Bio-organic fertilizer alleviates tobacco continuous cropping obstacles by coordinately reprogramming plant metabolism and the rhizosphere microbiome

ABSTRACT: Background Crop continuous cropping obstacles (CCO) severely threaten soil ecosystem health and sustainable agricultural production. Although bio-organic fertilizer (BF) has been widely applied to mitigate crop CCO, the underlying mechanisms remain poorly understood. Herein, an Aspergillus-amended BF was developed using an antagonistic strain isolated from tobacco rhizosphere. By integrating plant physiological responses with plant and rhizosphere metabolomics and microbiome analyses, we investigated the mechanisms underlying BF-mediated alleviation of tobacco CCO. Results We show that novel Aspergillus-amended BF markedly alleviates tobacco CCO by coordinately reprogramming host metabolism and the rhizosphere microbiome. BF application activated tobacco systemic acquired resistance through phenylalanine-derived salicylic acid signaling, as evidenced by the induction of PR genes, reactive oxygen species accumulation, and redox homeostasis regulation. Concurrently, BF significantly reshaped the composition, functional potential, and interaction networks of the rhizosphere microbiome, suppressing pathogen survival and virulence while enriching beneficial taxa, including Aspergillus, Flavobacterium, Pseudomonas, and Galbibacter, along with functional pathways related to quorum sensing and ABC transporters. BF also enhanced positive microbial interactions, thereby strengthening microbial network stability. Critically, microbiome reconstitution assays demonstrated that this protective effect depended on viable rhizosphere microbial communities, highlighting a causal role of the microbiome. Field trials further confirmed the efficacy of BF in mitigating tobacco CCO, resulting in a 31.0% reduction in disease incidence and significant improvements in economic traits compared with chemical fertilizer alone. Conclusions Collectively, our findings reveal a coordinated host-microbiome mechanism underlying BF-mediated alleviation of tobacco CCO and highlight microbiome priming as a promising strategy for microbiome-based disease suppression and sustainable agricultural production.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse-phase, Liquid Chromatography MS - positive - reverse-phase

PROVIDER: MTBLS14267 | MetaboLights | 2026-04-13

REPOSITORIES: MetaboLights