Utilization of diverse culture media to enrich bacterial communities in humus soils and mitigate continuous cropping obstacles in Gentiana scabra Bge.

Continuous cropping often leads to soil degradation and hampers crop growth, particularly in medicinal plants like Gentiana scabra Bge., which suffers from reduced yield and quality due to limited cultivation land and fixed practices. This study aimed to evaluate the effects of microbial communities enriched from humus soil on G. scabra growth under continuous cropping conditions and to explore their impact on soil health and plant metabolites. Bacterial communities from humus soil were cultivated using three media—Luria-Bertani broth (LB), Gause’s No. 1 (G1), and R2A—and applied in G. scabra pot experiments. Rhizosphere bacterial and fungal communities were analyzed via high-throughput sequencing, and plant metabolomics was conducted to elucidate microbial influences on plant growth. Bacterial communities enriched with G1 and R2A media significantly promoted G. scabra growth, increasing biomass, gentian polysaccharide, and gentiopicroside content. Enhanced soil enzyme activity and improved microbial diversity were observed, with dominant bacteria such as Massilia in R2A and Burkholderia in G1. Notably, in situ cultivation enriched previously unculturable microorganisms, contributing to improved plant growth and metabolite synthesis. These findings underscore the profound impact of enriched microbial communities on the rhizosphere under continuous cropping stress. Enriched microbial communities from humus soil effectively alleviate continuous cropping barriers for G. scabra. Our results offer valuable perspectives on establishing ecologically sound farming methods and enhancing the growth of therapeutic plants via microbial community implementations. • Developed a novel microbial enrichment method using three culture media. • Bacterial communities enhanced growth and stress resistance in Gentiana scabra. • Key taxa identified: Actinobacteria and Massilia with unique traits and roles. • R2A and G1 groups affected metabolites and pathways differently in plants. • Proposed a novel framework for microbial community transplantation into soils.