Analysis of soft rot Pectobacteriaceae population diversity in US potato growing regions between 2015 and 2022

Authors: MA, XING - Cornell University; ZHANG, XINYU - University Of Maine; Stodghill, Paul; RIOUX, RENEE - University Of Wisconsin; BABLER, BROOK - University Of Wisconsin; Rivedal, Hannah; FROST, KEN - Oregon State University; HAO, JIANJUN - University Of Maine; SECOR, GARY - North Dakota State University; Swingle, Bryan

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: In 2021, the total economic contribution of potato (including production, processing, retail sales, etc.) in the United States was valued at $101 billion and generated more than 714,000 jobs. Soft rot diseases are a long-term persistent problem affecting all stages of potato production. Soft rot diseases are caused by around 30 different species of bacteria, all of which cause disease by destroying the structural integrity of plant cells, causing the affected tissues to become rotten and inedible, and ultimately killing the plants. The most effective control is to avoid letting the bacteria infect the crop. In this study we made two important steps towards controlling potato soft rot. First, we determined the range of bacterial species responsible for soft rot diseases in most of the major American potato growing regions between 2015 and 2022. Second, we revealed that there are two sources of the disease. One is an endemic, highly diverse, population of bacteria appearing to have been present in the US for a very long time. The other is coming from recent introductions of highly virulent strains, derived from single of very few clones, that spread rapidly. These two pieces of information are critical for understanding how these pathogens enter our potato cropping systems and necessary for deciding how best to allocate resources to reduce the negative economic impact these diseases impose.

Technical Abstract: Soft rot Pectobacteriaceae (SRP) are globally dispersed pathogens that cause significant economic loss in potato and other crops. There are currently 34 recognized SRP species that produce plant cell wall degrading enzymes to break down plant tissues to extract nutrients and cause disease. Our understanding of the SRP species diversity has expanded in recent years due to advances and adoption of whole genome sequence technologies. In the present study, we used whole genome sequence analysis to describe the current distribution and epidemiology of SRP responsible for diseases in commercial potato cropping systems in the United States. We collected 118 SRP strains isolated from diseased potato plants and tubers in 14 states between 2015 and 2022. Our primary objectives were: 1) identify the species of these SRP isolates, 2) describe the variation among SRP isolates from various locations and track their temporal changes, and 3) evaluate the evolutionary relationships among these SRP isolates to deduce their source. As a result, we identified three Dickeya and eight Pectobacterium species responsible for diseases in potatoes. Especially, D. dianthicola, P. parmentieri, P. carotovorum, and P. versatile appeared to be the predominant species, constituting 83% of the isolates. Furthermore, all D. dianthicola strains studied here as well as 90% of US D. dianthicola isolates sequenced to date exhibit significant clonality. The prevalence of this specific group of D. dianthicola, temporally and geographically, aligns with the occurrence of blackleg and soft rot outbreaks in the northeastern US after 2014. The genomic diversity observed in P. parmentieri implies multiple introductions to the US from at least four distinct sources, earlier than the arrival of the predominant group of D. dianthicola. In contrast, P. carotovorum and P. versatile appear to be widespread, long-term endemic strains in the US