Searching for principles in microbial ecology: from individual physiology to collective metabolism in microbial communities

Microbial communities underpin nearly every ecosystem on Earth, from the open ocean to the human gut. They drive key biogeochemical cycles and affect the health of hosts and environments alike. Un-derstanding these communities is challenging because they are extraordinarily diverse and dynamic. In the first part of my talk, I will give a general introduction to microbial communities – why they mat-ter and how we think they work. I will argue that a central challenge in microbial ecology is connecting two very different kinds of knowledge: the detailed mechanistic understanding we have of a few model species, and the large-scale, sequence-based descriptions we now have of natural communi-ties that rarely contain those model species.
In the second part, I will show how my own research addresses this challenge by identifying simplify-ing principles for marine bacteria and their communities. Focusing on the important polysaccharide chitin, we found that the bacterial members of polysaccharide-degrading communities can be de-scribed in three stably coexisting functional groups, which interact by dynamically exchanging me-tabolites. To dive deeper into these metabolic strategies, we used high-throughput metabolic profiling and comparative genomics to show that the vast diversity of heterotrophic bacteria can be captured by a simple dichotomy: a preference for consuming sugars versus amino and organic acids. This preference is encoded in their genomes, enabling us to make predictions about the metabolic strate-gies underpinning complex communities from sequencing data. Together, these results illustrate how trait-based frameworks can bridge scales and enable more predictive, theory-driven approaches to microbial community ecology.