Toward predictive plant microbiomes: From assembly rules to deployment

Plants operate as holobionts whose productivity, resilience, and ecosystem functions are inseparable from their associated microbiomes. Recent advances in multi-omics and systems ecology have revealed how plant-microbe interactions regulate nutrient cycling, immunity, stress tolerance, and biogeochemical processes. Yet, much of this knowledge remains descriptive, limiting its translation into solutions for global challenges. This Review argues for a shift from microbiome cataloguing to predictive and application-oriented plant microbiome engineering. We synthesize fundamental principles of microbiome assembly-including rhizodeposition, host developmental control, functional trait selection, and microbial network dynamics-and connect them to emerging translational strategies. We examine how plant microbiomes can be harnessed to enhance crop biofortification and bioprotection, restore degraded ecosystems, modulate carbon and nitrogen cycling for climate resilience, and support sustainable bioenergy production on marginal lands. We highlight synthetic microbial communities, microbiome-aware breeding, and trait-based microbial selection as key frameworks for establishing causality. Finally, we discuss major constraints to field deployment, including ecological instability, host specificity, unintended greenhouse-gas feedbacks, and regulatory uncertainty. By integrating mechanistic insight with ecological realism, this review positions plant microbiomes as central levers for sustainable agriculture, climate action, and the bio-based economy.