Comparative genomics reveals high prophage diversity and horizontal gene transfer of effectors and phage defence systems in the Pseudomonas syringae complex

The mobilome, defined as the collection of mobile genetic elements within a bacterial genome, plays a role in the adaptation of bacteria to abiotic and biotic drivers. In particular, prophages have been reported to contribute to bacterial resistance to virulent bacteriophages, to competitive interactions among bacterial hosts within microbial communities and to pathogenicity and virulence. It is, therefore, critical to better understand the role of prophages in distributing genes and functions within and among bacterial species to predict how bacteria adapt to their biotic environment. Pseudomonas syringae offers an ideal study system to ask these questions, both because of its broad range of lifestyles (spanning from environmental growth to plant pathogens) and its high intraspecies diversity. To examine the role of prophages in this species complex, we compared 587 genomes available from public databases and annotated the defence mechanisms, effectors and prophages in the genomes. We found that this species complex has an elaborate phage pandefensome consisting of 139 defence mechanisms. Assessing taxonomical signatures of the observed prophages uncovered broad differences in the types and numbers of genes encoded by different phage families, emphasizing how the evolutionary advantages conferred to hosts can depend on the prophage composition and offering insight into how these genes might disperse within a community. Our study highlights the intimate association of specific phage families with their hosts and their potential role in shaping key ecological traits of these important species.