Root Microbiota Reprogram Aboveground Metabolite Allocation Across Tea Plant Tissues

Tea quality is determined by the composition and spatial distribution of specialized metabolites, such as amino acids, catechins, and caffeine, which vary across tissues and developmental stages. However, the mechanisms underlying metabolite allocation among tissues remain unclear. Plant-associated microbiota, particularly root communities, play important roles in regulating plant metabolism, yet their coordinated effects across plant compartments are poorly understood. Here, we combined metabolomic and microbiome analyses to investigate metabolic-microbial interactions in the white tea cultivar Zhenghe Dabai. Metabolite-associated microbial taxa identified from leaves were linked to root-derived isolates, and two synthetic communities (SynCom1 and SynCom2) were constructed and applied to the rhizosphere. Both SynComs enhanced flavan metabolite accumulation, especially proanthocyanidins, but exhibited distinct regulatory patterns. SynCom1 increased stem-enriched proanthocyanidins and multiple amino acids, including theanine, while SynCom2 promoted specific flavan derivatives and amino acids such as glutamate and tryptophan. Transcriptomic analysis revealed differential activation of flavonoid biosynthesis and amino acid transport pathways, with SynCom1 upregulating the transporter gene CsCAT1. Overall, our results demonstrate that root microbiota can differentially regulate host metabolism and metabolite allocation, providing new insights into microbiome-mediated quality formation in tea and highlighting the potential of synthetic microbial communities for crop improvement.