Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France

The genus Dickeya is an important group of plant pathogens that currently comprises eight recognized species. Although most Dickeya isolates originated from infected cultivated plants, they have also been repeatedly isolated from water. To better understand the natural diversity of Dickeya, a survey was performed in small lakes surrounded by wetlands in the French region of La Dombes. Several Dickeya isolates were obtained from water or plants from lakes protected from direct agricultural inputs. Sequencing of the gapA gene revealed that five isolates, S12, S15, S24, S29(T) and S39, belong to a phylogenetic group separated from other Dickeya species. The genomic sequence of strain S29(T) clearly established its separation from the other known Dickeya species. The in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) values (<33 and <88 %, respectively) obtained by comparing strain S29(T) with strains of characterized Dickeya species supported the delineation of a novel species. The closest species to strain S29(T) is Dickeya aquatica, previously isolated from rivers, suggesting that these strains have a common ancestor adapted to a water environment. Genomic and phenotypic comparisons enabled the identification of traits distinguishing isolates S12, S15, S24, S29(T) and S39 from D. aquatica and from other Dickeya species. The name Dickeya lacustris sp. nov. is proposed for this taxon with S29(T) (=CFBP 8647(T)=LMG 30899(T)) as the type strain.