Linking Nitrate-Modulated Plant Growth and Metabolic Reprogramming to Rhizobacterial Recruitment: Insights from the Plant Metabolome and Rhizosphere Microbiome

The growth-differentiation trade-off limits productivity in secondary metabolite-rich crops. Here, using Stevia rebaudiana as a model plant, we find that the N source strongly regulates the trade-off between biomass and steviol glycoside (SG) accumulation, with a nitrate [NO₃^-]-to-ammonium [NH₄⁺] ratio of 75:25 yielding optimal SG production. Metabolomics analyses attributed the benefits of a high proportion of NO₃^- supply to redirected carbon flux into phenolic and terpenoid pathways. While overall rhizomicrobial diversity remained unaffected by N forms, the composition of the bacterial, rather than fungal, community changed significantly. NO₃^- supply favored bacterial taxa from the Burkholderiales, Hyphalales, and Cytophagales orders while diminishing those belonging to Vicinamibacterales. Notably, NH₄⁺-associated bacteria were linked to amino acid synthesis, while NO₃^--enriched taxa, including Sphingomonadaceae and Thermoanaerobaculaceae, correlated with secondary metabolite accumulation. Our study highlighted the tight link between N-form-regulated trade-offs and rhizobacterial community assembly, providing insights into plant-microbe interactions and strategies for optimizing crop yield and bioactive compound accumulation.