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Cueva-Yesquén LG, Sartoratto A, da Silva Santos A, de Melo IS, Fantinatti-Garboggini F. Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata. Sci Rep 2024; 14:14285. [PMID: 38902258 PMCID: PMC11190252 DOI: 10.1038/s41598-024-64349-1] [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: 07/21/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
A polyphasic approach was applied to characterize taxonomically a novel endophytic bacterial strain, designated as EP178T, which was previously isolated from Passiflora incarnata leaves and characterized as plant-growth promoter. The strain EP178T forms Gram stain-negative and rod-shaped cells, and circular and yellow-pigmented colonies. Its growth occurs at 10-37 °C, at pH 6.0-8.0, and tolerates up to 7% (w/v) NaCl. The major cellular fatty acids found were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω6c /C16:1 ω7c), and C16:0, and the predominant ubiquinone was Q-9. The phylogenetic and nucleotide-similarity analysis with 16S rRNA gene sequences showed that strain EP178T belongs to Pseudomonas genus. The genomic-based G + C content was 65.5%. The average nucleotide identity and digital DNA-DNA hybridization values between strains EP178T and the closest type strain, P. oryzihabitans DSM 6835T, were 92.6% and 52.2%, respectively. Various genes associated with plant-growth promoting mechanisms were annotated from genome sequences. Based on the phenotypic, genomic, phylogeny and chemotaxonomic data, strain EP178T represents a new species of the genus Pseudomonas, for which the name Pseudomonas flavocrustae sp. nov. was proposed. The type strain is EP178T (= CBMAI 2609T = ICMP 24844T = MUM 23.01T).
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Affiliation(s)
- Luis Gabriel Cueva-Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
- Division of Microbial Resources, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil.
| | - Adilson Sartoratto
- Division of Organic and Pharmaceutical Chemical, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil
| | - Adriana da Silva Santos
- Division of Organic and Pharmaceutical Chemical, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Fabiana Fantinatti-Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
- Division of Microbial Resources, Research Center for Agriculture, Biological and Chemical, University of Campinas, Paulínia, SP, Brazil.
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Kundlacz C, Aldeia C, Eddoubaji Y, Campos-Madueno EI, Endimiani A. Complete genome sequence of Pseudomonas canadensis strain Pcan-CK-23 isolated from Zophobas morio larvae. Microbiol Resour Announc 2024; 13:e0002324. [PMID: 38682776 PMCID: PMC11237626 DOI: 10.1128/mra.00023-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
We present the complete genome sequence of Pseudomonas canadensis. The strain (Pcan-CK-23) was isolated from Zophobas morio (superworm) larvae. The genome consisted of a 6,424,469 bp chromosome with a GC content of 60.3% and 5,973 genes. Pcan-CK-23 can be used as a reference genome for further studies with P. canadensis.
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Affiliation(s)
- Cindy Kundlacz
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Yasmine Eddoubaji
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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3
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Gladysh NS, Bogdanova AS, Kovalev MA, Krasnov GS, Volodin VV, Shuvalova AI, Ivanov NV, Popchenko MI, Samoilova AD, Polyakova AN, Dmitriev AA, Melnikova NV, Karpov DS, Bolsheva NL, Fedorova MS, Kudryavtseva AV. Culturable Bacterial Endophytes of Wild White Poplar ( Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential. BIOLOGY 2023; 12:1519. [PMID: 38132345 PMCID: PMC10740426 DOI: 10.3390/biology12121519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology.
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Affiliation(s)
- Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Vsevolod V. Volodin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anastasia I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Nikita V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Geography, Russian Academy of Sciences, Staromonetny Pereulok, 29/4, 119017 Moscow, Russia
| | - Aleksandra D. Samoilova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Aleksandra N. Polyakova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Dmitry S. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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Shi Z, Guo X, Lei Z, Wang Y, Yang Z, Niu J, Liang J. Screening of high-efficiency nitrogen-fixing bacteria from the traditional Chinese medicine plant Astragalus mongolicus and its effect on plant growth promotion and bacterial communities in the rhizosphere. BMC Microbiol 2023; 23:292. [PMID: 37845638 PMCID: PMC10578054 DOI: 10.1186/s12866-023-03026-1] [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: 05/27/2023] [Accepted: 09/20/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Astragalus mongolicus Bunge is used in traditional Chinese medicine and is thus cultivated in bulk. The cultivation of A. mongolicus requires a large amount of nitrogen fertilizer, increasing the planting cost of medicinal materials and polluting the environment. Isolation and screening of plant growth-promoting rhizobacteria (PGPR) and exploring the nitrogen fixation potential of A. mongolicus rhizosphere microorganisms would effectively reduce the production cost of A. mongolicus. RESULTS This study used A. mongolicus roots and rhizosphere soil samples from Longxi County of Gansu Province, Jingle County, and Hunyuan County of Shanxi Province, China, to isolate and identify nitrogen-fixing bacteria. Through nitrogen fixation efficiency test, single strain inoculation test, and plant growth-promoting characteristics, three strains, Bacillus sp. J1, Arthrobacter sp. J2, and Bacillus sp. G4 were selected from 86 strains of potential nitrogen-fixing bacteria, which were the most effective in promoting the A. mongolicus growth and increasing the nitrogen, phosphorus, and potassium content in plants. The antagonistic test showed that these bacteria could grow smoothly under the co-culture conditions. The J1, J2, and G4 strains were used in a mixed inoculum and found to enhance the biomass of A. mongolicus plants and the accumulation of the main medicinal components in the field experiment. Mixed bacterial agent inoculation also increased bacterial diversity and changed the structure of the bacterial community in rhizosphere soil. Meanwhile, the relative abundance of Proteobacteria increased significantly after inoculation, suggesting that Proteobacteria play an important role in plant growth promotion. CONCLUSIONS These findings indicate that specific and efficient PGPRs have a significant promoting effect on the growth of A. mongolicus, while also having a positive impact on the structure of the host rhizosphere bacteria community. This study provides a basis for developing a nitrogen-fixing bacterial fertilizer and improving the ecological planting efficiency of A. mongolicus.
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Affiliation(s)
- Zhiyong Shi
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xu Guo
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Zhenhong Lei
- Shanxi Zhendong Pharmaceutical (China), Changzhi, 047000, China
| | - Yuanyuan Wang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Zhenyu Yang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Jingping Niu
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Jianping Liang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
- Shanxi Key Laboratory of Chinese Veterinary Medicine Modernization, Shanxi Agricultural University, Jinzhong, 030801, China.
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Tambong JT, Xu R, Chi SI, Birugu I, Bachelet S, Hutter C, Duceppe MO, Brière S. Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326615 DOI: 10.1099/ijsem.0.005890] [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: 06/17/2023] Open
Abstract
Four bacterial strains (S1Bt3, S1Bt7, S1Bt30 and S1Bt42T) isolated from soil collected from the rhizosphere of a native legume, Amphicarpaea bracteata, were investigated using a polyphasic approach. Colonies were fluorescent, white-yellowish, circular and convex with regular margins on King's B medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming rods. Oxidase- and catalase-positive. The optimal growth temperature of the strains was 37 °C. Phylogenetic analysis of the 16S rRNA gene sequences placed the strains within the genus Pseudomonas. Analysis of the 16S rRNA-rpoD-gyrB concatenated sequences clustered the strains and well separated from Pseudomonas rhodesiae CIP 104664T and Pseudomonas grimontii CFM 97-514T with the type strains of the closest species. Phylogenomic analysis of 92 up-to-date bacterial core gene and matrix-assisted laser desorption/ionization-time-of-flight MS biotyper data confirmed the distinct clustering pattern of these four strains. Digital DNA-DNA hybridization (41.7 %-31.2 %) and average nucleotide identity (91.1 %-87.0 %) values relative to closest validly published Pseudomonas species were below the species delineation thresholds of 70 and 96 %, respectively. Fatty acid composition results validated the taxonomic position of the novel strains in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests differentiated the novel strains from closely related Pseudomonas species. In silico prediction of secondary metabolite biosynthesis gene clusters in the whole-genome sequences of the four strains revealed the presence of 11 clusters involved in the production of siderophore, redox-cofactor, betalactone, terpene, arylpolyene and nonribosomal peptides. Based on phenotypic and genotypic data, strains S1Bt3, S1Bt7, S1Bt30 and S1Bt42T represent a novel species for which the name Pseudomonas quebecensis sp. nov. is proposed. The type strain is S1Bt42T (=DOAB 746T=LMG 32141T=CECT 30251T). The genomic DNA G+C content is 60.95 mol%.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvia I Chi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Canadian Blood Services, Ottawa, Ontario, Canada
| | - Isabelle Birugu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvia Bachelet
- Ottawa Plant Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Conrad Hutter
- Ottawa Plant Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Marc-Olivier Duceppe
- Ottawa Plant Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Stephan Brière
- Ottawa Plant Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
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Ghasemi S, Harighi B, Ashengroph M. Biosynthesis of silver nanoparticles using Pseudomonas canadensis, and its antivirulence effects against Pseudomonas tolaasii, mushroom brown blotch agent. Sci Rep 2023; 13:3668. [PMID: 36871050 PMCID: PMC9985599 DOI: 10.1038/s41598-023-30863-x] [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: 01/05/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
This study reports the biosynthesis of silver nanoparticles (AgNPs) using a Pseudomonas canadensis Ma1 strain isolated from wild-growing mushrooms. Freshly prepared cells of P. canadensis Ma1 incubated at 26-28 °C with a silver nitrate solution changed to a yellowish brown color, indicating the formation of AgNPs, which was confirmed by UV-Vis spectroscopy, scanning electron microscopy (SEM), and X-ray diffraction. SEM analysis showed spherical nanoparticles with a distributed size mainly between 21 and 52 nm, and the XRD pattern revealed the crystalline nature of AgNPs. Also, it provides an evaluation of the antimicrobial activity of the biosynthesized AgNPs against Pseudomonas tolaasii Pt18, the causal agent of mushroom brown blotch disease. AgNPs were found to be bioactive at 7.8 μg/ml showing a minimum inhibitory concentration (MIC) effect against P. tolaasii Pt18 strain. AgNPs at the MIC level significantly reduced virulence traits of P. tolaasii Pt18 such as detoxification of tolaasin, various motility behavior, chemotaxis, and biofilm formation which is important for pathogenicity. Scanning electron microscopy (SEM) revealed that bacterial cells treated with AgNPs showed a significant structural abnormality. Results showed that AgNPs reduced brown blotch symptoms in vivo. This research demonstrates the first helpful use of biosynthesized AgNPs as a bactericidal agent against P. tolaasii.
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Affiliation(s)
- Samira Ghasemi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Behrouz Harighi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Morahem Ashengroph
- Department of Biological Sciences, Faculty of Sciences, University of Kurdistan, Sanandaj, Iran
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Tambong JT, Xu R, Cuppels D, Chapados J, Gerdis S, Eyres J, Koziol A, Dettman J. Whole-Genome Resources and Species-Level Taxonomic Validation of 89 Plant-Pathogenic Xanthomonas Strains Isolated from Various Host Plants. PLANT DISEASE 2022; 106:1558-1565. [PMID: 35100028 DOI: 10.1094/pdis-11-21-2498-sc] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacterial spot disease caused by Xanthomonas spp. is a global threat to tomato and pepper plants. A recent classification of these pathogens indicated the need for a diverse dataset of whole-genome resources. We report whole-genome resources of 89 Xanthomonas strains isolated from Canada (n = 44), the United States (n = 29), Argentina (n = 4), Brazil (n = 3), Costa Rica (n = 3), New Zealand (n = 1), Australia (n = 1), Mexico (n = 1), Taiwan (n = 1), Thailand (n = 1), and unknown (n = 1). Of these strains, 48 were previously identified to species-level based on nongenome-based approaches while 41 strains were classified only at the genus level. The average coverage of the sequencing reads was 103×. The draft genome sizes ranged from 4.53 to 5.46 Mbp with a G + C content of 63.53 to 67.78% and comprised 4,233-5,178 protein-coding sequences. Using average nucleotide identity (ANI) and genome-based DNA-DNA hybridization (gDDH) values, the taxonomic classifications were validated for 38 of the 48 strains previously assigned to species level using other methods. Ten strains previously identified as Xanthomonas campestris, X. axonopodis, X. vasicola, and X. arboricola were incorrectly assigned, and new species-level delineations are proposed. Data from ANI, gDDH, and pangenome phylogeny of shared protein families were used to assign the 41 strains, previously identified only to genus level, into five distinct species: X. euvesicatoria (pv. euvesicatoria or pv. perforans), X. hortorum pv. gardneri, X. vesicatoria, X. campestris, and X. arboricola. These 89 whole-genome sequences of Xanthomonas strains, the majority (49.4%) of which are from Canada, could be useful resources in our understanding of the global population structure and evolution of these pathogens.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Diane Cuppels
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada (Retired)
| | - Julie Chapados
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jackson Eyres
- BICoE, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Adam Koziol
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Tambong JT, Xu R, Cuppels D, Chapados J, Gerdis S, Eyres J, Koziol A, Dettman J. Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato Isolated Between 1992 and 2008 Reveals Achromobactin Virulence Cluster that Is Absent in the Reference Strain DC3000. PHYTOPATHOLOGY 2022; 112:968-972. [PMID: 34543057 DOI: 10.1094/phyto-08-21-0353-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Diane Cuppels
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada (Retired)
| | - Julie Chapados
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jackson Eyres
- BICoE, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Adam Koziol
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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9
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Ilahi H, Hsouna J, Ellouze W, Gritli T, Chihaoui SA, Barhoumi F, Najib Elfeddy M, Bachkouel S, Ouahmane L, Tambong JT, Mnasri B. Phylogenetic study of rhizobia nodulating pea (Pisum sativum) isolated from different geographic locations in Tunisia. Syst Appl Microbiol 2021; 44:126221. [PMID: 34119907 DOI: 10.1016/j.syapm.2021.126221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Nodulated Pisum sativum plants showed the presence of native rhizobia in 16 out of 23 soil samples collected especially in northern and central Tunisia. A total of 130 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, dnaK and glnII) assigned 35 isolates to Rhizobium laguerreae, R. ruizarguesonis, Agrobacterium radiobacter, Ensifer meliloti and two putative genospecies. R. laguerreae was the most dominant species nodulating P. sativum with 63%. The isolates 21PS7 and 21PS15 were assigned to R. ruizarguesonis, and this is the first report of this species in Tunisia. Two putative new lineages were identified, since strains 25PS6, 10PS4 and 12PS15 clustered distinctly from known rhizobia species but within the R. leguminosarum complex (Rlc) with the most closely related species being R. indicum with 96.4% sequence identity. Similarly, strains 16PS2, 3PS9 and 3PS18 showed 97.4% and 97.6% similarity with R. sophorae and R. laguerreae, respectively. Based on 16S-23S intergenic spacer (IGS) fingerprinting, there was no clear association between the strains and their geographic locations. According to nodC and nodA phylogenies, strains of Rlc species and, interestingly, strain 8PS18 identified as E. meliloti, harbored the symbiotic genes of symbiovar viciae and clustered in two different clades showing heterogeneity within the symbiovar. All these strains nodulated and fixed nitrogen with pea plants. However, the strains belonging to A. radiobacter and the two remaining strains of E. meliloti were unable to nodulate P. sativum, suggesting that they were non-symbiotic strains. The results of this study further suggest that the Tunisian Rhizobium community is more diverse than previously reported.
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Affiliation(s)
- Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario L0R 2E0, Canada
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Mohamed Najib Elfeddy
- Phytobacteriology Laboratory, Plant Protection Research Unit, CRRA Marrakesh, National Institute for Agronomical Research, Marrakesh 40000, Morocco
| | - Sarra Bachkouel
- Research Support and Technology Transfer Unity, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - James T Tambong
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia.
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10
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Tambong JT, Xu R, Gerdis S, Daniels GC, Chabot D, Hubbard K, Harding MW. Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. Front Microbiol 2021; 12:666689. [PMID: 34093484 PMCID: PMC8170138 DOI: 10.3389/fmicb.2021.666689] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3CT = DOAB 1063T = CECT 30248T = LMG 32139T), Pseudomonas triticumensis sp. nov. (type strain 32L3AT = DOAB 1067T = CECT 30249T = LMG 32140T) and Pseudomonas foliumensis sp. nov. (type strain 10L4BT = DOAB 1069T = CECT 30250T = LMG 32142T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Greg C Daniels
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael W Harding
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
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11
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Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L. Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Int J Syst Evol Microbiol 2021; 71. [PMID: 33480838 DOI: 10.1099/ijsem.0.004652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a project focusing on the diversity of meat microbiota associated with beef ripening, a Pseudomonas strain was isolated exhibiting high 16S rRNA gene sequence similarities (>99 %) to Pseudomonas carnis DSM 107652T, P. lactis DSM 29167T, P. paralactis DSM 29164T and P. azotoformans DSM 18862T. Phylogenetic analysis of the complete rpoB gene sequences of the isolate V5/DAB/2/5T indicated a separate branch with about 99.0 % nucleotide identities to the closest relatives P. carnis DSM 107652T, P. lactis DSM 29167T and P. paralactis DSM 29164T, while average nucleotide identities (ANIb) calculated from the draft genomes were 94.8, 94.2 and 90.2 %, respectively. Pairwise genome-to-genome distance calculations (GGDC) resulted in values of 67.7, 63.5 and 45.7 %, respectively, lying below the actual species demarcation line as well. A second isolate, UBT403, was detected some years later by using matrix-assisted laser desorption ionization-time of flight MS of the microbiota of minced beef. The fatty acid profile of V5/DAB/2/5T consisted of C16 : 0, summed feature C 16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c, C17 : 0 cyclo, C12 : 0, C12 : 0 3-OH, C10 : 0 3-OH and C12 : 0 2-OH. The major cellular lipids were aminopholipids, phospholipids, phosphatidylethanolamine and phosphatidylglycerol; the major quinone was Q9 with a minor proportion of Q8. Based on phenotypic and chemotaxonomic characterizations, the isolates can be considered as representing a novel species, for which the name Pseudomonas paracarnis sp. nov. is proposed. The type strain is V5/DAB/2/5T (=DSM 111363T=LMG 31846T); a second strain is UBT403 (=DSM 111362=LMG 31847).
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Affiliation(s)
- Sonja Lick
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Annika Winkler
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- Chair of Bioanalytical Sciences and Food Analysis, University Bayreuth, Universitätsstraße 30, D-95447 Bayreuth and Max Rubner-Institut, E.C.-Baumann Straße 20, D-95326 Kulmbach, Germany.,Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Lothar Kröckel
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
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12
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Hofmann K, Woller A, Huptas C, Wenning M, Scherer S, Doll EV. Pseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream. Int J Syst Evol Microbiol 2020; 71. [PMID: 33289627 DOI: 10.1099/ijsem.0.004597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106T and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106T was most closely related to Pseudomonas nabeulensis CECT 9765T and Pseudomonas kairouanensis CECT 9766T. The G+C content of strain WS 5106T was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas, with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106T (=DSM 111143T=LMG 31863T) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.
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Affiliation(s)
- Katharina Hofmann
- Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Alexandra Woller
- Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Christopher Huptas
- Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Mareike Wenning
- Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764 Oberschleißheim, Germany.,Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Siegfried Scherer
- Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Etienne V Doll
- Chair of Microbial Ecology, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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13
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Analysis of Draft Genome Sequences of Two New Pantoea Strains Associated with Wheat Leaf Necrotic Tissues Caused by Xanthomonas translucens Reveals Distinct Species. Microbiol Resour Announc 2020; 9:9/30/e00638-20. [PMID: 32703837 PMCID: PMC7378036 DOI: 10.1128/mra.00638-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report whole-genome sequences of two new Pantoea strains (DOAB1048 and DOAB1050) isolated from necrotic wheat leaves caused by Xanthomonas translucens. The draft genome sequences of DOAB1048 and DOAB1050 consist of 52 and 57 scaffolds and have sizes of 4,795,525 bp and 4,962,883 bp with 4,418 and 4,517 coding sequences, respectively. We report whole-genome sequences of two new Pantoea strains (DOAB1048 and DOAB1050) isolated from necrotic wheat leaves caused by Xanthomonas translucens. The draft genome sequences of DOAB1048 and DOAB1050 consist of 52 and 57 scaffolds and have sizes of 4,795,525 bp and 4,962,883 bp with 4,418 and 4,517 coding sequences, respectively.
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14
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Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 2020; 70:2339-2347. [DOI: 10.1099/ijsem.0.004043] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains, WS 5063T and WS 5067, isolated from raw cow’s milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown,
Pseudomonas
species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel
Pseudomonas
species. It was most closely related to
Pseudomonas synxantha
DSM 18928T with an ANIm of 91.4 %. The DNA G+C content of WS 5063T was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4–34 °C and at pH values of pH 5.5–8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for
Pseudomonas
species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063T (=DSM 108987T=LMG 31232T) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).
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15
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Ramírez-Bahena MH, Salazar S, Santín PJ, Sánchez-Rodríguez JA, Fernández-Pascual M, Igual JM, Santa-Regina I, Peix Á. Pseudomonas edaphica sp. nov., isolated from rhizospheric soil of Cistus ladanifer L. in Spain. Int J Syst Evol Microbiol 2019; 69:3141-3147. [PMID: 31334698 DOI: 10.1099/ijsem.0.003603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study on biodiversity of bacteria inhabiting rhizospheric soil of rockrose (Cistus ladanifer L.), we isolated a strain coded RD25T in a soil from Northern Spain. The 16S rRNA gene sequence showed 99.5 % identity with respect to the closest related species Pseudomonas brenneri DSM15294T, and 99.4 % with respect to P. paralactis WS4672T. The following related Pseudomonas species showed 99.3 % or less identity, and therefore RD25T was classified within genus Pseudomonas. The phylogenetic analysis of 16S rRNA and the housekeeping genes rpoB, rpoD and gyrB suggested that this strain could be a novel species. The strain RD25T has several polar-subpolar flagella. It can grow at 36 °C, at 0-6 % NaCl concentration and a range of pH 5-9. Positive for arginine dihydrolase and urease production, and negative for reduction of nitrate. The strain is catalase and oxidase positive. Major fatty acids are C16 : 1 ω7c / C16 : 1 ω6c in summed feature 3, C16 : 0, and C18 : 1 ω7c / C18 : 1 ω6c in summed feature 8. The respiratory ubiquinone is Q9. The DNA G+C content was 59.9 mol%. The digital DNA-DNA hybridisation average values (dDDH) ranged between 30-61.2 % relatedness and the ANIb values ranged between 93.9-80.5 % with respect to the type strains of the closely related species. Therefore, the genotypic, genomic, phenotypic and chemotaxonomic data support the classification of strain RD25 as a novel species of genus Pseudomonas, for which the name P. edaphica sp. nov. is proposed. The type strain is RD25T (=LMG 30152T=CECT 9373T).
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Affiliation(s)
- Martha Helena Ramírez-Bahena
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC).,Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | - Sergio Salazar
- Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | | | | | | | - José Mariano Igual
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC).,Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | - Ignacio Santa-Regina
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC).,Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología. IRNASA-CSIC, Salamanca, Spain.,Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC)
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16
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Tchagang CF, Xu R, Overy D, Blackwell B, Chabot D, Hubbard K, Doumbou CL, Bromfield ESP, Tambong JT. Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov. Heliyon 2018; 4:e00761. [PMID: 30186983 PMCID: PMC6120581 DOI: 10.1016/j.heliyon.2018.e00761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 11/15/2022] Open
Abstract
Bacteria associated with corn roots inoculated with soils collected from the Canadian woodlands were isolated and characterized. Genus-level identification based on 16S rRNA sequence analysis classified the 161 isolates in 19 genera. The majority (64%) of the isolates were affiliated with the genus Pseudomonas. Further analysis of the Pseudomonas isolates based on BLASTn and rpoD-rpoB-gyrB concatenated gene phylogeny revealed three unique clusters that could not be assigned to known species. This study reports the taxonomic description of one of the distinct lineages represented by two strains (S1E40T and S1E44) with P. lurida LMG 21995T, P. costantinii LMG 22119T, P. palleroniana LMG 23076T, P. simiae CCUG 50988T and P. extremorientalis LMG 19695T as the closest taxa. Both strains showed low ANIm (<90%) and genome-based DNA-DNA hybridization (<50%) values, which unequivocally delineated the new strains from the closest relatives. These findings were supported by multilocus sequence analysis (MLSA) and DNA fingerprinting. In addition, growth characteristics and biochemical tests revealed patterns that differed from the related species. Strains S1E40T and S1E44 are Gram-negative, aerobic, rod-shaped and motile by at least one flagellum; and grew optimally at 30 °C. The predominant polar lipid is phosphatidylethanolamine while the major respiratory quinone is ubiquinone-9. Based on phenotypic and genotypic data presented here, strains S1E40T and S1E44 represent a novel species for which the name Pseudomonas aylmerense sp. nov. is proposed. The type strain is S1E40T (= LMG 30784T = DOAB 703T = HAMI 3696T) with a G + C content of 61.6%.
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Affiliation(s)
- Caetanie F Tchagang
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada.,Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - David Overy
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Cyr Lézin Doumbou
- Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Eden S P Bromfield
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - James T Tambong
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
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17
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Chen P, Li S, Li QX. Pseudomonas tianjinensis sp. nov., isolated from domestic sewage. Int J Syst Evol Microbiol 2018; 68:2760-2769. [DOI: 10.1099/ijsem.0.002799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Peizhen Chen
- 1Agro-Environmental Protection Institute (AEPI) of Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Safe-Product, Tianjin, 300191, PR China
| | - Shaopeng Li
- 1Agro-Environmental Protection Institute (AEPI) of Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Safe-Product, Tianjin, 300191, PR China
- 2College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, PR China
| | - Qing X. Li
- 3Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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18
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Cyanotrophic and arsenic oxidizing activities of Pseudomonas mendocina P6115 isolated from mine tailings containing high cyanide concentration. Arch Microbiol 2018; 200:1037-1048. [DOI: 10.1007/s00203-018-1514-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/25/2018] [Accepted: 04/04/2018] [Indexed: 10/17/2022]
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19
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Tchagang CF, Xu R, Doumbou CL, Tambong JT. Genome analysis of two novel Pseudomonas strains exhibiting differential hypersensitivity reactions on tobacco seedlings reveals differences in nonflagellar T3SS organization and predicted effector proteins. Microbiologyopen 2018; 7:e00553. [PMID: 29464939 PMCID: PMC5911992 DOI: 10.1002/mbo3.553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 11/06/2022] Open
Abstract
Multilocus sequence analysis (MLSA) of two new biological control strains (S1E40 and S3E12) of Pseudomonas was performed to assess their taxonomic position relative to close lineages, and comparative genomics employed to investigate whether these strains differ in key genetic features involved in hypersensitivity responses (HRs). Strain S3E12, at high concentration, incites HRs on tobacco and corn plantlets while S1E40 does not. Phylogenies based on individual genes and 16S rRNA-gyrB-rpoB-rpoD concatenated sequence data show strains S1E40 and S3E12 clustering in distinct groups. Strain S3E12 consistently clustered with Pseudomonas marginalis, a bacterium causing soft rots on plant tissues. MLSA data suggest that strains S1E40 and S3E12 are novel genotypes. This is consistent with the data of genome-based DNA-DNA homology values that are below the proposed cutoff species boundary. Comparative genomics analysis of the two strains revealed major differences in the type III secretion systems (T3SS) as well as the predicted T3SS secreted effector proteins (T3Es). One nonflagellar (NF-T3SS) and two flagellar T3SSs (F-T3SS) clusters were identified in both strains. While F-T3SS clusters in both strains were relatively conserved, the NF-T3SS clusters differed in the number of core components present. The predicted T3Es also differed in the type and number of CDSs with both strains having unique predicted protease-related effectors. In addition, the T1SS organization of the S3E12 genome has protein-coding sequences (CDSs) encoding for key factors such as T1SS secreted agglutinin repeats-toxins (a group of cytolysins and cytotoxins), a membrane fusion protein (LapC), a T1SS ATPase of LssB family (LapB), and T1SS-associated transglutaminase-like cysteine proteinase (LapP). In contrast, strain S1E40 has all CDSs for the seven-gene operon (pelA-pelG) required for Pel biosynthesis but not S3E12, suggesting that biofilm formation in these strains is modulated differently. The data presented here provide an insight of the genome organization of these two phytobacterial strains.
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Affiliation(s)
- Caetanie F. Tchagang
- Ottawa Research and Development CentreOttawaONCanada
- Institut des sciences de santé et de la vie Collège La CitéOttawaONCanada
| | - Renlin Xu
- Ottawa Research and Development CentreOttawaONCanada
| | - Cyr Lézin Doumbou
- Institut des sciences de santé et de la vie Collège La CitéOttawaONCanada
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Li X, Tambong J, Yuan KX, Chen W, Xu H, Lévesque CA, De Boer SH. Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses. Int J Syst Evol Microbiol 2017; 68:234-240. [PMID: 29160202 PMCID: PMC5882085 DOI: 10.1099/ijsem.0.002492] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.
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Affiliation(s)
- Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - James Tambong
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Kat Xiaoli Yuan
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Wen Chen
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Huimin Xu
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - C André Lévesque
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Solke H De Boer
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
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