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

Xing Ma; Xiuyan Zhang; Paul Stodghill; Renee Rioux; Smita Shrestha; Brooke Babler; Hannah Rivedal; Kenneth Frost; Jianjun Hao; Gary Secor; Bryan Swingle

doi:10.3389/fmicb.2024.1403121

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

Front Microbiol. 2024 Sep 16:15:1403121. doi: 10.3389/fmicb.2024.1403121. eCollection 2024.

Authors

Xing Ma¹, Xiuyan Zhang², Paul Stodghill^{1

3}, Renee Rioux⁴, Smita Shrestha⁴, Brooke Babler⁵, Hannah Rivedal⁶, Kenneth Frost⁷, Jianjun Hao², Gary Secor⁸, Bryan Swingle^{1

3}

Affiliations

¹ Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.
² School of Food and Agriculture, University of Maine, Orono, ME, United States.
³ Emerging Pests and Pathogens Research Unit, United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, United States.
⁴ Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States.
⁵ Wisconsin Seed Potato Certification Program, Department of Plant Pathology, University of Wisconsin-Madison, Middleton, WI, United States.
⁶ Forage Seed and Cereal Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, United States.
⁷ Department of Botany and Plant Pathology and Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States.
⁸ Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.

Abstract

Introduction: Soft rot Pectobacteriaceae (SRP) bacteria are globally dispersed pathogens that cause significant economic loss in potato and other crops. Our understanding of the SRP species diversity has expanded in recent years due to advances and adoption of whole-genome sequence technologies. There are currently 34 recognized SRP species that belong to the Dickeya and Pectobacterium genera.

Methods: We used whole-genome sequencing based analysis to describe the current distribution and epidemiology of SRP isolated from diseased potato samples obtained from commercial potato cropping systems in the United States. Our primary objectives in the present study were to: (1) identify the species of these SRP isolates recovered from potato samples across 14 states in the US, (2) describe the variation among SRP isolates from various US locations and track their temporal changes, and (3) evaluate the evolutionary relationships among these SRP isolates to deduce their source. We collected 118 SRP strains from diseased potato plants and tubers in 14 states between 2015 and 2022.

Results: We identified three Dickeya and eight Pectobacterium species from diseased potato samples. Dickeya dianthicola, Pectobacterium 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.

Discussion: 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.

Keywords: Dickeya; Pectobacteriacea; potato; soft rot and blackleg disease; whole genome sequencing.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was partially funded by the National Institute for Food and Agriculture, Specialty Crops Research Initiative (2017-51181-26827). The sampling and isolation conducted at University of Wisconsin-Madison was also funded by Specialty Crop Block Grant and Wisconsin Potato and Vegetable Growers Association under the project title “Development of next-generation detection methods and improved biological understanding for tuber necrotic viruses in Wisconsin seed potato production.”