Compartment-specific root microbiomes are associated with regional variation in Salvia miltiorrhiza quality with functional assessment of a Pseudomonas putida isolate

Danshen ( Salvia miltiorrhiza Bunge) exhibits marked regional differences in secondary metabolism, but their relationships with root-associated microbiomes remain insufficiently understood. Relationships between root-associated microbiomes and regional quality traits of Danshen were examined using samples from 19 cultivated fields in five major production regions of China. Root biomass, major bioactive constituents, and bacterial and fungal communities in root-inhabiting and rhizosphere compartments were analyzed. Regional patterns were distinct. Samples from Shandong (SD) had higher root biomass and tanshinone (TS) contents, whereas those from Sichuan (SC) had higher salvianolic acid B levels. Root-inhabiting bacterial alpha diversity was lowest in SD samples, where specific taxa, including Pseudomonas and Pantoea , were enriched. Salvianolic acid variation exhibited distinct associations with fungal communities. Variance partitioning also indicated that soil properties and microbiome variation explained both shared and independent fractions of regional quality differences. Network and trait-correlation analyses identified a Pseudomonas -affiliated operational taxonomic unit closely associated with both root biomass and TS accumulation. A bioaugmentation assay examined the functional potential of a culturable Pseudomonas isolate, Pseudomonas putida strain 3–37, obtained from Danshen roots. Under the tested conditions, strain 3–37 treatment promoted plant growth and increased total TS accumulation. These findings indicate closer associations of root-inhabiting bacterial communities with root biomass and tanshinone accumulation and of fungal communities with salvianolic acid variation. Therefore, strain 3–37 may serve as a candidate microbial resource for Danshen cultivation.