Dynamic co-existence of bacteriophages and their hosts in the Arabidopsis thaliana phyllosphere

Bacterial communities and the bacteriophages infecting them are the basis of every ecosystem, including holobionts. The various ways in which these microorganisms interact with each other in complex communities over the life of the host affects the holobiont fitness. Despite being ubiquitous and environmentally relevant, plant-associated microbial communities remain understudied, especially in the phyllosphere, mainly because of the low abundance of microbes and the complexity of the system. In this work we followed bacteria and phage community dynamics in the phyllosphere over a growing cycle of Arabidopsis thaliana, to understand the ecology and relevance of bacteriophages in complex bacterial communities. We focused on Pseudomonas, a common plant pathogen and commensal, and the phages infecting them, in three setups of increasing complexity: in vitro, controlled experiments in planta and in wild populations of A. thaliana. We found that bacterial communities are resilient to phage infection, and more dynamic than the phages infecting them over the growing season, suggesting that although ubiquitous and abundant, bacteriophages exert selective pressures on leaf bacterial communities only intermittently.