The cultivation of Paeonia suffruticosa ‘Luoyang Hong’, a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa ‘Luoyang Hong’. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa ‘Luoyang Hong’, offering deeper insights into replanting issues and supporting future mitigation strategies.
Sun et al. (Tue,) studied this question.