Background The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation. We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology (NGS).

Methods Lily bulbs were soaked in a seed treating agent containing beneficial microbes (SP treatment) for 4 hours. Subsequently, they were planted in soil in July and sampled in September to assess plant growth, rhizosphere soil physicochemical properties, and microorganism community structures. In addition, we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.

Results Under SP treatment, there were significant alterations in fungi and bacteria community structures, accompanied by improved soil nutrient status. Notably, the relative abundance of dominant microorganism groups, such as the fungi Basidiomycota, Pseudeurotium, Cladophialophora, Microascus, and Dactylonectria, as well as the bacteria Proteobacteria, Chloroflexi, Ochrobactrium, Lysobacter, and RB41, underwent notable changes. Microorganism function prediction results indicated a reduction in pathotrophic fungi (including plant pathogens) and an increase in endophytic and saprotrophic fungi under SP treatment. Among the top 20 metabolism pathways, 80% were upregulated in SP treatment compared to the CK.

Conclusions Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs. The beneficial microorganisms play a crucial role in regulating soil microbial structures, enhancing the accumulation of endophytic fungi, reducing the abundance of pathogens, and improving soil functions. Furthermore, specific microbial groups are found to be involved in maintaining soil health.