Inoculation of stigma-colonizing microbes to apple stigmas alters microbiome structure and reduces the occurrence of fire blight disease

Abstract

Flowers secrete nutrient-rich exudates that support the growth of an assemblage of microorganisms, including both beneficial and pathogenic members, most of which belong to the phylum Proteobacteria. Given the potential role of the microbiome in plant health, manipulating the microbiome to promote growth of beneficial members holds promise in controlling plant diseases. In this study, we inoculated four different bacterial strains that were originally isolated from apple stigmas, alone or in mixtures of increasing complexity, onto apple flowers during bloom. We tested whether such treatments would influence fire blight occurrence, a disease caused by Erwinia amylovora, and whether we could detect a shift in the structure of the microbiome due to the treatments. We show that various inoculations did influence the occurrence of fire blight, although the level of disease suppression was dependent upon specific bacterial strains. Furthermore, treatments using different strains or strain mixtures predominantly resulted in increased representation of the inoculated strains, suggesting that disease suppression was due to an alteration of the stigma microbiome structure. Compared with treatments using single strains, a Pantoea–Pseudomonas strain mixture produced a homogeneous microbiome structure with less interflower variability. Findings from this study suggest that the microbiome on the flower stigma can be manipulated through microbial inoculation. Due to flowers’ short life span yet important role in plant disease infection, even a short-term influence on microbiome composition may result in significant decreases in disease susceptibility.