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

Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were identified tentatively as P. polaris and then subjected to polyphasic analyses to characterise their genomic and phenotypic features. Phylogenetic analysis based on 376 core proteins showed that the isolates clustered closest to P. polaris but could be divided into two clades with high bootstrap values. Average Nucleotide Identity (ANI) with their sequenced genomes revealed that one of the isolate groups included P. polaris type strain, whereas the second group was at the borderline to P. polaris species with 96% ANI value, but formed a distinct group separated from P. polaris isolates due to high internal ANI values (<99%) and higher alignment coverage when compared to P. polaris isolates. In silico Genome-to-Genome comparisons between the groups were below 70%, suggesting that the two groups can be placed into separate species. Further verification for the delineation of the atypical isolates from P. polaris was obtained by AFLP, BIOLOG and ERIC-PCR analyses, which clearly separated these two groups of bacteria. Genomic comparisons between the genomes of the atypical isolates and P. polaris showed that the atypical isolates harboured genomic islands homologous to SPI-1-type Type III secretion genes typically found in animal pathogens and in Pantoea and Erwinia species that interact with insect vectors. Also, genes coding for proteins known for toxic effects on nematodes or insects were identified in the genome comparisons, whereas many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria were not found in the genomes of the atypical isolates, but were present in P. polaris. Furthermore, the atypical isolates were separated from P. polaris due to their low virulence in potato maceration assay, production of antibacterial metabolites against other soft rot bacteria and citrate-negative phenotype. Based on the polyphasic analyses, including the GGDC data, genome comparisons, and biochemical and virulence characteristics presented in this report, we propose delineation of the atypical isolates to as novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T = LMG 30828T) is suggested as a type strain.