Location and growth period influence the bioactive compounds of Angelica sinensis (Oliv.) diels: multi-omics insights

Angelica sinensis, a traditional medicinal herb, exhibits significant variations in efficacy quality linked to geographical origin and rhizosphere microbiome composition. However, the microbial factors driving the synthesis of its bioactive compounds in authentic (historically recognized for superior quality geoherbs, Min County) and adjacent regions remain poorly understood. This study integrated transcriptomic profiling of plant tissues with 16 S rRNA (bacteria) and ITS (fungi) sequencing of rhizosphere soils over multiple growth stages in authentic and near-authentic regions (the latter characterized by a similar climate but differing soil ecology). By combining these data with targeted metabolomics and soil property analysis, substantial regional and temporal variations in bioactive compound levels and soil properties were identified. Specifically, 2,367 differentially expressed genes (DEGs), 417 bacterial amplicon sequence variants (ASVs), and 295 fungal ASVs were detected with significant abundance shifts. Key genera, including Vicinamibacter and Bacillus (bacteria), and Bisifusarium and Longitudinalis (fungi), were linked to secondary metabolite production. Functional differences, such as those related to chitinolysis and fermentation pathways, were also observed. Co-occurrence networks revealed correlations between plant genes and microbial communities. Notably, soil parameters, including organic matter, total nitrogen, and soil alkaline phosphatase, were identified as key factors influencing microbial community structure. The rhizosphere microbiome was further associated with nutrient absorption, potentially impacting bioactive compound accumulation. This multi-omics analysis highlights the role of regional and growth-period variations in A. sinensis quality, offering valuable insights for optimizing its cultivation and efficacy across diverse regions.