Abstract
Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA–DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.
Highlights
Pseudomonas is a highly diverse and metabolically versatile genus of Gammaproteobacteria [1] ubiquitously found in the environment
Using a polyphasic approach we propose the reclassification of P. fluorescens F113 into the novel species P. ogarae sp. nov., type strain F113, which is substantiated by phylogenomics, functional genomics and phenotypic analyses
Genomes belonging to the P. corrugata phylogenomic subgroup were determined based on the genome blast distance phylogeny (GBDP) distance threshold of 0.132915 previously established for the P. fluorescens complex of species [15] using the genome of P. ogarae F113T as a reference, which has been previously classified into the P. corrugata subgroup in several previous studies [15, 26, 40, 41]
Summary
Pseudomonas is a highly diverse and metabolically versatile genus of Gammaproteobacteria [1] ubiquitously found in the environment. Members of this genus thrive from tropics to polar and desertic habitats [2,3,4,5] and have been found in fresh and sea waters [6, 7] and soils worldwide [8]. P. syringae is a known pathogen of a wide range of plant. Multiple Pseudomonas species are recognized for their beneficial plant role, known as plant growth-promoting rhizobacteria (PGPR), and are mainly found within isolates and species from the Pseudomonas fluorescens complex of species [15, 16], including P. brassicacearum, P. chlororaphis and P. protegens [17,18,19]
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