1Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, UMR5240 Microbiologie Adaptation et Pathogénie, F-69621 Villeurbanne, France.
2Univ Lyon, Université Claude Bernard Lyon 1, CNRS, plateforme DTAMB, FR3728 BioEnviS, F-69621 Villeurbanne, France.
Int J Syst Evol Microbiol. 2019 Mar;69(3):721-726. doi: 10.1099/ijsem.0.003208. Epub 2019 Feb 6.
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 and S39, belong to a phylogenetic group separated from other Dickeya species. The genomic sequence of strain S29 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 with strains of characterized Dickeya species supported the delineation of a novel species. The closest species to strain S29 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 and S39 from D. aquatica and from other Dickeya species. The name Dickeya lacustris sp. nov. is proposed for this taxon with S29 (=CFBP 8647=LMG 30899) as the type strain.
迪凯亚属是一类重要的植物病原菌，目前包含 8 个已被认可的种。虽然大多数迪凯亚分离株起源于受感染的栽培植物，但它们也被反复从水中分离出来。为了更好地了解迪凯亚的自然多样性，我们对法国拉当布地区被湿地环绕的小湖泊进行了调查。从受直接农业投入保护的湖泊的水或植物中获得了一些迪凯亚分离株。gapA 基因的序列分析表明，5 个分离株 S12、S15、S24、S29 和 S39 属于与其他迪凯亚种分离的一个系统发育群。S29 菌株的基因组序列明确表明其与其他已知的迪凯亚种分离。通过比较 S29 菌株与特征明确的迪凯亚种菌株，获得的 DNA-DNA 杂交（isDDH）和平均核苷酸同一性（ANI）值（分别<33%和<88%）支持了一个新种的划定。与 S29 菌株最接近的种是迪凯亚水生亚种，先前从河流中分离出来，表明这些菌株有一个适应水生环境的共同祖先。基因组和表型比较使我们能够识别出 S12、S15、S24、S29 和 S39 分离株与 D. aquatica 以及其他迪凯亚种之间的区别特征。建议将该分类群命名为迪凯亚湖泊亚种（Dickeya lacustris sp. nov.），其模式菌株为 S29（=CFBP 8647=LMG 30899）。
