Pathogenic and Genetic Bases of Species and Intraspecies Dynamics in Bacteria Causing Potato Blackleg and Soft Rot

Potato blackleg and soft rot (PBSR), caused by Dickeya and Pectobacterium species, poses a significant threat to potato production, leading to economic losses through seedling emergence failure, stem rot, and storage decay. This study aimed to characterize the dynamics of bacterial species responsible for PBSR in the Northeastern U.S. and assess their genetic and pathogenic bases behind the epidemic. A total of 300 symptomatic potato samples were collected from 2021 to 2023, along with an additional 800 samples from previous years. Using PCR, average nucleotide identity, and digital DNA-DNA hybridization analyses, single or multiple bacterial species were identified from diseased potato tissues. Co-infections involving multiple PBSR species were common and likely influenced disease severity and pathogen competition. The predominant species changed over time. Dickeya dianthicola genotype I was the most prevalent strain in the PBSR outbreak, but over two years, its population declined, while Pectobacterium parmentieri and P. versatile increased. Whole-genome sequencing revealed virulence factors, including plant cell wall-degrading enzymes, secretion systems, and quorum-sensing mechanisms, which provide insights into bacterial adaptation. These findings underscore the complex epidemiology of PBSR and the potential influence of climate change and agricultural practices, offering valuable insights for targeted control measures and sustainable potato disease management strategies.