Linking genomic and phenotypic traits to interaction outcomes in a synthetic phyllosphere community

Abstract

Predicting microbiome function remains challenging as microbial interactions scale from pairwise encounters to emergent community properties. This is particularly true of disease protective microbial consortia, where pathogen invasion has typically been studied either in terms of single biocontrol agents or in terms of microbiome diversity at the full community level, but rarely in between. Focusing on a 16-member synthetic tomato phyllosphere bacterial community, we combined reciprocal spent-media growth assays of over 600 pairwise and community-level combinations with comparative genomics to dissect the ecological and metabolic drivers of community interactions. Across the interaction network, negative interactions dominated, with community-derived spent media consistently exerting stronger inhibitory effects on bacterial growth across the community than any single-species filtrate. While two isolates (Exiguobacterium sibiricum and Bacillus thuringiensis) exhibited strong inhibitory effects in monoculture assays, community spent media analyses revealed that no single strain was responsible for the pathogen-suppressive phenotype observed in community, indicating that protection against Pseudomonas syringae is an emergent property of the particular community composition. Furthermore, using correlations and cross-validated multivariate models, inhibition strengths were poorly predicted by either genomic annotations or phenotypic strategies. Instead, community context strongly constrained environmental modification and buffered strain-specific effects observed in isolation. Together, these results demonstrate that microbial community function cannot easily be inferred from pairwise interactions or individual strain properties alone, and that both direct and indirect interactions shape phyllosphere community structure and function, with emergent properties such as pathogen suppression arising from collective properties rather than the presence/absence or dominance of individual keystone taxa.