Edible lily (Lilium davidii var. unicolor) has economic value in China, particularly in Gansu Province, due to its uses as food and in gardening. Edible lily is usually cultivated in a long-term continuous monoculture resulting in the so-called consecutive replant problem (CRP), which is associated with severe soil degradation and significant yield and quality losses. This study was conducted to investigate the fungal community structure and specific fungal members related to lily’s CRPs using metabarcoding analysis. Fungal diversity of rhizosphere soil was analyzed by high-throughput DNA sequencing (Miseq) of samples collected in fields at 0, 3, 6, and 9 replant years (L0, L3, L6, and L9, respectively). The results show that long-term replanting significantly decreased both soil fungal diversity and abundance at the OTUs levels. Furthermore, replanting altered the soil microbial communities, where 4 to 5 years of replanting is a key transition period for substantial change of fungal community structure, resulting in new fungal community structures in L6 and L9 compared to in L0 and L3. The fungal diversity loss and fungal community structure simplification contributes to the negative effect of replanting in lily, and after 6 years of replanting, accumulation of highly abundant pathogenic fungal genera and depletion of the putative plant-beneficial fungal genera exacerbate the lily CRP. In addition, changes in the soil physiochemical properties strongly contributes to the new structure of fungal communities, and the genera Cryptococcus and Guehomyces could be regarded as potential indicators to monitor and manage sustainable soil health in the lily cropping system.

Aims Consecutive replant problems (CRPs) in Lanzhou lily are linked to soil degradation, autotoxin accumulation, and pathogen proliferation. This study investigated how cinnamic acid, a model autotoxin, interacts with soilborne pathogens to influence plant health, soil properties, and rhizosphere fungal communities under simulated CRP conditions. Methods An artificial simulation was conducted by adding cinnamic acid to soil to induce autotoxic stress and concurrently inoculating lily plants with pathogens ( Fusarium oxysporum and Ilyonectria sp. ) to induce wilt. Growth parameters, disease incidence, root activity, leaf defense enzymes, proline, soil properties, and fungal community composition were analyzed. Results Cinnamic acid at 0.24–2.40 mg/L promoted pathogen growth in vitro and soil colonization. In planta, it induced autotoxic stress, inhibiting growth and root activity while elevating leaf defense responses. Co-application with pathogens significantly increased disease index and incidence compared to pathogen-only treatments. Rhizosphere soil properties and fungal community structure were markedly altered, with enrichment of pathogenic genera ( Fusarium , Ilyonectria , Gibberella ) and species ( Fusarium_oxysporum , Ilyonectria_liriodendri ). RDA showed soil properties (OM, pH, AK) explained 63.92–66.97% of community variation, with stronger effects than cinnamic acid. Conclusion Cinnamic acid exacerbates lily wilt by promoting pathogen proliferation and modifying soil properties, which collectively reshape the fungal community. Its indirect regulation of the microbial community via alterations in soil properties outweighs its direct effects. The synergy between autotoxin accumulation and pathogen enrichment drives CRP severity in lily.