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.
Nie et al. (2026) studied this question.