Abstract
The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans–P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.
Highlights
The genus Pseudomonas is considerably diverse and consists of more than 100 characterized species to date (Mulet et al, 2013)
A total of 373 Pseudomonas genome sequences were selected for phylogenomic tree reconstruction
A wgMLST analysis restricted to strains from closely related Pseudomonas species will likely identify more conserved loci which can be used to refine their evolutionary relationships which is beyond the scope of this study
Summary
The genus Pseudomonas is considerably diverse and consists of more than 100 characterized species to date (Mulet et al, 2013). Some species of Pseudomonas are well-known and characterized such as P. aeruginosa (Oliver et al, 2000). Some are plant-associated such as Pseudomonas fluorescens and Pseudomonas syringae and define or are present in numerous plant-microbe system. Genome-Based Taxonomy of Pseudomonas (Pieterse et al, 2014). Pseudomonas fluorescens in general, is known for its ability to colonize plant rhizospheres and produce antimicrobial compounds targeting pathogens; protecting plants from diseases (Hol et al, 2013). P. syringae is commonly associated with plant disease and has been known to invade a variety of plant species with its extracellular flagella and pili appendages. Infection with P. syringae can predispose the host plant to environmental stresses such as frost damage (Maki et al, 1974)
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