Fire Blight Canker Microbiome: Insights into the Key Ecological Niche for Erwinia amylovora

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 (single molecule, real-time) 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 was detected in the apple cultivar 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 cooccurrence and coexclusion, 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 the healthy wood tissue microbiome. The increasing number of amplicon sequence variants assigned to different bacterial taxa indicated 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 the way for the development of potential synthetic microbial communities that can effectively manage fire blight. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .