Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies
Microbial community dynamics are deeply impacted by parasites, such as their latent viruses (aka prophages).
In this study we sought to understand the long-term effect of prophages during competition and how infection may alter evolutionary outcomes by driving the emergence and maintenance of different phage resistance mechanisms.
We followed the coevolution of a phage-sensitive strain and a polylysogenized multi-drug resistant strain belonging to the Klebsiella pneumoniae species.
In populations with higher phage pressure, phage-sensitive bacteria would be rapidly outcompeted, yet, the latter are still present in the population and at higher relative frequencies compared to environments with milder phage pressure.
Contrary to expectation, resistance to temperate phages emerges rarely by the incorporation of the phage in the new host (lysogeny). Our experimental results and the individual-based simulations that quantify the cost of lysogeny versus other mechanisms of resistance show that lysogeny is expensive and thus counterselected.
At first, most populations become resistant to phages by receptor (capsule) loss, but eventually capsulated clones increase in frequency. Al longer time scales, adaptive process change and resistance emerges either by receptor modification or by non-genetic transient resistance. Such resistance is quickly lost in absence of phage pressure and suggest the existence of transient mechanisms of phage resistance that do not require the fixation of costly mutations. This could constitute an important wide-spread phage-resistance mechanism.
Overall, we highlight the complexity of the adaptive process is increased in the presence of lysogens and depend on trade-offs between resistance to phages and cell fitness.