Dismantling and reorganizing Pseudomonas marginalis sensu lato

Until recently, it had been a common practice in the field of plant disease control to identify bacterial strains with the following characteristics as Pseudomonas marginalis: fluorescent; oxidase-, potato soft rot- and arginine dihydrolase-positive; soft rot-causing (here referred to as P. marginalis sensu lato). In contrast, as phylogenetic and genomic analyses have been introduced into the bacterial taxonomy, it became clear that P. marginalis sensu lato is heterogeneous, suggesting that it might be a species complex containing many cryptic species. Therefore, a preliminary survey was performed targeting the P. marginalis sensu lato strains preserved in the NARO (National Agriculture and Food Research Organization, Japan) Genebank to sort these into strains corresponding to P. marginalis sensu stricto (i.e., strains that would be included in the same species range as the type strain of P. marginalis) and strains that might not fit this category. Since then, attempts have been made to examine the taxonomic affiliations of the latter by using a polyphasic approach. As a result, some strains were proven to differ from any known species and are described as the following novel species: Pseudomonas kitaguniensis, Pseudomonas allii, Pseudomonas cyclaminis, Pseudomonas petroselini, Pseudomonas brassicae, Pseudomonas lactucae, Pseudomonas aegrilactucae and Pseudomonas morbosilactucae. In this article, the profiles of each of these novel species and a scheme for their identification are briefly introduced. In addition to the problem of cryptic species, reorganizing P. marginalis sensu lato still faces various challenges, which we discuss.

Automated summary

In the field of plant disease control, the identification of bacterial strains as Pseudomonas marginalis was based on characteristics such as fluorescence, oxidase negativity, potato soft rot, and positive arginine dihydrolase. However, with the introduction of phylogenetic and genomic analyses, it was discovered that Pseudomonas marginalis is heterogeneous and may contain many cryptic species. A survey was conducted to sort the strains preserved in the NARO Genebank into Pseudomonas marginalis sensu stricto and other strains. Some of these strains were found to be novel species, including Pseudomonas kitaguniensis, Pseudomonas allii, Pseudomonas cyclaminis, Pseudomonas petroselini, Pseudomonas brassicae, Pseudomonas lactucae, Pseudomonas aegrilactucae, and Pseudomonas morbosilactucae. This article briefly introduces the profiles of these novel species and discusses the challenges in reorganizing Pseudomonas marginalis sensu lato.