Modeling the influence of metabolic trade-offs on microbiota diversity

Metagenomics has revealed huge diversity in nature, with thousands of microbial species coexisting in microbiota. However, classical resource-competition models predict that the number of species in steady coexistence cannot exceed the number of resources. To investigate the role of environmental conditioning and trade-offs in promoting diversity, we physically modeled the population dynamics of microbes that compete for resources in a chemostat. The model reproduces several notable features of natural ecosystems, including high diversity, keystone species, and characteristics of neutral theory, despite an underlying non-neutral competition for resources. Do metabolic trade-offs still promote diversity if nutrient supplies vary in time or if populations are spatially structured? The answer is yes in both cases. Serial dilutions preserve diversity, but with a surprising non-monotonic dependence on nutrient supply. Spatial structure selects one diverse solution, rather than a degenerate set. Importantly, we find that temporal or spatial variation permit diversity even when trade-offs are only approximate.