Plasmids encode and can mobilize onion pathogenicity inPantoea agglomerans

Abstract

AbstractPantoea agglomeransis one of fourPantoeaspecies for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not allP. agglomeransstrains are pathogenic to onion. We characterized onion-associated strains ofP. agglomeransto elucidate the genetic and genomic signatures of onion-pathogenicP. agglomerans. We collected >300P. agglomeransstrains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87P. agglomeransstrains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, publicP. agglomeransgenome assemblies identified two well-represented and well-supportedP. agglomeransphylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, theP. agglomeransHiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conservedP. agglomeransplasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes ofP. agglomeransrevealed that the pOnion plasmids harboredaltgenes responsible for encoding tolerance to the thiosulfinate defensive chemistry inAlliumspp. Additionally, many of these pOnion plasmids harboredcopgene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir andaltclusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transformsP. agglomeransPhylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediatingP. agglomeransinteractions with onion plants, with potential implications for onion bacterial disease management.