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Microorganisms
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Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas
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Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (30 December 2021) | Viewed by 12433

Special Issue Editors

Prof. Dr. Margarita Gomila

E-Mail Website
Guest Editor
Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
Interests: microbial evolution; phylogeny; bacterial systematics and taxonomy; bacterial identification; genomics and metagenomics; Pseudomonas
Prof. Dr. Jorge Lalucat

E-Mail Website
Guest Editor
Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
Interests: Pseudomonas; phylogeny; taxonomy and systematics; genomics
Dr. Antonio Busquets

E-Mail Website
Guest Editor
Microbiology, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
Interests: microbial ecology; molecular biology; genomics; Pseudomonas; plant-pathogens

Special Issue Information

Dear Colleagues,

The genus Pseudomonas is one of the most complex bacterial genera and is currently the genus of Gram-negative bacteria with the largest number of species, a number which is increasing every year. Strains of species in this genus are metabolically versatile, able to dwell in many environments with different lifestyles, and have attracted attention for their capability to use many different organic compounds, but also for the pathogenicity of some species against plants and animals (humans, fishes, or insects), as well as their role as biological control agents and in biodegradation, among others. The difficulty in phenotypically identifying Pseudomonas species has been highlighted through the years, the use of phylogenetic molecular markers in taxonomic studies being necessary. The introduction of genomics is profoundly changing the current bacterial taxonomy. Phylogenomic approaches based on comparative genomics and phylogenetic analyses have also been applied to clarify the taxonomy of the genus and are currently the choice methods for a stable 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.

In this context, this Special Issue on “Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas” of Microorganisms welcomes researchers all over the world to contribute with original articles addressing the latest knowledge about the taxonomy of the genus Pseudomonas and of species within the genus using the genomic approach.

Prof. Dr. Margarita Gomila
Prof. Dr. Jorge Lalucat
Dr. Antonio Busquets
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genomics
  • phylogenomics
  • evolution
  • taxonomy
  • phylogeny
  • comparative genomics
  • horizontal gene transfer
  • phytopathogenic Pseudomonas
  • biological control agent
  • clinical Pseudomonas
  • plant growth promotors
  • biodegradation
  • habitat correlation with genomics
  • Pseudomonas
  • ecological distribution
  • novel species

Published Papers (2 papers)

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Research

22 pages, 2956 KiB  
Article
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
by Margarita Gomila, Magdalena Mulet, Elena García-Valdés and Jorge Lalucat
Microorganisms 2022, 10(7), 1363; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071363 - 06 Jul 2022
Cited by 18 | Viewed by 3474
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 [...] Read more.
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). Full article
(This article belongs to the Special Issue Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas)
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25 pages, 3485 KiB  
Article
The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group
by Léa Girard, Cédric Lood, Monica Höfte, Peter Vandamme, Hassan Rokni-Zadeh, Vera van Noort, Rob Lavigne and René De Mot
Microorganisms 2021, 9(8), 1766; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081766 - 18 Aug 2021
Cited by 70 | Viewed by 7551
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 [...] Read more.
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 constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled 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 incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 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. Full article
(This article belongs to the Special Issue Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas)
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