Multi-omics analysis reveals the differential mechanism of host growth and metabolism promotion by endophytic fungus and bacteria in <i>Atractylodes lancea</i>

Microbial agents are expected to become effective tools for boosting both biomass and bioactive compound accumulation, to solve the challenges of poor quality and low yield in medicinal plants. Nevertheless, limited research has been conducted on the differential responses in plant growth and metabolism elicited by various types of endophytes, which constitute a significant natural microbial resource. In this study, the endophytic fungus Paraphoma sp. (F9) and the endophytic bacteria Paraburkholderia aromaticivorans (Pa) were inoculated into Atractylodes lancea. We found that both F9 and Pa exhibit a simultaneous enhancement on A. lancea's growth and specialized metabolism. In fibrous roots, F9 notably increased biomass, root length, and flavonoid accumulation more than Pa. However, in rhizomes, the accumulation of medicinal terpenoids exhibited slight differences between F9 and Pa treatments. In both fibrous roots and rhizomes, F9 had a greater impact on gene expression changes in the A. lancea transcriptome compared to Pa. In fibrous roots, the flavonoid tricin-7-O-glucoside and genes (CABs and LHC) from the photosynthetic pathway, along with transcription factors (five MYBs and three WRKYs), showed a significant positive correlation. Thus, F9 has a greater effect on A. lancea's photosynthesis, promoting better growth than Pa. In rhizomes, the terpenoid atractylon showed a strong positive correlation with genes, primarily enriched in immune response pathways. Therefore, most terpenoids exhibit comparable defense responses to various endophytes. This study will help optimize the utilization of endophyte resources in cultivating A. lancea and other plants.