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 ideal candidates for sustainable farm management practices with a lower carbon footprint. However, developing effective, stable, and environmentally friendly PGP consortia remains a major challenge. We developed a novel strategy for designing microbial consortia by integrating natural microbial interactions and metabolic complementarity among selected microbes, using network analysis and genome-scale metabolic modelling, respectively and thereby constructed a three-member microbial consortium (SAB). Both microbiological and genomic analyses demonstrated the significant PGP potential and stability of SAB, which outperformed its individual members. Phenotypic data indicated that SAB treatment enhanced plant growth rate and biomass without disrupting the native soil microbial community. Furthermore, experiments confirmed the consistent and significant performance of SAB treatment on Choy Sum and other plants across different setups and soil conditions, demonstrating its broad-spectrum beneficial activity. Transcriptomic analysis revealed that SAB triggered a parallel activation of growth and defense responses in the shoot, effectively bypassing the typical growth-defense trade-off through microbiome-mediated signaling and beneficial functions. Overall, our 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.