Date of Award

Spring 5-7-2021

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Doctor of Philosophy (PhD)


Ecology and Environmental Sciences


Jianjun Hao

Second Committee Member

Robert P. Larkin

Third Committee Member

Gregory Porter

Additional Committee Members

Seanna L. Annis

Ek Han Tan


Potato blackleg and soft rot (PBSR), which can be caused by Dickeya spp. and Pectobacterium spp., is a serious problem worldwide. The recent outbreak of PBSR in the Northeastern USA, caused primarily by D. dianthicola, has resulted in significant economic losses since 2015. This seedborne disease is highly associated with and therefore spread by seed tuber distribution. To understand how the outbreak occurred and where the pathogen originated, a total of 1204 potato samples were collected from 11 northeastern states from 2015 to 2020. All the samples were processed for bacterial isolation and DNA extraction. Dickeya dianthicola and P. parmentieri were detected using conventional polymerase chain reaction (PCR). Dickeya dianthicola and P. parmentieri were found in 38.1% and 53.3% of the samples, respectively, and 20.6% of samples contained both D. dianthicola and P. parmentieri. Seventeen isolates of D. dianthicola were obtained from the samples and classified into three genotypes (Type I, II, III). Results based on 258 samples showed that Maine mainly had Type I but no Type III, while Type II appeared to be distributed throughout the Northeastern USA. By pan-genomic analysis, D. dianthicola strains collected worldwide were classified into eight distinguished clades. Type I strains had an extraordinarily high homogeneity and distinct discrimination from other countries,

indicating a single-strain population. Virulence-related systems, such as plant cell-wall degrading enzymes, flagellar and chemotaxis related features, two-component regulatory system, and type I/II/III secretion systems were highly conserved, but type IV/VI secretion systems varied, in which type I strain had an additional set T4SS cluster, implying more aggressiveness and virulence. Thus, the PBSR outbreak was proposed to be associated with a new strain derived by mutation.

Bacterial communities were analyzed on the samples using Illumina sequencing targeting on the V3-V4 region of 16S rRNA gene. Genera Dickeya or Pectobacterium prevailed in the microbial community when they each existed alone, while Dickeya surpassed Pectobacterium when they coexisted. Among the pathogen complex, D. dianthicola was the only species in the Dickeya genus, while species varied in the Pectobacterium genus, with P. parmentieri, P. polaris, P. carotovora subsp. carotovora, P. carotovora subsp. odoriferum being the most prevalent presumptive species. Isolates of the four presumptive species and P. c. subsp. brasiliensis were identified by sequencing the gapA gene and were confirmed to be pathogenic on potatoes. Thus, PBSR was caused by intergeneric or intrageneric species of Dickeya and Pectobacterium that contribute collectively to the disease complex. To further investigate the relationship between the two bacterial species and their interaction, field trials were established. Three varieties of potato seed pieces were inoculated with bacterial suspensions of D. dianthicola and planted in the field. Two-year results showed that there was a significant linear correlation (P < 0.01) between relative yield loss and percentage of inoculated seed pieces. Furthermore, D. dianthicola was more virulent than P. parmentieri in the field, but the co-inoculation of the two species resulted in increased disease severity compared to single-species inoculation with either pathogen.