Genome-Based Species Diversity Assessment in the Pseudomonas chlororaphis Phylogenetic Subgroup and Proposal of Pseudomonas danubii sp. nov. Isolated from Freshwaters, Soil, and Rhizosphere

Abstract

The Pseudomonas chlororaphis phylogenetic subgroup of species, within the Pseudomonas fluorescens group, currently includes seven bacterial species, all of which have environmental relevance. Phylogenomic analyses help clarify the taxonomy of strains in the group and allow for precise identification. Thirteen antibiotic-resistant strains isolated in a previous study from nine different sampling sites in the Danube River were suspected to represent a novel species and are investigated taxonomically in the present study, together with four other strains isolated from the Woluwe River (Belgium) that were phylogenetically closely related in their rpoD gene sequences. The strains were characterized phenotypically, chemotaxonomically (fatty acid composition and main protein profiles), and phylogenetically. They could not be assigned to any known Pseudomonas species. Three genomes of representative strains were sequenced and analyzed in the context of the genome sequences of closely related strains available in public databases. The phylogenomic analysis demonstrates the need to differentiate new genomic species within the P. chlororaphis subgroup and that Pseudomonas piscis and Pseudomonas aestus are synonyms. This taxonomic study demonstrates that 14 of the characterized isolates are members of the Pseudomonas_E protegens_A species in the GTDB taxonomy and that they represent a novel species in the genus Pseudomonas, for which we propose the name Pseudomonas danubii sp. nov. with strain JDS02PS016T (=CECT 30214T = CCUG 74756T) as the type strain. The other three strains (JDS08PS003, rDWA16, and rDWA64) are members of the species Pseudomonas_E protegens_B in the GTDB taxonomy and need further investigation for proposal as a new bacterial species.