Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere

Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.