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Shain DH, Klein EA. Genome assembly of Pseudomonas sp. strain SED1 T, a psychrotolerant bacterium isolated from Deception Glacier (Washington, USA). Microbiol Resour Announc 2024; 13:e0012524. [PMID: 38526093 PMCID: PMC11008169 DOI: 10.1128/mra.00125-24] [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: 02/07/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
Strain SED1T was isolated from glacial samples collected on Mount Deception, Washington, USA. Genome sequencing and assembly identified a DNA G + C content of 60.4 mol% with 6,125 predicted proteins. Analysis by the Type Strain Genome Server is consistent with the isolate representing a previously undescribed species in the genus Pseudomonas.
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Affiliation(s)
- Daniel H. Shain
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
| | - Eric A. Klein
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
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2
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Ratnawati SE, Kuuliala L, Verschuere N, Cnockaert M, Vandamme P, Devlieghere F. The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing. Food Microbiol 2024; 118:104407. [PMID: 38049269 DOI: 10.1016/j.fm.2023.104407] [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: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.
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Affiliation(s)
- S E Ratnawati
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - L Kuuliala
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - N Verschuere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - M Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - P Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - F Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Lick S, Wibberg D, Busche T, Blom J, Grimmler C, Goesmann A, Kalinowski J. Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. Int J Syst Evol Microbiol 2024; 74. [PMID: 38587505 DOI: 10.1099/ijsem.0.006293] [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: 04/09/2024] Open
Abstract
By investigating wet and dry age-related ripening of beef, Pseudomonas strains V3/3/4/13T and V3/K/3/5T were isolated. Strain V3/3/4/13T exhibited more than 99 % 16S rRNA gene-based similarity to Pseudomonas fragi and other members of this group, while isolate V3/K/3/5T was very close to Pseudomonas veronii and a number of relatives within the Pseudomonas fluorescens group. Additional comparisons of complete rpoB sequences and draft genomes allowed us to place isolate V3/3/4/13T close to Pseudomonas deceptionensis DSM 26521T. In the case of V3/K/3/5T the closest relative was P. veronii DSM 11331T. Average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13T and P. deceptionensis DSM 26521T were 88.5 and 39.8 %, respectively. For V3/K/3/5T and its closest relative P. veronii DSM 11331T, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13T and V3/K/3/5T were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and summed feature C16 : 1 ω7ct/C15 : 0 iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5T, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5T, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13T and V3/K/3/5T should be considered as representatives of two novel Pseudomonas species. The type strain of the newly proposed Pseudomonas kulmbachensis sp. nov. is V3/3/4/13T (=DSM 113654T=LMG 32520T), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed Pseudomonas paraveronii sp. nov. is V3/K/3/5T (=DSM 113573T=LMG 32518T) with a second isolate FLM 11 (=DSM 113572=LMG 32519).
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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, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- ELIXIR DE Administration Office, Institute of Bio- and Geosciences IBG-5, Forschungszentrum Jülich GmbH - Branch office Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- 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, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
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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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Chan DTC, Baldwin GS, Bernstein HC. Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology. BIODESIGN RESEARCH 2023; 5:0016. [PMID: 37849456 PMCID: PMC10432152 DOI: 10.34133/bdr.0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/17/2023] [Indexed: 10/19/2023] Open
Abstract
Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to "model status," synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the "chassis effect." It remains a major challenge to uncover which genome-encoded and biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of genetic circuit performance. This was accomplished using a comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis effect and characterize the performance dynamics of a genetic inverter circuit operating within 6 Gammaproteobacteria. Our results solidify the notion that genetic devices are strongly impacted by the host context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar performance of the genetic inverter, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.
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Affiliation(s)
- Dennis Tin Chat Chan
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Geoff S. Baldwin
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Hans C. Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
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Identification of phenotypic and genotypic properties and cold adaptive mechanisms of novel freeze–thaw stress-resistant strain Pseudomonas mandelii from Antarctica. Polar Biol 2023. [DOI: 10.1007/s00300-023-03114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Pseudomonas marianensis sp. nov., a marine bacterium isolated from deep-sea sediments of the Mariana Trench. Arch Microbiol 2022; 204:638. [PMID: 36131209 DOI: 10.1007/s00203-022-03250-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/14/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
A novel marine Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain PS1T, was isolated from the deep-sea sediments of the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 35 °C (ranging 10-45 °C), pH 6 (ranging pH 5-10) and with 11% (w/v) NaCl (ranging 0-17%). The 16S rRNA gene sequence similarity results revealed that strain PS1T was most closely related to Pseudomonas stutzeri ATCC 17588T, Pseudomonas nitrititolerans GL14T, Pseudomonas zhaodongensis NEAU-ST5-21T, Pseudomonas xanthomarina DSM 18231T and Pseudomonas kunmingensis HL22-2T with 98.3-98.7%. The digital DNA-DNA hybridization values and the average nucleotide identity between strain PS1T and the reference strains were 20.4-40.1% and 78.7-79.4%, respectively. The major respiratory quinone is ubiquinone Q-9. The major polar lipids were phosphatidylethanolamine, diphosphatidyglycerol, phosphatidylglycerol, phosphatidylcholine, aminoglycolipid, two unidentified glycolipids and one unidentified lipid. The predominant cellular fatty acids of strain PS1T were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and cyclo-C19:0 ω8c. The G + C content of the genomic DNA was 63.0%. The combined genotypic and phenotypic data indicated that strain PS1T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas marianensis sp. nov. is proposed, with the type strain PS1T (= DSM 112238T = MCCC 1K05112T).
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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Cabezas A, Azziz G, Bovio-Winkler P, Fuentes L, Braga L, Wenzel J, Sabaris S, Tarlera S, Etchebehere C. Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems. Front Microbiol 2022; 13:827228. [PMID: 35923392 PMCID: PMC9339992 DOI: 10.3389/fmicb.2022.827228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.
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Affiliation(s)
- Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Durazno, Uruguay
| | - Gastón Azziz
- Laboratorio de Microbiología, Departamento de biología, Facultad de Agronomía, UdelaR, Montevideo, Uruguay
| | - Patricia Bovio-Winkler
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Laura Fuentes
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Lucía Braga
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jorge Wenzel
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvia Sabaris
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvana Tarlera
- Laboratorio de Ecología Microbiana Medioambiental, Departamento Biociencias, Facultad de Química, Montevideo, Uruguay
| | - Claudia Etchebehere
- Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- *Correspondence: Claudia Etchebehere,
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Armandeh M, Mahmoudi N, Fallah Nosratabad AR. Screening and evaluation of phosphate-solubilizing bacteria isolated from aquaculture ponds in a step-by-step strategy as potential biofertilizer. J Appl Microbiol 2022; 133:1581-1596. [PMID: 35689807 DOI: 10.1111/jam.15660] [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: 09/12/2020] [Revised: 05/03/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
AIMS The application of phosphate-solubilizing bacteria (PSB) has received little attention in aquaculture. In addition, the low efficiency of PSB as a biofertilizer in farm conditions is a major concern. Therefore, this study aims to isolate the PSB from sediment of earthen fishponds and evaluate with a more appropriate approach to ensure their effectiveness in increasing the bioavailability of phosphorus (P) in farm conditions. METHODS AND RESULTS PSB was first isolated and selected using the National Botanical Research Institute's Phosphate (NBRIP) medium-containing tri-calcium phosphate (TCP) in solid and liquid media. Among 96 strains that were isolated, 11 strains identified by 16 s rRNA, belonging to the genera Pseudomonas and Acinetobacter, showed a higher ability to release P from TCP (48-170 mg L-1 ). Then, the efficiency of 11 strains was evaluated by combining different criteria. Among 11 selected strains, based on the ability to dissolve TCP and Ca-Phytate in culture medium, release P in sediment microcosm, and growth in a wide range of environmental conditions in fishponds, especially optimum growth at 4°C and pH above 8, Ps. deceptionensis strain Persian10 was selected as the most efficient strain for testing in aquarium conditions. In the last step, incubation of Persian10 in aquarium sediment (sterilized under gamma-ray) increased soluble P and had an impact on calcium phosphate, organic P and alkaline phosphatase activity; however, Persian10 had no impact on the concentration of iron phosphate and aluminium phosphate. CONCLUSIONS Persian 10 strain can be considered a bio-fertilizer candidate in earthen fishponds as it expressed the ability to solubilize P in different conditions. SIGNIFICANCE AND IMPACT OF THE STUDY It is very important to evaluate PSB in an appropriate process using a combination of different criteria to ensure optimal performance of PSB in farm conditions.
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Affiliation(s)
- Mostafa Armandeh
- Department of Aquaculture, Faculty of Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nemat Mahmoudi
- Department of Aquaculture, Faculty of Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Reza Fallah Nosratabad
- Soil and Water Research Institute (SWRI), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
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11
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Wang X, Cui Y, Sang C, Wang B, Yuan Y, Liu L, Yuan Y, Yue T. Fungi with potential probiotic properties isolated from Fuzhuan brick tea. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Vieto S, Rojas-Gätjens D, Jiménez JI, Chavarría M. The potential of Pseudomonas for bioremediation of oxyanions. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:773-789. [PMID: 34369104 DOI: 10.1111/1758-2229.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Non-metal, metal and metalloid oxyanions occur naturally in minerals and rocks of the Earth's crust and are mostly found in low concentrations or confined in specific regions of the planet. However, anthropogenic activities including urban development, mining, agriculture, industrial activities and new technologies have increased the release of oxyanions to the environment, which threatens the sustainability of natural ecosystems, in turn affecting human development. For these reasons, the implementation of new methods that could allow not only the remediation of oxyanion contaminants but also the recovery of valuable elements from oxyanions of the environment is imperative. From this perspective, the use of microorganisms emerges as a strategy complementary to physical, mechanical and chemical methods. In this review, we discuss the opportunities that the Pseudomonas genus offers for the bioremediation of oxyanions, which is derived from its specialized central metabolism and the high number of oxidoreductases present in the genomes of these bacteria. Finally, we review the current knowledge on the transport and metabolism of specific oxyanions in Pseudomonas species. We consider that the Pseudomonas genus is an excellent starting point for the development of biotechnological approaches for the upcycling of oxyanions into added-value metal and metalloid byproducts.
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Affiliation(s)
- Sofía Vieto
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - José I Jiménez
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
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13
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Bendia AG, Lemos LN, Mendes LW, Signori CN, Bohannan BJM, Pellizari VH. Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica. Environ Microbiol 2021; 23:4054-4073. [PMID: 34245102 DOI: 10.1111/1462-2920.15649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 11/27/2022]
Abstract
Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers and active fumaroles, which creates steep gradients that have been shown to affect microbial diversity. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore the metabolic potentials and survival strategies of microbial communities along an extreme temperature gradient in fumarole and glacier sediments on Deception Island. We observed that communities from a 98 °C fumarole were significantly enriched in genes related to hyperthermophilic (e.g. reverse gyrase, GroEL/GroES and thermosome) and oxidative stress responses, as well as genes related to sulfate reduction, ammonification and carbon fixation. Communities from <80 °C fumaroles possessed more genes related osmotic, cold- and heat-shock responses, and diverse metabolic potentials, such as those related to sulfur oxidation and denitrification, while glacier communities showed abundant metabolic potentials mainly related to heterotrophy. Through the reconstruction of genomes, we were able to reveal the metabolic potentials and different survival strategies of underrepresented taxonomic groups, especially those related to Nanoarchaeota, Pyrodictiaceae and thermophilic ammonia-oxidizing archaeal lineages.
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Affiliation(s)
- Amanda Gonçalves Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Leandro Nascimento Lemos
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Lucas William Mendes
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Camila Negrão Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Vivian Helena Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
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14
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Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L. Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. Int J Syst Evol Microbiol 2021; 71. [PMID: 34097596 DOI: 10.1099/ijsem.0.004822] [Citation(s) in RCA: 6] [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
A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2aT with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains Pseudomonas versuta DSM 101070T, Pseudomonas saxonica DSM 108989T, Pseudomonas deceptionensis DSM 26521T and Pseudomonas weihenstephanensis DSM 29166T, placing it within the Pseudomonas fragi / lundensis branch of the genus Pseudomonas. Additional rpoB based comparison revealed P. versuta DSM 101070T as the nearest relative, with 98.5 % nucleotide identity. Calculation of ANIb values of the V4/DAB/S4/2aT draft genome identified P. versuta DSM 101070T with 90.1 %, P. deceptionensis DSM 26521T with 85.1 %, P. fragi DSM 3456T with 84.4 %, Pseudomonas psychrophila DSM 17535T and Pseudomonas bubulae DSM 107389T with 84.2 % similarities each. Pairwise genome-to-genome distance calculations [digital DNA-DNA hybridization (dDDH)] resulted in values of 47.1, 35.1, 34.8, 34.2 and 34.1 %, respectively. A second isolate was detected years later in ground beef and showed ANIb values of 99.3 % and dDDH of 96.1 % relatedness to V4/DAB/S4/2aT. The DNA G+C content was 58.6 mol% for both isolates. The predominant cellular fatty acids of V4/DAB/S4/2aT were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and a summed feature containing C16 : 1ω7c and/or C15 : 0 iso 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, the major respiratory quinone was Q9, with a small portion of Q8. The combined data on genotypic and phenotypic features support the proposal of a novel species, for which the name Pseudomonas paraversuta sp. nov. is proposed. The type strain is V4/DAB/S4/2aT (=DSM 111361T=LMG 31844T) and a second isolate is UBT376 (=DSM 111360=LMG 31845).
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Affiliation(s)
- Sonja Lick
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Annika Winkler
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 58, 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.,Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 58, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Lothar Kröckel
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
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15
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Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang Q. Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium. Int J Syst Evol Microbiol 2021; 71. [PMID: 33411665 DOI: 10.1099/ijsem.0.004632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902T, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902T were 30 °C and pH 6.0, respectively. Strain LAM1902T could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902T was closely related to the members of the family Pseudomonadaceae to the genus Pseudomonas, with the highest similarity to Pseudomonas nitroreducens DSM 14399T (99.6 %), Pseudomonas nitritireducens WZBFD3-5A2T (99.3 %) and Pseudomonas panipatensis Esp-1T (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (gyrB, rpoB and rpoD) further confirmed the intrageneric phylogenetic position of strain LAM1902T. The genomic DNA G+C content of LAM1902T was 64.8 mol%. The low values of in silico DNA-DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus Pseudomonas. The major fatty acids were C16 : 0, C17 : 0 cyclo and anteiso C15 : 0. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902T represents a novel species, for which the name Pseudomonas nicosulfuronedens sp. nov. is proposed. The type strain is LAM1902T (=JCM 33860T=KCTC 72830T).
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Affiliation(s)
- Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Juan Che
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China.,Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
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16
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Gallardo-Benavente C, Campo-Giraldo JL, Castro-Severyn J, Quiroz A, Pérez-Donoso JM. Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source. Genes (Basel) 2021; 12:genes12020187. [PMID: 33514061 PMCID: PMC7912247 DOI: 10.3390/genes12020187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.
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Affiliation(s)
- Carla Gallardo-Benavente
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, 4780000 Temuco, Chile;
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
| | - Jessica L. Campo-Giraldo
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, 1240000 Antofagasta, Chile;
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
- Correspondence: (A.Q.); (J.M.P.-D.)
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
- Correspondence: (A.Q.); (J.M.P.-D.)
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17
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Pavlov MS, Lira F, Martinez JL, Olivares-Pacheco J, Marshall SH. Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from Antarctic soil of King George Island, South Shetland Islands. Int J Syst Evol Microbiol 2020; 70:3255-3263. [PMID: 32375985 DOI: 10.1099/ijsem.0.004165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The strain KG01T was isolated from a soil sample from King George Island, Antarctica. Cells of KG01T are rod-shaped and motile by means of multiple polar flagella. The absence of arginine dihydrolase activity could be a key feature to readily distinguish KG01T from its closest phylogenetic relative species. The main fatty acids of the strain include summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1 ω7c. Phylogenetic analysis based on the 16S rRNA gene sequence and on a multilocus sequence analysis (MLSA) using housekeeping genes (16S rRNA, rpoB, rpoD, gyrB) were carried out. These analyses allowed us to include the strain within the Pseudomonas fluorescens group, presenting the highest similarity of multilocus sequence with Pseudomonas veronii LMG 17761T (96.67 %). The genome of KG01T was sequenced and in silico compared with genomes of the most closely related species of the P. fluorescens group. The average nucleotide identity (ANIb) and average amino acid identity (AAI) values of the species phylogenetically closest to KG01T were less than 95-96 %, threshold currently accepted to define strain as belonging to a bacterial species, the highest scores being those to Pseudomonas veronii LMG 17761T (87.98 %) and Pseudomonas marginalis ICMP 3553T (91.90 %). Therefore, the phenotypic and genotypic analyses results, allow us to propose that KG01T represents a member of a novel species of the genus Pseudomonas, for which the name Pseudomonas fildesensis is proposed, and KG01T (=CECT 9084T;=DSM 102036T) is established as the type strain .
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Affiliation(s)
- Maria S Pavlov
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
| | - Felipe Lira
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - José Luis Martinez
- Centro Nacional de Biotecnología, CNB, CSIC, Darwin 3, Campus de Cantoblanco, Madrid, Spain
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R). Santiago, Chile.,Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso, Chile
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18
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Nováková D, Švec P, Zeman M, Busse HJ, Mašlaňová I, Pantůček R, Králová S, Krištofová L, Sedláček I. Pseudomonas leptonychotis sp. nov., isolated from Weddell seals in Antarctica. Int J Syst Evol Microbiol 2020; 70:302-308. [PMID: 31617844 DOI: 10.1099/ijsem.0.003753] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A taxonomic study was carried out on four Gram-stain-negative strains P5773T, P6169, P4708 and P6245, isolated from anus or mouth samples of Weddell seals at James Ross Island, Antarctica. The results of initial 16S rRNA gene sequence analysis showed that all four strains formed a group placed in the genus Pseudomonas and found Pseudomonas guineae and Pseudomonas peli to be their closest neighbours with 99.9 and 99.2 % sequence similarity, respectively. Sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of isolates to P. peli (rpoD) and to P. guineae (rpoB and gyrB). The average nucleotide identity value below 86 %, as calculated from the whole-genome sequence data, showed the low genomic relatedness of P5773T to its phylogenetic neighbours. The complete genome of strain P5773T was 4.4 Mb long and contained genes encoding proteins with biotechnological potential. The major fatty acids of the seal isolates were summed feature 8 (C18 : 1 ω7c), summed feature 3 (C16 : 1 ω 7 c/C16 : 1 ω6c) and C16:0. The major respiratory quinone was Q9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Putrescine and spermidine are predominant in the polyamine pattern. Further characterization performed using repetitive sequence-based PCR fingerprinting and MALDI-TOF MS analysis showed that the studied isolates formed a coherent cluster separated from the remaining Pseudomonas species and confirmed that they represent a novel species within the genus Pseudomonas, for which the name Pseudomonas leptonychotis sp. nov. is suggested. The type strain is P5773T (=CCM 8849T=LMG 30618T).
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Affiliation(s)
- Dana Nováková
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Zeman
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institute of Microbiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Ivana Mašlaňová
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Roman Pantůček
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucie Krištofová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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19
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Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M. Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 2020; 70:935-943. [DOI: 10.1099/ijsem.0.003851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Katharina Hofmann
- 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
| | - Etienne V. Doll
- 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
| | - 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
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20
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21
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Lezcano MÁ, Moreno-Paz M, Carrizo D, Prieto-Ballesteros O, Fernández-Martínez MÁ, Sánchez-García L, Blanco Y, Puente-Sánchez F, de Diego-Castilla G, García-Villadangos M, Fairén AG, Parro V. Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and Cold. ASTROBIOLOGY 2019; 19:1490-1504. [PMID: 31339746 PMCID: PMC6918857 DOI: 10.1089/ast.2018.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Substrate-atmosphere interfaces in Antarctic geothermal environments are hot-cold regions that constitute thin habitable niches for microorganisms with possible counterparts in ancient Mars. Cerro Caliente hill in Deception Island (active volcano in the South Shetland Islands) is affected by ascending hydrothermal fluids that form a band of warm substrates buffered by low air temperatures. We investigated the influence of temperature on the community structure and metabolism of three microbial mats collected along the geothermal band of Cerro Caliente registering 88°C, 8°C, and 2°C at the time of collection. High-throughput sequencing of small subunit ribosomal ribonucleic acid (SSU rRNA) genes and Life Detector Chip (LDChip) microarray immunoassays revealed different bacterial, archaeal, and eukaryotic composition in the three mats. The mat at 88°C showed the less diverse microbial community and a higher proportion of thermophiles (e.g., Thermales). In contrast, microbial communities in the mats at 2°C and 8°C showed relatively higher diversity and higher proportion of psychrophiles (e.g., Flavobacteriales). Despite this overall association, similar microbial structures at the phylum level (particularly the presence of Cyanobacteria) and certain hot- and cold-tolerant microorganisms were identified in the three mats. Daily thermal oscillations recorded in the substrate over the year (4.5-76°C) may explain the coexistence of microbial fingerprints with different thermal tolerances. Stable isotope composition also revealed metabolic differences among the microbial mats. Carbon isotopic ratios suggested the Calvin-Benson-Bassham cycle as the major pathway for carbon dioxide fixation in the mats at 2°C and 8°C, and the reductive tricarboxylic acid cycle and/or the 3-hydroxypropionate bicycle for the mat at 88°C, indicating different metabolisms as a function of the prevailing temperature of each mat. The comprehensive biomarker profile on the three microbial mats from Cerro Caliente contributes to unravel the diversity, composition, and metabolism in geothermal polar sites and highlights the relevance of geothermal-cold environments to create habitable niches with interest in other planetary environments.
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Affiliation(s)
- María Ángeles Lezcano
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Address correspondence to: María Ángeles Lezcano, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Daniel Carrizo
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Olga Prieto-Ballesteros
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | - Laura Sánchez-García
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | | | | | - Alberto G. Fairén
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca, New York, USA
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
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22
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Snopková K, Čejková D, Dufková K, Sedláček I, Šmajs D. Genome sequences of two Antarctic strains of Pseudomonas prosekii: insights into adaptation to extreme conditions. Arch Microbiol 2019; 202:447-454. [PMID: 31691844 DOI: 10.1007/s00203-019-01755-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/26/2019] [Accepted: 10/22/2019] [Indexed: 01/20/2023]
Abstract
Pseudomonas prosekii is a recently described species isolated exclusively from James Ross Island close to the Antarctic Peninsula at 64° south latitude. Here, we present two P. prosekii genome sequences and their analyses with respect to phylogeny, low temperature adaptation, and potential biotechnological applications. The genome of P. prosekii P2406 comprised 5,896,482 bp and 5324 genes (GC content of 59.71%); the genome of P. prosekii P2673 consisted of 6,087,670 bp and 5511 genes (GC content of 59.50%). Whole genome sequence comparisons confirmed a close relationship between both investigated strains and strain P. prosekii LMG 26867T. Gene mining revealed the presence of genes involved in stress response, genes encoding cold shock proteins, oxidative stress proteins, osmoregulation proteins, genes for the synthesis of protection molecules, and siderophores. Comparative genome analysis of P. prosekii and P. aeruginosa PAO1 highlighted differences in genome content between extremophile species and a mesophilic opportunistic pathogen.
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Affiliation(s)
- Kateřina Snopková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Kristýna Dufková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Faculty of Science, Czech Collection of Microorganisms, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
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Gallardo-Benavente C, Carrión O, Todd JD, Pieretti JC, Seabra AB, Durán N, Rubilar O, Pérez-Donoso JM, Quiroz A. Biosynthesis of CdS Quantum Dots Mediated by Volatile Sulfur Compounds Released by Antarctic Pseudomonas fragi. Front Microbiol 2019; 10:1866. [PMID: 31456780 PMCID: PMC6700389 DOI: 10.3389/fmicb.2019.01866] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
Previously we reported the biosynthesis of intracellular cadmium sulfide quantum dots (CdS QDs) at low temperatures by the Antarctic strain Pseudomonas fragi GC01. Here we studied the role of volatile sulfur compounds (VSCs) in the biosynthesis of CdS QDs by P. fragi GC01. The biosynthesis of nanoparticles was evaluated in the presence of sulfate, sulfite, thiosulfate, sulfide, cysteine and methionine as sole sulfur sources. Intracellular biosynthesis occurred with all sulfur sources tested. However, extracellular biosynthesis was observed only in cultures amended with cysteine (Cys) and methionine (Met). Extracellular nanoparticles were characterized by dynamic light scattering, absorption and emission spectra, energy dispersive X-ray, atomic force microscopy, transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy. Purified QDs correspond to cubic nanocrystals of CdS with sizes between 2 and 16 nm. The analysis of VSCs revealed that P. fragi GC01 produced hydrogen sulfide (H2S), methanethiol (MeSH) and dimethyl sulfide (DMS) in the presence of sulfate, Met or Cys. Dimethyl disulfide (DMDS) was only detected in the presence of Met. Interestingly, MeSH was the main VSC produced in this condition. In addition, MeSH was the only VSC for which the concentration decreased in the presence of cadmium (Cd) of all the sulfur sources tested, suggesting that this gas interacts with Cd to form nanoparticles. The role of MeSH and DMS on Cds QDs biosynthesis was evaluated in two mutants of the Antarctic strain Pseudomonas deceptionensis M1T: megL - (unable to produce MeSH from Met) and mddA - (unable to generate DMS from MeSH). No biosynthesis of QDs was observed in the megL - strain, confirming the importance of MeSH in QD biosynthesis. In addition, the production of QDs in the mddA - strain was not affected, indicating that DMS is not a substrate for the biosynthesis of nanoparticles. Here, we confirm a link between MeSH production and CdS QDs biosynthesis when Met is used as sole sulfur source. This work represents the first report that directly associates the production of MeSH with the bacterial synthesis of QDs, thus revealing the importance of different VSCs in the biological generation of metal sulfide nanostructures.
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Affiliation(s)
- Carla Gallardo-Benavente
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Ornella Carrión
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Joana C. Pieretti
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - Amedea B. Seabra
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - Nelson Durán
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
- Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Olga Rubilar
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
- Departamento de Ingeniería Química, Universidad de La Frontera, Temuco, Chile
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
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Mohammed A, Abdul-Wahab MF, Hashim M, Omar AH, Md Reba MN, Muhamad Said MF, Soeed K, Alias SA, Smykla J, Abba M, Ibrahim Z. Biohydrogen Production by Antarctic Psychrotolerant Klebsiella sp. ABZ11. Pol J Microbiol 2019; 67:283-290. [PMID: 30451444 PMCID: PMC7255690 DOI: 10.21307/pjm-2018-033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
Lower temperature biohydrogen production has always been attractive, due to the lower energy requirements. However, the slow metabolic rate of psychrotolerant biohydrogen-producing bacteria is a common problem that affects their biohydrogen yield. This study reports on the improved substrate synthesis and biohydrogen productivity by the psychrotolerant Klebsiella sp. strain ABZ11, isolated from Antarctic seawater sample. The isolate was screened for biohydrogen production at 30°C, under facultative anaerobic condition. The isolate is able to ferment glucose, fructose and sucrose with biohydrogen production rate and yield of 0.8 mol/l/h and 3.8 mol/g, respectively at 10 g/l glucose concentration. It also showed 74% carbohydrate uptake and 95% oxygen uptake ability, and a wide growth temperature range with optimum at 37°C. Klebsiella sp. ABZ11 has a short biohydrogen production lag phase, fast substrate uptake and is able to tolerate the presence of oxygen in the culture medium. Thus, the isolate has a potential to be used for lower temperature biohydrogen production process.
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Affiliation(s)
- Abdullahi Mohammed
- Ibrahim Badamasi Babangida University, Lapai, Niger State, Nigeria ; Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Mazlan Hashim
- Geoscience and Digital Earth Centre (INSTeG), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Abdul Hafidz Omar
- Sports Innovation Technology Centre (SITC), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Mohd Nadzri Md Reba
- Geoscience and Digital Earth Centre (INSTeG), Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Kamaruzaman Soeed
- Sports Innovation Technology Centre (SITC), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia ; National Antarctic Research Centre, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Jerzy Smykla
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, USA ; Department of Biodiversity, Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Mustapha Abba
- Department of Microbiology, Bauchi State University Gadau, Bauchi, Nigeria
| | - Zaharah Ibrahim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
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25
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Ye Y, Chen C, Ren Y, Wang R, Zhang C, Han S, Ju Z, Zhao Z, Sun C, Wu M. Pseudomonas mangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2019; 69:377-383. [PMID: 30601113 DOI: 10.1099/ijsem.0.003141] [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
A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated as strain TC11T, was isolated from rhizosphere soil of mangrove forest (Kandeliaobovata) in Fugong village, Zhangzhou, Fujian, China. Strain TC11T grew at 15-45 °C (optimum, 35 °C), 0-8 % (w/v) NaCl (optimum, 1 %, w/v) and pH 5.5-9.5 (optimum, pH 7.5). Phylogenetic analyses revealed that strain TC11T belonged to a clade of the genus Pseudomonas and showed the highest sequence similarity of 98.4 % to Pseudomonas fluvialis ASS-1T, followed by Pseudomonas oleovorans subsp.oleovorans DSM 1045T (97.9 %), Pseudomonas indoloxydans JCM 14246T (97.7 %), Pseudomonas guguanensis JCM 18416T(97.6 %) and Pseudomonas alcaliphila JCM 10630T (97.5 %) on the basis of their 16S rRNA gene sequences. The DNA G+C content was 64.3 mol%. In silico DNA-DNA hybridization and average nucleotide identity values between strain TC11T and the reference strains were 19-22 % and 72-78 %, respectively. Studies based on the three housekeeping genes, rpoB, gyrB and rpoD, further confirmed that strain TC11T is a novel member of the genus Pseudomonas. The major fatty acids of strain TC11Twere C16 : 0, summed feature 8 (C18 : 1ω6c/C18 : 1ω7c) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The sole isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strain TC11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonasmangrovi sp. nov., is proposed. The type strain is TC11T (=KCTC 62159=MCCC 1K03499).
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Affiliation(s)
- Yanghui Ye
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Can Chen
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Yanhu Ren
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Ruijun Wang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Chongya Zhang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Shuaibo Han
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhao Ju
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhu Zhao
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- 3College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
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26
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Diversity and characterization of spoilage-associated psychrotrophs in food in cold chain. Int J Food Microbiol 2018; 290:86-95. [PMID: 30317110 DOI: 10.1016/j.ijfoodmicro.2018.09.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 01/24/2023]
Abstract
In this work, psychrotrophs known to cause food spoilage were isolated from commercial food products. Further, temperature sensitivities and volatile organic compounds of the representative strains were characterized to evaluate the population heterogeneity. A total of 490 isolates belonging to 38 genera of 20 families were identified from 30 psychrotroph-positive samples, among which Gram-negative bacteria occurred frequently. The genus Pseudomonas exhibited a clear predominance, especially Pseudomonas fragi, followed by Psychrobacter, Brochothrix, Serratia, and Stenotrophomonas, with the dominant bacteria varying with origin. Aquatic products related to Hafnia and quick-frozen food corresponding to Stenotrophomonas, as well as livestock products were shown to be good ecological niches for growth of psychrotrophs. The genus Pantoea was shown to have an intimate relationship with fruits. While in bean, cereal grain and dairy products, only Pseudomonas was present. The fits of the growth curves demonstrated good adaptability and tolerance of the tested strains under 4 °C, and multifarious growth also reflected intra-species differences and phenotypic diversity. Various kinds of esters, aromatic compounds, alcohols, and ketones were frequently detected by GC-MS. High alcohols were seen in Psychrobacter, but hydrocarbons and ethers were more often found in Pseudomonas. In particular, since high amounts of isophorone were only discovered in bacteria samples, it is speculated to be the characteristic substance of psychrotrophs.
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27
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Bendia AG, Araujo GG, Pulschen AA, Contro B, Duarte RTD, Rodrigues F, Galante D, Pellizari VH. Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica. Extremophiles 2018; 22:917-929. [PMID: 30109444 DOI: 10.1007/s00792-018-1048-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Polar volcanoes harbor unique conditions of extreme temperature gradients capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located at Maritime Antarctica that is notable for its pronounced temperature gradients over very short distances, reaching values up to 100 °C in the fumaroles, and subzero temperatures next to the glaciers. Due to these characteristics, Deception can be considered an interesting analogue of extraterrestrial environments. Our main goal in this study was to isolate thermophilic and psychrophilic bacteria from sediments associated with fumaroles and glaciers from two geothermal sites in Deception Island, comprising temperatures between 0 and 98 °C, and to evaluate their survivability to desiccation and UV-C radiation. Our results revealed that culturable thermophiles and psychrophiles were recovered among the extreme temperature gradient in Deception volcano, which indicates that these extremophiles remain alive even when the conditions do not comprise their growth range. The viability of culturable psychrophiles in hyperthermophilic environments is still poorly understood and our work showed the importance of future studies about their survival strategies in high temperatures. Finally, the spore-forming thermophilic isolates which we found have displayed good survival to desiccation and UV-C irradiation, which suggests their potential to be further explored in astrobiological studies.
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Affiliation(s)
- Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil.
| | - Gabriel G Araujo
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
| | - André A Pulschen
- Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Bruna Contro
- Undergraduate Program in Biology, Universidade Estadual Paulista "Julio de Mesquisa Filho", São Paulo, Brazil
| | - Rubens T D Duarte
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil
| | - Fábio Rodrigues
- Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil
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28
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Wei Y, Mao H, Xu Y, Zou W, Fang J, Blom J. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462-2467. [DOI: 10.1099/ijsem.0.002785] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuli Wei
- 2National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
- 3The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Haiyan Mao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yunping Xu
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Wencai Zou
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- 4Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
- 5Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Jochen Blom
- 6Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
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29
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30
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Vásquez-Ponce F, Higuera-Llantén S, Pavlov MS, Marshall SH, Olivares-Pacheco J. Phylogenetic MLSA and phenotypic analysis identification of three probable novel Pseudomonas species isolated on King George Island, South Shetland, Antarctica. Braz J Microbiol 2018; 49:695-702. [PMID: 29598976 PMCID: PMC6175711 DOI: 10.1016/j.bjm.2018.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 02/03/2018] [Accepted: 02/14/2018] [Indexed: 02/07/2023] Open
Abstract
Antarctica harbors a great diversity of microorganisms, including bacteria, archaea, microalgae and yeasts. The Pseudomonas genus is one of the most diverse and successful bacterial groups described to date, but only eight species isolated from Antarctica have been characterized. Here, we present three potentially novel species isolated on King George Island. The most abundant isolates from four different environments, were genotypically and phenotypically characterized. Multilocus sequence analysis and 16S rRNA gene analysis of a sequence concatenate for six genes (16S, aroE, glnS, gyrB, ileS and rpoD), determined one of the isolates to be a new Pseudomonas mandelii strain, while the other three are good candidates for new Pseudomonas species. Additionally, genotype analyses showed the three candidates to be part of a new subgroup within the Pseudomonas fluorescens complex, together with the Antarctic species Pseudomonas antarctica and Pseudomonas extremaustralis. We propose terming this new subgroup P. antarctica. Likewise, phenotypic analyses using API 20 NE and BIOLOG® corroborated the genotyping results, confirming that all presented isolates form part of the P. fluorescens complex. Pseudomonas genus research on the Antarctic continent is in its infancy. To understand these microorganisms’ role in this extreme environment, the characterization and description of new species is vital.
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Affiliation(s)
- Felipe Vásquez-Ponce
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sebastián Higuera-Llantén
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - María S Pavlov
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Jorge Olivares-Pacheco
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile.
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31
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Danilovich ME, Sánchez LA, Acosta F, Delgado OD. Antarctic bioprospecting: in pursuit of microorganisms producing new antimicrobials and enzymes. Polar Biol 2018. [DOI: 10.1007/s00300-018-2295-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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The current status on the taxonomy of Pseudomonas revisited: An update. INFECTION GENETICS AND EVOLUTION 2017; 57:106-116. [PMID: 29104095 DOI: 10.1016/j.meegid.2017.10.026] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.
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Higuera-Llantén S, Vásquez-Ponce F, Núñez-Gallegos M, Pavlov MS, Marshall S, Olivares-Pacheco J. Phenotypic and genotypic characterization of a novel multi-antibiotic-resistant, alginate hyperproducing strain of Pseudomonas mandelii isolated in Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2206-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Vandeweyer D, Crauwels S, Lievens B, Van Campenhout L. Metagenetic analysis of the bacterial communities of edible insects from diverse production cycles at industrial rearing companies. Int J Food Microbiol 2017; 261:11-18. [PMID: 28881263 DOI: 10.1016/j.ijfoodmicro.2017.08.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/28/2017] [Accepted: 08/22/2017] [Indexed: 02/02/2023]
Abstract
Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by (Para)bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas. In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies.
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Affiliation(s)
- D Vandeweyer
- KU Leuven, Department of Microbial and Molecular Systems (M(2)S), Lab4Food, Campus Geel, B-2440 Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), B-3001 Leuven, Belgium
| | - S Crauwels
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), B-3001 Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M(2)S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - B Lievens
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), B-3001 Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M(2)S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - L Van Campenhout
- KU Leuven, Department of Microbial and Molecular Systems (M(2)S), Lab4Food, Campus Geel, B-2440 Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), B-3001 Leuven, Belgium.
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35
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See-Too WS, Salazar S, Ee R, Convey P, Chan KG, Peix Á. Pseudomonas versuta sp. nov., isolated from Antarctic soil. Syst Appl Microbiol 2017; 40:191-198. [DOI: 10.1016/j.syapm.2017.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 10/19/2022]
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36
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Predicting the biotechnological potential of bacteria isolated from Antarctic soils, including the rhizosphere of vascular plants. Polar Biol 2017. [DOI: 10.1007/s00300-016-2065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Wang MQ, Sun L. Pseudomonas oceani sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:4250-4255. [PMID: 27468709 DOI: 10.1099/ijsem.0.001343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we identified a novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, strain KX 20T, isolated from the deep seawater in Okinawa Trough, northwestern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KX 20T was related to members of the genus Pseudomonas and shares the highest sequence identities with Pseudomonas aestusnigri CECT 8317T (99.4 %) and Pseudomonas pachastrellae JCM 12285T (98.5 %). The 16S rRNA gene sequence identities between strain KX 20T and other members of the genus Pseudomonaswere below 96.6 %. The gyrB and rpoD genes of strain KX 20T shared 82.0 to 89.3 % sequence identity with the gyrB and rpoD genes of the closest phylogenetic neighbours of KX 20T. The predominant cellular fatty acids of strain KX 20T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (29.2 %), C16 : 0 (24.5 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (21.5 %) and C12 : 0 (8.2 %). The major polar lipids of strain KX 20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The genomic DNA G+C content of strain KX 20T was 62.9 mol%. On the basis of phylogenetic analysis and phenotypic characteristics, a novel species, Pseudomonas oceani sp. nov. is proposed. The type strain is KX 20T (=CGMCC 1.15195T=DSM 100277T).
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Affiliation(s)
- Ming-Qing Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.,Function Laboratory for Marine Biology and Biotechnology, Qingdao National Oceanography Laboratory, Qingdao, PR China
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von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M, Stressler T, Fischer L, Hinrichs J, Scherer S, Wenning M. Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk. Int J Syst Evol Microbiol 2016; 66:1163-1173. [DOI: 10.1099/ijsem.0.000852] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- M. von Neubeck
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner, Berg 3, 85354 Freising, Germany
| | - C. Huptas
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner, Berg 3, 85354 Freising, Germany
| | - C. Glück
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599 Stuttgart, Germany
| | - M. Krewinkel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599 Stuttgart, Germany
| | - M. Stoeckel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Soft Matter Science and Dairy Technology, Garbenstr. 21, 70599 Stuttgart, Germany
| | - T. Stressler
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599 Stuttgart, Germany
| | - L. Fischer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599 Stuttgart, Germany
| | - J. Hinrichs
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Soft Matter Science and Dairy Technology, Garbenstr. 21, 70599 Stuttgart, Germany
| | - S. Scherer
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner, Berg 3, 85354 Freising, Germany
| | - M. Wenning
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner, Berg 3, 85354 Freising, Germany
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Jo JH, Singh P, Kim YJ, Wang C, Mathiyalagan R, Jin CG, Yang DC. Pseudomonas deceptionensis DC5-mediated synthesis of extracellular silver nanoparticles. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015. [DOI: 10.3109/21691401.2015.1068792 [pii]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jae H. Jo
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Priyanka Singh
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Yeon J. Kim
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Chao Wang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Republic of Korea
| | - Chi-Gyu Jin
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Deok C. Yang
- Department of Oriental Medicine Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Republic of Korea
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Jo JH, Singh P, Kim YJ, Wang C, Mathiyalagan R, Jin CG, Yang DC. Pseudomonas deceptionensis DC5-mediated synthesis of extracellular silver nanoparticles. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015; 44:1576-81. [PMID: 26232081 DOI: 10.3109/21691401.2015.1068792] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The biological synthesis of metal nanoparticles is of great interest in the field of nanotechnology. The present work highlights the extracellular biological synthesis of silver nanoparticles using Pseudomonas deceptionensis DC5. The particles were synthesized in the culture supernatant within 48 h of incubation. Extracellular synthesis of silver nanoparticles in the culture supernatant was confirmed by ultraviolet-visible spectroscopy, which showed the absorption peak at 428 nm, and also under field emission transmission electron microscopy which displayed the spherical shape. In addition, the particles were characterized by X-ray diffraction spectroscopy, which corresponds to the crystalline nature of nanoparticles, and energy-dispersive X-ray analysis which exhibited the intense peak at 3 keV, resembling the silver nanoparticles. Further, the synthesized nanoparticles were examined by elemental mapping which displayed the dominance of the silver element in the synthesized product, and dynamic light scattering which showed the distribution of silver nanoparticles with respect to intensity, volume, and number of particles. Moreover, the silver nanoparticles have been found to be quite active in antimicrobial activity and biofilm inhibition activity against pathogenic microorganisms. Thus, the present work emphasized the prospect of using the P. deceptionensis DC5 to achieve the extracellular synthesis of silver nanoparticles in a facile and environmental manner.
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Affiliation(s)
- Jae H Jo
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea
| | - Priyanka Singh
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea
| | - Yeon J Kim
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea
| | - Chao Wang
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea
| | - Ramya Mathiyalagan
- b Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University , Republic of Korea
| | - Chi-Gyu Jin
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea
| | - Deok C Yang
- a Department of Oriental Medicine Biotechnology and Ginseng Bank , College of Life Sciences, Kyung Hee University , Yongin , Republic of Korea.,b Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University , Republic of Korea
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Ramírez-Bahena MH, Cuesta MJ, Tejedor C, Igual JM, Fernández-Pascual M, Peix Á. Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain. Int J Syst Evol Microbiol 2015; 65:2110-2117. [DOI: 10.1099/ijs.0.000230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain named BSTT44T was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7 % identity with respect to that of its closest relative, Pseudomonas psychrophila E-3T, and the next most closely related type strains were those of Pseudomonas fragi, with 99.6 % similarity, Pseudomonas deceptionensis, with 99.2 % similarity, and Pseudomonas lundensis, with 99.0 % similarity; these results indicate that BSTT44T should be classified within the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation and showed identities lower than 92 % in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar–subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5–9.The DNA G+C content was 60.2 mol%. DNA–DNA hybridization results showed less than 48 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus Pseudomonas, for which the name Pseudomonas endophytica sp. nov. is proposed. The type strain is BSTT44T ( = LMG 28456T = CECT 8691T).
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Affiliation(s)
- Martha-Helena Ramírez-Bahena
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain
| | - Maria José Cuesta
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-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), Salamanca, Spain
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A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments. Nat Commun 2015; 6:6579. [DOI: 10.1038/ncomms7579] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/09/2015] [Indexed: 11/09/2022] Open
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Delgado L, Martínez G, López-Iglesias C, Mercadé E. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack. J Struct Biol 2015; 189:220-9. [PMID: 25617813 DOI: 10.1016/j.jsb.2015.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
Abstract
Cryo-electron tomography (CET) of plunge-frozen whole bacteria and vitreous sections (CETOVIS) were used to revise and expand the structural knowledge of the "Stack", a recently described cytoplasmic structure in the Antarctic bacterium Pseudomonas deceptionensis M1(T). The advantages of both techniques can be complementarily combined to obtain more reliable insights into cells and their components with three-dimensional imaging at different resolutions. Cryo-electron microscopy (Cryo-EM) and CET of frozen-hydrated P. deceptionensis M1(T) cells confirmed that Stacks are found at different locations within the cell cytoplasm, in variable number, separately or grouped together, very close to the plasma membrane (PM) and oriented at different angles (from 35° to 90°) to the PM, thus establishing that they were not artifacts of the previous sample preparation methods. CET of plunge-frozen whole bacteria and vitreous sections verified that each Stack consisted of a pile of oval disc-like subunits, each disc being surrounded by a lipid bilayer membrane and separated from each other by a constant distance with a mean value of 5.2±1.3nm. FM4-64 staining and confocal microscopy corroborated the lipid nature of the membrane of the Stacked discs. Stacks did not appear to be invaginations of the PM because no continuity between both membranes was visible when whole bacteria were analyzed. We are still far from deciphering the function of these new structures, but a first experimental attempt links the Stacks with a given phase of the cell replication process.
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Affiliation(s)
- Lidia Delgado
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain; Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Gema Martínez
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain.
| | - Elena Mercadé
- Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.
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Delgado L, Carrión O, Martínez G, López-Iglesias C, Mercadé E. The stack: a new bacterial structure analyzed in the Antarctic bacterium Pseudomonas deceptionensis M1(T) by transmission electron microscopy and tomography. PLoS One 2013; 8:e73297. [PMID: 24039905 PMCID: PMC3767748 DOI: 10.1371/journal.pone.0073297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/18/2013] [Indexed: 01/06/2023] Open
Abstract
In recent years, improvements in transmission electron microscopy (TEM) techniques and the use of tomography have provided a more accurate view of the complexity of the ultrastructure of prokaryotic cells. Cryoimmobilization of specimens by rapid cooling followed by freeze substitution (FS) and sectioning, freeze fracture (FF) and observation of replica, or cryoelectron microscopy of vitreous sections (CEMOVIS) now allow visualization of biological samples close to their native state, enabling us to refine our knowledge of already known bacterial structures and to discover new ones. Application of these techniques to the new Antarctic cold-adapted bacterium Pseudomonasdeceptionensis M1T has demonstrated the existence of a previously undescribed cytoplasmic structure that does not correspond to known bacterial inclusion bodies or membranous formations. This structure, which we term a “stack”, was mainly visualized in slow growing cultures of P. deceptionensis M1T and can be described as a set of stacked membranous discs usually arranged perpendicularly to the cell membrane, but not continuous with it, and found in variable number in different locations within the cell. Regardless of their position, stacks were mostly observed very close to DNA fibers. Stacks are not exclusive to P. deceptionensis M1T and were also visualized in slow-growing cultures of other bacteria. This new structure deserves further study using cryoelectron tomography to refine its configuration and to establish whether its function could be related to chromosome dynamics.
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Affiliation(s)
- Lidia Delgado
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Ornella Carrión
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Gema Martínez
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
| | - Elena Mercadé
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
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Pseudomonas prosekii sp. nov., a Novel Psychrotrophic Bacterium from Antarctica. Curr Microbiol 2013; 67:637-46. [DOI: 10.1007/s00284-013-0406-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/07/2013] [Indexed: 11/25/2022]
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