Potential new Dickeya sp. causing soft rot of Phalaenopsis orchids and bacteriophage biocontrol options

author: Špela Alič, National Institute of Biology
published: May 23, 2017,   recorded: April 2017,   views: 26
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Bacterial soft rots represent a serious limitation to the production of ornamental and others horticultural plants world-wide e.g. potatoes, tomatoes and orchids. There are currently no effective chemical agents for the soft rot disease, and this results in significant economic losses. The aim of our study was to isolate and characterize bacteria causing soft rot of orchids (Phalaenopsis sp.) and to investigate bacteriophages as biocontrol agents for their management.

Bacteria isolated from diseased tissues of Phalaenopsis orchids from a commercial production site were identified as Dickeya spp. based on morphological characteristics, partial sequencing of 16S rDNA, fliC and dnaX along with selected biochemical tests. However, none of the performed tests was able to resolve classification to a species level. Therefore, genomes of two representative Dickeya spp. isolates were sequenced using Ion Torrent technology, which has resulted in two draft genomes. As part of a comparative genomic study of genus Dickeya, average nucleotide analysis (ANI) and multilocus sequence analysis (MLSA) on six housekeeping genes were performed, placing the newly sequenced Dickeya isolates along with strains MK7 and NCCPB 3274 (isolated from water and an ornamental plant, respectively) as a new species within the Dickeya genus. To confirm the observed taxonomic and phylogenetic position of the putative new Dickeya sp. the phenotypic analysis was performed. The vast majority of the previously determined Dickeya virulence genes could be found in the core genome of the potential new species. Furthermore, some novel genes and genetic were identified including secondary metabolite biosynthesis pathways. Aggressiveness of the bacteria was tested phenotypically on the model plants, Belgian chicory and potato tubers, exhibiting extreme maceration potential of the new Dickeya isolates. Beside, inoculation of the viable potato plants was performed, showing the bacteria ability to survive and spread through the plant tissue. On the other hand, possible approaches for the Dickeya biocontrol were studied. Bacteriophages effective against new Dickeya strains were isolated from the diseased orchids and sewage water. Three different groups of bacteriophages were identified, each from different Caudovirales family. All bacteriophages were lytic and specific for the genus Dickeya, therefore represented suitable candidates for phage biocontrol. Furthermore, host range profile confirmed differences among bacterial isolates in the potential new Dickeya sp., indicating high inspecies phenotypic diversity.

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