Modeling Microbial Community Composition and Robustness in Changing Environments

Microbial communities are embedded in incredibly complex environments, shaped by abiotic factors such as pH, temperature, and aridity as well as metabolic factors such as nutrient and toxin levels driven by the microbes themselves. Environmental change can alter which taxa are present (composition) and how those taxa interact (dynamics). Predicting microbiome responses to environmental shifts requires understanding both processes: how environments filter community composition, and how the resulting interactions determine whether communities persist under perturbation.

In this dissertation, I develop two complementary frameworks for understanding these responses. First, I ask how the environment shapes community composition and whether environmental gradients filter for traits that reflect long-term evolutionary history or near-term adaptation.  This work suggests a two-scale view of microbial assembly: the dominant environmental axis structures community composition via deeply conserved traits, whereas secondary environmental effects structure the community via more evolutionarily labile traits. Second, I ask how complex interactions mediated by space, metabolism, and other mechanisms influence community robustness. This work suggests that diverse mechanisms of interactions between populations of microbes in a community promote robustness insomuch as they reduce the temporal overlap of rapid growth between species. Together, these results provide cross-cutting frameworks for understanding how microbial composition and robustness may change as environmental conditions shift.