Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Zaki Saati-Santamaría; Ezequiel Peral-Aranega; Encarna Velázquez; Raúl Rivas; Paula García-Fraile

doi:10.3390/biology10080782

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Biology (Basel). 2021 Aug 16;10(8):782. doi: 10.3390/biology10080782.

Authors

Zaki Saati-Santamaría^{1

2}, Ezequiel Peral-Aranega^{1

2}, Encarna Velázquez^{1

2

3}, Raúl Rivas^{1

2

3}, Paula García-Fraile^{1

2

3}

Affiliations

¹ Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain.
² Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain.
³ Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain.

Abstract

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

Keywords: Denitrificimonas; Neopseudomonas; Parapseudomonas; Pseudomonas; average nucleotide identity; bacterial taxonomy; comparative genomics; dDDH; genomics; phylogeny.