Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire

Abstract

BackgroundThe pectinolytic enterobacteria of the Pectobacterium and Dickeya genera are causative agents of maceration-associated diseases affecting a wide variety of crops and ornamentals. For the past decade, the emergence of a novel species D. solani was observed in potato fields in Europe and the Mediterranean basin. The purpose of this study is to search by comparative genomics the genetic traits that could be distinctive to other Dickeya species and be involved in D. solani adaptation to the potato plant host.ResultsD. solani 3337 exhibits a 4.9 Mb circular genome that is characterized by a low content in mobile elements with the identification of only two full length insertion sequences. A genomic comparison with the deeply-annotated model D. dadantii 3937 strain was performed. While a large majority of Dickeya virulence genes are shared by both strains, a few hundreds genes of D. solani 3337, mostly regrouped in 25 genomic regions, are distinctive to D. dadantii 3937. These genomic regions are present in the other available draft genomes of D. solani strains and interestingly some of them were not found in the sequenced genomes of the other Dickeya species. These genomic regions regroup metabolic genes and are often accompanied by genes involved in transport systems. A metabolic analysis correlated some metabolic genes with distinctive functional traits of both D. solani 3337 and D. dadantii 3937. Three identified D. solani genomic regions also regroup NRPS/PKS encoding genes. In addition, D. solani encodes a distinctive arsenal of T5SS and T6SS-related toxin-antitoxin systems. These genes may contribute to bacteria-bacteria interactions and to the fitness of D. solani to the plant environment.ConclusionsThis study highlights the genomic specific traits of the emerging pathogen D. solani and will provide the basis for studying those that are involved in the successful adaptation of this emerging pathogen to the potato plant host.

The effect of temperature on the phenotypic features and the maceration ability of Dickeya solani strains isolated in Finland, Israel and Poland

“…Genomic analysis of D. solani has stated that this species is most closely related to D. dadantii 3937 strain (94 % ANI), (Garlant et al 2013;Pedron et al 2014;van der Wolf et al 2014). This is fortunate, because this strain of D. dadantii appears to be the best studied in the terms of molecular determinants of virulence and its regulators.…”

“…Studies show that these pathogens are able to induce diseases at the lower inoculum levels, produce more PCWDE and in addition possess an arsenal of T5SS/T6SS secreted proteins exhibiting more diverse functions than just destroying the plant cell-wall (Toth et al 2011;Garlant et al 2013;Pedron et al 2014;Khayi et al 2015;Potrykus et al 2016). …”

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T

“…The strain IPO 2222 T grows in TY medium (tryptone 5 g/L, yeast extract 3 g/L and agar 1.5%) at 28 °C forming 1–2 mm colonies within 24 h. It produces phosphatase and indole and belongs to Dickeya biovar 3 as described previously [10]. Distinctive metabolic abilities of D. solani species were described using BIOLOG system [11]; among them, D. solani IPO 2222 T uses urea as sole nitrogen source (Additional file 1: Figure S1). D. solani IPO 2222 T was recovered form naturally infected potato plants showing blackleg and soft rot symptoms.…”

“…Recent comparative analyses underlined the major genetic and metabolic divergences between Dickeya solani species and the nearest clades that are D. dandatii (ANI 94%) and D. dianthicola (ANI 92%) [11, 19]. D. solani is characterized by a low content of phages elements and CRISPR system: in strain IPO 2222 T genome, only one CRISPR cluster (208 bp) was identified.…”

“…Using PHAST tool [22], the strain IPO 2222 T harbors one questionable prophage (11 CDSs) in a 10,687 bp region. In addition, some genomic regions were shown to be specific for D. solani species and contain some metabolic and NRPS/PKS encoding genes [11]. …”