Background The application of beneficial microbial seed soaking prior to sowing represents a novel technology that has yet to be employed in Lanzhou lily cultivation. We conducted an experiment to investigate 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 kind of seed treating agent containing beneficial microbial (SP treatment) for 4 hours, then planted in soil in July and sampled in September for investigation of the plant growth, and the rhizosphere soil physicochemical properties and the microorganism community structures. Furthermore, we utilized 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, companied by improved soil nutrient conditions. Nota, the relative abundance of dominant microorganism groups, such as the fungi Basidiomycota, Pseudeurotium, Cladophialophora, Microascus, and Dactylonectria; as well as the bacterial Proteobacteria, Chloroflexi and Ochrobactrium, Lysobacter and RB41, underwent notable changes. Microorganism function prediction results indicated a reduction in pathotrophic fungi (including the plant pathogens) and an increase in endophytic and saprotrophic fungi under SP treatment. Among the top 20 metabolism pathways, 80% were upregulated in SP treatments compared to the CK.

Conclusions Seed soaking with beneficial microbial strain promoted growth of Lanzhou lily bulbs. The beneficial microorganisms played a crucial role in regulating soil microbial structures, enhancing the accumulation of endophytic fungi, reducing pathogens, and improving soil function. Furthermore, specific microbial groups were fund to be involved in maintaining soil health.