Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations.

Katrina B Harris,Vaughn S Cooper,Kenneth M Flynn,Deepa Agashe

doi:10.1093/molbev/msab248

Katrina B Harris, Vaughn S Cooper + Show 2 more

Open Access

https://doi.org/10.1093/molbev/msab248

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Abstract

How biodiversity arises and can be maintained in asexual microbial populations growing on a single resource remains unclear. Many models presume that beneficial genotypes will outgrow others and purge variation via selective sweeps. Environmental structure like that found in biofilms, which are associated with persistence during infection and other stressful conditions, may oppose this process and preserve variation. We tested this hypothesis by evolving Pseudomonas aeruginosa populations in biofilm-promoting arginine media for 3 months, using both a bead model of the biofilm life cycle and planktonic serial transfer. Surprisingly, adaptation and diversification were mostly uninterrupted by fixation events that eliminate diversity, with hundreds of mutations maintained at intermediate frequencies. The exceptions included genotypes with mutator alleles that also accelerated genetic diversification. Despite the rarity of hard sweeps, a remarkable 40 genes acquired parallel mutations in both treatments and often among competing genotypes within a population. These incomplete soft sweeps include several transporters (including pitA, pntB, nosD, and pchF) suggesting adaptation to the growth media that becomes highly alkaline during growth. Further, genes involved in signal transduction (including gacS, aer2, bdlA, and PA14_71750) reflect likely adaptations to biofilm-inducing conditions. Contrary to evolution experiments that select mutations in a few genes, these results suggest that some environments may expose a larger fraction of the genome and select for many adaptations at once. Thus, even growth on a sole carbon source can lead to persistent genetic and phenotypic variation despite strong selection that would normally purge diversity.

Highlights

Bacterial populations inhabit countless environments along a continuum of spatial structure, ranging from a well-mixed liquid to rugged, solid surfaces
The culture medium was M63 media containing arginine as the sole carbon and nitrogen source and supplemented with 25 mM iron, a combination which has been shown to promote biofilm production in Pseudomonas species (Bernier et al 2011). We hypothesized that this media may select different adaptive mutations than those described in prior evolution experiments with P. aeruginosa (Barrett et al 2005; Wong et al 2012) because of its different metabolic demands and because biofilm production is externally induced, allowing us to identify subsequent steps of adaptation that are less known
We used experimental evolution to examine how the opportunistic pathogen P. aeruginosa adapts in laboratory culture in a medium known to promote biofilm formation (Ha et al 2014), comparing the results of propagation by simple serial dilution with a model simulating the biofilm life cycle (Poltak and Cooper 2011)

Summary

Introduction

Bacterial populations inhabit countless environments along a continuum of spatial structure, ranging from a well-mixed liquid to rugged, solid surfaces. This greater diversity increases competition between adaptive mutations, known as clonal interference (Rainey and Travisano 1998; Boles et al 2004; Habets et al 2006; Wong et al 2012; Traverse et al 2013; Flynn et al 2016; Santos-Lopez et al 2019) Despite this process of diversification, replicate populations propagated in both biofilm and planktonic conditions exhibit high levels of both phenotypic and genetic parallelisms, suggesting some measure of predictability within the same environment (Wong et al 2012; Tognon et al 2017; Yen and Papin 2017; Sanz-Garcıa et al 2018; Turner et al 2018). We still have much to learn about how the biofilm life cycle influences evolutionary dynamics and processes, including the relative roles of mutation and selection, and whether biofilm growth becomes the dominant selective force relative to other stresses like nutrient limitation or external toxins

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