Department Environmental Microbiology

Project MicroscapesX

Individual microbial cells rarely exist alone in the natural environment. Instead, they typically arrange themselves in space relative to other cells. Spatial positioning determines how different cells interact with each other (e.g., positive or negative effects on each other) and how those interactions lead to emergent community behaviors. The main objective of Microscapes is to understand the underlying processes that give rise to spatial self-organization and to predict the consequences of spatial self-organization on ecological processes.

To address our objective, we use synthetic microbial ecosystems where we impose specific types of interactions between different cell types. We then manipulate those interactions and measure the consequences on spatial self-organization and emergent community behaviors. We finally develop quantitative and predictive models for the formation and dynamical behavior of spatially assembled communities.

Microscapes is an inherently interdisciplinary project that encompasses a wide range of biological disciplines, including microbiology, ecology, evolution, and systems biology. We always strive to integrate experiments with mathematical modeling. The broader project therefore encompasses a total of five research groups that meet on a regular basis and have different expertise. Three groups focus on experimentation (Jan Roelof van der Meer, UNIL; Yok Que Ai, CHU; David R. Johnson, Eawag) while the other two focus on mathematical modeling (Dani Or, ETHZ; Vassily Hatzimanikatis, EPFL).

Publications

Metabolic specialization and the assembly of microbial communities

Metabolic specialization is a general biological principle that shapes the assembly of microbial communities. Individual cell types rarely metabolize a wide range of substrates within their environment. Instead, different cell types often specialize at metabolizing only subsets of the available substrates. What is the advantage of metabolizing subsets of the available substrates rather than all of them? In this perspective piece, we argue that biochemical conflicts between different metabolic processes can promote metabolic specialization and that a better understanding of these conflicts is therefore important for revealing the general principles and rules that govern the assembly of microbial communities. We first discuss three types of biochemical conflicts that could promote metabolic specialization. Next, we demonstrate how knowledge about the consequences of biochemical conflicts can be used to predict whether different metabolic processes are likely to be performed by the same cell type or by different cell types. We then discuss the major challenges in identifying and assessing biochemical conflicts between different metabolic processes and propose several approaches for their measurement. Finally, we argue that a deeper understanding of the biochemical causes of metabolic specialization could serve as a foundation for the field of synthetic ecology, where the objective would be to rationally engineer the assembly of a microbial community to perform a desired biotransformation.
Johnson, D. R.; Goldschmidt, F.; Lilja, E. E.; Ackermann, M. (2012) Metabolic specialization and the assembly of microbial communities, ISME Journal, 6(11), 1985-1991, doi:10.1038/ismej.2012.46, Institutional Repository