Differential microbial communities and metabolite profiles in the rhizosphere and bulk soils of rubber tree (Hevea brasiliensis) infected with red root rot disease

Red root rot disease, caused by the soil-borne pathogen Ganoderma pseudoferreum, is a severe threat to the natural rubber industry. However, the mechanisms by which pathogen invasion affects the composition, function, and metabolic products of the soil microbial community in rubber trees (Hevea brasiliensis) remain unclear. Here, we compared different soil management patterns, including rhizosphere healthy soil (RHS), rhizosphere diseased soil (RDS), bulk healthy soil (BHS), and bulk diseased soil (BDS), to investigate the diversity, functions, and metabolic characteristics of soil microbial communities using metagenomic and metabolomic techniques. In diseased rhizosphere soils, bacterial abundance increased significantly while diversity decreased; fungal diversity showed a declining trend. In diseased bulk soils, both bacterial richness and fungal diversity increased markedly. Co-occurrence network analysis revealed enhanced microbial interaction density (particularly among fungi) in the rhizosphere diseased soil. Ganoderma positively correlated with several functional microbial (e.g., Bradyrhizobium) groups but strongly negatively correlated with biocontrol agents (e.g., Trichoderma and Talaromyces). Lignin-degrading fungi Trametes and Dichomitus, which are significantly enriched in the diseased rhizosphere, significantly positively correlated with Ganoderma. Metagenomic analysis revealed significant enrichment of gene abundances related to latex and lignin degradation, carbon and nitrogen cycling, and fungal signal transduction in diseased soils. Metabolomic analysis revealed the upregulation of defense-related metabolites (e.g., 3-methylsalicylic acid, 5'-glucosyloxy-oxojasmonate, and abscisic acid) and plant cell wall-associated components (e.g., ferulic acid) in the diseased rhizosphere. These findings indicate that the invasion of Ganoderma leads to changes in the microbial community assembly process, elucidating the pathogenesis of red root rot in rubber trees from a soil microecological perspective. Simultaneously, this study provides direction for future research focused on mitigating crop losses caused by this pathogen.