Partial substitution of chemical fertilizer with chrysanthemum residue-derived biofertilizer alleviates continuous cropping obstacles of cut chrysanthemum by stimulating microbial cooperation and enzyme activities

Continuous cropping obstacles (CCOs) severely impede cut chrysanthemum ( Chrysanthemum morifolium Ramat.) cultivation by degrading soil health and suppressing yield. While excessive mineral fertilization exacerbates soil degradation, partial substitution with bio-fertilizers offers a promising mitigation strategy; however, the underlying microbial mechanisms remain elusive. To address this, a two-year trial was conducted in 12-year continuously cropped soil, substituting 20 % and 40 % of mineral fertilizer with chrysanthemum residue compost (OF) or Bacillus subtilis -inoculated bio-organic fertilizer (BF) on an equivalent nitrogen basis. Organic substitution, particularly high-rate BF in the second year, significantly enhanced plant biomass and quality parameters (e.g., chlorogenic acid and flavonoid), alongside markedly increasing the activities of urease and β-glucosidase, compared to conventional chemical fertilization ( P < 0.05). Concurrently, organic substitution effectively ameliorated soil acidification (increasing pH by 18.0–21.4 %) and compaction. Notably, BF treatments demonstrated the greatest potential for boosting soil fertility, with soil available phosphorus peaking at 114.6 g kg −1 . The BF treatments effectively suppressed the fungal community, notably reducing the abundance of the pathogen Fusarium oxysporum , while simultaneously promoting bacterial proliferation and enriching the inoculated Bacillus subtilis ( P < 0.05). Furthermore, BF application maintained bacterial alpha-diversity but reduced fungal diversity ( P < 0.05). Co-occurrence network analysis revealed that BF shifted the microbial interaction pattern from intense intra-kingdom bacterial competition (under chemical fertilization) toward enhanced inter-kingdom bacteria-fungi interactions, which fostered a more antagonistic profile among the core microbial taxa. Redundancy analysis identified soil pH and available phosphorus as primary drivers of this community reassembly. We conclude that bio-fertilizer substitution overcomes CCOs by restoring edaphic properties and fostering a specific, antagonistic core microbiome, providing a vital waste-to-value strategy to manage continuous cropping problems in the cut chrysanthemum industry. • B. subtilis- inoculated residues created a waste-to-value bio-fertilizer. • Bio-fertilizer strengthened soil bacterial-fungal network cooperation. • Bio-fertilizer enriched soil B. subtilis and suppressed F. oxysporum . • Synergistic antagonism among bacterial and fungal core taxa enhanced plant growth.