Metabolic adaptation to consume butyrate under prolonged resource exhaustion

Bacteria must often survive following the exhaustion of their external growth resources. Fitting with this need, many bacterial species that cannot sporulate, can enter a state known as long term stationary phase (LTSP) in which they can persist for years within spent media. Several recent studies have revealed the dynamics of genetic adaptation of Escherichia coli under LTSP. Yet, the metabolic consequences of such genetic adaptation were not addressed. Here, we characterized the metabolic changes LTSP populations experience, over the first 32 days under LTSP. This allowed us to link genetic adaptations observed in a convergent manner across LTSP populations back to their metabolic adaptive effect. Specifically, we demonstrate that through the acquisition of mutations combinations in specific sets of metabolic genes, E. coli acquires the ability to consume the short chain fatty acid butyrate. Intriguingly, this fatty acid is not initially present within the rich media we used in this study. Instead, it is E. coli itself that produces butyrate during its initial growth within fresh rich media. The mutations that enable butyrate consumption allow E. coli to grow on butyrate. However, the clones carrying these mutations rapidly decrease in frequency, once the butyrate is consumed, likely reflecting an associated cost to fitness. Yet despite this, E. coli populations show a remarkable capability of maintaining these genotypes at low frequency, as standing variation. This in turn allows them to more rapidly re-adapt to consume butyrate, once it again becomes available to them. Author summaryBacteria are able to survive prolonged periods of resource exhaustion. This ability is crucial for survival within many natural environments. Here, we link the metabolic changes the model bacterium Escherichia coli experiences during the first 32 days of growth under resource exhaustion to its genetic adaptation. We show that E. coli produces an important short chain fatty acid, butyrate, during the first 24 hours of growth within rich media. E. coli is not initially able to consume this metabolite but adapts to do so during our experiments. We show that these genetic adaptations enable growth on butyrate, but that the clones carrying them likely suffer a cost, when no butyrate is available. Despite these costs, and despite our populations being well mixed and subject to strong selection, these mutations are maintained at low frequencies within the evolving populations. This enables these populations to more rapidly re-adapt to consume butyrate. Our findings likely exemplify the more general ability of bacterial populations to maintain previous metabolic adaptations as standing variation, allowing rapid re-adaptation to previously met conditions.