Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer. Prophage cargo can determine ecological interactions of a bacterium with other community members, and even its pathogenic potential, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Interestingly, SPβ belongs to the so-called phage regulatory switches that precisely excise from the chromosome of sporulating mother cells, a phenomenon observed for phages infecting diverse spore-forming species. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes at global and local ecological scales indicates that these SPβ-like phages diversify rapidly, especially in the absence of other MGEs constraining their lytic cycle. Our study captures inter-phage recombination under an experimentally imposed selection regime, and reveals the ubiquity of similar phenomena in Bacillus sp. genomic data. Therefore, our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages.
Competing Interest Statement
The authors have declared no competing interest.