The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp.

The mycosphere is a hot spot for bacterial activity in soil. Bacteria must show a plethora of capacities to adapt to this habitat, and horizontal gene transfer processes like transduction may be key in the adaptation. However, studies focusing on the role of viruses in the mycosphere are currently absent. My research addressed this issue in three aspects. First, I dissects genomes of mycosphere-inhabiting Paraburkholderia strains, in order to provide a basis for bioinformatics-assisted identification of prophages. Second, I provides insight into the state-of-the-art of conceptualization of roles of (soil) viruses. Third, I contributes to the understanding of the ecological role and evolutionary trajectory of Paraburkholderia phages. To obtain a meaningful integrative perspective of the role of viromes in soil ecosystems, I advocate that hypothesis-based rather than broadly descriptive studies, based on both culture-dependent and –independent approaches are performed. By using these techniques in my research, I discovered the unexplored viral communities that interact with Paraburkholderia spp. One particular prophage, named ϕ437, was found to be spontaneously induced upon MMC induction. In the population context, such as in a biofilm, the inducibility of ϕ437 may contribute to the biofilm formation and fungal-interactivity in the mycosphere. However, this phenomenon needs further scrutiny. Furthermore, I showed complex evolutionary relationships between Paraburkholderia spp. and their phages. I propose that niche sharing over evolutionary time may have been at the basis of these genetic changes and evolutionary events. The extent of the diversity of viral communities in the mycosphere is unprecedented