Characterization and Genomics of Pectinolytic Bacteria Isolated from Soft Rot Symptomatic Produce

Bacterial soft rot causes major crop losses annually and can be caused by several species from multiple genera. These bacteria have a broad host range and often infect produce through contact with soil. The main genera causing bacterial soft rot are Pectobacterium and Dickeya, both of which have widespread geographical distribution. Because of many recent renaming and reclassifications of bacteria causing soft rot, identification and characterization of the causative agents can be challenging. In this work, we surveyed commercially available produce exhibiting typical soft rot symptoms, isolating pectinolytic bacteria and characterizing them genetically and phenotypically. We found that in our sampling, many samples were from the genus Pectobacterium; however, other genera were also capable of eliciting symptoms in potatoes, including an isolate from the genus Chryseobacterium. Genomic analyses revealed that many of the Pectobacterium isolates collected share prophages not found in other soft rot species, suggesting a potential role for these prophages in the evolution or fitness of these isolates. Our Chryseobacterium isolate was most similar to C. scophthalmum, a fish pathogen, suggesting that this isolate may be a crossover pathogen.