A synthetic microbial community for soybean biofertilization designed via chlorophyll-based iterative selection

ABSTRACT Improving the effectiveness of microbial inoculants for soybean is essential to enhance biological nitrogen fixation and reduce fertilizer dependence; however, inoculated Bradyrhizobium strains frequently display inconsistent field performance. Inoculation is usually carried out with single-strain formulations, overlooking the possible influence of the native soil microbiota on nodulation success. This limitation may be addressed by formulating inoculants with consortia that include selected members of the soil microbiota. To this end, a synthetic microbial community (SynCom) was developed through a host-mediated microbiome engineering approach guided by leaf chlorophyll content as a rapid, non-destructive plant trait. The experiment was initiated by inoculating soybean plants with a consortium of 9 Bradyrhizobium spp. and 14 non-rhizobial soil isolates. Across eight consecutive selection rounds under gnotobiotic conditions, rhizosphere communities associated with superior plant performance were pooled and propagated. Recurrent selection induced significant shifts in community composition, consistently favoring Bradyrhizobium diazoefficiens as the dominant nodulating member and enriching taxa from Pseudomonadales, Burkholderiales, and Sphingomonadales. Sequencing-based profiling and network analysis suggested the emergence of a cohesive and functionally enriched community, with increased potential for nitrogen transformations and organic matter turnover. When evaluated in non-sterile soil, the SynCom derived from the sixth selection round increased nodule number and biomass relative to an uninoculated control and a commercial inoculant strain. These results suggest that plant-guided selection can steer rhizosphere community assembly toward beneficial configurations and support the development of improved soybean bioinoculants. IMPORTANCE Soybean [ Glycine max (L.) Merr.] is a major global crop characterized by high seed protein content, which demands elevated nitrogen assimilation. To meet this demand, the crop can utilize atmospheric nitrogen through the process of biological nitrogen fixation in symbiosis with Bradyrhizobium bacteria, thus mitigating soil nitrogen depletion. Although Bradyrhizobium -based inoculants are applied at sowing, their interplay with other members of the rhizosphere microbiota remains poorly understood. It is well documented that plants and rhizosphere microbiota interact to shape plant growth and soil productivity. Therefore, this work evaluated the inoculation of soybean with a synthetic microbial consortium as a strategy to develop new-generation inoculants. These bioinputs are designed to harness plant-soil-microbe interactions to improve soybean productivity while preserving soil properties.