Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov.

Abstract

The genus Dickeya comprises plant pathogens that cause diseases in a large range of economically important crops and ornamentals. Strains previously assigned to the species Dickeya zeae are major pathogens attacking vital crops such as maize and rice. They are also frequently isolated from surface water. The newly described species Dickeya oryzae is closely related to D. zeae members, so that the limit between the two species can be difficult to define. In order to clearly distinguish the two species, globally described by the term ‘ D. zeae complex’, we sequenced the genome of four new water isolates and compared them to 14 genomes available in databases. Calculation of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values confirmed the phylogenomic classification into the two species D. zeae and D. oryzae . It also allowed us to propose a new species, Dickeya parazeae sp. nov., to characterize a clade distinct from those containing the D. zeae type strain NCPPB2538T. Strain S31T (CFBP 8716T=LMG 32070T) isolated from water in France is proposed as the type strain of the new species. Phenotypic analysis of eight publically available strains revealed traits common to the five tested D. oryzae members but apparently not shared by the D. oryzae type strain. Genomic analyses indicated that a simple distinction between the species D. zeae , D. parazeae and D. oryzae can be obtained on the basis of the recA sequence. D. oryzae can be distinguished from the two other species by growth on l-tartaric acid. Based on the recA marker, several strains previously identified as D. zeae were re-assigned to the species D. parazeae or D. oryzae . This study also highlighted the broad host range diversity of these three species.