Nonselective Bottlenecks Control the Divergence and Diversification of Phase-Variable Bacterial Populations

Abstract

Phase variation occurs in many pathogenic and commensal bacteria and is a major generator of genetic variability. A putative advantage of phase variation is to counter reductions in variability imposed by nonselective bottlenecks during transmission. Genomes of Campylobacter jejuni, a widespread food-borne pathogen, contain multiple phase-variable loci whose rapid, stochastic variation is generated by hypermutable simple sequence repeat tracts. These loci can occupy a vast number of combinatorial expression states (phasotypes) enabling populations to rapidly access phenotypic diversity. The imposition of nonselective bottlenecks can perturb the relative frequencies of phasotypes, changing both within-population diversity and divergence from the initial population. Using both in vitro testing of C. jejuni populations and a simple stochastic simulation of phasotype change, we observed that single-cell bottlenecks produce output populations of low diversity but with bimodal patterns of either high or low divergence. Conversely, large bottlenecks allow divergence only by accumulation of diversity, while interpolation between these extremes is observed in intermediary bottlenecks. These patterns are sensitive to the genetic diversity of initial populations but stable over a range of mutation rates and number of loci. The qualitative similarities of experimental and in silico modeling indicate that the observed patterns are robust and applicable to other systems where localized hypermutation is a defining feature. We conclude that while phase variation will maintain bacterial population diversity in the face of intermediate bottlenecks, narrow transmission-associated bottlenecks could produce host-to-host variation in bacterial phenotypes and hence stochastic variation in colonization and disease outcomes.

Domestication ofCampylobacter jejuniNCTC 11168

“…A shared frameshift mutation was identified in two hyper-motile isolates (11 and 16) within the core motor protein, fliR [85–87]. Isolate motility is also influenced by phase-variable gene expression as a result of upstream homopolymeric repeat regions [24, 88, 89]. Several motility associated genes ( maf1/Cj1348 , maf4/Cj1335 and maf7/Cj1342c ) were among 31 phase-variable regions recently identified in NCTC 11168 [90] and were among SNPs we identified in non-coding intergenic regions (196 of 632; 31%; Table 1 ).…”

“…Several motility associated genes ( maf1/Cj1348 , maf4/Cj1335 and maf7/Cj1342c ) were among 31 phase-variable regions recently identified in NCTC 11168 [90] and were among SNPs we identified in non-coding intergenic regions (196 of 632; 31%; Table 1 ). Twelve genes contained nucleotide substitutions in 10 or more NCTC 11168 isolates, of which five have been shown to be subject to phase variation [89]. Growth of motile bacteria in culture media can result in loss of motility as flagella construction is energetically expensive [91, 92].…”

The impact of bottlenecks on microbial survival, adaptation, and phenotypic switching in host-pathogen interactions

“…The impact of nonselective bottlenecks on bacterial phase variation was recently studied in (Aidley et al. ), where the effect of bottleneck size on patterns of diversity was analyzed. It was shown that populations that are passaged through single cell bottlenecks exhibited patterns of diversity that varied significantly from their ancestral populations, in contrast to the case of wide bottlenecks where the ancestral composition was largely maintained.…”

“…A nonselective bottleneck affects the population size, which sets the magnitude of demographic fluctuations, but it does not impact the mean composition of the transmitted population and thus has no effect on the fitness landscape. The impact of nonselective bottlenecks on bacterial phase variation was recently studied in (Aidley et al 2017), where the effect of bottleneck size on patterns of diversity was analyzed. It was shown that populations that are passaged through single cell bottlenecks exhibited patterns of diversity that varied significantly from their ancestral populations, in contrast to the case of wide bottlenecks where the ancestral composition was largely maintained.…”

Selective and non‐selective bottlenecks as drivers of the evolution of hypermutable bacterial loci

“…the number and prevalence of phasotypes). Aidley and Colleagues () explored PV of C. jejuni strain NCTC11168, which has 28 phase‐variable genes. A randomly selective bottleneck model with no selective inference was applied to populations containing multiple phasotypes.…”