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Carrasco V, Roldán DM, Valenzuela-Ibaceta F, Lagos-Moraga S, Dietz-Vargas C, Menes RJ, Pérez-Donoso JM. Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., two new species with the ability to degrade TNT isolated from soil samples at Deception Island, maritime Antarctica. Arch Microbiol 2023; 206:39. [PMID: 38142428 DOI: 10.1007/s00203-023-03768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Two motile, rod-shaped, Gram-stain-negative bacterial strains, TNT11T and TNT19T, were isolated from soil samples collected at Deception Island, Antarctica. According to the 16S rRNA gene sequence similarity, both strains belong to the genus Pseudomonas. Further genomic analyses based on ANI and dDDH suggested that these strains were new species. Growth of strain TNT11T is observed at 0-30 ℃ (optimum, 20 ℃), pH 4.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum, 1% NaCl), while for TNT19T is observed at 0-30 ℃ (optimum between 15 and 20 ℃), pH 5.0-9.0 (optimum, pH 6.0) and in the presence of 0-5.0% NaCl (optimum between 0 and 1% NaCl). The fatty acid profile consists of the major compounds; C16:0 and C16:1 ω6 for TNT11T, and C16:0 and C12:0 for TNT19T. Based on the draft genome sequences, the DNA G + C content for TNT11T is 60.43 mol% and 58.60 mol% for TNT19T. Based on this polyphasic study, TNT11T and TNT19T represent two novel species of the genus Pseudomonas, for which the proposed names are Pseudomonas violetae sp. nov. and Pseudomonas emilianonis sp. nov., respectively. The type strains are Pseudomonas violetae TNT11T (= RGM 3443T = LMG 32959T) and Pseudomonas emilianonis TNT19T (= RGM 3442T = LMG 32960T). Strains TNT11T and TNT19T were deposited to CChRGM and BCCM/LMG with entry numbers RGM 3443/LMG 32959 and RGM 3442/LMG 32960, respectively.
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Affiliation(s)
- Valentina Carrasco
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, Universidad Andres Bello, Av. República 330, Santiago, Chile
| | - Diego M Roldán
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - Felipe Valenzuela-Ibaceta
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, Universidad Andres Bello, Av. República 330, Santiago, Chile
| | - Sebastián Lagos-Moraga
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, Universidad Andres Bello, Av. República 330, Santiago, Chile
| | - Claudio Dietz-Vargas
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, Universidad Andres Bello, Av. República 330, Santiago, Chile
| | - Rodolfo Javier Menes
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, Universidad Andres Bello, Av. República 330, Santiago, Chile.
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Duman M, Altun S, Saticioglu IB, Romalde JL. A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022. JOURNAL OF FISH DISEASES 2023. [PMID: 37965781 DOI: 10.1111/jfd.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Jesús L Romalde
- Cross-disciplinary Research Center in Environmental Technologies (CRETUS), Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Sorty AM, Zervas A, García de Salamone IE, Nelson LM, Stougaard P. Pseudomonas hormoni sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37889848 DOI: 10.1099/ijsem.0.006119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Abstract
Bacterial strain G20-18T was previously isolated from the rhizosphere of an Arctic grass on Ellesmere Island, Canada and was characterized and described as Pseudomonas fluorescens. However, new polyphasic analyses coupled with phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 5-25 °C (optimum, 20-25 °C), at pH 5-9 (optimum, pH 6-7) and with 0-4 % NaCl (optimum, 2 % NaCl). The major fatty acids are C16 : 0 (35.6 %), C17 : 0 cyclo ω7c (26.3 %) and summed feature C18 : 1/C18 : 1 ω7c (13.6 %). The respiratory quinones were determined to be Q9 (93.5 %) and Q8 (6.5 %) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain G20-18T was shown to synthesize cytokinin and auxin plant hormones and to produce 1-aminocyclopropane-1-carboxylate deaminase. The DNA G+C content was determined to be 59.1 mol%. Phylogenetic analysis based on the 16S rRNA gene and multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) showed that G20-18T was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas. Comparisons of the G20-18T genome sequence and related Pseudomonas type strain sequences showed an average nucleotide identity value of ≤93.6 % and a digital DNA-DNA hybridization value of less than 54.4 % relatedness. The phenotypic, phylogenetic and genomic data support the hypothesis that strain G20-18T represents a novel species of the genus Pseudomonas. As strain G20-18T produces or modifies hormones, the name Pseudomonas hormoni sp. nov. is proposed. The type strain is G20-18T (=LMG 33086T=NCIMB 15469T).
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Affiliation(s)
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | - Louise M Nelson
- Biology Department, University of British Columbia, Vancouver, Canada
| | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Hu YQ, Zeng YX, Du Y, Zhao W, Li HR, Han W, Hu T, Luo W. Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments. BMC Genomics 2023; 24:534. [PMID: 37697269 PMCID: PMC10494350 DOI: 10.1186/s12864-023-09638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Biological denitrification has been commonly adopted for the removal of nitrogen from sewage effluents. However, due to the low temperature during winter, microorganisms in the wastewater biological treatment unit usually encounter problems such as slow cell growth and low enzymatic efficiency. Hence, the isolation and screening of cold-tolerant aerobic denitrifying bacteria (ADB) have recently drawn attention. In our previous study, two Pseudomonas strains PMCC200344 and PMCC200367 isolated from Arctic soil demonstrated strong denitrification ability at low temperatures. The two Arctic strains show potential for biological nitrogen removal from sewage in cold environments. However, the genome sequences of these two organisms have not been reported thus far. RESULTS Here, the basic characteristics and genetic diversity of strains PMCC200344 and PMCC200367 were described, together with the complete genomes and comparative genomic results. The genome of Pseudomonas sp. PMCC200344 was composed of a circular chromosome of 6,478,166 bp with a G + C content of 58.60% and contained a total of 5,853 genes. The genome of Pseudomonas sp. PMCC200367 was composed of a circular chromosome of 6,360,061 bp with a G + C content of 58.68% and contained 5,801 genes. Not only prophages but also genomic islands were identified in the two Pseudomonas strains. No plasmids were observed. All genes of a complete set of denitrification pathways as well as various putative cold adaptation and heavy metal resistance genes in the genomes were identified and analyzed. These genes were usually detected on genomic islands in bacterial genomes. CONCLUSIONS These analytical results provide insights into the genomic basis of microbial denitrification in cold environments, indicating the potential of Arctic Pseudomonas strains in nitrogen removal from sewage effluents at low temperatures.
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Affiliation(s)
- Yong-Qiang Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Yin-Xin Zeng
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yu Du
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Wei Zhao
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Hui-Rong Li
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Wei Han
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Ting Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China
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Saticioglu IB, Ay H, Altun S, Karakaya E, Gunduz ES, Aydogdu D, Yarim D, Erkek N, Duman M. Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss). Antonie Van Leeuwenhoek 2023; 116:291-302. [PMID: 36586048 DOI: 10.1007/s10482-022-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Duygu Aydogdu
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Dogancan Yarim
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Neslihan Erkek
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
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Pseudomonas citri sp. nov., a potential novel plant growth promoting bacterium isolated from rhizosphere soil of citrus. Antonie Van Leeuwenhoek 2023; 116:281-289. [PMID: 36596938 DOI: 10.1007/s10482-022-01803-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023]
Abstract
A novel potential plant growth promoting bacterium, designated OPS13-3T, was isolated from rhizosphere soil of citrus in Aotou Town of Guangzhou, Guangdong Province, PR China. It showed high ability to dissolve insoluble inorganic phosphate and organic phosphorus and to produce 3-indoleacetic acid (IAA) and siderophore. Cells of the novel strain were Gram-stain-negative, rod-shaped, aerobic and motile with polar flagellum. It shared the highest 16S rRNA gene similarity with Pseudomonas mucoides CCUG 74874T (98.7%) and P. bijieensis LMG 31948T (98.7%). Phylogenetic analyses based the 16S rRNA gene and genome sequences revealed that strain OPS13-3T belonged to the genus Pseudomonas, and was most closely related to P. mediterranea ICMP 14184T and P. corrugate ICMP 5819T. The average nucleotide identity (ANI) and DNA-DNA hybridization (dDDH) values between the novel strain and closely relatives with high 16S rRNA gene similarities were 80.8‒87.5% and 24.7‒34.6%, respectively, which were much below the threshold values for species delimitation. The major fatty acids included C16:0, C10:0 3-OH and summed feature 3 (C16:1ω7c and/or C16:1ω6c). It took ubiquinone 9 as the predominant respiratory quinone and the polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), three unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenetic, phenotypic and chemotaxonomic analyses and genome comparison, strain OPS13-3T should be considered as a novel species of the genus Pseudomonas, for which the name Pseudomonas citri sp. nov. is proposed (type strain OPS13-3T = GDMCC 1.3118T = JCM 35385T).
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
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Ntana F, Hennessy RC, Zervas A, Stougaard P. Pseudomonas nunensis sp. nov. isolated from a suppressive potato field in Greenland. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749687 DOI: 10.1099/ijsem.0.005700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The bacterial strain In5T was previously isolated from a suppressive potato field in southern Greenland and has been characterized and described as Pseudomonas fluorescens. However, the results of new polyphasic analyses coupled with those of phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 4-28 °C (optimum temperature 20-25 °C) and at pH 5-9 (optimum pH 6-7). Major fatty acids were C16 : 0 (38.2 %), a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c) (20.7 %), C17 : 0cyclo ω7c (14.3 %) and a summed feature consisting of C18 : 1ω6c and/or C18 : 1ω7c (11.7 %). The respiratory quinones were determined to be Q9 (95.5 %) and Q8 (4.5 %) and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was determined to be 59.4 mol%. The results of phylogenetic analysis based on the 16S rRNA gene and multi-locus sequence analysis (MLSA; concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) indicated that In5T was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas. Comparison of the genome sequence of In5T and those of related type strains of species of the genus Pseudomonas revealed an average nucleotide identity (ANI) of 87.7 % or less and digital DNA-DNA hybridization (dDDH) of less than 34.5 % relatedness, respectively. Two more strains, In614 and In655, isolated from the same suppressive soil were included in the genome analysis. The ANI and dDDH of In614 and In655 compared with In5T were ANI: 99.9 and 97.6 and dDDH (GGDC) 99.9 and 79.4, respectively, indicating that In5T, In614 and In655 are representatives of the same species. The results of the phenotypic, phylogenetic and genomic analyses support the hypothesis that strain In5T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nunensis sp. nov. is proposed. The type strain is In5T(=LMG 32653T=NCIMB 15428T).
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Affiliation(s)
- Fani Ntana
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Rosanna C Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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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] [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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