Mikrobiol. Z. 2018; 80(2):92-103. Ukrainian.
doi: https://doi.org/10.15407/microbiolj80.02.092

The Identification of Cucumber Soft Rot and Wilting in Ukraine
Based on 16S rRNA Gene Sequencing Analysis

Dankevych L.A.

Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
154 Akad. Zabolotny Str., Kyiv, 03143, Ukraine

Aim. To determine the 16SrRNA gene nucleotide sequences of 5 isolated Pectobacterium sp. and 9 collection "Erwinia toxica" strains with typical members of genera Pectobacterium, Erwinia, Dickeya to be identificated correctly at the species level. Materials and methods. Objects − 5 isolated from diseased cucumbers plants Pectobacterium sp. strains and 9 "Erwinia toxica" collection strains. The 16S rRNA gene was amplifed using universal pA and pH primers. Building a complementary sequence and alignment sequence was performed using the Multalin and Sequence Manipulation Suite software. The search of 16S rRNA nucleotide similar sequences of gene, that were placed and deposited in GenBank, was performed using the BLASTN program. The phylogenetic trees constructing was performed using MEGA5 program. Results. Nucleotide sequence analysis of the 16S rRNA gene revealed a high level of identity (99 - 98%) of the researched strains with the following typical strains P. carotovorum susp. carotovorum ICMP 5702, P. carotovorum susp. odoriferum LMG 17566, P. carotovorum susp. brasiliensis NZEC1. Also a signifcant level of strains phylogenetic similarity (97 - 98 % of 16S rRNA gene sequences identity) with members of the species P. atrosepticum, P. betavasculorum, P. wasabiae, P. aroidearum has researched. Conclusion. A significant level identity of 16S rRNA gene nucleotide sequences (98 - 99 %) of collection “Erwinia toxica” and isolated by our team the Pectobacterium sp. strains with typical representatives of the Pectobacterium genus can suggest that the existence of a separate  “Erwinia toxica” species is inappropriate, and also the possible belonging of this group to existing species. Since, according to the literature, the subspecies mentioned above are closely related species and poorly diferentiated by homology of the16SpPHK gene nucleotide sequences. Probably, for the final identification at the species level of the strains, studied by us, there is necessary to research other genotypic properties.

Keywords: Pectobacterium sp., "Erwinia toxica", genus Pectobacterium, 16SpPHK genе.

Full text (PDF, in Ukrainian)

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