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

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

doi:10.3390/biology10080782

Zaki Saati-Santamaría, Paula García-Fraile + Show 3 more

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https://doi.org/10.3390/biology10080782

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Abstract

Simple SummaryPseudomonas represents a very important bacterial genus that inhabits many environments and plays either prejudicial or beneficial roles for higher hosts. However, there are many Pseudomonas species which are too divergent to the rest of the genus. This may interfere in the correct development of biological and ecological studies in which Pseudomonas are involved. Thus, we aimed to study the correct taxonomic placement of Pseudomonas species. Based on the study of their genomes and some evolutionary-based methodologies, we suggest the description of three new genera (Denitrificimonas, Parapseudomonas and Neopseudomonas) and many reclassifications of species previously included in Pseudomonas.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.

Highlights

Pseudomonas is one of the most diverse and adaptable prokaryotic genera and their metabolic versatility allows their members to survive in many different environments [1,2].Members of the genus Pseudomonas have been identified in human and animal related sources, plants, soil, water environments, psychrophilic environments, and other environmental niches and hosts [3,4,5]
overall genome related index (OGRI) values shows that they have lower ANIb values with those type strains included in the main Pseudomonas clade than some thresholds that have been suggested for genera delimitation (75–76%) [25,26]
The ANIb and amino acid identities (AAI) values between P. hussaini JMC 19513T and other Pseudomonas species are below 75.3% and 70%, respectively (Tables S2 and S6 and Figure 7)

Summary

Introduction

Pseudomonas is one of the most diverse and adaptable prokaryotic genera and their metabolic versatility allows their members to survive in many different environments [1,2]. Members of the genus Pseudomonas have been identified in human and animal related sources, plants, soil, water environments, psychrophilic environments, and other environmental niches and hosts [3,4,5]. The multiplicity of environments where Pseudomonas grow and diversify has led to the broad evolution of its members, making it one of the most diverse bacterial genera. Pseudomonas’ diversity, together with the fact that these bacteria are tremendously versatile and easy to grow under laboratory conditions, has led to the continuous discovery of new species of this genus [4]. The large number of species belonging to Pseudomonas and related taxa has made their taxonomic classification challenging, involving constant reshaping and reclassifications [11,12]

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