From natural assemblages to synthetic communities in the Lupinus microbiome

Introduction Plant roots harbour complex microbial communities that enhance nutrient acquisition, stress tolerance, and pathogen defence, yet their assembly and functional dynamics remain incompletely understood. Results In this work, we isolated over 700 bacterial strains from wild Lupinus angustifolius across multiple compartments and soil types, capturing both dominant and rare bacterial taxa. Using co-occurrence network analysis, we selected representative strains to assemble synthetic communities (SynComs) of varying complexity, which were inoculated under sterile and non-sterile conditions. Plants were inoculated with SynComs of increasing complexity under both non-sterile soil and gnotobiotic conditions. SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. Increasing SynCom complexity enhanced plant growth and triggered host transcriptional responses involving hormone signaling, defence pathways, and metabolic reprogramming. Discussion These findings indicate that soil-driven filtering and microbial interactions govern microbiome assembly and plant responses. Incorporating taxa with distinct ecological roles, including low-abundance members, improves SynCom functionality and advances understanding of plant-microbe interactions in natural and agricultural systems.