Natural Escherichia coli isolates rapidly acquire genetic changes upon laboratory domestication

The adaptation of environmental bacteria to laboratory conditions was analysed through the exploration of genomic changes in four strains of Escherichia coli freshly isolated from their natural habitats and belonging to different taxonomic clusters. Up to 25 mutations were present in all cultures of natural isolates within 10 days of transfer in rich media or with a single growth cycle involving an extended stationary phase. Among numerous individual mutations, two genes were affected in parallel in distinct backgrounds. Mutations in rpoS (encoding sigma factor RpoS), altering a multiplication-survival trade-off in E. coli, were present in isolates derived from all four different ancestors. More surprisingly, two different natural isolates acquired mutations in mutL, affecting DNA mismatch repair, and a third also involved higher mutation rates. The elevated mutation rates in these isolates indicate the danger of increased genetic instability arising from laboratory domestication. Neither rpoS nor mutator mutations were detected in the already-acclimatized MG1655 laboratory strain; only one or no new mutations were present in the laboratory strain under the same culture conditions. Our results indicate rapid adaptation to the laboratory environment. Ancestor-specific responses also arise in the laboratory and mutational events are also sensitive to culture conditions such as extended stationary phase. To maintain natural isolates in a stable state, our data suggest that the transition of strains to the laboratory should minimize culture cycles and extended stationary phase.