Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans

Authors: SHING, GI - University Of Georgia; Asselin, Jo Ann; SMITH, AMY - University Of Georgia; AEGERTER, BRENNA - University Of California - Cooperative Extension Service; COUTINHO, TERESA - University Of Pretoria; ZHAO, MEI - China Agricultural University; DUTTA, BHABESH - University Of Georgia; MAZZONE, JENNIE - Pennsylvania State University; NEUPANE, RAM - Pennsylvania State University; GUGINO, BETH - Pennsylvania State University; HOEPTING, CHRISTY - Cornell University; KHANAL, MANZEAL - Texas A&M University; MALLA, SUBAS - Texas A&M University; NISCHWITZ, CLAUDIA - Utah State University; SIDHU, JASPREET - University Of California - Cooperative Extension Service; BURKE, ANTOINETTE - Eagle Point Farm; DAVEY, JANE - Colorado State University; UCHANSKI, MARK - Colorado State University; DERIE, MICHAEL - Washington State University; DU TOIT, LINDSEY - Washington State University; STRESOW, STEPHEN - Michigan State University; BONASERA, JEAN - Cornell University; Stodghill, Paul; KVITKO, BRIAN - University Of Georgia

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Center rot of onions is caused by several bacterial species in the genus Pantoea and can result in significant pre- and post-harvest losses. Disease management is difficult because there are no known commercially available cultivars of onion with resistance to these pathogens. In order to better understand this pathogen, we collected isolates of Pantoea agglomerans (Pag) from onions from across the USA and tested the strains for onion pathogenicity and resistance to copper bactericides. Combining this information with whole genome sequencing analysis of a subset of the strains revealed that strains fell into two groups, with the onion-pathogenic strains clustering together in a single group. We looked at the distribution of several gene clusters (onion virulence, survival in onion tissue, and copper tolerance) and found they are located on a small extra-chromosomal piece of DNA called a plasmid. One strain contained a plasmid with all three gene clusters plus a system that allowed the plasmid to transfer to other strains conferring pathogenicity to onions. This work shows that there is an association between a Pag strain's possession of plasmids containing specific genes associated with copper resistance, ability to survive in onion tissue, and capacity to cause disease in onions. Because plasmids can shape the emergence of virulence, managing bacterial diseases caused by Pantoea continues to be challenging.

Technical Abstract: Pantoea agglomerans is one of four Pantoea species for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected \>300 P. agglomerans strains 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 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. 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, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene 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 and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.