Integrated Multiomics Analysis Indicates Seasonal and Geographical Drivers of Rhizosphere Microbiome–Metabolome Interactions and Dihydrochalcone Accumulation in Lithocarpus litseifolius (Hance) Chun

Lithocarpus litseifolius (L. litseifolius) is a valuable economic crop rich in dihydrochalcones (DHCs), with wide applications in medicines, tea, and sweeteners. By integrating multiomics approaches, the relationship between rhizosphere microecology and quality formation in L. litseifolius was systematically elucidated. Key bacterial groups, such as Burkholderia–Caballeronia-Paraburkholderia, Conexibacter, and Bradyrhizobium, were driven by soil physicochemical properties (available copper, exchangeable manganese, alkali-hydrolyzable nitrogen, and organic matter) and rhizosphere metabolome and were strongly associated with the up-regulation of key genes in phenylpropanoid biosynthesis (phenylalanine ammonia lyase, cinnamate 4 hydroxylase, chalcone synthase, phloretin 4′-O-glucosyltransferase), thereby promoting DHC accumulation. A pot experiment confirmed the functional contribution of Burkholderia in promoting the growth of L. litseifolius and the accumulation of its secondary metabolites. The mechanisms by which soil characteristics and microbial communities regulate DHC biosynthesis in L. litseifolius were elucidated, providing insights into the coupling mechanism of “soil–microbiome–metabolome–plant secondary metabolism”.