Amino acid cross-feeding in E. coli globally and idiosyncratically alters mutant fitness

Abstract

Cross-feeding between microbes is believed to be common in many natural ecosystems, especially between species that are auxotrophic for essential nutrients such as amino acids. Several recent studies have demonstrated that cross-feeding and other ecological interactions between microbes alter their evolution and the fitness of mutations. However, these studies focused on interactions between different species, where the nature of the interaction is complex due to the large genetic differences between species, making it difficult to directly attribute changes in mutant fitness to a specific interaction. To address this problem, we use a synthetic cross-feeding interaction between isoleucine and methionine auxotrophs of Escherichia coli, two commonly observed auxotrophies in bacterial genomes. Using a library of genome-wide knockout mutants from transposon insertions, we measure the fitness of these mutants in the presence and absence of cross-feeding. We find that cross-feeding either isoleucine or methionine globally shifts mutant fitness to become more beneficial on average by inducing strong positive selection on a few mutants and rescuing strongly deleterious mutants. However, cross-feeding also affects mutants idiosyncratically: the most beneficial mutants under cross-feeding are neutral or deleterious without cross-feeding, and cross-feeding isoleucine affects different genes than cross-feeding methionine does. We discover one spontaneous mutant, with especially dramatic idiosyncratic effects under isoleucine cross-feeding, that achieves this phenotype by becoming a partial threonine auxotroph and reversing its ancestral isoleucine auxotrophy. This work directly demonstrates the statistical patterns and possible mechanisms by which a common ecological interaction between microbes alters their mutant fitness.