Bacterial soft rot of Oncidium orchids caused by Dickeya fangzhongdai , Dickeya zeae , and Pectobacterium aroidearum : Pathogen characterization and screening of resistant germplasm

Dickeya and Pectobacterium are globally important soft rot pathogens causing significant crop losses. From 2024 to 2025, 120 Oncidium plants with soft rot symptoms were collected from six areas in Fujian Province, China, yielding 91 bacterial isolates. 16S rRNA gene sequencing revealed that 69 isolates (75.82%) belonged to Dickeya and Pectobacterium. Subsequent gapA phylogenetic analysis identified these as three species: 61 Dickeya fangzhongdai (88.41%), 6 Dickeya zeae (8.70%), and 2 Pectobacterium aroidearum (2.90%). Multilocus sequence analysis based on sixteen housekeeping genes, together with whole-genome sequencing and in silico analyses (average nucleotide identity, ANI; and in silico DNA-DNA hybridization, isDDH), confirmed the species-level identification, with all values exceeding established thresholds. This is the first report of D. fangzhongdai, D. zeae, and P. aroidearum causing soft rot in Oncidium orchids. Pathogenicity assays on 137 accessions (comprising commercial cultivars, breeding lines, and wild accessions) showed that Dickeya strains exhibited strong virulence (mean lesion: 21.63–23.34 mm), while P. aroidearum was significantly weaker (8.83 mm). Wild accessions displayed the highest resistance (7.62–16.91 mm), followed by commercial cultivars (8.75–24.47 mm), with breeding lines most susceptible (10.22–31.13 mm). Five resistant accessions were identified, including two broad-spectrum resistant wild accessions (86 and 130) with stable resistance to all five tested strains (lesion: 2.36–3.48 mm). Host range assays showed the pathogens could infect eight additional orchid genera, indicating broad pathogenic potential. This study provides the first comprehensive characterization of these three pathogens in Oncidium soft rot and identifies valuable resistant germplasm for breeding programs.