Low intra-microbiota antagonism underlies stable and protective barley root microbiota

Plants rely on root-associated microbiota for growth and pathogen protection, yet the community properties underlying stable beneficial functions remain unclear. Here, we show that low intra-microbiota antagonism is associated with stability and pathogen protection in the barley root microbiota. Using a comprehensive culture collection of barley root endophytes, we reconstructed bacterial synthetic communities (SynComs) and compared a core SynCom resembling the natural microbiota with a trait-prioritized SynCom assembled from strains selected for predicted host benefits. Although strains from both communities exhibited broad pathogen-inhibitory potential, the communities behaved differently in planta. The core SynCom showed low internal antagonism, remained stable, and protected barley roots against fungal pathogens without impairing growth. In contrast, the trait-prioritized SynCom exhibited strong internal antagonism, unstable assembly, loss of protection, and reduced root growth. Together, our findings indicate that microbiota function cannot be predicted from individual strain traits alone. Rather, low intra-microbiota antagonism promotes community stability and enables protective functions to emerge in barley roots. Significance statementPlants rely on root microbiota for disease protection, yet the principles governing community stability and protective function remain poorly understood. Here, we show that low intra-microbiota antagonism is associated with a stable and protective barley root microbiota, whereas strong internal antagonism destabilizes communities, impairs root growth, and abolishes pathogen protection. These findings show that microbiota function depends not only on beneficial traits of individual strains, but also on compatibility among community members. HighlightsO_LILow intra-microbiota antagonism is associated with stable and protective barley root microbiota. C_LIO_LITrait-prioritized SynCom assembly with higher intra-microbiota antagonism can lead to dysbiosis. C_LIO_LIA highly antagonistic Pseudomonas strain is buffered by the core SynCom but detrimental in an unstable community. C_LIO_LICommunity compatibility better explains protection than individual strain traits. C_LIO_LIStable bacterial communities support fungal endophyte-mediated protection and maintain pathogen protection across barley genotypes. C_LI