Abstract

Microbial fertilizers represent a promising strategy for sustainable agriculture in phosphorus-deficient acidic red soils. However, whether microbial inoculation provides additional agronomic benefits within an organically amended system remains unclear. This study integrates field experiments and transcriptomics to investigate whether supplementation with a Bacillus velezensis BJCP3 and Aspergillus spinosus ISP018 consortium enhances peanut performance within an organically amended system. Compared with the organic amendment control (CK), the consortium (BI) increased peanut yield by 35.97% and kernel protein by 14.39% ( p  < 0.05), while improving soil available phosphorus (+26.12%), dissolved total nitrogen (+79.40% p  < 0.05), and organic matter (+30.95%). Crucially, microbial community diversity and richness were significantly affected by microbial inoculants, and changes occurred in the community composition. Quantitative PCR revealed that microbial inoculants increased the abundance of genes associated with organic P mineralization (OPM). This upregulation correlated strongly with higher soil AP. Transcriptomic analysis of peanut roots further revealed the consortium-induced upregulation of key genes involved in nutrient acquisition (including AMT, PHT, and HAK families for N, P, and K uptake, respectively) and defense responses (e.g., Pit6, PR1). Collectively, these findings suggest that the enhancement of peanut yield and quality by the microbial inoculant is associated with correlated dual responses: (1) changes in soil microecology linked to enhanced P bioavailability via OPM gene upregulation, and (2) co-activation of plant root pathways for nutrient assimilation and defense. This integrated analysis provides a plausible model linking microbial consortium application to improved crop performance within an organically amended system in acidic red soils.