Physiological and molecular drivers of Kiwifruit Vine Decline Syndrome: microbial community shifts, defence gene expression, and hormone dynamics

Kiwifruit Vine Decline Syndrome (KVDS) arises from a tangled interplay of environmental stresses, aggressive soil-borne pathogens, and the plant’s defence responses. To better understand this dynamic process, the root endosphere of healthy-looking and symptomatic vines was examined at two key phenological stages, integrating microbiome profiling, host transcriptomic analysis, and phytohormone quantification. Symptomatic roots exhibited a progressive and stage-dependent restructuring of their microbial communities, affecting both bacterial and fungal assemblages and resulting in a dysbiotic configuration associated with disease progression. In contrast, asymptomatic plants retained richer and more balanced microbial consortia across phenological stages, consistent with a more stable and resilient root ecosystem. Transcriptome data revealed sustained activation of defence-related genes, indicating chronic immune engagement in diseased vines, while phytohormone profiling revealed a marked temporal imbalance. Early reductions in growth-promoting hormones, including gibberellins, indole-3-acetic acid (IAA), and cytokinins, were followed by later increases in gibberellic acid (GA 3 ), 6-benzyladenine (6-BA), jasmonic acid (JA), and salicylic acid (SA). These hormones often exert antagonistic effects, suggesting a dysregulated coordination of defence responses. Concurrently, the expression of abscisic acid (ABA) biosynthetic genes increased, yet the hormone itself remained undetectable, suggesting post-transcriptional constraints on accumulation. Together, these findings depict KVDS as a systems-level disorder in which microbial dysbiosis, persistent immune signalling, and mis-regulated phytohormone crosstalk create a self-reinforcing spiral of root deterioration. Targeting this triad through microbiome management, hormonal balancing, and reinforcement of key immune pathways offers a way to achieve long-term control of KVDS and improve kiwifruit resilience. • Kiwifruit Vine Decline Syndrome induces root microbiome dysbiosis with reduced diversity • Dysbiosis correlates with the host health status and phenological stage • KVDS-plants show upregulated defence genes and hormonal imbalances • A microbiome dysbiosis vs. host immunity feedback loop may exacerbate vines' decline • Combined analyses of the microbiome and omics will support management strategies