Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas Putida Group

Léa Girard
ORCID logo ,
Cédric Lood
ORCID logo ,
Monica Höfte
ORCID logo ,
Peter Vandamme
ORCID logo ,
Hassan Rokni-Zadeh
,
Vera van Noort
,
Rob Lavigne
* ,
René De Mot
* ORCID logo
Version 1 : Received: 13 July 2021 / Approved: 14 July 2021 / Online: 14 July 2021 (13:11:32 CEST)

A peer-reviewed article of this Preprint also exists.

Girard, L.; Lood, C.; Höfte, M.; Vandamme, P.; Rokni-Zadeh, H.; van Noort, V.; Lavigne, R.; De Mot, R. The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group. Microorganisms 2021, 9, 1766. Girard, L.; Lood, C.; Höfte, M.; Vandamme, P.; Rokni-Zadeh, H.; van Noort, V.; Lavigne, R.; De Mot, R. The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group. Microorganisms 2021, 9, 1766.

Abstract

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution. In this study, whole genome se-quencing enabled us to define 43 new Pseudomonas species and to provide an update of the Pseu-domonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including 316 and 313 type strains of Pseudomonas, respectively, re-vealed sixteen groups of Pseudomonas and justified the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incor-rectly assigned at the species level and among those, 19 strains were shown to represent an addi-tional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle and metabolic potential of Pseudomonas spp.

Keywords

Pseudomonadaceae; long-read sequencing; hybrid assembly; Taxonomy; Phylogeny; Non-Ribosomal Peptide Synthetases (NRPS); Cyclic Lipopeptides (CLPs).

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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