PriME Project: Optimal Foraging and Community Assembly in Microbial Ecosystems
The ecological interactions of microbes govern the cycling of the elements and the health and productivity of the planet. However, despite their fundamental importance, we know relatively little about how microbial communities are assembled and how they function.
This project will use micro-scale engineering, real-time visualization approaches, Raman microspectroscopy and mathematical modeling to tease apart the influences on the organization of microbial communities in marine ecosystems. We will develop microdevices to create experimental microenvironments, in the form of an array of patches with precisely controlled nutrient availability. This will allow us to manipulate the spatial and temporal nutrient landscape, in order to study community assembly in laboratory-assembled panels of microbial strains. Integration with epifluorescent microscopy, confocal microscopy and Raman microspectroscopy will provide real-time measurements of community dynamics and metabolism. Our experimental approaches will both direct and gain inspiration from the development of optimal foraging models, with the aim of integrating microbial physiology, behavior and community ecology.
Roman Stocker is a professor of environmental engineering at ETH Zürich. Stocker is Italian and grew up in Nigeria, Yemen and Venice. He studied engineering and fluid mechanics and completed 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 the Massachusetts Institute of Technology, and he then became an assistant professor there. In 2015 he moved to ETH Zürich. Stocker 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: how to study marine microbes quantitatively, with explicit consideration of their highly dynamic processes at the micro-scale. Stocker’s research group, which brings together more than 20 physicists, biologists, mathematicians and engineers, uses quantitative experiments in combination with individual-based and continuum models to understand micro-scale 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. Stocker has brought to the field a unique combination of (i)imaging and image analysis, revealing previously unseen processes; (ii) new engineering tools, primarily microfabrication and 3-D printing, providing unprecedented access to quantitative experiments on marine microbes; and (iii) an intimate connection between observations and mathematical models for the purpose of identifying general principles of microbial ecosystems. Stocker’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.