Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets.

Philip Ruelens,J Arjan G M De Visser

doi:10.3390/genes12020223

Abstract

Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment. Yet, our knowledge about adaptation in very small populations, where selection strength and mutation supplies are limited, is scant. In this study, wild-type and mutator strains of the bacterium Escherichia coli were evolved for about 100 generations towards increased resistance to the β-lactam antibiotic cefotaxime in millifluidic droplets of 0.5 µL and effective population size of approximately 27,000 cells. The small effective population size limited the adaptive potential of wild-type populations, where adaptation was limited to inactivating mutations, which caused the increased production of outer-membrane vesicles, leading to modest fitness increases. In contrast, mutator clones with an average of ~30-fold higher mutation rate adapted much faster by acquiring both inactivating mutations of an outer-membrane porin and particularly inactivating and gain-of-function mutations, causing the upregulation or activation of a common efflux pump, respectively. Our results demonstrate how in very small populations, clonal interference and mutation bias together affect the choice of adaptive trajectories by mediating the balance between high-rate and large-benefit mutations.

Highlights

In contrast to the common perception that evolution happens over long timescales, pathogens and cancer cells may change evolutionarily within a timescale of days
By characterizing the evolved populations phenotypically and genotypically, we show that while adaptation of these small populations is limited by the supply of beneficial mutations, increasing the overall mutation rate by ~30-fold can alleviate this limitation and result in substantially increased adaptation through similar high-benefit mutations upregulating and activating a multidrug efflux pump, removing an outer-membrane porin, or increasing the production of outermembrane vesicles
Experimental evolution was performed in the presence of a sub-lethal concentration of β-lactam antibiotic cefotaxime with Escherichia coli B strain REL606, which has been regularly used for experimental evolution [11,12,22]

Summary

Introduction

In contrast to the common perception that evolution happens over long timescales, pathogens and cancer cells may change evolutionarily within a timescale of days. Such fast evolution can cause health problems when, for example, bacterial infections or cancer cells become resistant to the drugs used to cure them [1,2]. Predicting these unwanted evolutionary trajectories would present possibilities to intervene and control the problems they pose [3,4]. In small populations adaptation relies more heavily on the chance occurrence of beneficial mutations and, mutation bias has a relatively stronger impact [9,10]

Methods

Results

Conclusion