Escherichia colicultures maintain stable subpopulation structure during long-term evolution

Abstract

How genetic variation is generated and maintained remains a central question in evolutionary biology. When presented with a complex environment, microbes can take advantage of genetic variation to exploit new niches. Here we present a massively parallel experiment where WT and repair-deficient () populations have evolved over 3 y in a spatially heterogeneous and nutritionally complex environment. Metagenomic sequencing revealed that these initially isogenic populations evolved and maintained stable subpopulation structure in just 10 mL of medium for up to 10,000 generations, consisting of up to five major haplotypes with many minor haplotypes. We characterized the genomic, transcriptomic, exometabolomic, and phenotypic differences between clonal isolates, revealing subpopulation structure driven primarily by spatial segregation followed by differential utilization of nutrients. In addition to genes regulating the import and catabolism of nutrients, major polymorphisms of note included insertion elements transposing into (regulator of the type I fimbriae) and upstream of (global regulator of environmental-change and stress-response genes), both known to regulate biofilm formation. Interestingly, these genes have also been identified as critical to colonization in uropathogenic infections. Our findings illustrate the complexity that can arise and persist even in small cultures, raising the possibility that infections may often be promoted by an evolving and complex pathogen population.

Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

“…Whole‐population (metagenome) sequencing across different time points of an evolution experiment makes it possible to track the dynamics of individual mutations that arise and segregate in an evolving population . Studies that employ this technique provide a direct view of the trajectories of mutations and how they interact during adaptation.…”

Clonal reconstruction from time course genomic sequencing data

“…Long-term evolution experiment (LTEE) has long been adopted to study how genetic variations are generated and maintained in a period of time and how novel variations are associated with the adaptation of the species to novel environmental conditions [1]. Due to their high genetic diversity and rapid evolution, unicellular microbes, predominantly E. coli, are used in LTEEs [2,3,4], although LTEE was also conducted on multi-cellular model animals such as Drosophila [5]. The E. coli long-term evolution experiment conducted by Lenski and colleagues is the longest on-going LTEE, in which twelve initially identical E. coli strains (i.e., the founder clones) were grown in parallel, each under a daily serial passage for 30 years [6,7,3].…”

“…To address this issue, in a recent study, metagenome sequencing coupled with clonal sequencing was adopted for the study of populations of wild-type (WT) and repair-deficient E. coli evolving over three years [4]. To characterize the haplotypes in the populations, whole genome sequencing was carried out on randomly selected clones at the end of the experiments.…”

“…We also discuss the effect of varying the number of clones in the population and the number of time points. Finally, we test our algorithms on a real LTEE dataset [4] from an E. coli population. Our algorithms successfully reconstruct clonal haplotypes that are not characterized by clonal sequencing, and reveal the evolutionary dynamics of the clones during the LTEE.…”

“…Metagenome sequencing data from an evolving E. coli population We used data from the LTEE study on an E. coli population [4] to validate our methods. We used the paired-end Illumina sequencing reads data for the population 125, on which the metagenome sequencing was performed at six months interval during the course of three years, and eight clones were isolated and sequenced separately at the end of the experiment.…”