Rhizosphere metabolite–microbiome synergism mitigates 6 years continuous cropping obstacle in pepper plants

Aims Continuous cropping of pepper ( Capsicum annuum L.) results in yield decline, but the underlying mechanisms through which rhizosphere metabolites and the microbiome interact remain unclear. Methods In this study, we integrated soil physicochemical analysis, microbial community profiling (16S/ITS), and non-targeted metabolomics after 2, 6, and 10 years of continuous cropping (CC2, CC6, and CC10, respectively). Results CC6 soils significantly enriched Sphingomonas , a beneficial bacterium that was positively correlated with available phosphorus. It was recruited by root-exuded glucoerucin and glucosylsphingosine to combat pathogens. But compared with CC6, the contents of these two metabolites were reduced in CC10 soil, which diminished the abundance of Sphingomonas , while the pathogens such as Rigidoporus increased significantly. Nutrient levels (nitrate nitrogen, soil organic carbon, available phosphorus/potassium) were elevated in CC10, likely due to pepper death, resulting in an inability to utilize nutrients. Conclusions Integrated analysis revealed that rhizosphere metabolites drove beneficial microorganism recruitment, alleviating continuous cropping obstacles (CCOs) in CC6. However, the exhaustion of key metabolites fostered pathogen dominance in CC10. These results provide new insights for enhancing crop yield and quality and enhancing sustainable agricultural development.