Interactions between native soil microbiome and a synthetic microbial community reveals bacteria with persistent traits

Synthetic microbial communities (SynComs) are curated microbial groups that can be designed to optimize microbial functions, such as enhancing plant growth or disease resistance. Attaining SynCom stability in the presence of native soil communities remains a key challenge. This study investigated the survival, persistence, and chemical interactions of a SynCom with a native soil microbial community using a transwell system that spatially constrains bacteria while permitting chemical interactions. The SynCom, composed of six compatible <i>Pseudomonas</i> species identified through whole-genome sequencing, was analyzed for antagonistic interactions with native microbes over time and assessed using biomass and viability measurements. Over time, the SynCom exhibited reduced growth in the presence of native soil microbes compared to the SynCom not exposed to the native microbes. Flow cytometry analysis showed an 81% reduction of live cells for the persistent strain in the presence of native microbes and a 78% and 99% increase in dead and unstained cells, respectively. Compared to a non-persistent strain, one persistent SynCom strain showed lower metabolic utilization across five key compound classes: polymers, carboxylic acids, amino acids, amines, and phenols when exposed to the native soil microbes. These findings underscore the importance of understanding complex SynCom-environment interactions to enhance SynCom stability and optimize <i>in situ</i> applications.IMPORTANCESynComs are an emerging technology that can augment plant health. Still, their application <i>in situ</i> depends on deciphering the complex interactions between SynCom microbes and native microbial communities. This study provides insight into several <i>Pseudomonas</i> strains displaying persistent characteristics. Understanding the persistent traits of these bacteria is a vital advancement in SynCom technology and an important next step toward implementing SynComs in agricultural systems.