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. 2022 Jul 6;10(7):1363.
doi: 10.3390/microorganisms10071363.

Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans

Margarita Gomila  1 , Magdalena Mulet  1 , Elena García-Valdés  1   2 , Jorge Lalucat  1   2
Affiliations

Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans

Margarita Gomila et al. Microorganisms. .

Abstract

Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans).

Keywords: S. chloritidismutans; S. degradans; S. frequens; S. perfectomarina; Stutzerimonas; core-genome phylogeny; phylogenomic species.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Core-genome phylogeny based on the concatenated sequences of 1054 core genes of 200 genomes of species in the Stutzerimonas genus. Tree was constructed using the maximum likelihood method. Bootstrap values of 100 replicates are indicated in the nodes with different symbols: circles indicate bootstrap values of 100, squares indicate values higher than 90%, and stars indicate values higher than 70%.
Figure 2
Figure 2
UPGMA dendrogram of the average nucleotide identities (ANIb) analysis of the 200 genomes of Stutzerimonas strains. Members of each phylogenomic species (pgs) are indicated with the same color.
Figure 3
Figure 3
Splitstree representation of the phyletic pattern obtained in the analysis of the orthologous genes of 148 genomes selected from the 200 Stutzerimonas strains analyzed. Different pgs are indicated in different colors.
See this image and copyright information in PMC

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