Rhizosphere engineering in Camellia sinensis intercropping reveals hierarchical regulation of defense, nutrient cycling, and aromatic metabolism

AIMS: This study aimed to elucidate the transcriptional and metabolic reprogramming of Camellia sinensis rhizosphere under intercropping conditions, to understand its implications for ecological intensification and enhanced tea quality. METHODS: Intercropping-induced rhizosphere effects transcriptionally reprogram Camellia sinensis metabolism, as determined through integrated transcriptomic‒metabolomic analysis. RESULTS: Rhizosphere restructuring activated 159 (93.71 % upregulated) KEGG pathways, prioritizing flavonoid biosynthesis, plant‒pathogen interactions, and starch‒sucrose metabolism. The results revealed that the activation of the JA-mediated defense signaling pathway and phenylpropanoid pathway increased the secretion of pathogen-inhibiting phenolics; the coordinated upregulation of nitrogen fixation (nifH), ammonia oxidation (amo), and phosphate solubilization (phoC/D) pathways coupled with denitrification suppression (nirK) increased nitrogen retention and mitigated greenhouse gas emissions; C‒N metabolic crosstalk stimulated glycosylated metabolite synthesis and foliar aroma precursor enrichment; and systemic flavonoid metabolism synchronization between roots and leaves, which was mediated by CHS/PAL induction. Metabolic network analysis revealed malonyl-CoA channeling toward defense-associated terpenoids and carbohydrate reserves. CONCLUSIONS: This hierarchical regulation, microbial recruitment, nutrient optimization, and carbon flux redirection could establish rhizosphere engineering as a dual strategy for ecological intensification and tea quality enhancement in agroforestry.