Exogenous <i>Bacillus</i> promotes enrichment of native microbes to assemble synthetic communities for plant growth promotion

Abstract Plants recruit beneficial microbes to support growth and defense, but how exogenous inoculants interact with native microbiomes to influence plant performance remains unclear. We found that Bacillus thuringiensis NL-11 promoted the enrichment of indigenous taxa, including 45 Amplicon Sequence Variants (ASVs). From a non-redundant isolate collection, we linked enriched ASVs to isolates (based on 16S rRNA identity) to build a 12-member SynCom (SynCom12), and adding B. thuringiensis NL-11 produced BSynCom12 to test the growth effects. Neither SynCom12 nor BSynCom12 exceeded the growth promotion of B. thuringiensis NL-11 alone. Therefore, we designed a simplified synthetic community, SynComC, which consists of two strains (NJ158 and NJ63) with strong rhizosphere colonization capabilities and high abundance with the help of NL-11, and whose growth-promoting ability exceeds that of SynCom12 and BSynCom12. Moreover, co-inoculation of B. thuringiensis NL-11 with SynComC yielded the highest stability in bacterial co-occurrence networks. Community assembly analyses further showed that NL-11 alone increased deterministic assembly, whereas NL-11/SynComC co-inoculation restored stochastic dominance. Metagenomics revealed an enrichment of plant hormone signaling, plant-pathogen interactions, MAPK signaling, and isoflavonoid biosynthesis in the inoculated groups (NL-11, SynComC, and BSynComC). Our SynCom assembly strategy, guided by colonization capacity and co-inoculation with native partners, effectively promotes plant growth and informs rational design of synthetic communities.