Dynamics of adaptation during three years of evolution under long-term stationary phase

Many bacterial species that cannot sporulate, such as the modelbacterium Escherichia coli, can nevertheless survive for years underresource exhaustion, in a state termed long-term stationary phase(LTSP). Here we describe the dynamics of E. coli adaptation during thefirst three years spent under LTSP. We show that during this time E.coli continuously adapts genetically, through the accumulation ofmutations. For non-mutator clones, the majority of mutationsaccumulated appear to be adaptive under LTSP, reflected in anextremely convergent pattern of mutation accumulation. Despite therapid and convergent manner in which populations adapt under LTSP,they continue to harbor extensive genetic variation. The dynamics ofevolution of mutation rates under LTSP are particularly interesting.The emergence of mutators, affects overall mutation accumulation ratesas well as the mutational spectra and the ultimate spectrum ofadaptive alleles acquired under LTSP. With time, mutators can evolveeven higher mutation rates, through the acquisition of additionalmutation-rate enhancing mutations. Different mutator and non-mutatorclones within a single population and time point can display extremevariation in their mutation rates, resulting in differences in boththe dynamics of adaptation and their associated deleterious burdens.Despite these differences, clones that vary greatly in their mutationrates tend to co-exist within their populations for many years, underLTSP.