Genomic DNA-seq datasets for 69 Raoultella isolates

A major unresolved question is how bacteria living in complex communities respond to environmental changes. The evolution of single species in isolation has been well studied; however, in nature species are embedded within complex communities. In communities, biotic interactions may either facilitate or constrain evolution depending on whether the interactions expand or contract the range of ecological opportunities. A fundamental challenge is to understand how the surrounding biotic community alters evolutionary trajectories as species adapt to novel environmental conditions. Here we show how community context can dramatically alter the evolutionary dynamics of bacterial populations. We find that evolution of focal bacterial strains depends on properties both of the focal strain and of the surrounding community. In particular, there was a stronger evolutionary response in low-diversity communities, and when the focal species had a larger genome and were initially poorly adapted. We see how community context affects resource usage and detect genetic changes involved in carbon metabolism and inter-specific interaction. The findings demonstrate that adaptation to new environmental conditions can only be understood in the context of interspecific interactions.