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

Abstract

A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya , with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). 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 ZYY5T 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 ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T 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 ZYY5T 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 ZYY5T.

Genomic and phenotypic biology of novel strains of Dickeya zeae isolated from pineapple and taro in Hawaii: insights into genome plasticity, pathogenicity, and virulence determinants

“…High genome dissimilarity was observed among the D. zeae species complex with a dDDH value of 56-68.20 %, which is lower than the recommended cut-off value (70%) (Wayne et al, 1987;Goris et al, 2007). Additionally, the ANI value within the D. zeae species was 94.33-96.27%, which overlaps the threshold value (ANI 95-96%) (Richter et al, 2009;Goris et al, 2007;Kim et al, 2014;Chun et al, 2018;Wang et al 2020 Figure S1). The dDDH phylogenetic tree was inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences (Meier-Kolthoff et al 2013).…”

“…was reclassified as D. oryzae (Wang et al, 2020), a novel species within genus Dickeya. However, we included the genome of EC1 in our analyses because of the close relationships with D. zeae strains.…”

“…oryzae-recently separated from D. zeae (Wang et al, 2020;). Dickeya dadantii have two subspecies, D. dadantii subsp.…”

Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain

“…Pairwise isDDH analysis ( S5 Fig) found that these previously identified strains from rice reached the cut-off (90.00%) for a subspecies [43], and they were also suggested to be a subspecies within D. zeae [15].On other hand, ANI and AP analyses suggested EC2 was also close to the other two strains from non-rice hosts, NCPPB 3531 and CSL_RW192 (S5 Fig). In accordance with this, strains EC1, ZJU1202, DZ2Q, NCPPB 3531, and CSL RW192, were classified into a genomospecies named D. oryzae [44]. However, most of the genome sequences used in ANI and AP analyses were draft genomes, and ANI and AP analyses were based on pairwise comparisons.…”

“…In accordance with this, strains EC1, ZJU1202, DZ2Q, NCPPB 3531, and CSL RW192, were classified into a genomospecies named D . oryzae [ 44 ]. However, most of the genome sequences used in ANI and AP analyses were draft genomes, and ANI and AP analyses were based on pairwise comparisons.…”