High-quality draft genome sequences of Pseudomonas monteilii DSM 14164T, Pseudomonas mosselii DSM 17497T, Pseudomonas plecoglossicida DSM 15088T, Pseudomonas taiwanensis DSM 21245T and Pseudomonas vranovensis DSM 16006T: taxonomic considerations

Abstract

Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164 T ), Pseudomonas mosselii (DSM 17497 T ), Pseudomonas plecoglossicida (DSM 15088 T ) , Pseudomonas taiwanensis (DSM 21245 T ) and Pseudomonas vranovensis (DSM 16006 T ). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species.

Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

“…The important group of phytopathogens represented by Pseudomonas syringae has been analyzed under a phylogenomic point of view by Gomila and collaborators, considering 149 genes in the core genome of 139 strains in the group, including 15 type strains [13]. Similarly, whole genome sequences have been used to clarify the taxonomy of species in the fluorescens phylogenetic group of species [14], in a comparison of P. aeruginosa and Azotobacter [15] and in the Pseudomonas putida group of species [16].…”

“…The currently accepted taxonomy of 217 species type strains in the genus Pseudomonas based on a 4-gene MLSA study is presented in this study, whose main aim is the comparison of the current taxonomy with the results obtained by genomic analyses in previous studies performed by our research group [11,16] and those obtained by Hesse et al [17] and Parks et al [8]. The results demonstrate that: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by the 4-gene MLSA analysis are concordant with the groupings in the genomic analyses.…”

Pseudomonas Species Diversity Along the Danube River Assessed by rpoD Gene Sequence and MALDI-TOF MS Analyses of Cultivated Strains

“…The rpoD sequence analysis, however, indicated that these assignations are correct at the level of phylogenetic group, P. fluorescens G, and P. putida G as defined by Mulet et al (2010) , but they can be now identified more precisely at the phylospecies level. The P. fluorescens group contains at the moment more than sixty different species and the P. putida group is composed of at least by 20 species ( Keshavarz-Tohid et al, 2019 ; Peña et al, 2019 ). Table 4 shows the assignation by rpoD of the 14 MDR strains resistant to three or more antibiotic classes.…”

Biosorption of Lead(ii) Ions by Dead Bacterial Biomass Isolated From Mine Water

“…The Pseudomonas genus has the highest number of recognized species and different members have been reported for its application in different bioremediation processes. High-quality draft genome sequence of type strain Pseudomonas monteilii DSM 14164T was recently reported [14]. Different strains of P. monteilii have been reported for its contaminant removal ability from liquid samples [15,16].…”