Sequencing-based quantification of Erwinia amylovora strains identifies contribution of strain × strain × host interactions underlying apple fire blight severity

Multiple pathogen strains coexist in the field, and their interactions with host genotypes can strongly affect disease severity and management. Fire blight, caused by the bacterium Erwinia amylovora , is one of the most devastating bacterial diseases of apple and pear worldwide. The interaction between the genetics and phenological stage of the host, the genetics of pathogen strains, and environmental conditions results in outbreaks and changes the severity of the fire blight infection. Multiple E. amylovora strains are present in apple orchards, yet the effects of strain × strain interactions on disease development remain poorly understood. This is partially due to the low genetic diversity of E. amylovora, which presents a challenge for strain differentiation and quantification. We developed and utilized an amplicon sequence (AmpSeq) based approach to identify SNPs between strains to investigate strain-strain interactions in vitro and in planta . In vitro assays showed that the fire blight strain E2002a exhibited the fastest growth and outcompeted the other strains (Ea273 and E4001a) as cultures approached the stationary phase. Plant inoculation assays of four apple genotypes in two separate experiments demonstrated that both strain composition and host genotype influenced disease severity. Generally, E2002a and E4001a and strain mixtures containing them resulted in the most severe fire blight infections in the apple genotypes (‘Empire’, ‘Gala’, and ‘G.935’), suggesting the dominance of these strains in determining infection severity. The severity of infection was also strongly host dependent. E2002a was the dominant strain isolated from infected tissue. Our results show that host genotype × strain interaction was the most important predictor of fire blight severity, highlighting the need for in depth understanding of strain × strain × host genotype interaction for sustainable fire blight management.