Bacterial Community Expansion and Nutrient Activation Underlie Yield Improvement Following Diazotrophic Inoculant Application in Paddy Soil

Reducing reliance on chemical nitrogen fertilizers while maintaining rice productivity is a key challenge in sustainable agriculture. In this study, a composite inoculant of three diazotrophic strains (Paenibacillus azotifigens, Paenibacillus azotofixans, and Phytobacter diazotrophicus) was applied by root drenching at the heading stage of field-grown rice. Soil physicochemical properties, rice yield, and soil bacterial and fungal communities were assessed at harvest using spike-in-based absolute quantification amplicon sequencing. Inoculation increased rice yield by 5.5% and significantly elevated soil nitrate nitrogen (NO3−-N) (+343%), with a trend toward higher available phosphorus, while total nitrogen, phosphorus, and carbon remained unchanged. Bacterial absolute abundance was approximately 2.6-fold higher in inoculated plots, while fungal abundance declined, resulting in a substantially elevated bacteria-to-fungi ratio; community composition and diversity indices showed no significant changes. The inoculant strains were not detectably enriched at harvest, yet functional groups associated with nitrification, nitrogen fixation, and organic matter decomposition were consistently elevated and positively associated with reactive nutrient fractions. These results suggest that diazotrophic inoculants may promote yield through transient microbial community activation and nutrient form transformation rather than persistent colonization, and highlight the value of absolute quantification for detecting inoculation-induced shifts in microbial community size.