Dickeya oryzae sp. nov., isolated from the roots of rice

A novel Gram-stain-negative strain, designated ZYY5 T , was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5 T was a member of the genus Dickeya , with a highest similarity to Dickeya zeae DSM 18068 T (98.5%). The major fatty acids were summed feature 3 (C 16:1 ω7 c and/or C 16:1 ω6 c ), C 16:0 and summed feature 8 (C 18:1 ω7 c and/or C 18:1 ω6 c ). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD , infB , recA and gyrB ) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5 T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5 T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068 T , which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5 T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya . Based on the results of the polyphasic approaches, we propose that strain ZYY5 T represents a novel species in the genus Dickeya , for which the name Dickeya oryzae sp. nov. (=JCM 33020 T =ACCC 61554 T ) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5 T .