Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments

Abstract

Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via the transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle that releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, it remains unclear how costs/benefits of prophages vary across environments. Here, studying prophages with/without ARGs in Escherichia coli, we disentangled the effects of prophages alone and adaptive genes they carry. In competition with prophage-free strains, benefits from prophages and ARGs peaked in different environments. Prophages were most beneficial when induction of the lytic lifecycle was common, whereas ARGs were more beneficial upon antibiotic exposure and with reduced prophage induction. Acquisition of prophage-encoded ARGs by competing strains was most common when prophage induction, and therefore free phages, were common. Thus, selection on prophages and adaptive genes they carry varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in evolution.

Keywords: Antibiotic resistance; fitness; lysogen; mobile genetic elements; prophage; temperate phage.

Figure 1

Competitive fitness of lysogens relative to the antibiotic‐susceptible and phage‐susceptible Wild Type in the (A) absence and (B) presence of mitomycin C. Each row of panels shows data from a different combination of antibiotic (given at right of panel C) and prophage type (given at right of panel B). Shown are single data points as well as means ± s.e. from six replicate populations. Black/grey points indicate lysogens without/with ARGs, assayed in competition with the WT at different antibiotic concentrations (x‐axis). Lysogens have higher fitness than the WT when the selection rate constant r > 0. (c) Benefits of ARGs (left column) and prophages (right column) in different treatment groups (labeled at the right of the heatmap), clustered by k‐means clustering (see Methods). Data have been scaled using the scale function implemented in R prior to the cluster analysis.

Figure 2

Production of free phages in the presence (grey) and absence (black) of mitomycin C. The number of cultures (y‐axis) with each amount of produced phages (x‐axis) is shown for competition cultures involving ARG‐free lysogens (left panel) and ARG‐carrying lysogens (right panel). Further details, including variation depending on all of the factors we tested and among replicates within each treatment group, are shown in Figure S3.

Figure 3

Competitive fitness of new WT‐lysogens relative to each of three competing ancestral strains (left: in competition with the phage‐free, ARG‐free Wild Type; middle: in competition with an ARG‐free lysogen with the same prophage type; right: in competition with an ARG‐carrying lysogen with the same prophage type). Fitness was measured in the absence and presence of antibiotics (x‐axis). Different colors correspond to different ARGs (see legend). Each line gives the mean ± s.e. across all of the new‐WT lysogens we isolated for each ARG; individual reaction norms for every new WT‐lysogen (each isolated from one of the 16 populations where we detected new lysogens, Table 2) are given in Figure S8. New WT‐lysogens have a higher fitness than the competing strain when r > 0.