Competitive hierarchies, antibiosis, and the distribution of bacterial life history traits in a microbiome

Microbiome manipulation requires an understanding of how species interact within communities. Can outcomes of ecological interactions be predicted from microbial life history traits, the identity of the species, or both? We addressed these questions by studying the competitive interaction network in a community of 40 endophytic Pseudomonas spp. bacterial isolates from a native plant. Pairwise competition experiments revealed competitive dominance of P. fluorescens over P. syringae strains within this microbiome-derived community. P. syringae strains with higher growth rates won more contests, while P. fluorescens strains with shorter lag times and lower growth rates won more contests. Adding to their competitive dominance, P. fluorescens strains often produced antibiotics to which few P. syringae strains were resistant. Many competitive outcomes among P. syringae strains were predicted to be reversed by P. fluorescens inhibitors because indirect benefits accrued to less competitive strains. P. fluorescens strains frequently changed competitive outcomes, suggesting a critical role of strains within this bacterial clade in structuring plant microbiome communities. Microbial traits also may provide a handle for directing the outcome of colonization processes within microbiomes.