Identification of a Burkholderia Species Causing Onion Bulb Rot Disease

This short communication reports two bacterial strains (22PA0099 and 22PA0106) of a previously undescribed Burkholderia species causing bulb rot in onion. These strains were recovered from symptomatic onion plants collected from Pennsylvania during the routine scouting of onion fields in 2022. The strains were identified as Burkholderia sp. through 16S ribosomal RNA sequencing with the highest percentage of identity, coverage, and e-value of 98.7%, 98 to 100%, and zero, respectively. In addition, primers targeting the recA gene were used to characterize species. Both strains had the closest hits with B. perseverans and B. gladioli, with 94 to 100% coverage and 92 to 95% identity in the recA gene. The whole genomes of both strains were sequenced using long-read sequencing. Comparisons with available genomes indicated that these strains had the closest identity with B. gladioli, with 92% average nucleotide identity. Furthermore, the two strains shared 97% sequence identity, suggesting they belong to the same species. These percentages indicate that the strains likely represent a novel Burkholderia species not reported previously on onion. A whole onion bulb assay confirmed the two strains’ pathogenicity. The proper identification and monitoring of this pathogen is important to help growers make informed decisions regarding disease diagnosis and management.