Size fractionated carbohydrate data collected in the Sargasso Sea during BIOS-SCOPE cruises AE2114 and AE2123 in August and November 2021

Website: https://www.bco-dmo.org/dataset/964801
Data Type: Cruise Results
Version: 1
Version Date: 2025-06-13

Project
» Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology (BIOSSCOPE)
ContributorsAffiliationRole
Carlson, Craig A.University of California-Santa Barbara (UCSB)Principal Investigator
Close, Hilary G.University of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS)Principal Investigator
English, ChanceUniversity of California-Santa Barbara (UCSB)Scientist
Henderson, LillianUniversity of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS)Scientist
Popendorf, KimberlyUniversity of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS)Scientist
Jeng, DailenUniversity of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS)Student
Halewood, ElisaUniversity of California-Santa Barbara (UCSB)Data Manager
Gerlach, Dana StuartWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Included in this dataset are chemical analyses of size-fractionated particle samples collected during BIOS-SCOPE project cruises in the Sargasso Sea (2021). Samples were collected using McLane WTS-LV in-situ pumps and analyzed for carbohydrate monomers.


Coverage

Location: North Atlantic Subtropical Gyre - Bermuda Atlantic Time Series (BATS) site
Spatial Extent: N:32.17 E:-64.08 S:30.75 W:-64.5
Temporal Extent: 2021-08-06 - 2021-11-13

Methods & Sampling

Samples were collected during August 2021 and November 2021 at or near the BATS site (31°40’ N, 64°10’ W) or at Hydrostation S (32°10’ N, 64°30’ W) on R/V Atlantic Explorer cruises AE2114 and AE2123.

Size-fractionated particle samples were collected using McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.) during all sampling periods. Five to eight depths were sampled between the surface and 200 meters during each cruise. Most pumps were dual-flow, collecting water through two filter holders simultaneously for geochemical and taxonomic analyses, as described by Henderson et al. (2024) and Comstock et al. (2024). Each filter holder was a vertical-intake (McLane) or mini-MULVFS style and contained four 142 mm diameter filter tiers equipped as follows (from top to bottom) for the geochemical analyses reported here: [1] 20 μm Nitex filter, [2] 6 μm Nitex filter (5 μm polyester filter), [3] two stacked 1.2 μm glass fiber filters (GF/C), [4] two stacked 0.3 μm glass fiber filters (GF75). A 150 μm Nitex backing filter was placed beneath the filter(s) of interest on the first three tiers of all filter holders to ensure filter structural integrity. Nitex filters were acid-and methanol-washed before use, and glass fiber filters were pre‑combusted (450°C) for 5 hours. After pump recovery, filter holders were drained with a weak vacuum to remove excess seawater. Filters were photographed, removed and folded with clean forceps, stored in combusted foil, and transported and stored at ‑80°C. Flow meters were placed in-line on each flow path of the pumps, and exact filtered volumes for each flow path were determined; flow rates through filter stacks used for organic analyses averaged <3 Liters per minutes (L/min). We collected dip blanks – filters that did not have any water pumped through them, but were submerged in natural seawater – along with our samples.

Processing of large particle (>20 µm) samples
Samples were stored at ‑80°C until processing. Once in the lab, particles collected on 20 µm Nitex filters were rinsed off the filters onto 47-mm diameter, pre-combusted (450°C, for 5 hr) glass fiber filters with a nominal pore size of 0.7 μm (GF/F) using 0.2 µm-filtered seawater and combusted glass filter towers. Briefly, particles were rinsed from the Nitex filters using an acid-clean squirt bottle to spray across the filter. The Nitex mesh was then sonicated for three minutes in an acid-clean polypropylene Nalgene bottle with more filtered seawater. After sonication, this water was poured into the filter tower. The process was repeated three times, with all filtered seawater being drained from the filter tower with gentle vacuum after each rinse and sonication onto the same GF/F filter. Samples were then freeze-dried and inspected under a dissecting microscope to visually characterize the particles and remove intact zooplankton swimmers or contaminant fibers, which were both rare in the samples.

Analysis of individual carbohydrate monomers
Freeze-dried filters of the 0.3 µm, 1.2 µm, and 20 µm size fractions were also quantitatively split radially by weight for analysis of carbohydrate content for selected samples from August and November 2021.

For carbohydrate monomer analysis, two or three filter splits (replicates/triplicates) were prepared per sample. Filter splits were hydrolyzed (20 h, 100°C) using 0.4 N hydrochloric acid, and hydrolysate was separated from filter material by pushing through combusted glass syringes with combusted glass wool in the tip and 0.2 μm polyethersulfone syringe-tip filters. Samples were neutralized by evaporating acid under nitrogen (N2), reconstituted in ultrapure water, and filtered again through combusted quartz wool to remove any residual particulates before quantitative aliquots (by volume) were taken for analysis. Frozen samples were transported to the University of California Santa Barbara for analysis via high performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD). Here, we quantified neutral, amino, and acidic carbohydrate monomers following Engel and Händel (2011). The mobile phase was as follows: eluent A was 100 mmol L-1 sodium hydroxide and 200 mmol L-1 sodium acetate, eluent B was 18 mmol L-1 sodium hydroxide, eluent C was 1000 mmol L-1 sodium hydroxide, and eluent D was ultrapure water. Eluent A was filtered through a 0.2 μm nylon membrane filter, and subsequently all eluents were bubbled with N2 gas for 45 min and degassed before being attached to the system and pressurized with N2 gas. Individual carbohydrates were separated on a Dionex CarboPac PA10 analytical column (4x250 mm) with a Dionex CarboPac PA10 guard column (4x50 mm). The column, detector, and autosampler were temperature controlled, held constant at 25°C, 30°C, and 4°C, respectively. The flow rate was 1 mL min-1 and the elution gradient was as follows:

  • -15 to 22 min: 100% eluent B
  • 23 min: 9:1 eluent D/C
  • 27 to 37 min: 100% eluent A
  • 42 to 57 min: 4:1 eluent D/C
  • 60 min: 100% eluent B

A standard curve was analyzed alongside samples during each run. A stock solution was prepared in ultrapure water to achieve concentrations of 1 mmol L-1 fucose, rhamnose, arabinose, galactose, glucose, mannose/xylose, ribose, galacturonic acid, and glucuronic acid, and 0.5 mmol L-1 galactosamine, glucosamine, and muramic acid. The solution was prepared all at once, and then aliquoted and stored at ‑20°C until analysis. Standard aliquots were thawed alongside samples and diluted to concentrations of 10 to 10000 nmol L-1 per monomer for analysis. Standards of appropriate sizes (i.e., bracketing those of each monomer sample peak) were to determine sample concentrations. To verify consistent instrument performance, a 1000 nmol L-1 standard was analyzed after every eight samples and compared to the original standard curve. An aliquot of a sample with ample material was also analyzed during every day of analysis to confirm day-to-day consistency. Sample concentrations were calculated from recorded peak areas using the calibration from the standard curve. Blanks of ultrapure water and full process blanks were analyzed alongside samples to check for background carbohydrate content in reagents or contamination. Full process blanks consisted of dip blank filter splits and 0.4 M hydrochloric acid blanks that were processed exactly as samples. Seawater particulate carbohydrate concentrations (nmol L‑1) were calculated based on the original amount of seawater filtered through the portion of sample analyzed during each run (material extracted from 0.1 to 2.5 L of seawater injected for a single run). We report concentrations here as total carbohydrate carbon as a proportion of POC, where carbon from individual monomers was calculated from the molecular formula for each monomer, summed, and divided by the total POC concentration in that particle size fraction.


BCO-DMO Processing Description

- Imported data from source file "SizeFrac_Carbos_BIOSSCOPE_2021.xlsx" into the BCO-DMO data system.
- Modified parameter (column) names to conform with BCO-DMO naming conventions.
- Converted latitude and longitude columns to decimal degrees
- Changed date format to ISO format of yyyy-mm-dd
- Moved standard deviation values to be adjacent to the associated carbohydrate values
- Rounded values according to submitter's indicated precision


[ table of contents | back to top ]

Data Files

File
964801_v1_pump_carbohydrates_biosscope_2021.csv
(Comma Separated Values (.csv), 7.58 KB)
MD5:43aac3a5d5c8c48df49050a172094884
Primary data file for dataset ID 964801, version 1. Size-fractionated Carbohydrate data collected during BIOS-SCOPE cruises AE2114 and AE2123 in 2021

[ table of contents | back to top ]

Related Publications

Bishop, J. K. B., Lam, P. J., & Wood, T. J. (2012). Getting good particles: Accurate sampling of particles by large volume in-situ filtration. Limnology and Oceanography: Methods, 10(9), 681–710. doi:10.4319/lom.2012.10.681
Methods
Comstock, J., Henderson, L. C., Close, H. G., Liu, S., Vergin, K., Worden, A. Z., Wittmers, F., Halewood, E., Giovannoni, S., & Carlson, C. A. (2024). Marine particle size-fractionation indicates organic matter is processed by differing microbial communities on depth-specific particles. ISME Communications, 4(1). https://doi.org/10.1093/ismeco/ycae090
Methods
Doherty, S. C., Maas, A. E., Steinberg, D. K., Popp, B. N., & Close, H. G. (2021). Distinguishing zooplankton fecal pellets as a component of the biological pump using compound‐specific isotope analysis of amino acids. Limnology and Oceanography, 66(7), 2827–2841. Portico. https://doi.org/10.1002/lno.11793
Methods
Engel, A., & Händel, N. (2011). A novel protocol for determining the concentration and composition of sugars in particulate and in high molecular weight dissolved organic matter (HMW-DOM) in seawater. Marine Chemistry, 127(1–4), 180–191. https://doi.org/10.1016/j.marchem.2011.09.004
Methods
Goldberg, S. J., Carlson, C. A., Hansell, D. A., Nelson, N. B., & Siegel, D. A. (2009). Temporal dynamics of dissolved combined neutral sugars and the quality of dissolved organic matter in the Northwestern Sargasso Sea. Deep Sea Research Part I: Oceanographic Research Papers, 56(5), 672–685. doi:10.1016/j.dsr.2008.12.013
Methods
Grosse, J., Nöthig, E.-M., Torres-Valdés, S., & Engel, A. (2021). Summertime Amino Acid and Carbohydrate Patterns in Particulate and Dissolved Organic Carbon Across Fram Strait. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.684675
Methods
Hannides, C. C. S., Popp, B. N., Choy, C. A., & Drazen, J. C. (2013). Midwater zooplankton and suspended particle dynamics in the North Pacific Subtropical Gyre: A stable isotope perspective. Limnology and Oceanography, 58(6), 1931–1946. doi:10.4319/lo.2013.58.6.1931
Methods
Henderson, L.C., Wittmers, F., Carlson, C. A., Worden, A.Z., & Close, H. G. (2024. Variable carbon isotope fractionation of photosynthetic communities over depth in an open-ocean euphotic zone. Proceedings of the National Academy of Sciences, 121(10). https://doi.org/10.1073/pnas.2304613121
Results
Kaiser, K., & Benner, R. (2005). Hydrolysis-induced racemization of amino acids. Limnology and Oceanography: Methods, 3(8), 318–325. doi:10.4319/lom.2005.3.318
Methods
Lindroth, Peter., & Mopper, Kenneth. (1979). High performance liquid chromatographic determination of subpicomole amounts of amino acids by precolumn fluorescence derivatization with o-phthaldialdehyde. Analytical Chemistry, 51(11), 1667–1674. https://doi.org/10.1021/ac50047a019
Methods
Liu, S., Longnecker, K., Kujawinski, E. B., Vergin, K., Bolaños, L. M., Giovannoni, S. J., Parsons, R., Opalk, K., Halewood, E., Hansell, D. A., Johnson, R., Curry, R., & Carlson, C. A. (2022). Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.833252
Methods
Wojtal, P. K., Doherty, S. C., Shea, C. H., Popp, B. N., Benitez‐Nelson, C. R., Buesseler, K. O., Estapa, M. L., Roca‐Martí, M., & Close, H. G. (2023). Deconvolving mechanisms of particle flux attenuation using nitrogen isotope analyses of amino acids. Limnology and Oceanography. Portico. https://doi.org/10.1002/lno.12398
Results

[ table of contents | back to top ]

Related Datasets

IsRelatedTo
Carlson, C. A., Giovannoni, S., Liu, S., Halewood, E. (2025) BIOS-SCOPE survey biogeochemical data as collected on Atlantic Explorer cruises (AE1614, AE1712, AE1819, AE1916) from 2016 through 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-17 doi:10.26008/1912/bco-dmo.861266.1 [view at BCO-DMO]
Henderson, L., Close, H. G., Carlson, C. A., Saied, A., Ortiz, A., Garley, R., Halewood, E. (2024) Chemical analyses of size-fractionated particle samples collected during the BIOS-SCOPE cruise AE1819 in the Sargasso Sea in July 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-02-22 doi:10.26008/1912/bco-dmo.920443.1 [view at BCO-DMO]
Henderson, L., English, C., Jeng, D., Popendorf, K., Carlson, C. A., Close, H. G. (2025) Size fractionated Amino Acid data collected in the Sargasso Sea during BIOS-SCOPE cruises AE2114 and AE2123 in August and November 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-13 doi:10.26008/1912/bco-dmo.964684.1 [view at BCO-DMO]

[ table of contents | back to top ]

Parameters

ParameterDescriptionUnits
Sample_ID

Internal sample ID

unitless
Cruise

BIOSSCOPE cruise identifier

unitless
Latitude

Latitude of sampling

decimal degrees
Longitude

Longitude of sampling

decimal degrees
Date

Date of sampling

unitless
Size_fraction

Particle size range for water fraction

micrometers (um)
Filter_type

Filter type used for particle fraction (Nitex, GF/C ,GF75)

unitless
Depth

Water column depth of sample

meters (m)
Fucose

Carbohydrate monomer average concentration: Fucose

nanomoles carbon per liter (nmol C/L)
Fucose_sd

Standard deviation of Fucose concentration

nanomoles carbon per liter (nmol C/L)
Rhamnose

Carbohydrate monomer average concentration: Rhamnose

nanomoles carbon per liter (nmol C/L)
Rhamnose_sd

Standard deviation of Rhamnose concentration

nanomoles carbon per liter (nmol C/L)
Galactosamine

Carbohydrate monomer average concentration: Galactosamine

nanomoles carbon per liter (nmol C/L)
Galactosamine_sd

Standard deviation of Galactosamine concentration

nanomoles carbon per liter (nmol C/L)
Arabinose

Carbohydrate monomer average concentration: Arabinose

nanomoles carbon per liter (nmol C/L)
Arabinose_sd

Standard deviation of Arabinose concentration

nanomoles carbon per liter (nmol C/L)
Glucosamine

Carbohydrate monomer average concentration: Glucosamine

nanomoles carbon per liter (nmol C/L)
Glucosamine_sd

Standard deviation of Glucosamine concentration

nanomoles carbon per liter (nmol C/L)
Galactose

Carbohydrate monomer average concentration: Galactose

nanomoles carbon per liter (nmol C/L)
Galactose_sd

Standard deviation of Galactose concentration

nanomoles carbon per liter (nmol C/L)
Glucose

Carbohydrate monomer average concentration: Glucose

nanomoles carbon per liter (nmol C/L)
Glucose_sd

Standard deviation of Glucose concentration

nanomoles carbon per liter (nmol C/L)
MannoseXylose

Carbohydrate monomer average concentration: Mannose+Xylose

nanomoles carbon per liter (nmol C/L)
MannoseXylose_sd

Standard deviation of Mannose+Xylose concentration

nanomoles carbon per liter (nmol C/L)
Ribose

Carbohydrate monomer average concentration: Ribose

nanomoles carbon per liter (nmol C/L)
Ribose_sd

Standard deviation of Ribose concentration

nanomoles carbon per liter (nmol C/L)
MurAc

Carbohydrate monomer average concentration: Muramic acid

nanomoles carbon per liter (nmol C/L)
MurAc_sd

Standard deviation of Muramic acid concentration

nanomoles carbon per liter (nmol C/L)
GalURA

Carbohydrate monomer average concentration: Galacturonic acid

nanomoles carbon per liter (nmol C/L)
GalURA_sd

Standard deviation of Galacturonic acid concentration

nanomoles carbon per liter (nmol C/L)
GlcURA

Carbohydrate monomer average concentration: Glucuronic acid

nanomoles carbon per liter (nmol C/L)
GlcURA_sd

Standard deviation of Glucuronic acid concentration

nanomoles carbon per liter (nmol C/L)


[ table of contents | back to top ]

Instruments

Dataset-specific Instrument Name
flow meter
Generic Instrument Name
Flow Meter
Dataset-specific Description
Flow meters were placed in-line on each flow path of the pumps, and exact filtered volumes for each flow path were determined.
Generic Instrument Description
General term for a sensor that quantifies the rate at which fluids (e.g. water or air) pass through sensor packages, instruments, or sampling devices. A flow meter may be mechanical, optical, electromagnetic, etc.

Dataset-specific Instrument Name
autosampler
Generic Instrument Name
Laboratory Autosampler
Dataset-specific Description
The column, detector, and autosampler were temperature controlled, held constant at 25°C, 30°C, and 4°C, respectively. 
Generic Instrument Description
Laboratory apparatus that automatically introduces one or more samples with a predetermined volume or mass into an analytical instrument.

Dataset-specific Instrument Name
McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.)
Generic Instrument Name
McLane Large Volume Pumping System WTS-LV
Dataset-specific Description
Size-fractionated particle samples were collected using McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.) during all sampling periods.
Generic Instrument Description
The WTS-LV is a Water Transfer System (WTS) Large Volume (LV) pumping instrument designed and manufactured by McLane Research Labs (Falmouth, MA, USA). It is a large-volume, single-event sampler that collects suspended and dissolved particulate samples in situ. Ambient water is drawn through a modular filter holder onto a 142-millimeter (mm) membrane without passing through the pump. The standard two-tier filter holder provides prefiltering and size fractioning. Collection targets include chlorophyll maximum, particulate trace metals, and phytoplankton. It features different flow rates and filter porosity to support a range of specimen collection. Sampling can be programmed to start at a scheduled time or begin with a countdown delay. It also features a dynamic pump speed algorithm that adjusts flow to protect the sample as material accumulates on the filter. Several pump options range from 0.5 to 30 liters per minute, with a max volume of 2,500 to 36,000 liters depending on the pump and battery pack used. The standard model is depth rated to 5,500 meters, with a deeper 7,000-meter option available. The operating temperature is -4 to 35 degrees Celsius. The WTS-LV is available in four different configurations: Standard, Upright, Bore Hole, and Dual Filter Sampler. The high-capacity upright WTS-LV model provides three times the battery life of the standard model. The Bore-Hole WTS-LV is designed to fit through a narrow opening such as a 30-centimeter borehole. The dual filter WTS-LV features two vertical intake 142 mm filter holders to allow simultaneous filtering using two different porosities.

Dataset-specific Instrument Name
dissecting microscope
Generic Instrument Name
Microscope - Optical
Dataset-specific Description
Samples were inspected under a dissecting microscope to visually characterize the particles and remove intact zooplankton swimmers or contaminant fibers, which were both rare in the samples.
Generic Instrument Description
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

Dataset-specific Instrument Name
Ion chromatography system
Generic Instrument Name
Thermo Fisher Scientific Dionex ICS-5000 ion chromatography (IC) system
Dataset-specific Description
Frozen samples were transported to the University of California Santa Barbara for analysis via high performance anion exchange chromatography.
Generic Instrument Description
The Thermo Fisher Scientific Dionex ICS-5000 ion chromatography (IC) system is an ion chromatography system that offers a full range of reagent-free components. This instrument can be configured to use single or dual pumps. The single-channel Dionex ICS-5000 can be configured to run capillary, microbore or standard bore IC applications. A dual Dionex ICS-5000 system can be configured with any combination of these applications. This system uses an eluent generator (EG) to generate high purity acid or base eluents from deionized water, in the amount and concentration needed for sample analysis, configurable for single or dual channel operation. Eluent regeneration may also be used without an EG - eluent regeneration uses the suppressor to reconstitute the starting eluent, allowing use of a single 4-liter bottle of eluent for up to four weeks. An eluent organizer (EO) module is used to contain eluent spills and leaks. The ICS-5000 detector/chromatography module (DC) can accommodate components for two channels, plumbed either serially or in parallel, in a temperature-controlled environment. Available DC components include conductivity detectors, electrochemical detectors, injection valves, switching valves, guard and separator columns, suppressors, and Dionex IC cubes or ICS-5000 Automation Manager. Detectors outside of the DC include a Dionex ICS Series Photodiode Array Detector (PDA); Dionex ICS Series Variable Wavelength Detector (VWD); MSQ Plus Mass Spectrometer.

Dataset-specific Instrument Name
sonicator
Generic Instrument Name
ultrasonic cell disrupter (sonicator)
Dataset-specific Description
The mesh filter was sonicated for three minutes in an acid-clean polypropylene Nalgene bottle with filtered seawater.
Generic Instrument Description
Instrument that applies sound energy to agitate particles in a sample.


[ table of contents | back to top ]

Deployments

AE2114

Website
Platform
R/V Atlantic Explorer
Start Date
2021-08-05
End Date
2021-08-08

AE2123

Website
Platform
R/V Atlantic Explorer
Start Date
2021-11-10
End Date
2021-11-13


[ table of contents | back to top ]

Project Information

Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology (BIOSSCOPE)


Coverage: North Atlantic Subtropical Gyre, Bermuda Atlantic Time Series (BATS) site


The aim of BIOS-SCOPE is to expand knowledge about the BATS ecosystem and achieve a better understanding of ocean food web sources, sinks and transformations of DOM. Advances in knowledge and technology now poise us to investigate the specific mechanisms of DOM incorporation, oxidation and transformation by zooplankton and the distinct microbial plankton communities that have been discovered at BATS.

The overarching goal of the BIOS-SCOPE is to form and foster collaborations of cross disciplinary science that utilize a broad suite of genomic, chemical, ecological, and biogeochemical approaches to evaluate microbial process, structure and function on various scales. These scales will range from organism-compound and organism-organism interactions to large biogeochemical patterns on the ecosystem scale. For this purpose we have assembled a cross-disciplinary team including microbial oceanographers (Carlson and Giovannoni), a chemical oceanographer (Kujawinski), biological oceanographer / zooplankton ecologists (Maas and Blanco-Bercial) and microbial bioinformatician (Temperton) with the expertise and technical acuity that are needed to study complex interactions between food web processes, microbes and DOM quantity and quality in the oligotrophic ocean. This scientific team has a vision of harnessing this potential to produce new discoveries that provide a mechanistic understanding of the carbon cycle and explain the many emergent phenomenon that have yet to be understood.

For additional details:

BIOSSCOPE I: November 1st, 2015 through October 31st, 2020
Current: November 1st, 2020 to October 31st, 2025



[ table of contents | back to top ]

Funding

Funding SourceAward
Simons Foundation (Simons)

[ table of contents | back to top ]