Table of Contents

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

Seawater was collected aboard R/V Endeavor during the research cruise EN683 (2022-05-24 to 2022-06-12). Samples were collected in one of three ways: bulk seawater from each station was collected into acid-washed 50 mL Falcon tubes from Niskin bottles mounted on a rosette, equipped with a CTD and triggered at specific depths; or from large volume (LV) mesocosm experiments sampled by pouring water from each mesocosm into an acid-washed 50 mL Falcon tube; or from Sargassum mesocosm experiments by submerging acid-washed 50 mL Falcon tubes into the incubation tank to collect surrounding water.

To 1.7ml triplicate subsamples and one killed control, isotopically diluted L-[3,4,5-3H(N)]-Leucine (PerkinElmer, NET460250UC, specific activity of 3.7 TBq/mmol) was added (20 nM final concentration). Samples and killed control were incubated between 6 and 36 hours at near in-situ temperature.  Live samples were killed with 100% (w/v) TCA and centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.  The supernatant liquid was removed and 1 mL of ice-cold 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation. Supernatant removal, mixing, and centrifugation were repeated using 1 mL of ice-cold 80% ethanol solution. Again, the supernatant liquid was removed and each sample was left to dry in a hood overnight.  After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and left overnight so that precipitated proteins dissolve into scintillation fluid.  Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter for bulk, and PerkinElmer Tri-Carb 3110TR LSA for large volume (mesocosm) samples.  Radioactivity was compared to 1 mL of scintillation cocktail spiked with an identical amount of isotopically diluted L-[3,4,5-3H(N)]-Leucine that was added to samples. Incorporation rate was calculated by dividing sample radioactivity by incubation time.

For experiments using Exetainer vials, isotopically diluted L-[3,4,5-3H(N)]-Leucine addition was scaled to achieve 20 nM final concentrations in the ~ 3.0 mL volume Exetainer vial subsample.  The addition of TCA was also scaled accordingly. Vials were carefully and fully filled with subsample prior to capping to prevent leaking or cracking when pressure was applied. 

Data were processed using Microsoft Excel.

- Imported "2025.09.24_EN683 Bulk_ LVs_Sar_Press_3H-Leucine_incorporation.csv" into the BCO-DMO system
- Combined "date" and "time" (local EST time) and converted the value into a UTC ISO datetime value
- Removed MPa unit from the "incubation_pressure" field
- Renamed fields to comply with BCO-DMO naming guidelines, removing spaces, units, and parentheses
- Exported file as "985783_v1_en683_bacterial_productivity.csv"

Substrate Structural Complexity and Abundance Control Distinct Mechanisms of Microbially-Driven Carbon Cycling in the Ocean

Almost half of the organic carbon produced in the ocean is processed by bacteria. Bacteria use extracellular (outside the cell) enzymes to break down large organic molecules to small sizes that can be transported into their cells. It has recently been discovered that bacteria use extracellular enzymes in two ways: ‘selfish uptake’ and ‘external hydrolysis’. External hydrolysis releases low molecular weight products to the environment where they can be used by other organisms. ‘Selfish uptake’ releases little or no products. This research will determine the extent and location of ‘selfish uptake’ in ocean waters. This process affects the distribution of organic carbon in the ocean, the flow of small organic molecules to feed a wider range of bacteria, and the composition and dynamics of the bacterial community. Recent results show that ‘selfish’ bacteria are active in deep ocean waters, where they take up complex polysaccharides (sugars) that are not hydrolyzed externally. These results inspired a new model that links ‘selfish uptake’ and external hydrolysis to the amount and complexity of the organic matter that is used by bacteria. This project will test the model by describing the polysaccharide fraction of marine organic matter, and studying the relationships between organic matter abundance, structural complexity, and extracellular enzyme use. Graduate and undergraduate students will participate in the project as members of the research team in the field and in the laboratory.

This research will test the hypothesis that the mechanism of polysaccharide processing is related to the cost to a cell of producing the enzymes required for its hydrolysis, and the probability that a cell will receive sufficient return on investment for producing the enzymes. The conceptual model that will be tested suggests that external hydrolysis is favored when organic matter is abundant, or when enzyme production costs can be shared (e.g., on particles, in biofilms); selfish uptake would be a better strategy when high molecular weight (HMW) organic matter is scarce, and particularly when the HMW organic matter is very complex. This study will test this model by characterizing the structure of polysaccharide-containing components of dissolved organic matter (DOM) and particulate organic matter (POM) collected from the ocean, by determining the extent of selfish uptake and rates of external hydrolysis of different polysaccharides by natural microbial communities from the surface and the deep ocean, and by incubation experiments that control for the abundance of polysaccharides of different structural complexity. This project will be carried out in collaboration with colleagues at the Max Planck Institute for Marine Microbiology, whose expertise in carbohydrate chemistry and structural analyses, and in advanced microscopy and analysis of complex microbial communities, are central to the project.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.