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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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2
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Zhang J, Wu D, Zhao Y, Liu D, Guo X, Chen Y, Zhang C, Sun X, Guo J, Yuan D, Xiao D, Li F, Song H. Engineering Shewanella oneidensis to efficiently harvest electricity power by co-utilizing glucose and lactate in thin stillage of liquor industry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158696. [PMID: 36108833 DOI: 10.1016/j.scitotenv.2022.158696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Thin stillage, rich in glucose and lactate, can seriously pollute water resources when directly discharged into the natural environment. Microbial fuel cells (MFC), as a green and sustainable technology, could utilize exoelectrogens to break down organics in wastewater and harvest electricity. Nevertheless, Shewanella oneidensis MR-1, cannot utilize thin stillage for efficient power generation. Here, to enable S. oneidensis to co-utilize glucose and lactate from thin stillage, an engineered S. oneidensis G7∆RSL1 was first created by constructing glucose metabolism pathway, promoting glucose and lactate co-utilization, and enhancing biofilm formation. Then, to enhance biofilm conductivity, we constructed a 3D self-assembled G7∆RSL1-rGO/CNT biohybrid with maximum power density of 560.4 mW m-2 and 373.7 mW m-2 in artificial and actual thin stillage, respectively, the highest among the reported genetically engineered S. oneidensis with thin stillage as carbon source. This study provides a new strategy to facilitate practical applications of MFC in wastewater remediation and efficient power recovery.
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Affiliation(s)
- Junqi Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China; Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Yakun Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China
| | - Dingyuan Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Xi Sun
- College of Biological Engineering, Tianjin Agricultural University, Tianjin, PR China
| | - Ju Guo
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dezhi Yuan
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Feng Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China.
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3
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Ford K, Kaste JAM, Shachar-Hill Y, TerAvest MA. Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1. ACS Synth Biol 2022; 11:3405-3413. [PMID: 36219726 PMCID: PMC9595118 DOI: 10.1021/acssynbio.2c00323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/24/2023]
Abstract
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.
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Affiliation(s)
- Kathryne
C. Ford
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Microbiology and Molecular Genetics, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Joshua A. M. Kaste
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yair Shachar-Hill
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Michaela A. TerAvest
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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4
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Teel HR, Likit-Anurak K, Shimpalee S, Turick CE. Imaginary admittance and charge transfer resistance correlate to the physiological status of Shewanella oneidensis cultures in real time. Bioelectrochemistry 2022; 147:108210. [PMID: 35872371 DOI: 10.1016/j.bioelechem.2022.108210] [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: 01/26/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022]
Abstract
Monitoring microbial activity is essential for industrial and environmental applications to proceed efficiently. To minimize time and labor-intensive monitoring, a new paradigm is required for in-situ, real time analysis. Since bioconversion of organics is accomplished by microorganisms through the oxidation of feedstocks linked to the reduction of electron acceptors, microorganisms can be viewed as electrochemical catalysts. In this respect, cell membranes have an electrical potential, which is analogous to a conventional capacitor and linked dynamically to cellular activity. Here we demonstrate the use of electrochemical impedance spectrometry (EIS) and cyclic voltammetry (CV) for monitoring microbial metabolic activity in real time, in-situ. The effect of organic electron donors as a function of concentration to the physiological status of strains of Shewanella oneidensis was determined. In this study, the pyomelanin overproducer (S. oneidensis ΔhmgA) and the pyomelanin deficient mutant (S. oneidensis ΔmelA) were chosen due to different surface electrochemical characteristics along with differences in oxygen utilization efficiency. CV, relative admittance, phase shift and permittivity changed with growth status and correlated with electron flow from organic carbon sources and terminal electron acceptor availability. This work offers a novel and inexpensive approach to real time monitoring with the advantage of abundant data.
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Affiliation(s)
| | | | | | - Charles E Turick
- ElectroBioDyne LLC, Aiken, SC, USA; Savannah River National Lab., Aiken, SC 29803.
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5
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Han HX, Tian LJ, Liu DF, Yu HQ, Sheng GP, Xiong Y. Reversing Electron Transfer Chain for Light-Driven Hydrogen Production in Biotic-Abiotic Hybrid Systems. J Am Chem Soc 2022; 144:6434-6441. [PMID: 35377628 DOI: 10.1021/jacs.2c00934] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biotic-abiotic photosynthetic system integrating inorganic light absorbers with whole-cell biocatalysts innovates the way for sustainable solar-driven chemical transformation. Fundamentally, the electron transfer at the biotic-abiotic interface, which may induce biological response to photoexcited electron stimuli, plays an essential role in solar energy conversion. Herein, we selected an electro-active bacterium Shewanella oneidensis MR-1 as a model, which constitutes a hybrid photosynthetic system with a self-assembled CdS semiconductor, to demonstrate unique biotic-abiotic interfacial behavior. The photoexcited electrons from CdS nanoparticles can reverse the extracellular electron transfer (EET) chain within S. oneidensis MR-1, realizing the activation of a bacterial catalytic network with light illumination. As compared with bare S. oneidensis MR-1, a significant upregulation of hydrogen yield (711-fold), ATP, and reducing equivalent (NADH/NAD+) was achieved in the S. oneidensis MR-1-CdS under visible light. This work sheds light on the fundamental mechanism and provides design guidelines for biotic-abiotic photosynthetic systems.
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Affiliation(s)
- He-Xing Han
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Li-Jiao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yujie Xiong
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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6
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Yi YC, Ng IS. Redirection of metabolic flux in Shewanella oneidensis MR-1 by CRISPRi and modular design for 5-aminolevulinic acid production. BIORESOUR BIOPROCESS 2021; 8:13. [PMID: 38650245 PMCID: PMC10992681 DOI: 10.1186/s40643-021-00366-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/01/2021] [Indexed: 11/10/2022] Open
Abstract
Programming non-canonical organisms is more attractive due to the prospect of high-value chemical production. Among all, Shewanella oneidensis MR-1 possesses outstanding heme synthesis ability and is well-known for electron transfer, thus has high potential in microbial fuel cell and bioremediation. However, heme, as the final product of C4 and C5 pathways, is regulated by heme cluster for the high-value 5-aminolevulinic acid (ALA) for cancer photodynamic therapy, which has never been explored in MR-1. Herein, the heme metabolism in MR-1 was firstly optimized for ALA production. We applied CRISPR interference (CRISPRi) targeted on the genes to fine-tune carbon flux in TCA cycle and redirected the carbon out-flux from heme, leading to a significant change in the amino acid profiles, while downregulation of the essential hemB showed a 2-fold increasing ALA production via the C5 pathway. In contrast, the modular design including of glucokinase, GroELS chaperone, and ALA synthase from Rhodobacter capsulatus enhanced ALA production markedly in the C4 pathway. By integrating gene cluster under dual T7 promoters, we obtained a new strain M::TRG, which significantly improved ALA production by 145-fold. We rewired the metabolic flux of MR-1 through this modular design and successfully produced the high-value ALA compound at the first time.
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Affiliation(s)
- Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
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7
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Cheng L, Min D, He R, Cheng Z, Liu D, Yu H. Developing a base‐editing system to expand the carbon source utilization spectra of
Shewanella oneidensis
MR‐1 for enhanced pollutant degradation. Biotechnol Bioeng 2020; 117:2389-2400. [DOI: 10.1002/bit.27368] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Lei Cheng
- School of Life Sciences, University of Science and Technology of China Hefei China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Ru‐Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Zhou‐Hua Cheng
- School of Life Sciences, University of Science and Technology of China Hefei China
| | - Dong‐Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Han‐Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
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8
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Gonzalez NM, Fitch A, Al-Bazi J. Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3-methyl-5-pyrazolone derivatization. PLoS One 2020; 15:e0229990. [PMID: 32163461 PMCID: PMC7067395 DOI: 10.1371/journal.pone.0229990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022] Open
Abstract
A method was developed and validated for low-level detection of glucose. The method involves quantitation of glucose though derivitization with 1-phenyl-3-methyl-5-pyrazolone (PMP) and HPLC-DAD analysis. The developed method was found to be accurate and robust achieving detection limits as low as 0.09 nM. The applicability of the method was tested against microbial samples with glucose acting as a carbon fuel source. The method was shown to be able to accurately discriminate and quantify PMP-glucose derivatives within Shewanella oneidensis MR-1 samples. The method proved capable at examining glucose usage during the early hours of microbial growth, with detectable usage occurring as early as two hours. S. oneidensis cultures were found to grow more effectively in the presence of oxygen which coincided with more efficient glucose usage. Glucose usage further increased in the presence of competing electron acceptors. The rate at which S. oneidensis reached exponential growth was affected by the presence of ferric iron under microaerobic conditions. Such samples reached exponential growth approximately two hours sooner than aerobic samples.
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Affiliation(s)
- Norberto M. Gonzalez
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
| | - Alanah Fitch
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
| | - John Al-Bazi
- Department of Chemistry, Northeastern Illinois University, Chicago, IL, United States of America
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9
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Hirose A, Kouzuma A, Watanabe K. Towards development of electrogenetics using electrochemically active bacteria. Biotechnol Adv 2019; 37:107351. [DOI: 10.1016/j.biotechadv.2019.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/09/2019] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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10
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Hirose A, Kasai T, Koga R, Suzuki Y, Kouzuma A, Watanabe K. Understanding and engineering electrochemically active bacteria for sustainable biotechnology. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0245-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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11
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Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 2018; 109:571-583. [PMID: 29995975 DOI: 10.1111/mmi.14067] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.
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Affiliation(s)
- Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Thea Bursac
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Catarina Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Ricardo Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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12
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Yu Q, Fein JB. Controls on Bacterial Cell Envelope Sulfhydryl Site Concentrations: The Effect of Glucose Concentration During Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7395-7402. [PMID: 28603975 DOI: 10.1021/acs.est.7b01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial sulfhydryl sites can form strong complexes with chalcophilic metals such as Hg and Cd, thereby affecting the fate, transport, and bioavailability of these metals in both natural and engineered systems. In this study, five bacterial species were cultured in M9 minimal media containing a range of glucose concentrations as carbon source and in a high-nutrient TSB medium enriched with 50 g/L of glucose, and the sulfhydryl site concentrations of the obtained biomass samples were determined through selective sulfhydryl site-blocking, potentiometric titrations, and surface complexation modeling. The experimental results show that the glucose concentration in the M9 minimal media strongly affects the concentration of sulfhydryl sites that are present on the bacteria, with higher glucose concentrations yielding higher bacterial sulfhydryl site concentrations for each species studied. In contrast, although adding 50 g/L of glucose to the TSB medium significantly increases the sulfhydryl site concentrations for the three Bacillus species studied, the elevated glucose concentration does not significantly affect sulfhydryl site concentrations for S. oneidensis and P. putida samples when grown in the TSB medium. Our results suggest that bacterial sulfhydryl site concentrations in natural systems are likely affected by the composition of the bacterial community and by the available nutrients, and that these factors must be considered in order to determine and model the effects of bacterial cells on metal cycling and metal bioavailability in the environment.
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Affiliation(s)
- Qiang Yu
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Jeremy B Fein
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
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13
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Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1. J Bacteriol 2017; 199:JB.00827-16. [PMID: 28289083 PMCID: PMC5424254 DOI: 10.1128/jb.00827-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/04/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved when Shewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism of N-acetylglucosamine are the common basis for evolved glucose metabolism across populations. The loss of nagR results in the constitutive expression of genes for an N-acetylglucosamine permease (nagP) and kinase (nagK). We demonstrate that promiscuous activities of both NagP and NagK toward glucose allow for the transport and phosphorylation of glucose to glucose-6-phosphate, the initial events of glycolysis otherwise thought to be absent in S. oneidensis. 13C-based metabolic flux analysis uncovered that subsequent utilization was mediated by the Entner-Doudoroff pathway. This is an example whereby gene loss and preexisting enzymatic promiscuity, and not gain-of-function mutations, were the drivers of increased metabolic capacity. However, we observed a significant decrease in the growth rate on lactate after adaptation to glucose catabolism, suggesting that trade-offs may explain why glycolytic function may not be readily observed in S. oneidensis in natural environments despite it being readily accessible through just a single mutational event. IMPORTANCE Gains in metabolic capacity are frequently associated with the acquisition of novel genetic material via natural or engineered horizontal gene transfer events. Here, we explored how a bacterium that typically consumes small organic acids and amino acids expands its metabolic capacity to include glucose via a loss of genetic material, a process frequently associated with a deterioration of metabolic function. Our findings highlight how the natural promiscuity of transporters and enzymes can be a key driver in expanding metabolic diversity and that many bacteria may possess a latent metabolic capacity accessible through one or a few mutations that remove regulatory functions. Our discovery of trade-offs between growth on lactate and on glucose suggests why this easily gained trait is not observed in nature.
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14
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Lin T, Bai X, Hu Y, Li B, Yuan Y, Song H, Yang Y, Wang J. Synthetic
Saccharomyces cerevisiae
‐
Shewanella oneidensis
consortium enables glucose‐fed high‐performance microbial fuel cell. AIChE J 2016. [DOI: 10.1002/aic.15611] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tong Lin
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Xue Bai
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yidan Hu
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Bingzhi Li
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Ying‐Jin Yuan
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Hao Song
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yun Yang
- School of Chemistry and EnvironmentBeihang UniversityBeijing100191 China
| | - Jingyu Wang
- Dept. of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis MN55455
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15
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Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis. Appl Environ Microbiol 2016; 82:3996-4005. [PMID: 27107127 DOI: 10.1128/aem.00881-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Shewanella oneidensis is unable to metabolize the sugar xylose as a carbon and energy source. In the present study, an otherwise silent xylose catabolic pathway was activated in S. oneidensis by following an adaptive evolution strategy. Genome-wide scans indicated that the S. oneidensis genome encoded two proteins similar to the xylose oxido-reductase pathway enzymes xylose reductase (SO_0900) and xylulokinase (SO_4230), and purified SO_0900 and SO_4230 displayed xylose reductase and xylulokinase activities, respectively. The S. oneidensis genome was missing, however, an Escherichia coli XylE-like xylose transporter. After 12 monthly transfers in minimal growth medium containing successively higher xylose concentrations, an S. oneidensis mutant (termed strain XM1) was isolated for the acquired ability to grow aerobically on xylose as a carbon and energy source. Whole-genome sequencing indicated that strain XM1 contained a mutation in an unknown membrane protein (SO_1396) resulting in a glutamine-to-histidine conversion at amino acid position 207. Homology modeling demonstrated that the Q207H mutation in SO_1396 was located at the homologous xylose docking site in XylE. The expansion of the S. oneidensis metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by S. oneidensis Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass. IMPORTANCE The activation of an otherwise silent xylose metabolic system in Shewanella oneidensis is a powerful example of how accidental mutations allow microorganisms to adaptively evolve. The expansion of the S. oneidensis metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by S. oneidensis Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass.
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16
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Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions. PLoS One 2015; 10:e0138813. [PMID: 26394222 PMCID: PMC4579138 DOI: 10.1371/journal.pone.0138813] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022] Open
Abstract
In bioelectrochemical systems, the electrode potential is an important parameter affecting the electron flow between electrodes and microbes and microbial metabolic activities. Here, we investigated the metabolic characteristics of a glucose-utilizing strain of engineered Shewanella oneidensis under electrode-respiring conditions in electrochemical reactors for gaining insight into how metabolic pathways in electrochemically active bacteria are affected by the electrode potential. When an electrochemical reactor was operated with its working electrode poised at +0.4 V (vs. an Ag/AgCl reference electrode), the engineered S. oneidensis strain, carrying a plasmid encoding a sugar permease and glucose kinase of Escherichia coli, generated current by oxidizing glucose to acetate and produced D-lactate as an intermediate metabolite. However, D-lactate accumulation was not observed when the engineered strain was grown with a working electrode poised at 0 V. We also found that transcription of genes involved in pyruvate and D-lactate metabolisms was upregulated at a high electrode potential compared with their transcription at a low electrode potential. These results suggest that the carbon catabolic pathway of S. oneidensis can be modified by controlling the potential of a working electrode in an electrochemical bioreactor.
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17
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TerAvest MA, Ajo‐Franklin CM. Transforming exoelectrogens for biotechnology using synthetic biology. Biotechnol Bioeng 2015; 113:687-97. [DOI: 10.1002/bit.25723] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Michaela A. TerAvest
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCalifornia94720
| | - Caroline M. Ajo‐Franklin
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
- Materials Science DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
- Synthetic Biology InstituteLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
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18
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Kouzuma A, Kasai T, Hirose A, Watanabe K. Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells. Front Microbiol 2015; 6:609. [PMID: 26136738 PMCID: PMC4468914 DOI: 10.3389/fmicb.2015.00609] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/02/2015] [Indexed: 12/12/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that respires using a variety of inorganic and organic compounds. MR-1 is also capable of utilizing extracellular solid materials, including anodes in microbial fuel cells (MFCs), as electron acceptors, thereby enabling electricity generation. As MFCs have the potential to generate electricity from biomass waste and wastewater, MR-1 has been extensively studied to identify the molecular systems that are involved in electricity generation in MFCs. These studies have demonstrated the importance of extracellular electron-transfer (EET) pathways that electrically connect the quinone pool in the cytoplasmic membrane to extracellular electron acceptors. Electricity generation is also dependent on intracellular catabolic pathways that oxidize electron donors, such as lactate, and regulatory systems that control the expression of genes encoding the components of catabolic and electron-transfer pathways. In addition, recent findings suggest that cell-surface polymers, e.g., exopolysaccharides, and secreted chemicals, which function as electron shuttles, are also involved in electricity generation. Despite these advances in our knowledge on the EET processes in MR-1, further efforts are necessary to fully understand the underlying intra- and extracellular molecular systems for electricity generation in MFCs. We suggest that investigating how MR-1 coordinates these systems to efficiently transfer electrons to electrodes and conserve electrochemical energy for cell proliferation is important for establishing the biological basis for MFCs.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Takuya Kasai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Atsumi Hirose
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
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19
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Tao L, Wang H, Xie M, Thia L, Chen WN, Wang X. Improving mediated electron transport in anodic bioelectrocatalysis. Chem Commun (Camb) 2015; 51:12170-3. [DOI: 10.1039/c5cc03188e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A microbial fuel cell loaded with bio-cocatalyst beads immobilized with recombinant riboflavin-secreting Escherichia coli shows significantly enhanced performance.
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Affiliation(s)
- Le Tao
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
| | - Haibo Wang
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
| | - Mingshi Xie
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
| | - Larissa Thia
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
| | - Xin Wang
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 62 Nanyang Avenue
- Singapore
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20
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Choi D, Lee SB, Kim S, Min B, Choi IG, Chang IS. Metabolically engineered glucose-utilizing Shewanella strains under anaerobic conditions. BIORESOURCE TECHNOLOGY 2014; 154:59-66. [PMID: 24384311 DOI: 10.1016/j.biortech.2013.12.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 05/20/2023]
Abstract
Comparative genome analysis of Shewanella strains predicted that the strains metabolize preferably two- and three-carbon carbohydrates as carbon/electron source because many Shewanella genomes are deficient of the key enzymes in glycolysis (e.g., glucokinase). In addition, all Shewanella genomes are known to have only one set of genes associated with the phosphotransferase system required to uptake sugars. To engineer Shewanella strains that can utilize five- and six-carbon carbohydrates, we constructed glucose-utilizing Shewanella oneidensis MR-1 by introducing the glucose facilitator (glf; ZMO0366) and glucokinase (glk; ZMO0369) genes of Zymomonas mobilis. The engineered MR-1 strain was able to grow on glucose as a sole carbon/electron source under anaerobic conditions. The glucose affinity (Ks) and glucokinase activity in the engineered MR-1 strain were 299.46 mM and 0.259 ± 0.034 U/g proteins. The engineered strain was successfully applied to a microbial fuel cell system and exhibited current generation using glucose as the electron source.
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Affiliation(s)
- Donggeon Choi
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan gwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Sae Bom Lee
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan gwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Sohyun Kim
- College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-gu, Seoul 136-701, Republic of Korea
| | - Byoungnam Min
- College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-gu, Seoul 136-701, Republic of Korea
| | - In-Geol Choi
- College of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-gu, Seoul 136-701, Republic of Korea.
| | - In Seop Chang
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), 261 Cheomdan gwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
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