Contributors | Affiliation | Role |
---|---|---|
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, Chance | University of California-Santa Barbara (UCSB) | Scientist |
Henderson, Lillian | University of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS) | Scientist |
Popendorf, Kimberly | University of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS) | Scientist |
Jeng, Dailen | University of Miami Rosenstiel School of Marine and Atmospheric Science (UM-RSMAS) | Student |
Halewood, Elisa | University of California-Santa Barbara (UCSB) | Data Manager |
Gerlach, Dana Stuart | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
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:
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.
- 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
File |
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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 |
Parameter | Description | Units |
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) |
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. |
Website | |
Platform | R/V Atlantic Explorer |
Start Date | 2021-08-05 |
End Date | 2021-08-08 |
Website | |
Platform | R/V Atlantic Explorer |
Start Date | 2021-11-10 |
End Date | 2021-11-13 |
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
Funding Source | Award |
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Simons Foundation (Simons) |