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Li S, Mao S, Mu W, Guo B, Li C, Zhu Q, Hou X, Zhao Y, Wei S, Liu H, Liu A. Flavobacterium potami sp. nov., a multi-metal resistance genes harbouring bacterium isolated from shallow river silt. Antonie Van Leeuwenhoek 2023; 116:265-280. [PMID: 36574165 DOI: 10.1007/s10482-022-01802-z] [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: 08/22/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
Environmental pollution by heavy metals is becoming an increasing problem and has become a matter of great concern due to the adverse effects worldwide. In this study, we report a novel strain of multi-metal resistant bacteria. A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped strain 17AT, was isolated from the shallow silt of Fuyang River located in Longdian town, Hengshui city, Hebei province, China. Strain 17AT grew at 20-35 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and 0-2% (w/v) NaCl (optimum, 1%). Phylogenetic analyses of 16S rRNA gene sequences showed that strain 17AT was closely related to members of the genus Flavobacterium, and had the highest 16S rRNA gene sequence similarity with 'Flavobacterium panacis' DCY106T (97.5%), followed by Flavobacterium johnsoniae subsp. johnsoniae UW101T (97.3%), Flavobacterium cutihirudinis E89T (97.2%), Flavobacterium limi THG-AG6.4T (97.2%), Flavobacterium hibisci THG-HG1.4T (97.2%) and Flavobacterium johnsoniae subsp. aurantiacum DSM 6792T (97.1%). The genome size of strain 17AT was 5.4 Mb and the DNA G + C content was 34.0%. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain 17AT and reference strains were in the ranges of 79.8-86.1%, 24.1-31.4% and 80.5-88.6%, respectively, lower than the threshold values for species delineation. Strain 17AT contained iso-C15:0 and C16:0 3-OH as the predominant fatty acids (≥ 10%). The main isoprenoid quinone of strain 17AT was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, two unidentified aminophospholipids and six unidentified lipids. Comparative genomics analysis between strain 17AT and its reference type strains revealed that there are a number of metal-resistant genes in strain 17AT, which are located in 15 gene clusters responsible for the copper homeostasis, cobalt-zinc-cadmium resistance, copper resistance, and arsenic/antimony resistance, with the copper resistance protein NlpE being unique to 17AT. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 17AT is a representative of a novel species within the genus Flavobacterium, for which the name Flavobacterium potami sp. nov. is proposed. The type strain is 17AT (= GDMCC 1.2723T = JCM 34833T).
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Affiliation(s)
- Shucheng Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Sidi Mao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Weidong Mu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Bai Guo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Chen Li
- Shandong International Talent Exchange Service Center, Jinan, 250101, People's Republic of China
| | - Qing Zhu
- Shandong Institute of Innovation and Development, Jinan, 250101, People's Republic of China
| | - Xiaoxiao Hou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yanfang Zhao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Shuzhen Wei
- Center for Wetland Conservation and Research, Hengshui University, Hengshui, 053000, People's Republic of China
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China
- Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, 053000, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
| | - Aiju Liu
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, 255000, People's Republic of China.
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Silver nanoparticles produced from Cedecea sp. exhibit antibiofilm activity and remarkable stability. Sci Rep 2021; 11:12619. [PMID: 34135368 PMCID: PMC8209203 DOI: 10.1038/s41598-021-92006-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022] Open
Abstract
With multidrug-resistant bacterial pathogens on the rise, there is a strong research focus on alternative antibacterial treatments that could replace or complement classical antibiotics. Metallic nanoparticles, and in particular silver nanoparticles (AgNPs), have been shown to kill bacterial biofilms effectively, but their chemical synthesis often involves environmentally unfriendly by-products. Recent studies have shown that microbial and plant extracts can be used for the environmentally friendly synthesis of AgNPs. Herein we report a procedure for producing AgNPs using a putative Cedecea sp. strain isolated from soil. The isolated bacterial strain showed a remarkable potential for producing spherical, crystalline and stable AgNPs characterized by UV–visible spectroscopy, transmission electron microscopy, dynamic light scattering, and Fourier transform infrared spectroscopy. The concentration of produced nanoparticles was 1.31 µg/µl with a negative surface charge of − 15.3 mV and nanoparticles size ranging from 10–40 nm. The AgNPs was tested against four pathogenic microorganisms S. epidermidis, S. aureus, E. coli and P. aeruginosa. The nanoparticles exhibited strong minimum inhibitory concentration (MIC) values of 12.5 and 6.25 µg/µl and minimum bactericidal concentration (MBC) values of 12.5 and 12.5 µg/mL against E. coli and P. aeruginosa, respectively. One distinguishing feature of AgNPs produced by Cedecea sp. extracts is their extreme stability. Inductively coupled plasma mass spectrometry and thermogravimetric analysis demonstrated that the produced AgNPs are stable for periods exceeding one year. This means that their strong antibacterial effects, demonstrated against E. coli and P. aeruginosa biofilms, can be expected to persist during extended periods.
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Kämpfer P, Glaeser SP, McInroy JA, Xu J, Busse HJ, Clermont D, Criscuolo A. Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum. Int J Syst Evol Microbiol 2020; 70:5824-5831. [PMID: 33034547 DOI: 10.1099/ijsem.0.004482] [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: 12/28/2022] Open
Abstract
A Gram-staining-negative non endospore-forming strain, PXU-55T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium. The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the PXU-55T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% (Flavobacterium defluvii), and 86.1 and 29.9% (Flavobacterium johnsoniae). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C16:0 3-OH, C16:0 3-OH and C15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium. Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55T (=CIP 111646T=CCM 8914T) represents a novel species with the name Flavobacterium panici sp. nov.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Jia Xu
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
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Singh P, Pandit S, Mokkapati VRSS, Garnæs J, Mijakovic I. A Sustainable Approach for the Green Synthesis of Silver Nanoparticles from Solibacillus isronensis sp. and Their Application in Biofilm Inhibition. Molecules 2020; 25:E2783. [PMID: 32560208 PMCID: PMC7355478 DOI: 10.3390/molecules25122783] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/31/2020] [Accepted: 06/09/2020] [Indexed: 11/29/2022] Open
Abstract
The use of bacteria as nanofactories for the green synthesis of nanoparticles is considered a sustainable approach, owing to the stability, biocompatibility, high yields and facile synthesis of nanoparticles. The green synthesis provides the coating or capping of biomolecules on nanoparticles surface, which confer their biological activity. In this study, we report green synthesis of silver nanoparticles (AgNPs) by an environmental isolate; named as AgNPs1, which showed 100% 16S rRNA sequence similarity with Solibacillus isronensis. UV/visible analysis (UV/Vis), transmission electron microscopy (TEM), atomic force microscopy (AFM), dynamic light scattering (DLS), and Fourier-transform infrared spectroscopy (FTIR) were used to characterize the synthesized nanoparticles. The stable nature of nanoparticles was studied by thermogravimetric analysis (TGA) and inductively coupled plasma mass spectrometry (ICP-MS). Further, these nanoparticles were tested for biofilm inhibition against Escherichia coli and Pseudomonas aeruginosa. The AgNPs showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 3.12 µg/mL and 6.25 µg/mL for E. coli, and 1.56 µg/mL and 3.12 µg/mL for P. aeruginosa, respectively.
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Affiliation(s)
- Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden; (S.P.); (V.M.)
| | - VRSS Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden; (S.P.); (V.M.)
| | - Jørgen Garnæs
- Danish Institute of Fundamental Metrology, Kogle Allé 5, DK 2970 Hoersholm, Denmark;
| | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark;
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden; (S.P.); (V.M.)
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Singh P, Kim YJ, Singh H, Farh MEA, Yang DC. Achromobacter panacis sp. nov., isolated from rhizosphere of Panax ginseng. J Microbiol 2017; 55:428-434. [PMID: 28551873 DOI: 10.1007/s12275-017-6612-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
Abstract
A novel strain DCY105T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY105T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5-7.0 and in the absence of NaCl. Phylogenetically, strain DCY105T is most closely related to Achromobacter marplatensis LMG 26219T (96.81%). The DNA G+C content of strain DCY105T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were amongst the major polar lipids. C16:00, C8:03OH and iso-C17:03OH were identified as the major fatty acids present in DCY105T. The results of physiological and biochemical tests allowed strain DCY105T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105T (=CCTCCAB 2015193T =KCTC 42751T).
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Affiliation(s)
- Priyanka Singh
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea. .,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea.
| | - Yeon Ju Kim
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea.
| | - Hina Singh
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Mohamed El-Agamy Farh
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Deok-Chun Yang
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea. .,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Singh P, Singh H, Kim YJ, Yang DC. Pedobacter panacis sp. nov., isolated from Panax ginseng soil. Antonie van Leeuwenhoek 2016; 110:235-244. [PMID: 27798744 DOI: 10.1007/s10482-016-0794-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/19/2016] [Indexed: 11/30/2022]
Abstract
A novel strain, DCY108T was isolated from soil of a Panax ginseng field, Yeoncheon province (38°04'N 126°57'E), Republic of Korea. Strain DCY108T is Gram-negative, non-motile, non-flagellate, rod-shaped, and aerobic. The bacterium grows optimally at 25-30 °C, pH 6.5-7.0 and 1 % NaCl. Phylogenetically, strain DCY108T is closely related to Pedobacter jejuensis JCM 18824T, Pedobacter aquatilis JCM 13454T, Pedobacter kyungheensis LMG 26577T and the type strain of the genus Pedobacter heparinus DSM 2366T. The DNA-DNA relatedness values between strain DCY108T and its close phylogenetic neighbors were below 30.0 %. The DNA G+C content of strain DCY108T was determined to be 45.1 mol%. The predominant quinone was menaquinone 7 (MK-7). The major polar lipids were identified as phosphatidylethanolamine and three unidentified aminolipids AL1, AL13 and AL17. Iso-C15:00, iso-C17:03OH and summed feature 3 (C16:1 ω7c/C16:1 ω6c) were identified as the major fatty acids present in strain DCY108T. The results of physiological and biochemical tests allowed strain DCY108T to be differentiated phenotypically from other recognized species belonging to the genus Pedobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Pedobacter panacis sp. nov is proposed with the type strain designated as DCY108T (=CCTCCAB 2015196T = KCTC 42748T).
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Affiliation(s)
- Priyanka Singh
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea. .,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea.
| | - Hina Singh
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea
| | - Yeon-Ju Kim
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea
| | - Deok-Chun Yang
- Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea. .,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, Gyeonggi-do, 446-701, Republic of Korea.
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