Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • BCO-DMO Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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 amino acids
Freeze-dried filters of the 0.3 µm, 1.2 µm, and 20 µm size fractions were quantitatively split radially by weight for analysis of amino acid content for selected samples from August and November 2021.

For amino acid analysis, one filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections). Filter splits were hydrolyzed (20 h, 110°C) using trace metal grade 6 N hydrochloric acid. Hydrolysate was separated from filter material using combusted glass syringes with glass wool in the tip and syringe-tip 0.2 μm polyethersulfone filters. Samples were neutralized by evaporating acid under nitrogen (N₂), reconstituted in 0.1 N hydrochloric acid, and purified via cation exchange chromatography. Notably, we found that cation exchange chromatography was crucial in achieving acceptable yields; trial samples analyzed without undergoing this purification step resulted in yields much lower than expected and much lower than when analyzed after the purification procedure, likely due to chromatographic interference from compound(s) that were effectively removed via the cation exchange procedure. Samples were aliquoted into individual 2 mL HPLC vials, and known quantities of the synthetic amino acid aminoadipic acid were added as an internal standard to confirm accurate analysis. Samples were then dried under N₂, reconstituted in 60/40 ultrapure water/methanol (v/v), and derivatized with o‑phthaldialdehyde and 2‑mercaptoethanol 2 minutes before injection for analysis via reverse‑phase high performance liquid chromatography (HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm). The mobile phase was as follows: eluent A was 50 mmol L^-1 sodium acetate (HPLC‑grade; adjusted to pH 5.7), and eluent B was 100% methanol (HPLC‑grade). The stationary phase was a C18 column (Kinetex^TM EVO-C18, 5 µm, 100 Å, 4.6x250 mm) with a C18 guard column (EVO-C18 ULTRA cartridge, 4.6 mm) at 20°C. The flow rate was constant at 0.9 mL min^-1 and the elution gradient of eluent B added to eluent A was as follows:

• -12 min to 0 min: 5% eluent B
• 4 min: 23% eluent B
• 8 min: 29% eluent B
• 24 min: 44% eluent B
• 37 to 44 min: 60% eluent B
• 52 min: 77% eluent B
• 57 to 62 min: 100% eluent B

A standard curve was analyzed alongside samples during each run. The standard used was a mixed amino acid standard solution initially prepared in 0.1 N hydrochloric acid. We measured the following amino acids: alanine, arginine, aspartic acid, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tyrosine, valine, γ-aminobutyric acid, and β-alanine. The standard also included cysteine and proline, though these amino acids are not detectable with the OPA derivatization method. The standard was prepared from the Pierce amino acid calibration standard H with the addition of non-protein forming amino acids γ-aminobutyric acid and β-alanine. The standard solution was prepared to a concentration of 92 μmol L^-1 for all amino acids except for γ-aminobutyric acid and β-alanine, which were prepared to concentrations of 30 and 34 μmol L^-1, respectively. The standard solution was aliquoted by weight to exact concentrations targeting a range of 0.2 to 50 μmol L^-1 for the protein-forming amino acids. As with the samples, standards were aliquoted directly into individual 2 mL HPLC vials, supplemented with known quantities of aminoadipic acid as an internal standard, dried under N₂, and reconstituted in 60/40 ultrapure water/methanol (v/v). The effect of cation exchange chromatography on measured amino acid yields in the standard was determined by subjecting two aliquots of the standard mixture to the procedure; average yields for each amino acid were 87-98% with the exception of arginine (40%) and lysine (71%). Yields were consistent for each amino acid across the duplicate standard aliquots. Sample concentrations were corrected assuming a yield of 40% for arginine, 71% for lysine, and 91% (average) for all other amino acids. Sample peak areas were converted to molar quantities using the calibration from the standard curve. Blanks of ultrapure water and full process blanks were analyzed alongside samples to check for any background amino acid content in reagents or contamination. Full process blanks consisted of dip blank filter splits that were processed exactly as sample filter splits. Seawater particulate amino acid concentrations (nmol L^‑1) were calculated based on the original volume of seawater filtered through the portion of sample analyzed during each run (material extracted from 0.7 to 10.5 L of seawater injected for a single run). We report concentrations here as (1) total amino acid carbon as a proportion of POC, where carbon from individual amino acids was calculated (via the molecular formula for each monomer), summed, and divided by the total POC concentration in that particle size fraction, and (2) individual amino acids as mol%, where the concentrations (in nmol L^-1) of individual amino acids were each divided by the total amino acid concentration in that sample (sum of individual concentrations in nmol L^‑1).

- Imported data from source file "SizeFrac_AminoAcids_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 amino acid values
- Rounded values according to submitter's indicated precision

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:

• BIOS-SCOPE Narrative: 
  https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/BIOS-SCOPE_Narrative_FINAL.pdf
• Physical Framework:
  https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/Physical_Framework.pdf

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