Characterization of Pectobacterium species isolated from vegetable crops in north-west of Iran

In August 2012, vegetable crops including potato, cabbage, bell pepper and carrot showing symptoms of maceration and water soaked lesions on their tuber, leaf and fruit were collected from major vegetable growing areas in north-west of Iran. Physiological and biochemical assays divided the isolates into two main groups according to their ability to grow at 37°C. In addition, these two groups were differentiated by some biochemical characteristics such as utilization of α –methyl glucoside and maltose, reducing substrates from sucrose and gelatin liquefaction. Partial sequence of polymerase chain reaction (PCR) product from reaction of putative Pectobacterium spp. with 16S rRNA confirmed the results obtained from physiological and biochemical assays used for identification of the bacterium. All of the causal organisms isolated from infected tissues were identified as Pectobacterium spp. based on biochemical characteristics and PCR amplification of the 16S rRNA gene with specific primers PCCSSF and PCCSSR. Twenty of the isolates were identified as Pectobacterium carotovorum subsp. carotovorum using a polyphasic approach including physiological, biochemical and molecular characteristics.  Only six isolates from infected bell peppers and five isolates from infected potatoes identified as Pectobacterium wasabiae and Pectobacterium atrosepticum respectively. Our findings based on physiological, biochemical and molecular assays indicated the occurrence of P. wasabiae as a novel species in bell pepper in Iran. Moreover, genetic diversity of Pcc strains in this study was also performed based on Repetitive extragenic palindromic-PCR (rep-PCR). High genetic variability was revealed among these Pcc strains by rep-PCR typing using two primers sets for ERIC-PCR and BOX-PCR.   Key words: 16S rRNA, repetitive extragenic palindromic- polymerase chain reaction (rep-PCR), Pectobacterium, soft rot, vegetable.