Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. We describe a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. We profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and detected significant phylogenetic diversity (e.g., Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs where an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in approximately 10% of SynComs that generally followed the diversity-invasion principle. Additionally, our approach enables analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work establishes a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessing persistence and interaction of a specific organism of interest with native consortia.