Research
We uncover the biochemical mechanisms that determine how microbes function and how they shape the ocean carbon cycle
The ocean is one of Earth's most powerful carbon reservoirs, and microbes are the engine behind it. But the biochemical rules that govern how microbial life controls carbon fate in the ocean remain poorly understood. Our lab investigates these rules at the most fundamental level: the chemistry happening inside and between microbial cells.
Our work targets two scales. At the biochemical level, we investigate how marine enzymes transform carbon-containing molecules, altering their structure and determining whether they get broken down, passed through the food web, or persist in the environment. At the microbial community level, we examine how interactions between microbes collectively shape which carbon compounds accumulate and which disappear. Together, these processes control how carbon moves between its possible fates in the ocean.
Microbes drive the formation of one of Earth's biggest carbon reservoirs
The ocean harbors one of Earth's largest carbon reservoirs, a vast pool of dissolved organic carbon (DOC) nearly as large as all the carbon in the atmosphere. The story begins with phytoplankton, which are responsible for roughly half of all photosynthetic carbon capture on Earth, matching the combined output of every plant on land. Once that carbon enters the ocean, its fate branches in several directions. Some is broken down by microbial cells for energy and returned to the water and air as CO₂. Some is released as molecules that feed bacteria at the base of the food web. Some becomes microbial biomass that sinks to the seafloor as particles, locking carbon in deep sediments for millennia.
And then there is something stranger: some carbon resists consumption entirely, accumulating as an enormous pool of small dissolved molecules that collectively contain more carbon than all the plants on land combined and can persist in seawater for thousands of years. How microbes produce these molecules, through what enzymatic reactions and cellular processes, and why they resist breakdown so effectively, remains one of the great open questions in ocean science. Even the apparent stability of these molecules is puzzling: on average they are only around 5,000 years old, far younger than their persistence would suggest.
Understanding what controls these different carbon fates, and what shifts the balance between them, is at the heart of what we do.
Combining mass spectrometry and enzyme assays to reveal how microbes transform carbon
Enzymes catalyze carbon transformations both within microbial cells, shaping metabolism and carbon flux, and outside them, influencing interactions with neighboring microbes and the broader chemistry of the ocean. To understand these transformations, we develop and apply high-throughput metabolomics platforms combined with enzyme assays, allowing us to quantify intracellular and extracellular chemistry across hundreds of strains, conditions, and timepoints simultaneously.
This scale is essential. Many of the biochemical principles that govern microbial behavior only become visible when you can compare across a large number of conditions at once. By combining throughput with molecular resolution, we aim to uncover the enzymatic and metabolic mechanisms that determine carbon fate, identify how environmental perturbations shift those mechanisms, and extract fundamental principles about how microbial life works that would remain invisible in smaller studies.
The insights we gain are not limited to the ocean. The biochemical principles that emerge from this work speak to how microbes function in any environment, and may ultimately inform how we think about engineering microbial metabolism for other applications.
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Pontrelli, S., Bigovic Villi, K., Sichert, A., Trouillon, J., Rutz, A., Landry, Z., Rudisser, S.H., Stocker, R. and Sauer, U., 2025. Degradation of extracellular polymeric substances shapes microbial community diversity Plos Biology
Clerc, E. E., Raina, J. B., Keegstra, J. M., Landry, Z., Pontrelli, S., Alcolombri, U., ... & Stocker, R. (2023). Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nature Communications
Pontrelli, S., Szabo, R., Pollak, S., Schwartzman, J., Ledezma-Tejeida, D., Cordero, O. X., & Sauer, U. (2022). Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. Science advances