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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Mulet M, Gomila M, Lalucat J, Bosch R, Rossello-Mora R, García-Valdés E. Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments. Syst Appl Microbiol 2023; 46:126400. [PMID: 36706672 DOI: 10.1016/j.syapm.2023.126400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/20/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
Strains 19SMN4T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as Pseudomonas stutzeri genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. P. stutzeri has been recently reclassified as a new genus, Stutzerimonas, and a preliminary analysis indicated that the strains in this study were distinct from any classified Stutzerimonas and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4T and ST27MN3 shared 3,995 genes and were closely related to members of the species "Stutzerimonas songnenensis" and Stutzerimonas perfectomarina, as well as to the Stutzerimonas phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %). We therefore conclude that strains 19SMN4T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4T (=CCUG44593T = DSM6084T = LMG18521T).
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Rafael Bosch
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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Gomila M, Mulet M, García-Valdés E, Lalucat J. 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. Microorganisms 2022; 10:microorganisms10071363. [PMID: 35889082 PMCID: PMC9320692 DOI: 10.3390/microorganisms10071363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
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 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).
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Affiliation(s)
- Margarita Gomila
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
| | - Magdalena Mulet
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
| | - Elena García-Valdés
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats (IMEDEA CSIC-UIB), 07190 Mallorca, Spain
| | - Jorge Lalucat
- Microbiology (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.G.); (M.M.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats (IMEDEA CSIC-UIB), 07190 Mallorca, Spain
- Correspondence:
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Mulet M, Gomila M, Ramírez A, Lalucat J, Garcia-Valdes E. Corrigendum: Pseudomonas nosocomialis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Antonio Ramírez
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122, Palma de Mallorca, Spain
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122, Palma de Mallorca, Spain
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Duman M, Mulet M, Altun S, Saticioglu IB, Gomila M, Lalucat J, García-Valdés E. Corrigendum: Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870571 DOI: 10.1099/ijsem.0.005125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Soner Altun
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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Lalucat J, Gomila M, Mulet M, Zaruma A, García-Valdés E. Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov. Syst Appl Microbiol 2021; 45:126289. [PMID: 34920232 DOI: 10.1016/j.syapm.2021.126289] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]
Abstract
Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.
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Affiliation(s)
- Jorge Lalucat
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain; Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), Spain.
| | - Margarita Gomila
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Magdalena Mulet
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Anderson Zaruma
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain
| | - Elena García-Valdés
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, Spain; Institut Mediterrani d'Estudis Avançats, IMEDEA (CSIC-UIB), Spain
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Duman M, Mulet M, Altun S, Saticioglu IB, Gomila M, Lalucat J, García-Valdés E. Corrigendum to "Pseudomonas anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish" [44(3) (2021) 126198]. Syst Appl Microbiol 2021; 45:126246. [PMID: 34758913 DOI: 10.1016/j.syapm.2021.126246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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Mulet M, Duman M, Altun S, Saticioglu IB, Gomila M, Matthijs S, Lalucat J, García-Valdés E. Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water. Int J Syst Evol Microbiol 2021; 71. [PMID: 34242155 DOI: 10.1099/ijsem.0.004860] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Bursa Uludag University, 16059, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Bursa Uludag University, 16059, Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Sandra Matthijs
- Institut de recherche LABIRIS, Avenue Emile Gryzon, 1 - 1070 Bruxelles, Belgium
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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Duman M, Mulet M, Altun S, Burcin Saticioglu I, Gomila M, Lalucat J, García-Valdés E. Pseudomonas anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish. Syst Appl Microbiol 2021; 44:126198. [PMID: 33838437 DOI: 10.1016/j.syapm.2021.126198] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022]
Abstract
In a study carried out between 2013 and 2018 in fish farms in Turkey, several putative novel species were isolated. The 16S rRNA nucleotide sequences of fourteen strains of Gram-negative rods, which were isolated from asymptomatic and symptomatic rainbow trouts (Onchorhynchus mykiss), placed them under the genus Pseudomonas. The similarity values of the concatenated nucleotide sequences of the rpoD, rpoB, gyrB and 16S rRNA genes clustered these isolates into the P. fluorescens phylogenetic group of species and into the Pseudomonas koreensis subgroup, close to Pseudomonas helmanticensis and Pseudomonas baetica. An isolate of a totally different origin, strain CCUG 67011, clustered with these isolates. Phenotypic characterization, together with the chemotaxonomic data, whole-cell MALDI-TOF MS and fatty acids methyl esters analyses were performed. The DNA G + C content was 58.7 mol% for isolate P9T and 58.8 mol% for isolate P42T. The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9T, P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9T as the type strain (=CCUG 74755T = CECT 3172T). The isolates P1, P2, P10, P27, P30, P24a, P42T, P117, P139, P152 and CCUG 67011 represent another novel sècies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42T as the type strain (=CCUG 74870T = CECT 3174T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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Duman M, Mulet M, Altun S, Saticioglu IB, Gomila M, Lalucat J, Garcia-Valdes E. Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov. , Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout. Int J Syst Evol Microbiol 2021; 71. [PMID: 33629945 DOI: 10.1099/ijsem.0.004714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50T, 154aT and P154b), Pseudomonas fluorescens (strain P115T) and Pseudomonas koreensis (strain P155T) phylogenetic subgroups in the genus Pseudomonas. The DNA G+C content ranged from 58.5 to 60 mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas. Based on these data, we concluded that strains P49, P50T, P115T, P154aT, P154b and P155T belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50T with P50T (=CECT 30175T=CCUG 74871T) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115T (CECT 30173T=CCUG 74873T); Pseudomonas mucoides sp. nov. for strains P154aT and P154b with P154aT (=CECT 30177T=CCUG 74874T) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155T (=CECT 30178T=CCUG 74875T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Soner Altun
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.,Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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11
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Oueslati M, Mulet M, Zouaoui M, Chandeysson C, Lalucat J, Hajlaoui MR, Berge O, García-Valdés E, Sadfi-Zouaoui N. Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia. AMB Express 2020; 10:198. [PMID: 33130970 PMCID: PMC7604283 DOI: 10.1186/s13568-020-01134-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 11/12/2022] Open
Abstract
The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.
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Peña A, Busquets A, Gomila M, Mulet M, Gomila RM, Garcia-Valdes E, Reddy TBK, Huntemann M, Varghese N, Ivanova N, Chen IM, Göker M, Woyke T, Klenk HP, Kyrpides N, Lalucat J. High-quality draft genome sequences of Pseudomonas monteilii DSM 14164 T, Pseudomonas mosselii DSM 17497 T, Pseudomonas plecoglossicida DSM 15088 T, Pseudomonas taiwanensis DSM 21245 T and Pseudomonas vranovensis DSM 16006 T: taxonomic considerations. Access Microbiol 2020; 1:e000067. [PMID: 32974501 PMCID: PMC7491935 DOI: 10.1099/acmi.0.000067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164T), Pseudomonas mosselii (DSM 17497T), Pseudomonas plecoglossicida (DSM 15088T), Pseudomonas taiwanensis (DSM 21245T) and Pseudomonas vranovensis (DSM 16006T). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species.
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Affiliation(s)
- Arantxa Peña
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Antonio Busquets
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Margarita Gomila
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Magdalena Mulet
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Rosa M Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
| | - T B K Reddy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Neha Varghese
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - I-Min Chen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Jorge Lalucat
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
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Mulet M, Montaner M, Román D, Gomila M, Kittinger C, Zarfel G, Lalucat J, García-Valdés E. Pseudomonas Species Diversity Along the Danube River Assessed by rpoD Gene Sequence and MALDI-TOF MS Analyses of Cultivated Strains. Front Microbiol 2020; 11:2114. [PMID: 32983072 PMCID: PMC7492575 DOI: 10.3389/fmicb.2020.02114] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/11/2020] [Indexed: 11/24/2022] Open
Abstract
A collection of 611 Pseudomonas isolated from 14 sampling sites along the Danube River were identified previously by MALDI-TOF MS with the VITEK MS system and were grouped in 53 clusters by their main protein profiles. The strains were identified in the present study at the phylospecies level by rpoD gene sequencing. Partial sequences of the rpoD gene of 190 isolates representatives of all clusters were analyzed. Strains in the same MALDI-TOF cluster were grouped in the same phylospecies when they shared a minimum 95% similarity in their rpoD sequences. The sequenced strains were assigned to 34 known species (108 strains) and to 32 possible new species (82 strains). The 611 strains were identified at the phylospecies level combining both methods. Most strains were assigned to phylospecies in the Pseudomonas putida phylogenetic group of species. Special attention was given to 14 multidrug resistant strains that could not be assigned to any known Pseudomonas species and were considered environmental reservoir of antibiotic resistance genes. Coverage indices and rarefaction curves demonstrated that at least 50% of the Pseudomonas species in the Danube River able to grow in the isolation conditions have been identified at the species level. Main objectives were the confirmation of the correlation between the protein profile clusters detected by MALDI-TOF MS and the phylogeny of Pseudomonas strains based on the rpoD gene sequence, the assessment of the higher species discriminative power of the rpoD gene sequence, as well as the estimation of the high diversity of Pseudomonas ssp. along the Danube river. This study highlights the Pseudomonas species diversity in freshwater ecosystems and the usefulness of the combination of MALDI-TOF mass spectrometry for the dereplication of large sets of strains and the rpoD gene sequences for rapid and accurate identifications at the species level.
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - María Montaner
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Daniela Román
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Clemens Kittinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gernot Zarfel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
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14
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Duman M, Mulet M, Saticioglu IB, Altun S, Gomila M, Lalucat J, García-Valdés E. Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey. Syst Appl Microbiol 2020; 43:126103. [PMID: 32690194 DOI: 10.1016/j.syapm.2020.126103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
A study of 91 isolates from fish farms in Turkey showed that isolates P7T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7T as a type strain (=CCUG 74260T= and CECT30107T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animals Disease, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Soner Altun
- Department of Aquatic Animals Disease, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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15
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Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas. Genes (Basel) 2020; 11:E139. [PMID: 32013079 PMCID: PMC7074058 DOI: 10.3390/genes11020139] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/11/2023] Open
Abstract
The introduction of genomics is profoundly changing current bacterial 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. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.
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Affiliation(s)
- Jorge Lalucat
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.M.); (M.G.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats, IMEDEA (CSIC-UIB), 07122 Palma de Mallorca, Spain
| | - Magdalena Mulet
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.M.); (M.G.); (E.G.-V.)
| | - Margarita Gomila
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.M.); (M.G.); (E.G.-V.)
| | - Elena García-Valdés
- Microbiologia, Departament Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; (M.M.); (M.G.); (E.G.-V.)
- Institut Mediterrani d’Estudis Avançats, IMEDEA (CSIC-UIB), 07122 Palma de Mallorca, Spain
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Mulet M, Gomila M, Ramírez A, Lalucat J, Garcia-Valdes E. Pseudomonas nosocomialis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 2019; 69:3392-3398. [DOI: 10.1099/ijsem.0.003628] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Antonio Ramírez
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122, Palma de Mallorca, Spain
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122, Palma de Mallorca, Spain
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17
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Oueslati M, Mulet M, Gomila M, Berge O, Hajlaoui MR, Lalucat J, Sadfi-Zouaoui N, García-Valdés E. New species of pathogenic Pseudomonas isolated from citrus in Tunisia: Proposal of Pseudomonas kairouanensis sp. nov. and Pseudomonas nabeulensis sp. nov. Syst Appl Microbiol 2019; 42:348-359. [PMID: 30910423 DOI: 10.1016/j.syapm.2019.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 11/25/2022]
Abstract
A collection of Pseudomonas strains was isolated in different regions of Tunisia in the period 2016-2017 from the fruits and leaves of Citrus sinensis cv. 'Valencia Late' and Citrus limon cv. 'Eureka' plants with symptoms of blast and black pit disease. A phylogenetic analysis of the housekeeping gene rpoD was used for strain identification at the species level. The results demonstrated the affiliation of these strains with the genus Pseudomonas and revealed the presence of 11 strains representing two putative new species in two monophyletic branches. These strains were analyzed morphologically and genotypically by multilocus sequence analyses of the rpoD, gyrB and 16S rRNA (rrs) gene sequences, and their phenotypic characteristics by API 20NE and Biolog GEN III. Plant pathogenic properties were confirmed on fruits and detached leaves of C. limon cv. 'Eureka'. Fatty acids and WC MALDI-TOF MS major protein profiles were determined. The genomes of both representatives were sequenced. The average nucleotide index and genome-to-genome distance from KC12T and E10BT are below the cut-off established for a described species. These results support the conclusion that the strains KC12T, KC17, KC20, KC22, KC24A, KC25 and KC26 represent a novel species of Pseudomonas, for which the name of Pseudomonas kairouanensis is proposed. The type strain is KC12T (=CECT9766 and CFBP 8662). The strains E10BT, E10AB, E10CB1 and Iy3BA represent another novel species of Pseudomonas for which the name of Pseudomonas nabeulensis is proposed; the type strain is E10BT (=CECT9765 and CFBP 8661).
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Affiliation(s)
- Maroua Oueslati
- Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Université de Tunis ElManar, 2092 Tunis, Tunisia
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Odile Berge
- INRA, UR 407, Unité de Recherche de Pathologie Végétale, Centre de Recherche Provence-Alpes-Côte d'Azur, Avignon, France
| | - Mohamed Rabeh Hajlaoui
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, INRA Tunisia, Université de Carthage, 2094 Ariana, Tunisia
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Najla Sadfi-Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Université de Tunis ElManar, 2092 Tunis, Tunisia
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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18
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Gomila M, Moralejo E, Busquets A, Segui G, Olmo D, Nieto A, Juan A, Lalucat J. Draft Genome Resources of Two Strains of Xylella fastidiosa XYL1732/17 and XYL2055/17 Isolated from Mallorca Vineyards. Phytopathology 2019; 109:222-224. [PMID: 30570447 DOI: 10.1094/phyto-08-18-0298-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xylella fastidiosa is a plant-pathogenic bacterium that causes serious diseases in many crops of economic importance and is a quarantine organism in the European Union. This study reports a de novo-assembled draft genome sequence of the first isolates causing Pierce's disease in Europe: X. fastidiosa subsp. fastidiosa strains XYL1732/17 and XYL2055/17. Both strains were isolated from grapevines (Vitis vinifera) showing Pierce's disease symptoms at two different locations in Mallorca, Spain. The XYL1732/17 genome is 2,444,109 bp long, with a G+C content of 51.5%; it contains 2,359 open reading frames and 48 tRNA genes. The XYL2055/17 genome is 2,456,780 bp long, with a G+C content of 51.5%; it contains 2,384 open reading frames and 48 tRNA genes.
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Affiliation(s)
- Margarita Gomila
- 1 Microbiology (Biology Department), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Eduardo Moralejo
- 2 Tragsa, Empresa de Transformación Agraria, Delegación de Baleares, 07005 Palma de Mallorca, Spain
| | - Antonio Busquets
- 1 Microbiology (Biology Department), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Guillem Segui
- 1 Microbiology (Biology Department), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Diego Olmo
- 3 Serveis de Millora Agrària, Govern Balear, 07009, Palma de Mallorca, Spain; and
| | - Alicia Nieto
- 3 Serveis de Millora Agrària, Govern Balear, 07009, Palma de Mallorca, Spain; and
| | - Andreu Juan
- 4 Servicio de Agricultura, Conselleria de Medi Ambient, Agricultura i Pesca, 07006 Palma de Mallorca, Spain
| | - Jorge Lalucat
- 1 Microbiology (Biology Department), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
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Häggblom MM, Song B, Lalucat J. Norberto J. Palleroni (1922-2018). Environ Microbiol 2018; 20:3459-3461. [DOI: 10.1111/1462-2920.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Max M. Häggblom
- Rutgers; The State University of New Jersey; New Brunswick NJ USA
| | - Bongkeun Song
- Virginia Institute of Marine Science; Gloucester Point VA USA
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Mulet M, Sánchez D, Rodríguez AC, Nogales B, Bosch R, Busquets A, Gomila M, Lalucat J, García-Valdés E. Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2018; 41:340-347. [DOI: 10.1016/j.syapm.2018.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
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Jaén-Luchoro D, Aliaga-Lozano F, Gomila RM, Gomila M, Salvà-Serra F, Lalucat J, Bennasar-Figueras A. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PLoS One 2017; 12:e0189459. [PMID: 29236773 PMCID: PMC5728571 DOI: 10.1371/journal.pone.0189459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Francisco Aliaga-Lozano
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Laboratorio de Biología Molecular, Clínica Rotger, Palma de Mallorca, Spain
| | - Rosa Maria Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francisco Salvà-Serra
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Antoni Bennasar-Figueras
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Area de Enfermedades Infecciosas, Instituto Universitario de Investigaciones en Ciencias de la Salud (IUNICS-UIB), Universitat de les Illes Balears, Palma de Mallorca, Spain
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22
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Gomila M, Busquets A, Mulet M, García-Valdés E, Lalucat J. Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis. Front Microbiol 2017; 8:2422. [PMID: 29270162 PMCID: PMC5725466 DOI: 10.3389/fmicb.2017.02422] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 11/22/2017] [Indexed: 11/13/2022] Open
Abstract
The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.
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Affiliation(s)
- Margarita Gomila
- Microbiology, Department of Biology, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Antonio Busquets
- Microbiology, Department of Biology, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Magdalena Mulet
- Microbiology, Department of Biology, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiology, Department of Biology, Universitat de les Illes Balears, Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (Consejo Superior de Investigaciones Científicas-Universidad de las Islas Baleares), Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiology, Department of Biology, Universitat de les Illes Balears, Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (Consejo Superior de Investigaciones Científicas-Universidad de las Islas Baleares), Palma de Mallorca, Spain
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Michael E, Gomila M, Lalucat J, Nitzan Y, Pechatnikov I, Cahan R. Proteomic Assessment of the Expression of Genes Related to Toluene Catabolism and Porin Synthesis in Pseudomonas stutzeri ST-9. J Proteome Res 2017; 16:1683-1692. [PMID: 28276695 DOI: 10.1021/acs.jproteome.6b01044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The organization and expression of Pseudomonas stutzeri ST-9 genes related to toluene catabolism and porin synthesis was investigated. Toluene-degrading genes were found to be localized in the chromosome close to a phage-type integrase. A regulatory gene and 21 genes related to an aromatics degradation pathway are organized as a putative operon. These proteins are upregulated in the presence of toluene. Fourteen outer membrane proteins were identified as porins in the ST-9 genome. The identified porins showed that the main detected porins are related to the OmpA and OprD superfamilies. The percentage of porins in the outer membrane protein fraction, as determined by mass spectrometry, was 73% and 54% when the cells were cultured with toluene and with glucose, respectively. Upregulation of OmpA and downregulation of OprD occurred in the presence of toluene. A porin fraction (90% OprD) from both cultures was isolated and examined as a toluene uptake system using the liposome-swelling assay. Liposomes were prepared with the porin fraction from a culture that was grown on toluene (T-proteoliposome) or glucose (G-proteoliposome). There was no significant difference in the permeability rate of the different solutes through the T-proteoliposome and the G-proteoliposome.
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Affiliation(s)
- Esti Michael
- Department of Chemical Engineering, Ariel University , Ariel, 40700, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan, 52900, Israel
| | - Margarita Gomila
- Microbiology, Biology Department, and IMEDEA, (CSIC-UIB) University of the Balearic Islands , Palma de Mallorca, 07122, Spain
| | - Jorge Lalucat
- Microbiology, Biology Department, and IMEDEA, (CSIC-UIB) University of the Balearic Islands , Palma de Mallorca, 07122, Spain
| | - Yeshayahu Nitzan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan, 52900, Israel
| | - Izabella Pechatnikov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan, 52900, Israel
| | - Rivka Cahan
- Department of Chemical Engineering, Ariel University , Ariel, 40700, Israel
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24
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Peña A, Busquets A, Gomila M, Mulet M, Gomila RM, Reddy TBK, Huntemann M, Pati A, Ivanova N, Markowitz V, García-Valdés E, Göker M, Woyke T, Klenk HP, Kyrpides N, Lalucat J. High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains. Stand Genomic Sci 2016; 11:55. [PMID: 27594974 PMCID: PMC5009691 DOI: 10.1186/s40793-016-0178-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/16/2016] [Indexed: 01/10/2023] Open
Abstract
Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6–4.9 Mb), with 4,119–4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.
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Affiliation(s)
- Arantxa Peña
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Antonio Busquets
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Magdalena Mulet
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Rosa M Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - T B K Reddy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Amrita Pati
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Victor Markowitz
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Elena García-Valdés
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain ; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698 USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jorge Lalucat
- Department of Biology-Microbiology, Universitat de les Illes Balears, Campus UIB, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain ; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
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25
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Mulet M, Sánchez D, Lalucat J, Lee K, García-Valdés E. Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol. Int J Syst Evol Microbiol 2015; 65:4013-4018. [DOI: 10.1099/ijsem.0.000529] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name ‘Pseudomonas alkylphenolia’ was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T with the Pseudomonas putida group, with Pseudomonas vranovensis DSM 16006T as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, gyrB, rpoD and rpoB partial gene sequences showed that isolate KL28T could be differentiated from P. vranovensis DSM 16006T (sequence similarity 93.7 %). Genomic comparisons of strain KL28T with the type strains of the species in the P. putida group using average nucleotide index based on blast (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with P. vranovensis DSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T ( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, ‘P. alkylphenolia’, is correctly latinized as Pseudomonas alkylphenolica sp. nov.
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
| | - David Sánchez
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Kyoung Lee
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 641-773, Republic of Korea
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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Abstract
The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.
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Affiliation(s)
- Margarita Gomila
- Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain
| | - Arantxa Peña
- Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain
| | - Magdalena Mulet
- Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain ; Institut Mediterrani d'Estudis Avançats (Consejo Superior de Investigaciones Científicas-Universidad de las Islas Baleares) Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain ; Institut Mediterrani d'Estudis Avançats (Consejo Superior de Investigaciones Científicas-Universidad de las Islas Baleares) Palma de Mallorca, Spain
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27
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Gomila M, Prince-Manzano C, Svensson-Stadler L, Busquets A, Erhard M, Martínez DL, Lalucat J, Moore ERB. Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses. PLoS One 2014; 9:e114356. [PMID: 25474264 PMCID: PMC4256396 DOI: 10.1371/journal.pone.0114356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/10/2014] [Indexed: 11/18/2022] Open
Abstract
The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected ‘house-keeping’ genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to support the identifications determined by the genotypic DNA sequence-based MLSA. The MALDI-TOF MS data showed good accordance in strain groupings and identifications by the MLSA data.
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Affiliation(s)
- Margarita Gomila
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
- * E-mail:
| | - Claudia Prince-Manzano
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | - Liselott Svensson-Stadler
- Department of Infectious Diseases, Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Antonio Busquets
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | | | - Deny L. Martínez
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
- Mediterranean Institute for Advanced Studies (IMEDEA) (CSIC-UIB), Palma de Mallorca, Islas Baleares, Spain
| | - Edward R. B. Moore
- Department of Infectious Diseases, Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
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Sánchez D, Gomila M, Bennasar A, Lalucat J, García-Valdés E. Genome analysis of environmental and clinical P. aeruginosa isolates from sequence type-1146. PLoS One 2014; 9:e107754. [PMID: 25329302 PMCID: PMC4198096 DOI: 10.1371/journal.pone.0107754] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/16/2014] [Indexed: 11/18/2022] Open
Abstract
The genomes of Pseudomonas aeruginosa isolates of the new sequence type ST-1146, three environmental (P37, P47 and P49) and one clinical (SD9) isolates, with differences in their antibiotic susceptibility profiles have been sequenced and analysed. The genomes were mapped against P. aeruginosa PAO1-UW and UCBPP-PA14. The allelic profiles showed that the highest number of differences were in “Related to phage, transposon or plasmid” and “Secreted factors” categories. The clinical isolate showed a number of exclusive alleles greater than that for the environmental isolates. The phage Pf1 region in isolate SD9 accumulated the highest number of nucleotide substitutions. The ORF analysis of the four genomes assembled de novo indicated that the number of isolate-specific genes was higher in isolate SD9 (132 genes) than in isolates P37 (24 genes), P47 (16 genes) and P49 (21 genes). CRISPR elements were found in all isolates and SD9 showed differences in the spacer region. Genes related to bacteriophages F116 and H66 were found only in isolate SD9. Genome comparisons indicated that the isolates of ST-1146 are close related, and most genes implicated in pathogenicity are highly conserved, suggesting a genetic potential for infectivity in the environmental isolates similar to the clinical one. Phage-related genes are responsible of the main differences among the genomes of ST-1146 isolates. The role of bacteriophages has to be considered in the adaptation processes of isolates to the host and in microevolution studies.
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Affiliation(s)
- David Sánchez
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain
| | - Antonio Bennasar
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain; Instituto Universitario de Investigación en Ciencias de la Salud (IUNICS-UIB) Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, Palma de Mallorca, Spain
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29
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Renom F, Gomila M, Garau M, Gallegos MDC, Guerrero D, Lalucat J, Soriano JB. Respiratory infection by Corynebacterium striatum: epidemiological and clinical determinants. New Microbes New Infect 2014; 2:106-14. [PMID: 25356355 PMCID: PMC4184579 DOI: 10.1002/nmi2.48] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/15/2014] [Accepted: 04/24/2014] [Indexed: 12/27/2022] Open
Abstract
The increasing prevalence of advanced chronic respiratory disease, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favours the emergence of nosocomial respiratory infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. There is little evidence about patterns of respiratory infection, transmission and adaptive ability of this pathogen. Seventy-two C. striatum isolates from 51 advanced respiratory patients, mainly chronic obstructive pulmonary disease, were studied during 38 months. Patients were 74.8 ± 8.6 years old and 81.9% were men, who had required an average of 2.2 hospitalizations and 63.5 days in the hospital in the previous year. Of 49 isolates from 42 patients we were able to identify 12 clones by multilocus sequence analysis (MLSA), nine phenotypic variants and 22 antibiotic susceptibility patterns, and we determined their clinical and epidemiological determinants. MLSA allows identification of the existence of nosocomial outbreaks by transmission of the same or different clones, the persistence of the same clone in the environment or in patient airways for months. The study showed the high variability and adaptive capacity of the isolates, the antibiotic multidrug-resistance in all of them, and their contribution to a high morbidity and mortality (41%) during the study period.
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Affiliation(s)
- F Renom
- Respiratory Department, Hospital Joan March Bunyola, Balearic Islands, Spain
| | - M Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Institut Mediterrani d'Estudis Avançats (CSIC-UIB) Palma de Mallorca, Balearic Islands, Spain
| | - M Garau
- Microbiology Service, Hospital Son Llàtzer Palma de Mallorca, Balearic Islands, Spain
| | - M D C Gallegos
- Microbiology Service, Hospital Son Llàtzer Palma de Mallorca, Balearic Islands, Spain
| | - D Guerrero
- Programme of Epidemiology and Clinical Research, Fundació Caubet-CIMERA Illes Balears, International Centre for Advanced Respiratory Medicine Bunyola, Balearic Islands, Spain
| | - J Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Institut Mediterrani d'Estudis Avançats (CSIC-UIB) Palma de Mallorca, Balearic Islands, Spain
| | - J B Soriano
- Programme of Epidemiology and Clinical Research, Fundació Caubet-CIMERA Illes Balears, International Centre for Advanced Respiratory Medicine Bunyola, Balearic Islands, Spain
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Sánchez D, Mulet M, Rodríguez AC, David Z, Lalucat J, García-Valdés E. Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2014; 37:89-94. [DOI: 10.1016/j.syapm.2013.09.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
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Scotta C, Gomila M, Mulet M, Lalucat J, García-Valdés E. Whole-cell MALDI-TOF mass spectrometry and multilocus sequence analysis in the discrimination of Pseudomonas stutzeri populations: three novel genomovars. Microb Ecol 2013; 66:522-532. [PMID: 23733171 DOI: 10.1007/s00248-013-0246-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/10/2013] [Indexed: 06/02/2023]
Abstract
Pseudomonas stutzeri is a widely distributed species with very high genetic diversity and metabolic capacities, occupying many diverse ecological niches. A collection of 229 P. stutzeri strains isolated from different habitats and geographical locations has been previously characterised phylogenetically by rpoD gene sequencing analysis and in the present study 172 of them phenotypically by whole-cell MALDI-TOF mass spectrometry. Fifty-five strains were further analysed by multilocus sequencing analysis to determine the phylogenetic population structure. Both methods showed coherence in strain grouping; 226 strains were allocated in the 18 genomovars known presently. The remaining three strains are proposed as references for three novel genomovars in the species. The correlation and usefulness of sequence-based phylogenetic analysis and whole-cell MALDI-TOF mass spectrometry, which are essential for autoecological studies in microbial ecology, is discussed for the differentiation of P. stutzeri populations.
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Affiliation(s)
- Claudia Scotta
- Microbiología, Departamento de Biología, Universidad de las Islas Baleares, 07122, Palma de Mallorca, Islas Baleares, Spain
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Gomila M, Del Carmen Gallegos M, Fernández-Baca V, Pareja A, Pascual M, Díaz-Antolín P, García-Valdés E, Lalucat J. Genetic diversity of clinical Pseudomonas aeruginosa isolates in a public hospital in Spain. BMC Microbiol 2013; 13:138. [PMID: 23773707 PMCID: PMC3706262 DOI: 10.1186/1471-2180-13-138] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 06/13/2013] [Indexed: 12/29/2022] Open
Abstract
Background Pseudomonas aeruginosa is an important nosocomial pathogen that exhibits multiple resistances to antibiotics with increasing frequency, making patient treatment more difficult. The aim of the study is to ascertain the population structure of this clinical pathogen in the Hospital Son Llàtzer, Spain. Results A significant set (56) of randomly selected clinical P. aeruginosa isolates, including multidrug and non-multidrug resistant isolates, were assigned to sequence types (STs) and compared them with their antibiotic susceptibility profile classified as follows: extensively drug resistant (XDR), multidrug resistant (MDR) and non-multidrug resistant (non-MDR). The genetic diversity was assessed by applying the multilocus sequence typing (MLST) scheme developed by Curran and collaborators, and by the phylogenetic analysis of a concatenated tree. The analysis of seven loci, acsA, aroE, guaA, mutL, nuoD, ppsA and trpE, demonstrated that the prevalent STs were ST-175, ST-235 and ST-253. The majority of the XDR and MDR isolates were included in ST-175 and ST-235. ST-253 is the third in frequency and included non-MDR isolates. The 26 singleton sequence types corresponded mainly to non-MDR isolates. Twenty-two isolates corresponded to new sequence types (not previously defined) of which 12 isolates were non-MDR and 10 isolates were MDR or XDR. Conclusions The population structure of clinical P. aeruginosa present in our hospital indicates the coexistence of nonresistant and resistant isolates with the same sequence type. The multiresistant isolates studied are grouped in the prevalent sequence types found in other Spanish hospitals and at the international level, and the susceptible isolates correspond mainly to singleton sequence types.
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Affiliation(s)
- Margarita Gomila
- Microbiología, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears 07198, Spain.
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Mulet M, García-Valdés E, Lalucat J. Phylogenetic affiliation of Pseudomonas putida biovar A and B strains. Res Microbiol 2013; 164:351-9. [DOI: 10.1016/j.resmic.2013.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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Mulet M, Gomila M, Scotta C, Sánchez D, Lalucat J, García-Valdés E. Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas. Syst Appl Microbiol 2013; 35:455-64. [PMID: 23140936 DOI: 10.1016/j.syapm.2012.08.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/31/2012] [Accepted: 08/10/2012] [Indexed: 10/27/2022]
Abstract
Multilocus sequence analysis (MLSA) is one of the most accepted methods for the phylogenetic assignation of Pseudomonas strains to their corresponding species. Furthermore, updated databases are essential for correct bacterial identification and the number of Pseudomonas species is increasing continuously. Currently, 127 species are validly described in Euzéby's List of Species with Standing in Nomenclature, and 29 novel species have been described since the publication of the last comprehensive MLSA phylogenetic study based on the sequences of the 16S rDNA, gyrB, rpoB and rpoD genes. Therefore, an update of the sequence database is presented, together with the analysis of the phylogeny of the genus Pseudomonas. Whole-cell matrix-assisted laser-desorption/ionization time-of-flight (WC-MALDI-TOF) mass spectrometry (MS) analysis has been applied very recently to the identification of bacteria and is considered to be a fast and reliable method. A total of 133 type strains of the recognized species and subspecies in the genus Pseudomonas, together with other representative strains, were analyzed using this new technique, and the congruence between the WC-MALDI-TOF MS and MLSA techniques was assessed for the discrimination and correct species identification of the strains. The utility of both methods in the identification of environmental and clinical strains is discussed.
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Affiliation(s)
- Magdalena Mulet
- Microbiología, Departamento de Biología, Universidad de las Islas Baleares, 07122 Palma de Mallorca, Islas Baleares, Spain
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Gomila M, Renom F, Gallegos MDC, Garau M, Guerrero D, Soriano JB, Lalucat J. Identification and diversity of multiresistant Corynebacterium striatum clinical isolates by MALDI-TOF mass spectrometry and by a multigene sequencing approach. BMC Microbiol 2012; 12:52. [PMID: 22475029 PMCID: PMC3348057 DOI: 10.1186/1471-2180-12-52] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 04/04/2012] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The genus Corynebacterium is composed of gram-positive bacteria that are widely distributed throughout the environment; these bacteria are also part of the normal microbiota of human skin and mucous membranes. Multiple studies have shown that species of this genus, including C. striatum, become pathogenic to humans under special conditions. Our aim was to determine the characteristics of clinical multiresistant strains of C. striatum that were isolated in our geographical region, to determine their diversity, and to compare them with the type strain and with related species. We studied fifty-two strains of C. striatum isolated from different hospitals from Mallorca, Spain, mainly from the Hospital Joan March in Bunyola, Mallorca. Most of the strains were isolated from sputum cultures of respiratory samples from patients with chronic obstructive pulmonary disease. To gain further insight into the genetic diversity of the strains, we analysed several housekeeping genes and other genes associated with antibiotic resistance. Strains were also characterised phenotypically by their antibiotic resistance profiles and by MALDI-TOF mass spectrometry analysis. RESULTS The ITS1 region, gyrA and rpoB were chosen as the appropriate genes in the C. striatum genome to study the genetic diversity of C. striatum species and to discriminate between strains. After analysing these three genes, four sequence types (ST2, ST4, ST1 and ST11) were found to be the most abundant. Splits tree analysis of the strains demonstrated that these clinical isolates did not share any alleles with the type strain of the species. Recombination was detected within all of the C. striatum isolates, and different clonal populations were detected within the samples. CONCLUSIONS Our results demonstrate that the isolates were best identified using gene-based molecular methods; using these methods, the isolated strains were determined to be different from the type strain of C. striatum. The ITS1 region and the gyrA and rpoB genes were selected because of their variability and were the most useful tools for discriminating between strains. The phenotype and antibiotype characteristics of the strains did not seem suitable for typing purposes. MALDI-TOF mass spectrometry can be a useful method for identifying and discriminating between C. striatum strains.
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Affiliation(s)
- Margarita Gomila
- Unidad de Investigación-Microbiología, Fundación Hospital Son Llàtzer, Ctra, Manacor, km, 4, 07198 Palma de Mallorca, Illes Balears, Spain.
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Scotta C, Mulet M, Sánchez D, Gomila M, Ramírez A, Bennasar A, García-Valdés E, Holmes B, Lalucat J. Identification and genomovar assignation of clinical strains of Pseudomonas stutzeri. Eur J Clin Microbiol Infect Dis 2012; 31:2133-9. [PMID: 22282021 DOI: 10.1007/s10096-012-1547-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/03/2012] [Indexed: 11/25/2022]
Abstract
The identification of Pseudomonas stutzeri clinical isolates through conventional phenotypic methods was compared with identification through partial rpoD gene sequencing. We observed that commercial phenotypic systems easily confuse P. stutzeri with other Pseudomonas species. We also demonstrated that most of the clinical strains of P. stutzeri herein studied (79%) belonged to genomovar 1 of the species. We propose the use of partial rpoD gene sequence analysis as a complementary molecular tool for the precise routine identification and genomovar assignation of P. stutzeri clinical isolates, as well as for typing and epidemiological studies.
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Affiliation(s)
- C Scotta
- Microbiología, Departamento de Biología, Universidad de las Islas Baleares, 07122, Palma de Mallorca, Islas Baleares, España.
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Gomila M, Tvrzová L, Teshim A, Sedláček I, González-Escalona N, Zdráhal Z, Šedo O, González JF, Bennasar A, Moore ERB, Lalucat J, Murialdo SE. Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol-contaminated soil. Int J Syst Evol Microbiol 2010; 61:2231-2237. [PMID: 20952547 DOI: 10.1099/ijs.0.025304-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic approach was applied to the study of a Gram-negative bacterium (B2(T)) isolated from soil by selective enrichment with pentachlorophenol. 16S rRNA gene sequence analysis of strain B2(T) showed that the strain belongs to the genus Achromobacter within the Betaproteobacteria. The 16S rRNA gene sequence displayed more than 99 % similarity to the sequences of the type strains of all species of Achromobacter, with the highest sequence similarity to those of Achromobacter spanius CCM 7183(T) and A. piechaudii CCM 2986(T) (99.8 %). On the basis of phylogenetic analysis, genomic DNA-DNA relatedness and phenotypic characteristics, including chemotaxonomic (cellular fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2(T) ( = CCM 7608(T) = CCUG 56371(T) = CECT 7342(T)).
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Affiliation(s)
- Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Ludmila Tvrzová
- Division of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 60200 Brno, Czech Republic
| | - Andrea Teshim
- Division of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 60200 Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, 60200 Brno, Czech Republic
| | - Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Zbyněk Zdráhal
- Division of Functional Genomics and Proteomics, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ondrej Šedo
- Division of Functional Genomics and Proteomics, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | | | - Antonio Bennasar
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.,Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Edward R B Moore
- Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Bacteriology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Silvia E Murialdo
- Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Buenos Aires, Argentina
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Bennasar A, Mulet M, Lalucat J, García-Valdés E. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species. BMC Microbiol 2010; 10:118. [PMID: 20409328 PMCID: PMC2873489 DOI: 10.1186/1471-2180-10-118] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. DESCRIPTION The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA) procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI). Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. CONCLUSIONS The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer-reviewed articles, and direct external links to more specialized strain information databases (StrainInfo) and GeneBank (NCBI). The PseudoMLSA is intended to provide helpful strain-sequence information for a better and more comprehensive discriminative multigenic sequence based analysis of this special group of bacteria, contributing to enhance our understanding of the evolution of Pseudomonas species.
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Affiliation(s)
- Antoni Bennasar
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Magdalena Mulet
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
- Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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Gomila M, Pinhassi J, Falsen E, Moore ERB, Lalucat J. Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae. Int J Syst Evol Microbiol 2010; 60:809-814. [DOI: 10.1099/ijs.0.011478-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, Gram-negative bacterium, strain KIN192T, isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA–DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192T (=CCUG 53117T =CECT 7319T).
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Affiliation(s)
- Margarita Gomila
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Jarone Pinhassi
- Marine Microbiology, Department of Pure and Applied Natural Sciences, University of Kalmar, SE-391 82 Kalmar, Sweden
| | - Enevold Falsen
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
| | - Edward R. B. Moore
- Sahlgrenska University Hospital, University of Göteborg, SE-413 46 Göteborg, Sweden
- CCUG – Culture Collection University of Göteborg, University of Göteborg, SE-413 46 Göteborg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
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Abstract
Partial sequences of four core 'housekeeping' genes (16S rRNA, gyrB, rpoB and rpoD) of the type strains of 107 Pseudomonas species were analysed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pseudomonas genus. Gene trees allowed the discrimination of two lineages or intrageneric groups (IG), called IG P. aeruginosa and IG P. fluorescens. The first IG P. aeruginosa, was divided into three main groups, represented by the species P. aeruginosa, P. stutzeri and P. oleovorans. The second IG was divided into six groups, represented by the species P. fluorescens, P. syringae, P. lutea, P. putida, P. anguilliseptica and P. straminea. The P. fluorescens group was the most complex and included nine subgroups, represented by the species P. fluorescens, P. gessardi, P. fragi, P. mandelii, P. jesseni, P. koreensis, P. corrugata, P. chlororaphis and P. asplenii. Pseudomonas rhizospherae was affiliated with the P. fluorescens IG in the phylogenetic analysis but was independent of any group. Some species were located on phylogenetic branches that were distant from defined clusters, such as those represented by the P. oryzihabitans group and the type strains P. pachastrellae, P. pertucinogena and P. luteola. Additionally, 17 strains of P. aeruginosa, 'P. entomophila', P. fluorescens, P. putida, P. syringae and P. stutzeri, for which genome sequences have been determined, have been included to compare the results obtained in the analysis of four housekeeping genes with those obtained from whole genome analyses.
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
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Lanfranconi MP, Christie-Oleza JA, MartÃn-Cardona CÃ, Suárez-Suárez LY, Lalucat J, Nogales B, Bosch R. Physiological role of NahW, the additional salicylate hydroxylase found inPseudomonas stutzeriAN10. FEMS Microbiol Lett 2009; 300:265-72. [DOI: 10.1111/j.1574-6968.2009.01787.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Vázquez S, Nogales B, Ruberto L, Hernández E, Christie-Oleza J, Lo Balbo A, Bosch R, Lalucat J, Mac Cormack W. Bacterial community dynamics during bioremediation of diesel oil-contaminated Antarctic soil. Microb Ecol 2009; 57:598-610. [PMID: 18685886 DOI: 10.1007/s00248-008-9420-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 06/19/2008] [Indexed: 05/26/2023]
Abstract
The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated using biostimulation with nutrients, and that this causes a change in the indigenous bacterial communities and in the genetic potential for hydrocarbon degradation.
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Affiliation(s)
- S Vázquez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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Mulet M, Bennasar A, Lalucat J, García-Valdés E. An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 2009; 23:140-7. [PMID: 19268522 DOI: 10.1016/j.mcp.2009.02.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Accepted: 02/12/2009] [Indexed: 11/30/2022]
Abstract
A polymerase chain reaction-based approach was developed for species identification of Pseudomonas strains and for the direct detection of Pseudomonas populations in their natural environment. A highly selective set of primers (PsEG30F and PsEG790R), giving an amplicon of 760 nucleotides in length, was designed based on the internal conserved sequences of 33 selected rpoD gene sequences (the sigma 70 factor subunit of the DNA polymerase) of Pseudomonas type strains, representing the entire intrageneric phylogenetic clusters described in the genus. The utility of the primer set was verified on 96 Pseudomonas type strains and on another 112 recognised Pseudomonas strains. The specificity of the primer set was also tested against strains from species not belonging to the genus Pseudomonas. These primers were also shown to be useful for the direct detection of Pseudomonas species in environmental DNA after a cloning procedure. These results were compared in parallel with other cloning procedures described previously, based on the analysis of other genes (16S rDNA and ITS1) and also by using primers designed for rpoD on sequences from gamma-proteobacteria. All of the cultured Pseudomonas strains tested could be amplified with these novel primers, indicating that this method is also a useful tool for the specific analysis of Pseudomonas populations from environmental samples without the need for cultivation.
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
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Gomila M, Ramirez A, Gascó J, Lalucat J. Mycobacterium llatzerense sp. nov., a facultatively autotrophic, hydrogen-oxidizing bacterium isolated from haemodialysis water. Int J Syst Evol Microbiol 2009; 58:2769-73. [PMID: 19060055 DOI: 10.1099/ijs.0.65857-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six mycobacterial isolates from haemodialysis water, conforming a homogeneous phylogenetic group in a previous multigenic analysis, were classified taxonomically. Physiological and biochemical characterization, as well as DNA-DNA hybridizations, demonstrated that the isolates were facultatively autotrophic, aerobic and hydrogen-oxidizing bacteria, representing a novel species in the rapid growing Mycobacterium group, for which the name Mycobacterium llatzerense sp. nov. is proposed. The type strain is MG13(T) (=CECT 7273(T)=CCUG 54744(T)).
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Affiliation(s)
- Margarita Gomila
- Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats CSIC, Palma de Mallorca, Illes Balears, Spain
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Mulet M, Gomila M, Gruffaz C, Meyer JM, Palleroni NJ, Lalucat J, Garcia-Valdes E. Phylogenetic analysis and siderotyping as useful tools in the taxonomy of Pseudomonas stutzeri: description of a novel genomovar. Int J Syst Evol Microbiol 2008; 58:2309-15. [DOI: 10.1099/ijs.0.65797-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Christie-Oleza JA, Nogales B, Martín-Cardona C, Lanfranconi MP, Albertí S, Lalucat J, Bosch R. ISPst9, an ISL3-like insertion sequence from Pseudomonas stutzeri AN10 involved in catabolic gene inactivation. Int Microbiol 2008; 11:101-110. [PMID: 18645960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A novel insertion sequence (IS), ISPst9, from Pseudomonas stutzeri AN10 was cloned and characterized. ISPst9 is a typical bacterial IS, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp AT-rich target duplications upon insertion. The sequence also contains a gene that encodes an active transposase (TnpA) with significant amino acid identity to members of the ISL3 family. Southern blot analysis of digested genomic DNA of strain AN10 and its 4-chlorosalicylate-degrading derivative strain AN142 demonstrated that native ISPst9 transposes in multiple copies, with one of them responsible for the nahH insertional inactivation observed in strain AN142. Precise excision of ISPst9 yielded NahH+ revertants of AN142 at high frequencies (up to 10-6). In vivo transposition, mainly in multiple copies, of an ISPst9 derivative containing a KmR cassette cloned into a suicide vector was also demonstrated. Hybridization experiments carried out with different strains of P. stutzeri and with 292 phylogenetically distinct environmental isolates suggested that the presence of an ISPst9-like IS occurs in diverse bacteria together with the presence of aromatic hydrocarbon-degrading determinants.
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Affiliation(s)
- Joseph A Christie-Oleza
- Microbiology, Department of Biology, University of the Balearic Islands, Palma, Mallorca, Spain
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Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J. Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water. Int J Syst Evol Microbiol 2008; 57:2629-2635. [PMID: 17978231 DOI: 10.1099/ijs.0.65149-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99% with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3% 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA-DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA-DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.
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Affiliation(s)
- Margarita Gomila
- Área Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
| | - Botho Bowien
- Abt. Molekularphysiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Enevold Falsen
- CCUG, Culture Collection University of Göteborg, Department of Clinical Bacteriology, 41346 Göteborg, Sweden
| | - Edward R B Moore
- CCUG, Culture Collection University of Göteborg, Department of Clinical Bacteriology, 41346 Göteborg, Sweden
| | - Jorge Lalucat
- Área Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
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Gomila M, Solis JJ, David Z, Ramon C, Lalucat J. Comparative reductions of bacterial indicators, bacteriophage-infecting enteric bacteria and enteroviruses in wastewater tertiary treatments by lagooning and UV-radiation. Water Sci Technol 2008; 58:2223-2233. [PMID: 19092200 DOI: 10.2166/wst.2008.584] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A two-year monitoring program of microbiological and physical-chemical parameters at 2 waste water treatment plants (WWTPs) in Mallorca (Spain) was performed in order to (1) evaluate the efficiency of lagooning and UV radiation as tertiary treatment processes; (2) determine the characteristics of wastewater effluent for its potential agricultural reuse; and (3) establish correlations between bacteriological and virological parameters. The presence of currently established bacterial indicators (total coliforms, faecal coliforms, Escherichia coli, enterococci, and spores of sulphite-reducing clostridia), virological (enteroviruses, somatic coliphages, F-specific coliphages, and phages infecting Bacteroides fragilis and Bacteroides thetaiotaomicron), and helminth eggs were tested during this study. Bacterial and viral indicators were removed at least with one log reduction in the lagooning system, and to a lesser extent with UV-radiation treatment. The lagooning system was less efficient in removing phages and viruses than were bacterial indicators, with the exception of F-specific phages. Phages of B. fragilis and B. thetaiotaomicron were less removed than all of the other microbiological parameters. In the UV-radiation treatment, however, the faecal coliforms proved the most sensitive, while clostridial spores, somatic coliphages, Bacteroides phages, and enteric viruses were the more resistant. Helminth eggs were not detected in any samples from effluents of either the secondary or tertiary treatments.Indicator levels in both treatments met the established regulations of both local and national authorities for the disposal or reuse of wastewater in irrigation for non-human crop. We demonstrate that somatic coliphages are effective indicators of enteric viruses in both of the WWTPs studied.
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Affiliation(s)
- Margarita Gomila
- Area Microbiologia, Departament de Biologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), 07122 Palma de Mallorca, Illes Balears, Spain
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Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J. Description of Roseateles aquatilis sp. nov. and Roseateles terrae sp. nov., in the class Betaproteobacteria, and emended description of the genus Roseateles. Int J Syst Evol Microbiol 2008; 58:6-11. [DOI: 10.1099/ijs.0.65169-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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