Impact of ecological interactions on mutant fitness and evolution in microbes

Project Summary/Abstract Microbes acquire an enormous number of new mutations every day in nature, which enables them to rapidly adapt to environmental changes. At the same time, these microbes are often dependent on interactions between species and strains, especially the exchange of nutrients (cross-feeding). Our ability to predict evolution of mi- crobes in different ecological environments is valuable for treating infectious diseases — for example, anticipating if and how fast a pathogen will evolve resistance to a treatment — as well as for designing personalized medicine based on an individual’s evolving microbiome. The overall goal of our lab’s research is therefore to understand the feedback between these evolutionary and ecological processes in microbial communities. A particular chal- lenge in this field is our ability to quantitatively predict the effects of mutations on fitness, and how those effects vary across ecological environments. The distribution of fitness effects — the set of fitness values for all spon- taneous mutations available to a population — is a key input to predicting how a population will evolve, and its variation across environments can reveal unknown gene functions. However, since we cannot empirically mea- sure the fitness of mutations across all possible environments, it is crucial that we develop general principles for how mutant fitness changes across these environments to predict evolution. We need to know these rules, for example, to predict whether cross-feeding certain nutrients is likely to make a species adapt more slowly or more quickly, and how it changes the genes and molecular pathways under selection. In the next five years, our lab seeks to develop principles by which ecological interactions affect mutant fitness by addressing three questions: 1) Do different kinds of interactions have different effects on mutant fitness? 2) Do different kinds of mutants respond differently to interactions? 3) What mechanisms cause interactions to alter mutant fitness? We will focus on Escherichia coli auxotrophs that allow us to engineer defined cross-feeding interactions, combined with DNA barcoding for generating and tracking high-throughput mutant libraries. We will experimentally measure the effect of cross-feeding different types of nutrients (amino acids, vitamins, carbon intermediates) on mutant fitness, as well as the effect of cross-feeding on different types of mutants (gene knockouts from transposon insertions vs. spontaneous mutations from an evolution experiment). In parallel we will use whole-genome metabolic models to make predictions for these experiments and investigate the underlying mechanisms. In particular, we seek to test how metabolic cheating and changes in nutrient limitation mediate the effect of cross-feeding on mutant fitness. Our long-term goal is to apply the principles we learn from this laboratory system to complex, naturalistic com- munities that involve a range of ecological interactions. Our work on this problem will contribute toward predicting microbial evolution across ecological environments as well as helping discover new functions of genes, especially secondary activities that arise under nutrient conditions not commonly tested in the lab.