Exploring the ecological landscape of microbial communities

• Applicant: Dr. Christoph Ratzke
• Subject Area: Microbial Ecology and Applied Microbiology ; Biophysics
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 468972576

Microbes usually don’t live isolated but with many other microbes in complex communities. Despite the importance of those communities for our health and well-being – especially given the complex microbial communities that live in and on our body – we have very limited understanding of how these systems function. Especially a mechanistic understanding how interactions between the microbes shape the overall community is largely missing. Other complex dynamical systems like evolving systems or folding proteins were described with “energy landscapes” in which the system of interest has the tendency to move towards the valleys (or tops) of this landscape. Recent publications – also of us - suggest that this concept might be also valid for complex microbial communities; as a kind of “ecological landscape”. Complex microbial systems would therefore - driven by microbial interactions – move towards states that correspond to valleys in this landscape. The number of those valleys would decide in how many final states the system can reside – eg mono- vs multistability.In this project we will test in how far the idea of “energy landscapes” can be transferred to microbial communities and function as a framework to describe and predict their properties. This will be achieved by integrating lab experiments, mathematical modeling and next generation sequencing. We are further interested if we can predict the overall shape of such ecological landscapes by knowing the prevalent type of interactions within the community.For that purpose we will first search for conditions that enrich specific types of microbial interactions (resource competition, toxic warfare, cross-feeding and cross-protection) in pairwise co-culture. Then we will use mathematical modeling to predict the shape of ecological landscapes for microbial communities that are enriched in one of those interaction types. Finally, we will experimentally scan ecological landscapes by building a large number of communities with same species compositions but different abundances. We will follow the trajectories of those communities by next generation sequencing to achieve a direct mapping of the ecological landscape, to see how they depend on the interactions within the communities and compare the results with our simulations. Overall, we aim to establish the concept of ecological landscapes as a framework to describe complex microbial systems and their behavior. Such a framework would be central to specifically manipulate and design microbial communities in the future which is the long term goal of our lab.

• DFG Programme: Research Grants