Fire Blight Canker Microbiome: Insights into the Key Ecological Niche for <i>Erwinia amylovora</i>

The invasion of Erwinia amylovora (Ea) from soft plant tissues to wood forms fire blight cankers, which serve as reservoirs for pathogen overwintering and infection in spring. Understanding the poorly explored ecological niche of Ea within cankers provides valuable insight into its biology, ecology and pathogenicity. This study analyzed bacterial communities in healthy and cankered wood samples from six apple cultivars in Augusta County, Virginia, using SMRT PacBio Hi-Fi metabarcoding. Significant differences in bacterial diversity and richness were found between healthy and cankered wood tissues, with Erwinia spp. dominating the cankered samples. The highest number of Ea Amplicon Sequence Variants (ASVs) was detected in apple cultivars Cripps Pink, followed by Gala, Aztec Fuji, Granniwinkle, Hewe's Crab and an unknown cultivar used as a blind control. Machine learning algorithms identified the prevalence of Erwinia, Sphingomonas, Massilia and Pantoea in cankered wood samples. Bacterial interactions in healthy and cankered wood networks showed a mixture of co-occurrence and co-exclusion, including significant negative (e.g. Rhizobia group) and positive (e.g. Pantoea spp.) correlations with Ea and several other bacterial species in the canker microbiome. The canker networks identified Novosphingobium, Variovorax, and Nocardioides as module hubs. Bacillus spp. were prominent in healthy wood tissue microbiome. The increasing number of ASVs assigned to different bacterial taxa indicates a shift in community composition from microbiome to pathobiome. Functional profiling revealed ecological differences between healthy tissues and cankers (e.g. canker phytopathogenic determinants enrichment). Our results pave way to potential synthetic microbial communities that could effectively manage fire blight.