPac Bishop MULVFS sampler vol_filt is reported in liters.

"}},{"_id":"988175","name":"epitope","format":"","frictionlessType":"string","description":"

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

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"988176","name":"H2O","format":"","frictionlessType":"number","description":"

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

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"988177","name":"EDTA","format":"","frictionlessType":"number","description":"

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

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"988178","name":"NaOH","format":"","frictionlessType":"number","description":"

The semi-quantiative signal output for each antibody when NAOH was used for extraction of the polysaccharides following H2O and EDTA

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}}],"related_publications":[{"id":"987355","citation":"Vidal-Melgosa, S., Sichert, A., Francis, T. B., Bartosik, D., Niggemann, J., Wichels, A., Willats, W. G. T., Fuchs, B. M., Teeling, H., Becher, D., Schweder, T., Amann, R., & Hehemann, J.-H. (2021). Diatom fucan polysaccharide precipitates carbon during algal blooms. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-21009-6\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[{"_id":"985784","name":"EN638 POC and Monosaccharide","url":"","relation_type":"IsRelatedTo","type_desc":"

The dataset is related to another dataset.

\n","relation_desc":"","citation":"Lloyd, C., Vidal, S., Arnosti, C., Ghobrial, S. (2025) Particulate organic carbon concentrations and monosaccharide composition of POM-derived carbohydrates from samples taken during 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 2025-10-03 http://lod.bco-dmo.org/id/dataset/985784"}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/985786/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/985786/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/985786/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/985786/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"809975","name":"A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation","acronym":"Microbial DOC Degradation","description":"$18"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.985786.1","url":"https://doi.org/10.26008/1912/bco-dmo.985786.1","date_assigned":"2026-10-02","version_date":"2025-10-03","archiver":"Woods Hole Oceanographic Institution (WHOI BCO-DMO)","archiver_id":"191"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":46},"downloads":{"count":66}}}}]