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Liu C, Guo D, Wen S, Dang Y, Sun D, Li P. Transcriptomic insights unveil the crucial roles of cytochromes, NADH, and pili in Ag(I) reduction by Geobacter sulfurreducens. CHEMOSPHERE 2024; 358:142174. [PMID: 38685325 DOI: 10.1016/j.chemosphere.2024.142174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Silver (Ag) is a pivotal transition metal with applications in multiple industries, necessitating efficient recovery techniques. Despite various proposed methods for silver recovery from wastewaters, challenges persist especially for low concentrations. In this context, bioreduction by bacteria like Geobacter sulfurreducens, offers a promising approach by converting Ag(I) to Ag nanoparticles. To reveal the mechanisms driving microbial Ag(I) reduction, we conducted transcriptional profiling of G. sulfurreducens under Ag(I)-reducing condition. Integrated transcriptomic and protein-protein interaction network analyses identified significant transcriptional shifts, predominantly linked to c-type cytochromes, NADH, and pili. When compared to a pilus-deficient strain, the wild-type strain exhibited distinct cytochrome gene expressions, implying specialized functional roles. Additionally, despite a down-regulation in NADH dehydrogenase genes, we observed up-regulation of specific downstream cytochrome genes, highlighting NADH's potential role as an electron donor in the Ag(I) reduction process. Intriguingly, our findings also highlight the significant influence of pili on the morphology of the resulting Ag nanoparticles. The presence of pili led to the formation of smaller and more crystallized Ag nanoparticles. Overall, our findings underscore the intricate interplay of cytochromes, NADH, and pili in Ag(I) reduction. Such insights suggest potential strategies for further enhancing microbial Ag(I) reduction.
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Affiliation(s)
- Chunmao Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dongchao Guo
- School of Computer Science, Beijing Information Science and Technology University, Beijing, 100101, China
| | - Su Wen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dezhi Sun
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Pengsong Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
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2
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Vaitiekūnaitė D, Snitka V. Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS). Microorganisms 2021; 9:1969. [PMID: 34576865 PMCID: PMC8466144 DOI: 10.3390/microorganisms9091969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022] Open
Abstract
Due to the harmful effects of chemical fertilizers and pesticides, the need for an eco-friendly solution to improve soil fertility has become a necessity, thus microbial biofertilizer research is on the rise. Plant endophytic bacteria inhabiting internal tissues represent a novel niche for research into new biofertilizer strains. However, the number of species and strains that need to be differentiated and identified to facilitate faster screening in future plant-bacteria interaction studies, is enormous. Surface enhanced Raman spectroscopy (SERS) may provide a platform for bacterial discrimination and identification, which, compared with the traditional methods, is relatively rapid, uncomplicated and ensures high specificity. In this study, we attempted to differentiate 18 bacterial isolates from two oaks via morphological, physiological, biochemical tests and SERS spectra analysis. Previous 16S rRNA gene fragment sequencing showed that three isolates belong to Paenibacillus, 3-to Pantoea and 12-to Pseudomonas genera. Additional tests were not able to further sort these bacteria into strain-specific groups. However, the obtained label-free SERS bacterial spectra along with the high-accuracy principal component (PCA) and discriminant function analyses (DFA) demonstrated the possibility to differentiate these bacteria into variant strains. Furthermore, we collected information about the biochemical characteristics of selected isolates. The results of this study suggest a promising application of SERS in combination with PCA/DFA as a rapid, non-expensive and sensitive method for the detection and identification of plant-associated bacteria.
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Affiliation(s)
- Dorotėja Vaitiekūnaitė
- Laboratory of Forest Plant Biotechnology, Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania
| | - Valentinas Snitka
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu Str. 65, 51369 Kaunas, Lithuania;
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Stricker L, Guido I, Breithaupt T, Mazza MG, Vollmer J. Hybrid sideways/longitudinal swimming in the monoflagellate Shewanella oneidensis: from aerotactic band to biofilm. J R Soc Interface 2020; 17:20200559. [PMID: 33109020 PMCID: PMC7653395 DOI: 10.1098/rsif.2020.0559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/06/2020] [Indexed: 11/12/2022] Open
Abstract
Shewanella oneidensis MR-1 are facultative aerobic electroactive bacteria with an appealing potential for sustainable energy production and bioremediation. They gather around air sources, forming aerotactic bands and biofilms. Here, we experimentally follow the evolution of the band around an air bubble, and we find good agreement with the numerical solutions of the pertinent transport equations. Video microscopy reveals a transition between motile and non-motile MR-1 upon oxygen depletion, preventing further development of the biofilm. We discover that MR-1 can alternate between longitudinal fast and sideways slow swimming. The resulting bimodal velocity distributions change in response to different oxygen concentrations and gradients, supporting the biological functions of aerotaxis and confinement.
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Affiliation(s)
- Laura Stricker
- ETH Zürich, Department of Materials, Polymer Physics, 8093 Zurich, Switzerland
| | - Isabella Guido
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
| | - Thomas Breithaupt
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
| | - Marco G. Mazza
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Loughborough University, Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough, Leicestershire LE11 3TU, UK
| | - Jürgen Vollmer
- University of Leipzig, Institute of Theoretical Physics, 04103 Leipzig, Germany
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Schkolnik G, Schmidt M, Mazza MG, Harnisch F, Musat N. Correction: In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy. PLoS One 2018; 13:e0199344. [PMID: 29902257 PMCID: PMC6002062 DOI: 10.1371/journal.pone.0199344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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5
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Cheng HY, Hou YN, Zhang X, Yang ZN, Xu T, Wang AJ. Activating electrochemical catalytic activity of bio-palladium by hybridizing with carbon nanotube as "e - Bridge". Sci Rep 2017; 7:16588. [PMID: 29185498 PMCID: PMC5707347 DOI: 10.1038/s41598-017-16880-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/17/2017] [Indexed: 11/09/2022] Open
Abstract
Nano metal catalysts produced by bacteria has received increasing attention owing to its environmental friendly synthesis route. However, the formed metal nanoparticles are associated with poorly conductive cells and challenged to be electrochemically applied. In this study, Palladium (Pd) nanoparticles were synthesized by Shewanella oneidensis MR-1. We demonstrated the limitation of palladized cells (Pd-cells) serving as electro-catalysts can be relieved by hybridizing with the conductive carbon nanotubes (Pd-cells-CNTs hybrid). Compared to the Pd-cells, the electrochemical active surface area of Pd in Pd-cells-CNTs10 (the ratio of Pd/CNTs is 1/10 w/w) were dramatically increased by 68 times to 20.44 m2·g-1. A considerable enhancement of electrocatalytic activity was further confirmed for Pd-cells-CNTs10 as indicated by a 5-fold increase of steady state current density for nitrobenzene reduction at -0.55 V vs Ag/AgCl. These results indicate that the biogenetic palladium could has been an efficient electro-catalyst but just limited due to lacking an electron transport path (e - Bridge). This finding may also be helpful to guide the way to electrochemically use other biogenetic metal nano-materials.
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Affiliation(s)
- Hao-Yi Cheng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ya-Nan Hou
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, China
| | - Xu Zhang
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
| | - Zhen-Ni Yang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Tiefu Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,School of Civil Engineering, Heilongjiang University, Harbin, 150080, China
| | - Ai-Jie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, China.
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Mosier-Boss PA. Review on SERS of Bacteria. BIOSENSORS-BASEL 2017; 7:bios7040051. [PMID: 29137201 PMCID: PMC5746774 DOI: 10.3390/bios7040051] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 12/16/2022]
Abstract
Surface enhanced Raman spectroscopy (SERS) has been widely used for chemical detection. Moreover, the inherent richness of the spectral data has made SERS attractive for use in detecting biological materials, including bacteria. This review discusses methods that have been used to obtain SERS spectra of bacteria. The kinds of SERS substrates employed to obtain SERS spectra are discussed as well as how bacteria interact with silver and gold nanoparticles. The roll of capping agents on Ag/Au NPs in obtaining SERS spectra is examined as well as the interpretation of the spectral data.
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Keleştemur S, Çulha M. Understanding and Discrimination of Biofilms of Clinically Relevant Microorganisms Using Surface-Enhanced Raman Scattering. APPLIED SPECTROSCOPY 2017; 71:1180-1188. [PMID: 27708179 DOI: 10.1177/0003702816670916] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Biofilm formation is a defense mechanism for microorganisms to survive under both natural and stress conditions. Clinically relevant microorganisms threaten patient health through biofilm formation on medical devices and implants. It is very important to identify biofilm formation in order to suppress their pathogenic activities in early stages. With the aim for better understanding biofilm formation and possibility of detection, in this study, biofilm formation of clinically important microorganisms, Pseudomonas aeruginosa, Staphylococcus epidermidis, and Candida albicans are monitored with surface-enhanced Raman scattering (SERS). The SERS spectra were collected by mapping a dried droplet area where a volume of colloidal silver nanoparticle (AgNP) suspension is placed on microorganism culture plate. The spectral changes on the SERS spectra with increasing incubation time of the model microorganisms from 4 to 120 h are monitored. The unique spectra originating from the biofilms of three pathogenic microorganisms and the spectral changes as a result of time-dependent concentration fluctuations of biomolecular species in their biofilms including carbohydrates, lipids, proteins, and genetic materials allow not only identification but also discrimination of biofilms using principal component analysis.
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Affiliation(s)
- Seda Keleştemur
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Atasehir, Istanbul, Turkey
| | - Mustafa Çulha
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Atasehir, Istanbul, Turkey
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Vasylevskyi SI, Kracht S, Corcosa P, Fromm KM, Giese B, Füeg M. Bildung von Nanopartikeln durch Elektronentransfer in Peptiden und c-Cytochromen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sonja Kracht
- Departement Chemie; Université de Fribourg; Chemin du Musée 9 1700 Fribourg Schweiz
| | - Paula Corcosa
- Departement Chemie; Université de Fribourg; Chemin du Musée 9 1700 Fribourg Schweiz
| | - Katharina M. Fromm
- Departement Chemie; Université de Fribourg; Chemin du Musée 9 1700 Fribourg Schweiz
| | - Bernd Giese
- Departement Chemie; Université de Fribourg; Chemin du Musée 9 1700 Fribourg Schweiz
| | - Michael Füeg
- Departement für Chemie und Biochemie; Universität Bern; Freiestrasse 3 3012 Bern Schweiz
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Vasylevskyi SI, Kracht S, Corcosa P, Fromm KM, Giese B, Füeg M. Formation of Silver Nanoparticles by Electron Transfer in Peptides and c-Cytochromes. Angew Chem Int Ed Engl 2017; 56:5926-5930. [DOI: 10.1002/anie.201702621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Serhii I. Vasylevskyi
- Department of Chemistry; University of Fribourg; Chemin du Musée 9 1700 Fribourg Switzerland
| | - Sonja Kracht
- Department of Chemistry; University of Fribourg; Chemin du Musée 9 1700 Fribourg Switzerland
| | - Paula Corcosa
- Department of Chemistry; University of Fribourg; Chemin du Musée 9 1700 Fribourg Switzerland
| | - Katharina M. Fromm
- Department of Chemistry; University of Fribourg; Chemin du Musée 9 1700 Fribourg Switzerland
| | - Bernd Giese
- Department of Chemistry; University of Fribourg; Chemin du Musée 9 1700 Fribourg Switzerland
| | - Michael Füeg
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
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