How clonal are bacteria over time?

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Highlights

  • Bacteria reproduce clonally but exchange genes horizontally by recombination.

  • Clonality is determined by the balance of recombination and natural selection.

  • Pathogens can arise as clonal expansions originating from a non-clonal (highly recombining) source population.

  • Clonality may vary over time, but can generally be considered a stable trait of a microbial population.

  • Therefore, a microbial population's evolutionary history may be used to predict its future evolutionary potential.

Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality  defined here as the balance between vertical and horizontal inheritance  is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively  but not completely  stable over evolutionary time.

Introduction

Here, I revisit the question posed in the title of a classic paper by John Maynard Smith and colleagues [1]: How clonal are bacteria, and more specifically how does clonality vary among different microbial populations and over time? First, what do we mean by clonality? Perfectly clonal bacteria replicate by cell division (vertical descent) and evolve by random mutations that occur during DNA replication. In this theoretical population, there is negligible horizontal transfer of DNA by recombination across the resulting tree of vertical descent. Very few (if any) natural bacterial populations fit this idealized, theoretical definition of clonality. Or, as discussed below, they might only fit it for a short amount of time. However, knowing where a bacterial population of interest happens to fall along a spectrum of clonality can help us understand its biology, and even make predictions about its evolution.

The opposite of clonality is panmixis  a situation in which the rate of horizontal transfer is higher than the rate of vertical cell division, resulting in random association (linkage equilibrium) among loci in the genome [1, 2]. However, rates of horizontal transfer (recombination) vary widely across the genome, such that a population can be mostly clonal, except for a few loci in the genome [3]. These loci came to be termed genomic islands  a metaphor I will build upon below. Some of the first islands identified were called pathogenicity islands because they contained virulence factors [4]. However, non-pathogenic environmental bacteria also contain islands, conferring adaptation to different ecological niches. For example, genes in Prochlorococcus genomic islands confer adaptation to light and nutrient conditions [5, 6]. But islands need not confer niche adaptation to their host genome; they can be neutral to host fitness or even detrimental, selfish parasites. Here, I define genomic islands broadly as any piece of DNA that is transferred horizontally (by either homologous or nonhomologous recombination) from cell to cell and therefore evolves independently (i.e. is unlinked) from the rest of the genome.

I will begin by extending the use of island analogies to include continents, peninsulas and archipelagos (Table 1). I will then use these analogies to discuss to what extent microbial populations are clonal or panmictic, and how often they transition between the two regimes.

Section snippets

Are some islands really peninsulas?

In the classic analogy, an island is totally disconnected from the mainland, meaning that genes in the island evolve independently of the genome (Table 1). Examples of islands that fit this strict independence might include integrated phages and other ‘selfish’ elements, or genes that reside in a particular niche but not in a particular genome (e.g. a gene ecology model [7]). Peninsulas provide an analogy that might better describe how islands are related to microbial genomes. A peninsula (or

Are some genomes archipelagos?

The very concept of one or a few islands implies a contrast with the large, clonal genomic mainland or continent. But some microbial genomes may contain so many islands that there is no mainland, only a vast archipelago (Table 1). A striking recent example is a population of hotspring cyanobacteria in which virtually every gene in the genome evolved independently due to frequent recombination [11], leading the authors to call the population ‘quasi-sexual’ (in other words, panmictic). Frequent

Clonal expansions from panmictic pools

I propose that archipelagos are not necessarily static over time, and that archipelagos can sometimes coalesce into continents. Given the right ecological opportunity, a genome from a panmictic gene pool can escape the ‘gravitational pull’ of recombination and take off into a clonal expansion. An example mentioned earlier is V. cholerae, a genetically diverse group of coastal marine bacteria, some of which cause cholera. Virulence is mainly determined by two loci in the genome: the cholera

The balance between recombination and selection

Let us consider the evolutionary forces that determine clonality: natural selection and recombination. The effect of recombination on clonality is straightforward: more recombination means less clonality. The effect of natural selection is more complex, but is defined here simply as a force which favors clonal expansions of adaptive mutants within an ecological niche. Selection, as defined here, therefore includes ecological effects. When driven by ecological selection, clonal expansions are

Modeling the recombination-selection balance

When rates of recombination are relatively low compared to rates of natural selection on adaptive genes within niches, entire genomes will sweep to fixation before they can be shuffled by recombination. Following previous modeling work, s is defined here as the selective coefficient of a niche-adaptive allele, and r is the recombination rate, per locus per generation [7•, 32, 33]. The s  r regime is well described in the Stable Ecotype Model [17], which predicts that most of the genome will

Genome-wide and gene-specific sweeps in nature

To date, empirical evidence for gene-specific and genome-wide sweeps has come mostly from cross-sectional studies of a single population of genomes at a single point in time, with recombination and selection inferred backward in time [11•, 13•, 14, 35]. Sequencing microbial genomes or metagenomes sampled over time  already a typical practice in genomic epidemiology (e.g. [28, 36])  promises to elucidate the rates of gene-specific and genome-wide sweeps in nature (Figure 1).

In a pioneering study,

Is clonality a stable trait?

As described in the V. cholerae example, some pathogenic bacterial populations can switch between panmictic and clonal lifestyles [11•, 13•, 14, 19•, 25, 34, 35]. Therefore clonality can vary over time, but how much and how often? To quantify the stability of clonality over time, not just in pathogens but in free-living environmental bacteria, I re-analyzed the lake time-course of Bendall et al. [37••]. Because estimates of selection and recombination rates were not readily available for this

History repeats itself

It appears that pathogens are more likely than free-living bacteria to undergo clonal expansions, due in part to their ecology and transmission dynamics [41]. Free-living aquatic bacteria, on the other hand, seem to be more likely to live in large, panmictic populations and behave like archipelagos [11•, 13•, 14, 37••]. If clonality is indeed a stable trait, this implies that history will repeat itself, and that the future behavior of microbial populations can be predicted with some confidence

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

I am grateful to Rex Malmstrom, Yan Boucher, and Salvador Almagro-Moreno for their thoughtful comments which improved the manuscript. I was supported by a Canada Research Chair.

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