Integrative microbiomics and co-occurrence network analyses decipher the mechanisms underlying organic fertilizer-driven yield and nucleoside content enhancement in Fritillaria unibracteata

Fritillaria unibracteata is a medicinal plant with high economic and medicinal value. The mechanistic understanding of how varying fertilization strategies influence its yield and phytochemical quality however remains largely unexplored. In this study, we aimed to comprehensively evaluate the effects of cow and sheep manures on the soil nutrient enzyme activities, microbiology, yield, and nucleoside content of F. unibracteata. A comprehensive evaluation of the physicochemical properties of the soil, enzyme activities, microbiomics, and co-occurrence networks was conducted at the time of F. unibracteata harvest with the application of cow and sheep manure. Our findings demonstrated that the application of cow manure (24.3 t·ha⁻¹), and sheep manure (43.7 t·ha⁻¹) resulted in remarkable yield increases of 119.45% and 97.22%, respectively. Organic fertilizer treatment significantly increased the concentrations of critical nucleosides—uridine, guanosine, and thymidine—by 119.65%, 105.26%, and 70.20%, respectively. Microbiome profiling and co-occurrence network analyses revealed that organic fertilizer enhanced the functional synergy and structural resilience of soil microbial communities, with notable proliferation of nutrient-cycling taxa, such as Comamonadaceae and Sphingomonadaceae significantly increasing by 31.7% and 27.0%, respectively. Pathogenic fungal taxa, including Heydenia and Solicoccozyma, showed significant reductions of 63.1% and 19.4%, respectively. Structural equation modeling identified the enhancement of soil enzyme activity and soil phosphorus as the principal factors driving the observed increases in F. unibracteata yield and nucleoside accumulation. The application of organic fertilizers enhances the yield and quality of F. unibracteata by recruiting beneficial microorganisms that promote soil nutrient cycling and improve the soil microbiological environment.