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Diversity
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Pseudomonas Biology and Biodiversity
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Pseudomonas Biology and Biodiversity

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 14528

Special Issue Editor

Dr. Dimitris Mossialos

E-Mail Website
Guest Editor
Department of Biochemistry & Biotechnology, University of Thessaly, School of Health Sciences, Larisa, Greece
Interests: Pseudomonas; high-affinity iron uptake systems; gene regulation; metagenomics; oxidative stress; antimicrobial natural producs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genus Pseudomonas comprises Gram-negative, gamma-proteobacteria that are thriving in diverse environments all over the world, because of their metabolic versatility. Pseudomonas species include those that are plant growth promoting, human and plant pathogens, and bacteria implicated in xenobiotic biodegradation. Their ease of culture in vitro, and the availability of big data with the advent of next generation sequencing and other -omic technologies (e.g., proteomics and metabolomics), has made the genus an excellent focus for scientific research and the development of biotechnological applications. This Special Issue provides a platform to highlight the exciting research and significant advances regarding Pseudomonas diversity, as it is reflected, for example, by community structure and phylogenomics, (meta)genomic, proteomic and metabolomic data, and biotechnological applications harnessing Pseudomonas diversity.

Dr. Dimitris Mossialos
Guest Editor

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. Diversity 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 2600 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

  • Pseudomonas;
  • Biodiversity;
  • Omic technologies;
  • Community structure;
  • Phylogenomics;
  • Metagenomics;
  • Biotechnological applications

Published Papers (4 papers)

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Research

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23 pages, 2862 KiB  
Article
Genome-Based Species Diversity Assessment in the Pseudomonas chlororaphis Phylogenetic Subgroup and Proposal of Pseudomonas danubii sp. nov. Isolated from Freshwaters, Soil, and Rhizosphere
by Magdalena Mulet, María José Martínez, Margarita Gomila, Johanna Dabernig-Heinz, Gabriel E. Wagner, Clemens Kittinger, Gernot Zarfel, Jorge Lalucat and Elena García-Valdés
Diversity 2023, 15(5), 617; https://0-doi-org.brum.beds.ac.uk/10.3390/d15050617 - 02 May 2023
Cited by 1 | Viewed by 1725
Abstract
The Pseudomonas chlororaphis phylogenetic subgroup of species, within the Pseudomonas fluorescens group, currently includes seven bacterial species, all of which have environmental relevance. Phylogenomic analyses help clarify the taxonomy of strains in the group and allow for precise identification. Thirteen antibiotic-resistant strains isolated [...] Read more.
The Pseudomonas chlororaphis phylogenetic subgroup of species, within the Pseudomonas fluorescens group, currently includes seven bacterial species, all of which have environmental relevance. Phylogenomic analyses help clarify the taxonomy of strains in the group and allow for precise identification. Thirteen antibiotic-resistant strains isolated in a previous study from nine different sampling sites in the Danube River were suspected to represent a novel species and are investigated taxonomically in the present study, together with four other strains isolated from the Woluwe River (Belgium) that were phylogenetically closely related in their rpoD gene sequences. The strains were characterized phenotypically, chemotaxonomically (fatty acid composition and main protein profiles), and phylogenetically. They could not be assigned to any known Pseudomonas species. Three genomes of representative strains were sequenced and analyzed in the context of the genome sequences of closely related strains available in public databases. The phylogenomic analysis demonstrates the need to differentiate new genomic species within the P. chlororaphis subgroup and that Pseudomonas piscis and Pseudomonas aestus are synonyms. This taxonomic study demonstrates that 14 of the characterized isolates are members of the Pseudomonas_E protegens_A species in the GTDB taxonomy and that they represent a novel species in the genus Pseudomonas, for which we propose the name Pseudomonas danubii sp. nov. with strain JDS02PS016T (=CECT 30214T = CCUG 74756T) as the type strain. The other three strains (JDS08PS003, rDWA16, and rDWA64) are members of the species Pseudomonas_E protegens_B in the GTDB taxonomy and need further investigation for proposal as a new bacterial species. Full article
(This article belongs to the Special Issue Pseudomonas Biology and Biodiversity)
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25 pages, 1905 KiB  
Article
Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis
by Marios Nikolaidis, Dimitris Mossialos, Stephen G. Oliver and Grigorios D. Amoutzias
Diversity 2020, 12(8), 289; https://0-doi-org.brum.beds.ac.uk/10.3390/d12080289 - 24 Jul 2020
Cited by 33 | Viewed by 6869
Abstract
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete [...] Read more.
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers. Full article
(This article belongs to the Special Issue Pseudomonas Biology and Biodiversity)
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17 pages, 3561 KiB  
Article
Comparative Genomic Analysis of the Biotechnological Potential of the Novel Species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T
by Dominik Rutz, David Frasson, Martin Sievers, Jochen Blom, Fabio Rezzonico, Joël F. Pothier and Theo H. M. Smits
Diversity 2019, 11(11), 204; https://0-doi-org.brum.beds.ac.uk/10.3390/d11110204 - 28 Oct 2019
Cited by 3 | Viewed by 3215
Abstract
In recent years, the use of whole-cell biocatalysts and biocatalytic enzymes in biotechnological applications originating from the genus Pseudomonas has greatly increased. In 2014, two new species within the Pseudomonas putida group were isolated from Swiss forest soil. In this study, the high [...] Read more.
In recent years, the use of whole-cell biocatalysts and biocatalytic enzymes in biotechnological applications originating from the genus Pseudomonas has greatly increased. In 2014, two new species within the Pseudomonas putida group were isolated from Swiss forest soil. In this study, the high quality draft genome sequences of Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T were used in a comparative genomics approach to identify genomic features that either differed between these two new species or to selected members of the P. putida group. The genomes of P. wadenswilerensis CCOS 864T and P. reidholzensis CCOS 865T were found to share genomic features for the degradation of aromatic compounds or the synthesis of secondary metabolites. In particular, genes encoding for biocatalytic relevant enzymes belonging to the class of oxidoreductases, proteases and isomerases were found, that could yield potential applications in biotechnology. Ecologically relevant features revealed that both species are probably playing an important role in the degradation of soil organic material, the accumulation of phosphate and biocontrol against plant pathogens. Full article
(This article belongs to the Special Issue Pseudomonas Biology and Biodiversity)
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Review

Jump to: Research

25 pages, 1590 KiB  
Review
Microbial Diversity in Bee Species and Bee Products: Pseudomonads Contribution to Bee Well-Being and the Biological Activity Exerted by Honey Bee Products: A Narrative Review
by Christina Tsadila, Chiara Amoroso and Dimitris Mossialos
Diversity 2023, 15(10), 1088; https://0-doi-org.brum.beds.ac.uk/10.3390/d15101088 - 16 Oct 2023
Cited by 2 | Viewed by 1806
Abstract
Bees are important pollinators worldwide, promoting sustainability in agriculture and natural ecosystems. Moreover, honey bees produce a variety of honey bee products (beehive products). Honey is the main edible bee product. The consumption of pollen, bee bread, royal jelly, and propolis is becoming [...] Read more.
Bees are important pollinators worldwide, promoting sustainability in agriculture and natural ecosystems. Moreover, honey bees produce a variety of honey bee products (beehive products). Honey is the main edible bee product. The consumption of pollen, bee bread, royal jelly, and propolis is becoming more popular nowadays. All these products are characterized by high nutritional value and/or bioactivity. A high microbial diversity has been reported in bees and beehive products, forming distinct microbial communities. The honey bee gut microbiome actively promotes good health and nutrient availability for the host. Furthermore, it prevents food spoilage and contributes to the maintenance of good hygiene conditions in the hive. Pseudomonads are often reported in investigations on bee and bee product microbiomes. Diverse Pseudomonas species demonstrate high metabolic adaptability, producing a wide range of bioactive enzymes and secondary metabolites. Several studies have provided evidence that Pseudomonads might play a role in bee well-being and the bioactivity exerted by honey bee products, though further research is warranted to fully understand the effects and mechanisms. The aim of this narrative review is to highlight the importance of Pseudomonads in the context of up-to-date knowledge regarding the bee and bee product microbiomes. Full article
(This article belongs to the Special Issue Pseudomonas Biology and Biodiversity)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type: Review 

Tentative title: Diversity of Pseudomonads present at hive microbiome: contribution to  biological activity of bee products and honeybee well being

Tentative Authors: Christina Tsadila, Marios Nikolaidis, Grigorios Amoutzias and Dimitris Mossialos

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