Metabolite-Guided Regulation of the Rhizosphere Microbiome by a Synthetic Microbial Consortium and Key Mixed Metabolites Suppresses Root Rot Disease in Fritillaria pallidiflora

Abstract Continuous cropping can weaken soil disease suppression, but its microbial and metabolic bases remain unclear. We compared first-planting and replant rhizospheres of Fritillaria pallidiflora at 2-, 3-, and 4-year cultivation stages sampled in different calendar years using soil analysis, sequencing, metabolomics, and pot experiments. Replant soils had a higher root rot incidence, greater Fusarium solani abundance, and lower microbial network complexity and stability. Nitrate, ammonium, and electrical conductivities were associated with community restructuring. Five metabolites were linked to disease incidence and microbial taxa. A synthetic community (SynCom) of four Bacillus strains and one Brevibacillus laterosporus strain reduced F. solani abundance and disease incidence, enriched beneficial bacteria, increased antioxidant enzyme activities, and promoted growth. All five strains were recovered from the rhizosphere after 30 days. Combining the SynCom with the five metabolites produced the strongest disease suppression and plant growth. These findings support the evaluation of metabolite-guided microbial consortia for disease management.