A Resident Prophage Metabolically Reprograms Root-Colonizing Pseudomonas to Modulate Plant Physiology

Microbiomes and their hosts influence one another in a complex and dynamic ecosystem. While bacteria in the root microbiome are recognized for their role in plant health, it still remains unclear whether their viral (phage) activity indirectly influences plant growth. Using machine learning-based viral detection tools, we identified a putative 63.7 kb double-stranded DNA prophage in the plant growth promoting rhizobacterium Pseudomonas simiae WCS417 and experimentally confirmed its lysogenic potential. We co-cultivated the GFP-labeled wild-type (WT) and prophage absent (Δphage) strains with Arabidopsis thaliana and Brachypodium distachyon to assess the prophage’s impact on both bacterial host and plant physiology. Our results demonstrate that prophage presence impacted plant root architecture, root exudate metabolic profiles, and shoot biomass under thermal stress without affecting bacterial colonization ability. Collectively, these findings reveal a triadic plant-bacterium-phage axis in the rhizosphere, underscoring a critical role of phages in shaping community dynamics and plant-microbiome interactions.