Field Evidence for Microbial Fertilization Improving Flue-Cured Tobacco Quality through Rhizosphere Shifts and Chemical Coordination

Flue-cured tobacco quality relies not only on yield but also on the coordination of chemical constituents and sensory traits, both of which are compromised by long-term overuse of chemical fertilizers. Microbial fertilization has emerged as a promising strategy to balance productivity, quality, and soil health, yet systematic field-scale evidence remains limited. Here, we conducted a two-year factorial field experiment in Sichuan, China, to evaluate two microbial fertilizers (a Bacillus-based inoculant and a commercial consortium) applied individually or in combination across dosage gradients. Agronomic traits, chemical composition, secondary metabolites, and rhizosphere microbial communities were comprehensively assessed. Co-application significantly improved plant height, leaf width, and overall appearance while optimizing sugar/nicotine and nitrogen/nicotine ratios within ideal coordination ranges. Secondary metabolite profiling showed that co-application enhanced chlorogenic and neochlorogenic acids alongside balanced organic acids, contributing to superior aroma and combustibility. Microbial diversity and community structure were reshaped, with Bacillus, Rhizobiales, and Sphingomonas emerging as key biomarkers positively associated with agronomic and sensory traits. Network and structural equation modeling confirmed an indirect pathway whereby fertilization type modulated rhizosphere communities, which in turn influenced metabolites and ultimately leaf quality. Collectively, these results provide field-based evidence that microbial fertilizer co-application improves flue-cured tobacco quality through rhizosphere shifts and chemical coordination, offering a mechanistic and practical basis for sustainable tobacco production.