Rhizosphere fungal generalists drive plant metabolic adaptability via regulating soil micronutrient availability.

The ecological characteristics of fungal generalists (FG) and specialists (FS) in rhizosphere, as well as their impact on soil micronutrient dynamics and plant metabolic adaptability are largely unknown. Through large-scale sampling of Panax notoginseng (with saponins as the primary specialized metabolite) and ecological analysis, we demonstrated that, compared to FS, the assembly of rhizosphere FG is more strongly governed by deterministic processes and that they play more crucial roles in maintaining network stability. Further, Mantel analysis and multiple machine learning models revealed that FG, rather than FS, are significant contributors to soil micronutrient availability, particularly for iron and zinc. This was substantiated by culture-based approaches, where we confirmed the zinc- and iron-solubilizing capabilities of candidate FG isolates both in vitro and in soil. A driver analysis of plant metabolic variation identified soil micronutrient availability as the predominant factor affecting plant metabolome and saponin accumulation, underscoring the significance of the FG-driven micronutrient availability in shaping plant metabolic adaptability. Among these micronutrients, available zinc exhibited the strongest positive effect on total saponin accumulation (R2 = 0.24, P < 0.001). A zinc-supplement pot experiment further validates the improving effects of zinc on root saponin accumulation, which was correlated to the upregulation of the PnCYP716A47 gene. Collectively, this study clarifies that deterministically assembled rhizosphere FG regulate plant adaptability by influencing soil micronutrient availability. These findings provide new insights for plant-microbe interactions in rhizosphere and are critical for the utilization of functional microbes to enhance plant performance.