Integrated Analysis of Transcriptomics and Metabolomics and High-throughput Amplicon Sequencing Reveals the Synergistic Effects of Secondary Metabolites and Rhizosphere Microbiota on Root Rot Resistance in Psammosilene tunicoides

This study examined healthy and diseased P. tunicoides roots and rhizosphere soil. Using transcriptomics, metabolomics and microbial sequencing to analyse changes in P. tunicoides after root rot occurrence, our results illustrated that flavonoid and triterpenoid metabolism actively dominates P. tunicoides resistance to root rot disease. We mined plant transcriptome, metabolome and microbiome resources, revealing that the expression of triterpenoid (e.g. HGMS, DXS, SQS) and flavonoid biosynthesis genes (e.g. PAL, CHS, CHI) were up-regulated in diseased P. tunicoides compared with their expression in healthy specimens. Furthermore, we hypothesise that when P. tunicoides plants are stimulated by external adverse factors, their roots accumulate and secrete large amounts of specific triterpenoid and flavonoid secondary metabolites through gene regulation. These secondary metabolites can directly resist pathogen invasion while also enriching growth-promoting and disease-resistant beneficial bacterial communities. This includes the endophytic Pseudomonas strain MG-2011-23-CX and antagonistic bacteria isolated and identified from the soil, as well as a series of actinomycetes enriched in the rhizosphere soil. Most of these actinomycetes exhibited positive correlations with triterpenoid and flavonoid compounds and their key genes. This study provides new insights and potential applications for the future ecological cultivation and management of P. tunicoides.