A novel internal reference microorganism-based method reveals wild-enriched Penicillium for enhancing growth and disease resistance in Fritillaria thunbergii

Introduction Fritillaria thunbergii Miq. is an important traditional Chinese medicinal herb, but bulb rot disease causes severe losses during its cultivation. Screening and reintroducing beneficial microorganisms from the wild rhizosphere is an effective strategy to increase disease resistance in cultivated plants. However, the absolute quantitative characteristics of microorganisms cannot be reflected by traditional methods based on relative abundance analysis due to compositional bias. Methods In this study, we identified Clavatospora as a host-specific internal reference microorganism (IRM) and established an IRM-based relative abundance differential microorganism analysis (IRMRADMA) method. Results Application of this method revealed that wild F. thunbergii possesses greater potential than cultivated plants for mining beneficial rhizosphere microorganisms. Specifically, Penicillium was identified as a key wild-enriched genus. Subsequently, two strains, Penicillium korosum and Penicillium aculeatum , were isolated from the rhizosphere of wild F. thunbergii . Functional tests confirmed that these strains demonstrated dual functions in disease suppression and plant growth promotion by solubilizing phosphate, producing siderophores, antagonizing pathogens, and upregulating defenserelated genes. Conclusion This study established the IRM-RADMA method and identified key Penicillium strains from the wild Fritillaria thunbergii rhizosphere. Their confirmed dual functions in growth promotion and disease suppression validate the ‘plant microbiome rewilding’ strategy, offering a new paradigm for the biological control of F. thunbergii diseases.