Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

Abstract

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (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 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.

Keywords: Pseudomonas; genomics; phylogenomics; taxonomy.

Figure 1

Phylogenetic tree based on the 4-genes MLSA for the 227 species or subspecies type strains analyzed using neighbor-joining reconstruction with Jukes–Cantor distances. (A) P. aeruginosa and P. pertucinogena lineages. (B) P. fluorescens lineage. Bootstrap values higher than 70% are indicated on the nodes. Bars indicate sequence divergence.

Figure 1

Phylogenetic tree based on the 4-genes MLSA for the 227 species or subspecies type strains analyzed using neighbor-joining reconstruction with Jukes–Cantor distances. (A) P. aeruginosa and P. pertucinogena lineages. (B) P. fluorescens lineage. Bootstrap values higher than 70% are indicated on the nodes. Bars indicate sequence divergence.

Figure 2

Maximum likelihood phylogenetic tree constructed with PhyML 3.0 based on the 4-genes MLSA for the different groups and subgroups defined in the Pseudomonas genus and closest-related genera. GTI+I+R was selected as the best evolutionary method. Number of species in each collapsed branch are indicated in brackets. Bootstrap values higher than 70% are indicated on the nodes. Bar indicates sequence divergence.

Figure 3

Phylogenetic tree of the Pseudomonadaceae genera based on the GTDB taxonomy. Triangles are proportional to the sequence divergence among species included in each genus. Bar indicates sequence divergence.

Figure 4

P. chlororaphis species and subspecies delineation based on the GBDP phylogenetic analyses retrieved from the TYGS website. The tree was inferred with FastME 2.1.6.1 [32] from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values >60% from 100 replications, with an average branch support of 83.0%. The tree was rooted at the midpoint [33].