Identifying and studying the genetic diversity of pathogenic Pseudomonas strains isolated from pepper, onion, and potato in east and west Azerbaijan provinces

The bacterial rot of pepper, onion, and potato is one of the most crucial diseases in the East and West Azerbaijan provinces of Iran. Therefore, accurate identification of the causes of these diseases and the study of their genetic diversity can be beneficial in preventing their occurrence. In the present study, in addition to studying and identifying their morphological and molecular characteristics, the genetic diversity of bacterial species from selected hosts in the provinces of East and West Azerbaijan is studied to obtain comprehensive information.

Infected potatoes, onions, and peppers with soft rot symptoms were collected from different areas in the East and West Azarbaijan provinces of Iran in the timeframe between 2019 and 2020. Infected samples were cultured on the NA medium. Moreover, purified bacterial colonies were streaked on the Kings’B medium. All isolates that produced fluorescent pigments were identified using biochemical, nutritional, and physiological tests, including LOPAT tests (levan production from sucrose (L), the presence of oxidase (O), the ability to cause rot on potato tubers (P), the presence of arginine dihydrolase (A), and the ability to induce hypersensitivity reaction (HR) on tobacco leaves (T)), nitrate reduction, and the utilization of various carbon sources. All isolates that produced fluorescent pigments were identified as Pseudomonas using phenotypic properties. To assess the genetic diversity within the strains, BOX and ERIC-PCR were analyzed. The UPGMA method was employed to evaluate the similarity matrix and clustering between the strains. For genetic identification, 16S rRNA, gyrB, and ropD genes of strains were amplified and sequenced. 

A total of 59 isolates were obtained from infected onion, pepper, and potato plants. The bacterial isolates revealed cream colonies with a low convex height, jagged edge, and rugged surface on the nutrient agar medium. All strains produced fluorescent pigments on the King’s B medium and demonstrated Gram-negative and positive reactions to the catalase. In pathogenicity tests, all strains were pathogenic on healthy plants. Moreover, clustering ERIC and BOX-PCR results with UPGMA and Jaccard’s similarity coefficients showed that the strains of potato, pepper, and onion were clustered into five and four main groups, respectively. The gyrB, rpoD, and 16S rRNA nucleotide sequences showed high similarity between the strains and Pseudomonas cichorii.

The results showed that Iranian P. marginalis strains are very diverse and are related to the isolation site and the host plant. This high diversity can be due to the long history of cultivating these plants in the provinces of Iran and the high genetic diversity in the bacterial population. Based on previous studies published on Iranian P. marginalis, this is the first report of isolation and identification of P. marginalis, the agent that causes soft rot in pepper, onion, and potato in East and West Azarbaijan provinces.