TRIADE

The composition and evolution of microbial communities depends on the interplay between bacteria and their many mobile genetic elements. The latter have their own interests, that are only sometimes aligned with the interests of their bacterial hosts. Because mobile genetic elements also interact with other mobile genetic elements, this results in a complex network of interactions, with important consequences for i) the stability of bacterial communities in (e.g.) host-associated environments, and ii) the rapid dissemination of virulence traits that lead to the emergence of bacterial pathogens. Bacteriophages (phages) are bacterial predators, but they can also be vehicles of horizontal gene transfer. Despite being parasites, phages also have their own parasites, the phage-satellites. These hyperparasites lack genes to form viral particles, and instead encode genes to steal viral particles assembled by phages that co-infect the same bacterial cell. They can both act as, and encode, anti-phage defense systems, and some phage-satellites also encode virulence traits. However, these observations came from a few dozens of known phage-satellites, which limited the study of their evolution, their distribution in bacterial clades, their impact for bacterial adaptation and their effect in microbial communities. I have recently identified >5000 phage-satellites in bacterial genomes, showing that they are very characteristic, abundant and diverse. This novel data allows me to propose the project TRIADE, which will use a multidisciplinary approach to better understand the role of phage-satellites in their tripartite relationship with phages and with the bacterial hosts. By combining comparative genomics, experimental evolution and agent-based simulations, I will explore different temporal and biological levels involved in the tripartite interactions. This will lead to novel insights on how phages and their satellites impact bacterial adaptation and pathogenicity.