PCR-identification of bacteria belonging to the genus Pectobacterium – agents of cucumber soft rot and wilting in Ukraine

  • L. A. Dankevych


Aim. Correct species identification of isolated Pectobacterium sp., collection «E. toxica» strains and typical representatives of some species of the genus Pectobacterium and Dickeya via PCR for individual species-specific regions of their genome. Methods. Microbiological and molecular genetic (PCR) methods Results. A specific PCR product of size 434 bp was amplified in the genome of isolated Pectobacterium sp., collection «E. toxica» and typical P. carotovorum susp. carotovorum UKM B1075T and P. atrosepticum UKM B-1084T strains. The 690 bp DNA fragment was detected solely in the genome of the typical P. atrosepticum UKM B-1084T strain and absent in strains which are agents of cucumber soft rot and wilting and a typical P. carotovorum susp. carotovorum UKM B1075T strain. Conclusions. PCR detection of specific DNA fragments allowed us to finally clarify the species status of the causative agent of cucumber soft rot and wilting and attribute it to P. carotovorum.

Keywords: identification, causative agent of cucumber soft rot and wilting.


Gvozdiak R.I., Pasichnik L.A., Yakovleva L.M., Moroz S.M., Litvinchuk O.O., Zhytkevich N.V., Hodos S.F., Butsenko L.M., Dankevich L.A., Grinnik I.V., Patty V.P. Phytopathogenic bacteria. Bacterial diseases of plants. K.: LLC "NVP" Interservis", 2011. 444 p. [in Ukrainian]

Czajkowski R., Perombelon M.C.M., Jafra S., Lojkowska E., Potrykus M., van der Wolf J.M., Sledz W. Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review. Annals of Applied Biology. 2015. No. 166. P. 18–38. doi: 10.1111/aab.12166.

Dankevych L.A. The identification of cucumber soft rot and wilting in Ukraine based on 16S rRNA gene sequencing analysis. Mikrobiolohichnyi zhurnal. 2018. Vol. 80, No. 2. P. 89–100. [in Ukrainian]

Dankevych L.A. Rep-PCR analysis of single agent of cucumber bacterial diseases. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2017. Vol. 15, No. 1. P. 25–31. [in Ukrainian]

Azadmanesh S., Marefat A., Azadmanesh K. Detection of Pectobacteria Causal Agents of Potato Soft Rot in North Western Provinces of Iran. J Plant Pathol Microb. 2013 Vol. 4, No.1. P. 1–6. doi: 10.4172/2157-7471.1000154.

Darrasse A., Priou S., Kotoujansky A., Bertheau Y. PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation of potato diseases. Applied and environmental microbiology. 1994. Vol. 60, No. 5. P. 1437–1444.

De Boer S.H., Ward L.J. PCR Detection of Erwinia carotovora subsp. atroseptica associated with potato tissue. Phytopathology. 1995. Vol. 85. P. 854–858.

Phokum C., Jitareerat P., Phochanachai S., Cheevadhanarak S. Detection and classification of soft rot Erwinia of vegetables in Thailand by DNA polymerase chain reaction. Acta horticulturae. 2006. Vol. 2. P. 917–925.

Yahiaoui-Zaidi R., Jouan B., Andrivon D. Biochemical and molecular diversity among Erwinia isolates from potato in Algeria. Plant Pathology. 2003. Vol. 52, No. 1. P. 2319–7706. doi: 10.1046/j.1365-3059.2003.00791.x.

Hrelias V., Le Roux A.-C., Bertheau Y., Andrivon D., Gauthier J.-P., Jouan B. Characterisation of Erwinia carotovora subspecies and detection of Erwinia carotovora subsp. atroseptica in potato plants, soil and water extracts with PCR-based methods. European Journal of Plant Pathology. 1998. No. 104. P. 685–699.

Prajapat R., Marwal A., Nath Jha P. Erwinia carotovora associated with potato: a critical appraisal with respect to Indian perspective. Int. J. Curr. Microbiol. App. Sci. 2013. Vol. 2, No. 10. P. 83–89.

Hyman L.J., Birch P.R.J., Dellagi A., Avrova A.O., Toth I.K. A competitive PCR-based method for the detection and quantification of Erwinia carotovora subsp.atroseptica on potato tubers. Letters in Applied Microbiology. 2000. Vol. 30. P. 330–335. doi: 10.1046/j.1472-765x.2000.00736.x.