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

Abstract

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 <i>Dickeya</i>, with a highest similarity to <i>Dickeya zeae</i> DSM 18068^T (98.5%). The major fatty acids were summed feature 3 (C_16:1 ω7<i>c</i> and/or C_16:1 ω6<i>c</i>), C_16:0 and summed feature 8 (C_18:1 ω7<i>c</i> and/or C_18:1 ω6<i>c</i>). Multi-locus sequence analysis using five concatenated genes (16S rRNA, <i>atpD</i>, <i>infB</i>, <i>recA</i> and <i>gyrB</i>) 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 <i>D. zeae</i>. 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 <i>D. zeae</i> 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 <i>Dickeya</i>. Based on the results of the polyphasic approaches, we propose that strain ZYY5^T represents a novel species in the genus <i>Dickeya</i>, for which the name <i>Dickeya oryzae</i> 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 <i>D. oryzae</i> same as ZYY5^T.