Soil moisture modulates rhizosphere microbiota and suppresses root rot in organic Panax ginseng cultivated under pine forests

Abstract Background The integration of agroforestry and understory cultivation offers a sustainable approach to producing high-value medicinal plants with ecological conservation. However, optimal irrigation management for organic Panax ginseng grown under pine forests (OPPF) remains poorly studied, particularly regarding its influence on root rot disease and rhizosphere microbial communities. Results This study evaluated four soil moisture treatments—PTh1 (55–60% field capacity, FC), PTh2 (70–75% FC), PTh3 (80–85% FC), and PTh4 (95–100% FC)—on the growth, quality, and root rot incidence of OPPF. We analyzed agronomic traits, secondary metabolites, soil properties, enzymatic activities, and rhizosphere microbial composition via high‑throughput sequencing and qPCR, and validated microbial isolates functionally through pot experiments. Moderate soil moisture (PTh2) significantly improved plant biomass, seedling survival, and the accumulation of flavonoids, polysaccharides, and ginsenosides. In contrast, high soil moisture (PTh4) increased the incidence of root rot and the abundance of pathogens such as Fusarium solani and Ilyonectria mors-panacis . Soil properties and enzyme activities were markedly influenced by moisture levels, with PTh2 maintaining a higher pH and beneficial nutrient profile. Rhizosphere microbiome analysis revealed that PTh2 enriched potential biocontrol agents, including Trichoderma , Penicillium , Bacillus , and Streptomyces , while reducing pathogenic taxa. Six antagonistic strains were isolated, with Penicillium ortum (F1) showing the strongest suppression of root rot and promotion of plant growth in pot trials. Conclusions Maintaining soil moisture at 70–75% FC optimizes the growth and health of OPPF by fostering beneficial microbial communities and inhibiting soil-borne pathogens. These findings provide science-based irrigation strategies to support the sustainable cultivation of organic ginseng in forest-based agroecosystems.