Role of metabolism and ecology in the emergence of microbial communities

Polymicrobial communities often show complex patterns of metabolic and ecological interactions, yet our understanding of how the properties of communities emerge from the metabolic rules of species interactions is still limited. A central feature of metabolic interactions within microbial communities is ‘cross-feeding’, where one species or lineage consumes the metabolic by-products of another. Cross-feeding bacteria excrete and consume a wide range of metabolites and this sets the stage for diverse intra- and inter-specific metabolic interactions. In this thesis, I use ecological and evolutionary theory to address a number of critical questions posed by cross-feeding bacteria, with a particular focus on the role played by microbial metabolism in driving the emergence and dynamics of microbial interactions. First, I explore the conditions that favour the emergence and maintenance of cooperative cross-feeding and show that the evolutionary outcome depends strongly on the shape of the trade-off curves between the costs and benefits of cooperation. Second, I investigate the origins of cross-feeding interactions via single lineage diversification and derive new predictions on the physiological mechanisms that may explain the stable coexistence of a cross-feeding polymorphism that evolved from a single clone. Third, I investigate what are the ecological consequences of cross-feeding metabolic interactions and demonstrate theoretically that a simple mechanism of trade can generate a diverse array of ecological relationships. Furthermore, I show the importance of the metabolic by-product properties in determining the ecological outcome. Fourth, I investigate how metabolic constraints of individual species shape the emergent functional and structural relationships among species. I show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Furthermore, I show that these emergent community properties are driven by demographic feedbacks. In general, these findings support the idea that bridging microbial ecology and metabolism is a critical step toward a better understanding of the factors governing the emergence and dynamics of polymicrobial interactions.