Pseudomonas Putida Dynamics of Adaptation under Prolonged Resource Exhaustion

Abstract

Many non-sporulating Bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase (LTSP). Here, we performed LTSP evolutionary experiments on the bacterium Pseudomonas putida, followed by whole genome sequencing of evolved clones. We show that P. putida is able to persist and adapt genetically under LTSP. We observed a gradual accumulation of mutations within the evolving P. putida populations. Within each population, independently evolving lineages are established early on and persist throughout the four-month-long experiment. Mutations accumulate in a highly convergent manner, with similar loci being mutated across independently evolving populations. Across populations, mutators emerge, that due to mutations within mismatch repair genes developed a much higher rate of mutation than other clones with which they co-existed within their respective populations. While these general dynamics of the adaptive process are quite similar to those we previously observed in the model bacterium Escherichia coli, the specific loci that are involved in adaptation only partially overlap between P. putida and E. coli. Significance statementBacteria often face conditions of prolonged nutrient limitation, following periods of growth. One strategy for dealing with this challenge is entry into a state termed long-term stationary phase (LTSP), in which a small minority of cells within a population can survive and persist, by recycling the remains of their deceased brethren. Here, we broaden our understanding of adaptation under LTSP, by studying it in the bacterium Pseudomonas putida. We show that many of the dynamics of LTSP genetic adaptation are quite general, as reflected by great similarity to what was previously observed in the model bacterium Escherichia coli. However, the specific loci that are involved in adaptation substantially vary between P. putida and E. coli.