An ecology-driven microbial consortium enhances plant growth and immunity while sustaining rhizospheric microbial balance

Plant growth-promoting (PGP) microbial consortia offer a promising alternative to reduce reliance on chemical fertilizers in crop production. Their regenerative potential makes them well suited for sustainable farm management practices with a lower carbon footprint. However, developing effective, stable, and environmentally friendly PGP consortia remains a major challenge. Here, we present a novel strategy for designing microbial consortia by integrating natural microbial interactions and metabolic complementarity among selected microbes, using co-occurrence network analysis and genome-scale metabolic modeling, respectively. Using this approach, we constructed a three-member microbial consortium comprising Streptomyces sp., Agromyces sp., and Bacillus sp. (SAB). Both microbiological and genomic analyses demonstrate the strong PGP potential and stability of SAB, which outperforms its individual members. Phenotypic analyses indicate that SAB treatment enhances plant growth rate and biomass without disrupting the native soil microbial community. Furthermore, experiments confirm the consistent and significant performance of SAB across choy sum and other plant species under different experimental setups and soil conditions, demonstrating its broad-spectrum beneficial activity. Transcriptomic analyses reveal that SAB induces parallel activation of growth and defense responses in shoots, effectively bypassing the typical growth-defense trade-off through microbiome-mediated signaling and beneficial functions. Overall, this study demonstrates the functional potential of an ecologically designed microbial consortium that enhances plant growth by rewiring resource allocation while exerting minimal impact on the rhizospheric microbial community.