Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence

Abstract

Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421 T (CFBP 8630 T =LMG 30828 T) is suggested as a type strain.

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

“…Out of the 136 strains isolated from potatoes, 31 were isolated from the stem or leaf and 33 from the tuber, and, unfortunately, it was not clearly documented for the remaining 71 strains ( Table 3 ). The 31 strains isolated from the stem or leaf belonged to six species: five of which— P. brasiliense, P. atrosepticum, P. parvum, P. parmentieri and P. punjabense —are well-known species triggering blackleg disease [ 4 , 23 , 26 ]. Interestingly, the newly described P. versatile species was also isolated from potato stems or leaves in the UK, Morocco and France from 1972 to 2016.…”

“…In addition, new Pectobacterium species were progressively described, most of them recently on the basis of whole-genome sequence analysis. Today, the Pectobacterium genus encompasses 17 recognised species: Pectobacterium actinidiae [ 15 ], Pectobacterium aquaticum [ 17 ], Pectobacterium aroidearum [ 18 ], Pectobacterium atrosepticum [ 14 ], Pectobacterium betavasculorum [ 14 ], Pectobacterium brasiliense [ 15 ], Pectobacterium cacticida [ 9 , 19 ], Pectobacterium carotovorum [ 8 , 15 , 20 ], Pectobacterium fontis [ 21 ], Pectobacterium odoriferum [ 15 ], Pectobacterium parmentieri [ 22 ], Pectobacterium parvum [ 23 ], Pectobacterium polaris [ 24 ], Pectobacterium polonicum [ 25 ], Pectobacterium punjabense [ 26 ], Pectobacterium versatile [ 15 ] and Pectobacterium wasabiae [ 14 ] and two proposed species not yet validated by ad hoc committees: “ Pectobacterium peruviense ” and “ Pectobacterium zantedeschiae” [ 27 , 28 ]. Given the taxonomic evolution in the past ten years, the ecological importance, repartition and habitat of most species need to be evaluated.…”

Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide

“…Additional complications have been presented by the recent numerous rearrangements of the taxonomy of Pectobacteria [3,10,41]. After the elevation of Pectobacterium carotovorum subspecies actinidiae, brasiliense, odoriferum and versatile to the species level [10], and the separation of new species P. fontis [6], P. polaris [7], P. aquaticum [8] and P. parvum [9] from P. carotovorum, the number of strains that are still considered as the members of the current P. carotovorum is limited. The current situation also promotes refinements in the estimation of the abundance of SRP in the pathogenesis of potatoes, as well as the attribution of previously found bacteriophages that were considered to be infective to P. carotovorum subspecies.…”

“…Most taxonomic alterations have been applied to the species Pectobacterium carotovorum (Pca), formerly Erwinia carotovora. Several species have been separated from Pca [6][7][8][9], and several subspecies have been elevated to species level [10]. Therefore, the number of bacterial strains still attributed as Pectobacterium carotovorum with genomic data deposited to the NCBI GenBank is now limited.…”

Host Specificity and Differential Pathogenicity of Pectobacterium Strains from Dicot and Monocot Hosts

“…According to the present taxonomy, the genus now includes 18 species: P. actinidiae, P. aquaticum, P. aroidearum, P. atrosepticum , P. betavasculorum, P. brasiliense, P. cacticida , P. carotovorum , P . odoriferum , P. parmentieri, P. parvum, P. peruviense, P. polaris, P. polonicum, P. punjabense, P. versatile, P. wasabiae and P. zantedeschiae, [ 4 , 7 , 8 , 9 , 10 , 11 ]. In spite of the clarifying taxonomy, the mechanisms underlying this natural segregation are largely unexplored.…”