Uncovering how microbes dismantle seaweed cell walls

Macroalgae (seaweeds) are major primary producers in coastal ecosystems and have existed for hundreds of millions of years. A large fraction of their biomass is their cell wall, built from distinctive polysaccharides that differ across algal groups. Red algae are rich in agar and carrageenans, while brown algae mainly contain alginate. These polymers help seaweeds withstand a harsh marine environment—high salt, drying during low tide and sun exposure, and strong waves—while also giving seaweed extracts useful properties such as gelation and thickening, widely exploited in food, cosmetics, and other industries. More recently, algal carbohydrates and their breakdown products have attracted interest for potential biomedical and biotechnological applications, intensifying research into how they are degraded.In nature, bacteria and fungi living on seaweeds feed on these cell-wall polysaccharides. To do so, they produce specialized enzymes tailored to the chemistry of each polymer. In our recent work, we clarified the catalytic strategies used by three key enzyme families involved in the degradation of algal cell walls: enzymes that break down red-algal polysaccharides (agar and carrageenans) and an alginate-degrading enzyme from brown algae that operates through a previously unrecognized mechanism. This research was carried out in close collaboration with teams at the Station Biologique de Roscoff (France) and the Technical University of Denmark, who provided high-resolution enzyme structures and kinetic measurements.Using high-performance computing resources, we performed atomistic simulations that combine quantum chemistry and molecular dynamics to follow the chemical reaction inside the enzyme active site. Beyond identifying “what reacts with what”, these calculations reveal short-lived but crucial steps—such as transition states—and how the carbohydrate chain is positioned and reshaped during catalysis [1-3]. Together with experimental data, this mechanistic understanding can guide the development of selective inhibitors and molecular probes, and support enzyme engineering to produce tailored algal oligosaccharides of biotechnological interest.