Species of Dickeya and Pectobacterium isolated in 2015-2016 from potatoes with soft rot disease in Northeastern and North Central United States

Authors: CURLAND, R. - University Of Minnesota; MAINELLO, A. - Pennsylvania State University; PERRY, K. - Cornell University; HAO, J. - University Of Maine; CHARKOWSKI, A. - Colorado State University; BULL, C. - Pennsylvania State University; MCNALLY, R. - University Of Minnesota; JOHNSON, S. - University Of Maine Cooperative Extension; ROSENZWEIG, N. - University Of Michigan; SECOR, G. - University Of North Dakota; Larkin, Robert - Bob; GUGINO, B. - University Of Pennsylvania; ISHIMARU, C. - University Of Minnesota

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/11/2021
Publication Date: 8/14/2021
Citation: Curland, R.D., Mainello, A., Perry, K.L., Hao, J., Charkowski, A.O., Bull, C.T., McNally, R.R., Johnson, S.B., Rosenzweig, N., Secor, G.A., Larkin, R.P., Gugino, B.K., Ishimaru, C.A. 2021. Species of Dickeya and Pectobacterium isolated in 2015-2016 from potatoes with soft rot disease in Northeastern and North Central United States. Microorganisms. https://doi.org/10.3390/microorganisms9081733.
DOI: https://doi.org/10.3390/microorganisms9081733

Interpretive Summary: A major outbreak of a serious and damaging disease of potato plants, known as blackleg and soft rot of potato, caused primarily by the bacterial species of Dickeya and Pectobacterium has resulted in significant economic losses in the Northeastern and North Central United States since 2015. In order to understand and clarify the extent and genetic diversity of soft rot pathogens present in the U.S. at this time, a phylogenetic study consisting of 121 pectolytic soft rot bacteria isolated from potato in those regions between 2015 and 2016, with 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains was conducted. Advanced molecular techniques based on multi-locus sequence alignments were used to provide a thorough analysis of genetic characterization and variability. Strains from the 2015-2016 collection clustered with type strains of several different known Dickeya and Pectobacterium species. Genetic diversity within strains of the predominant species, D. dianthicola, from 2015-2016 was low, with one sequence type (ST1) identified in 17/19 strains. Pectobacterium parmentieri was more diverse with ten sequence types detected among 37 of the 2015-2016 strains. This research confirmed that soft rot diseases of potato in the U.S. are caused by multiple species of Dickeya and Pectobacterium with varying genetic diversity. This study is useful for researchers to aid in monitoring future shifts in potato soft rot pathogens and can be useful in developing control strategies and mitigating disease losses.

Technical Abstract: Multiple species of Pectobacterium and Dickeya cause soft rot diseases during production and storage of potatoes. Significant losses from blackleg and non-emergence diseases in commercial and seed potato production occurred in the past decade in Northeastern and North Central United States. A phylogenetic study consisting of 121 pectolytic soft rot bacteria isolated from potato in those regions between 2015 and 2016, with 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains was conducted to clarify the soft rot agents present at that time in the U.S. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed strains from the 2015-2016 collection clustered with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains from 2015-2016 was low, with one sequence type (ST1) identified in 17/19 strains. Pectobacterium parmentieri was more diverse with ten sequence types detected among 37 of the 2015-2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management.