Crop rotation alleviates continuous cropping obstacles of lily and improves secondary metabolites in bulb through shifting Rhizospheric microbiota

• Rice rotation significantly alleviates lily continuous cropping obstacles through rhizosphere microbiome restructuring. • Crop rotation reduces fungal diversity and reshapes microbial community composition in the rhizosphere. • Aspergillus enrichment in rotation soils suppresses pathogenic fungi and activates plant defense mechanisms. • Rotation-induced metabolic changes enhance jasmonate biosynthesis and medicinal alkaloid accumulation. • The dual role of Aspergillus in pathogen suppression and metabolite promotion enables sustainable lily production. Lilies ( Lilium spp.) are important economic horticultural plants with applications in ornamental horticulture, food, and traditional medicine. However, continuous cropping obstacles (CCOs) severely impact lily cultivation, causing yield and quality losses. This study investigates application of crop rotation, particularly with rice, to mitigate CCOs in "multi-functional lily" hybrids. Through comparative field trials of continuous monoculture (NR), maize rotation (MR), and rice rotation (RR) systems, we demonstrate that RR significantly alleviates CCOs by restructuring rhizosphere microbial communities, enhancing secondary metabolite accumulation, and enriching Aspergillus populations. Rice rotation promotes Aspergillus proliferation, the average relative abundance (RA) of Aspergillus in RR increased to 59.00%, raising by nearly 60 times compared with that in NR condition (RA=1.05%). Rice rotation activates jasmonic acid (JA) biosynthesis, suppressing fungal pathogens ( Fusarium spp. and Botrytis spp.) and boosting medicinal alkaloid production in bulbs. Our findings provide a sustainable, cost-effective solution for CCO mitigation, highlighting the vital role of Aspergillus as a biocontrol agent and a promoter of plant defense mechanisms. This study offers novel insights into the agroecological benefits of rice-lily rotation, advancing sustainable lily cultivation practices through rice rotation and microbial management.