The interactions of bacteria with phytoplankton and with marine particles are central to the role of bacteria in global biogeochemical cycling and control over atmospheric carbon levels. As part of PriME, Roman Stocker’s group will lead three projects to understand how microscale interactions govern the assembly of microbial communities and so lay the foundations for the fundamental ecological functions of marine bacteria.
1. The signaling role of phytoplankton metabolites as a driver of microbial community assembly in phycospheres. Phytoplankton metabolites serve as growth substrates, but also as signals for bacteria. Through a combination of laboratory trials and experiments directly in the ocean, the group will study chemotaxis of bacteria toward (but also potentially away from) phytoplankton. The goal is to understand to what extent behavior contributes to community assembly in phycospheres (the metabolite-rich region surrounding individual phytoplankton cells).
2. The spatial and temporal interactions of bacteria and phytoplankton. Because of the substantially enhanced ability of bacteria and phytoplankton to exchange metabolites when they are in close proximity to each other, compared to when they are randomly dispersed in the water column, their interactions are expected to have an important spatial component. In this project, the group will study the spatial and temporal interactions between phytoplankton and bacteria, employing microfluidics to create precisely controlled laboratory environments and using long-term video tracking of individual bacteria to quantify their behavior.
3. Degradation of particles in flow by multi-species communities. One of the defining features of marine snow particles is their propensity to sink in the water column, transporting carbon from surface waters to the oceans’ depths. This phenomenon, which is key for the global cycling of carbon, implies that the interactions between bacteria and marine snow occur in conditions of constant fluid flow around the particles. In the first phase of PriME, Stocker’s group discovered that fluid flow can increase the rate of particle degradation by attached bacteria by over an order of magnitude, due to the removal of the degradation products that otherwise inhibit further degradation. In this project, the group will ask how interactions among bacterial species that colonize marine particles affect the degradation of the particle, by using a microfluidic model system to study the impact of fluid flow on the assembly and functioning of marine microbial communities.
Roman Stocker is a professor of environmental engineering at ETH Zürich. He is Italian, grew up in Nigeria, Yemen and Venice, and graduated from the University of Padova, where he studied engineering and fluid mechanics before completing his Ph.D. on the mathematical modeling and field observation of internal waves in lakes. From 2002 to 2005, he was an instructor in applied mathematics at MIT, where he then became an assistant professor in Environmental Engineering. In 2015, he moved to ETH. Roman pioneered a new approach to microbial ecology, based on the combination of microtechnology and mathematical modeling, which allowed him to address a long-standing challenge in oceanography: the need to study marine microbes quantitatively at the single-cell level and with explicit consideration of their highly dynamic processes at the microscale.
Roman’s research group, which brings together more than 30 physicists, biologists, mathematicians and engineers, uses quantitative experiments in combination with individual-based and continuum models to understand microscale processes in the ocean, including microbial motility and sensing, the role of microbes in the marine carbon cycle, harmful algal blooms, coral disease, oil degradation, viral infection and bacteria–phytoplankton interactions. Roman has brought to the field a unique combination of (1) imaging and image analysis, revealing previously unseen processes; (2) new engineering tools, primarily microfabrication and 3D printing, providing unprecedented access to quantitative experiments on marine microbes; and (3) an intimate connection between observations and mathematical models, as necessary to identify general principles of microbial ecosystems. Roman’s work has frequently appeared in high-profile journals including Science, Nature and the Proceedings of the National Academy of Sciences, and has been featured in popular media including the BBC, CNN and The New York Times.