Bacterial social interactions in synthetic Bacillus consortia enhance plant growth

Abstract

Plant growth-promoting rhizobacteria (PGPR) represent a sustainable method to improve crop productivity. Synthetic microbial consortia have emerged as a powerful tool for engineering rhizosphere microbiomes. However, designing functionally stable consortia remains challenging due to an insufficient understanding of bacterial social interactions. In this study, we investigated the effects of Bacillus velezensis SQR9 (i.e., a commercially important PGPR) on social interactions within the rhizosphere community, particularly among Bacillus species. SQR9 inoculation significantly enhanced cucumber plant growth and altered the structure of rhizosphere Bacillus and its related bacterial communities. The results of swarm boundary and carbon utilization assays, revealed that phylogenetically closer Bacillus strains exhibited increased social cooperation and increased metabolic niche overlap. Building on these social interactions, we designed 30 consortia comprising both highly related (HR) and moderately related (MR) types across four richness levels (1, 2, 3, and 4 strains), with MR consortia demonstrating superior PGP effects through enhanced plant growth, root colonization, indole-3-acetic acid production, and siderophore production, than the HR consortia. Expanding these findings to 300 consortia across four richness levels (1, 2, 4, and 8 strains) confirmed enhanced PGP effects in MR consortia with increasing richness. These findings highlight the importance of bacterial interactions and phylogenetic relationships in shaping rhizosphere communities and designing synthetic microbial consortia. Specifically, this study provides a framework for assembling Bacillus consortia that enhance cooperation, which would aid in improving their stability and effectiveness in agricultural applications.