Differential Microbial Communities and Metabolite Profiles in the Rhizosphere and Near-rhizosphere Soils of Rubber Tree (Hevea brasiliensis) Infected with Red Root Rot Disease

Background and aims Red root rot disease, caused by the soil-borne pathogen Ganoderma pseudoferreum, is a severe threat to the natural rubber industry. However, disparities in microbial composition and metabolic profiles between healthy and diseased rubber trees (Hevea brasiliensis) in rhizosphere and near-rhizosphere soils remain unclear. Thus, this study aimed to investigate the disease-induced changes in microbial community structure and function and elucidate the underlying mechanisms. Methods The microbial composition and metabolite profiles of healthy and diseased rubber trees in rhizosphere and near-rhizosphere soils were compared using metagenomic sequencing and ultra-performance liquid chromatography-tandem mass spectrometry. Results In diseased rhizosphere soils, bacterial abundance significantly increased, but bacterial diversity decreased; fungal abundance and diversity both decreased. In diseased near-rhizosphere soils, bacterial richness markedly increased, but bacterial diversity decreased; fungal richness remained statistically unchanged, and diversity was unaffected. Co-occurrence network analysis showed that microbial interaction density increased in diseased soil. Ganoderma positively correlated with several functional microbial groups but strongly negatively correlated with biocontrol agents. Lignin-degrading fungi Trametes and Dichomitus, which are significantly enriched in the diseased rhizosphere, significantly positively correlated with Ganoderma. 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. Conclusion This study offers scientific evidence elucidating the microecological mechanisms behind red root rot disease and lays the groundwork for developing microbiome-based ecological control strategies.