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Wang Z, Hu Y, Dong Y, Shi L, Jiang Y. Enhancing electrical outputs of the fuel cells with Geobacter sulferreducens by overexpressing nanowire proteins. Microb Biotechnol 2023; 16:534-545. [PMID: 36815664 PMCID: PMC9948223 DOI: 10.1111/1751-7915.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022] Open
Abstract
Protein nanowires are critical electroactive components for electron transfer of Geobacter sulfurreducens biofilm. To determine the applicability of the nanowire proteins in improving bioelectricity production, their genes including pilA, omcZ, omcS and omcT were overexpressed in G. sulfurreducens. The voltage outputs of the constructed strains were higher than that of the control strain with the empty vector (0.470-0.578 vs. 0.355 V) in microbial fuel cells (MFCs). As a result, the power density of the constructed strains (i.e. 1.39-1.58 W m-2 ) also increased by 2.62- to 2.97-fold as compared to that of the control strain. Overexpression of nanowire proteins also improved biofilm formation on electrodes with increased protein amount and thickness of biofilms. The normalized power outputs of the constructed strains were 0.18-0.20 W g-1 that increased by 74% to 93% from that of the control strain. Bioelectrochemical analyses further revealed that the biofilms and MFCs with the constructed strains had stronger electroactivity and smaller internal resistance, respectively. Collectively, these results demonstrate for the first time that overexpression of nanowire proteins increases the biomass and electroactivity of anode-attached microbial biofilms. Moreover, this study provides a new way for enhancing the electrical outputs of MFCs.
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Affiliation(s)
- Zhigao Wang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China.,Hubei Key Laboratory of Wetland Evolution and Eco-Restoration, Wuhan, Hubei, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China.,Hubei Key Laboratory of Wetland Evolution and Eco-Restoration, Wuhan, Hubei, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China.,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, Hubei, China.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, Hubei, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China.,Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, Hubei, China.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, Hubei, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China.,Hubei Key Laboratory of Wetland Evolution and Eco-Restoration, Wuhan, Hubei, China
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2
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Electric field stimulates production of highly conductive microbial OmcZ nanowires. Nat Chem Biol 2020; 16:1136-1142. [PMID: 32807967 PMCID: PMC7502555 DOI: 10.1038/s41589-020-0623-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 12/26/2022]
Abstract
Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of previously unknown cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S/cm), and 3-fold higher stiffness (1.5 GPa), than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function, and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modelling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically-produced, highly-conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.
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3
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Thirumurthy MA, Jones AK. Geobacter cytochrome OmcZs binds riboflavin: implications for extracellular electron transfer. NANOTECHNOLOGY 2020; 31:124001. [PMID: 31791015 DOI: 10.1088/1361-6528/ab5de6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Geobacter sulfurreducens is an important model organism for understanding extracellular electron transfer (EET), i.e. transfer of electrons from the cell's interior (quinone pool) to an extracellular substrate. This exoelectrogenic functionality can be exploited in bioelectrochemical applications. Nonetheless, key questions remain regarding the mechanisms of this functionality. G. sulfurreducens has been hypothesized to employ both multi-heme cytochromes and soluble, small molecule redox shuttles, as the final, redox-active species in EET. However, interactions between flavin redox shuttles and outer membrane, redox proteins in Geobacter have not been demonstrated. Herein, the heterologous expression and purification from E. coli of a soluble form of the multi-heme cytochrome OmcZs from G. sulfurreducens is reported. UV-vis absorption assays show that riboflavin can be reduced by OmcZs with concomitant oxidation of the protein. Fluorescence assays show that oxidized OmcZs and riboflavin interact with a binding constant of 34 μM. Furthermore, expression of OmcZs in E. coli enables EET in the host, and the current produced by these E. coli in a bioelectrochemical cell increases when riboflavin is introduced. These results support the hypothesis that OmcZs functions in EET by transiently binding riboflavin, which shuttles electrons from the outer membrane to the extracellular substrate.
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Affiliation(s)
- Miyuki A Thirumurthy
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
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Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell 2020; 177:361-369.e10. [PMID: 30951668 DOI: 10.1016/j.cell.2019.03.029] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/14/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022]
Abstract
Long-range (>10 μm) transport of electrons along networks of Geobacter sulfurreducens protein filaments, known as microbial nanowires, has been invoked to explain a wide range of globally important redox phenomena. These nanowires were previously thought to be type IV pili composed of PilA protein. Here, we report a 3.7 Å resolution cryoelectron microscopy structure, which surprisingly reveals that, rather than PilA, G. sulfurreducens nanowires are assembled by micrometer-long polymerization of the hexaheme cytochrome OmcS, with hemes packed within ∼3.5-6 Å of each other. The inter-subunit interfaces show unique structural elements such as inter-subunit parallel-stacked hemes and axial coordination of heme by histidines from neighboring subunits. Wild-type OmcS filaments show 100-fold greater conductivity than other filaments from a ΔomcS strain, highlighting the importance of OmcS to conductivity in these nanowires. This structure explains the remarkable capacity of soil bacteria to transport electrons to remote electron acceptors for respiration and energy sharing.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - J Patrick O'Brien
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Sophia M Yi
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Sibel Ebru Yalcin
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale University, New Haven, CT 06511, USA
| | - Dennis Vu
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Nicole L Ing
- Department of Materials Science & Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Allon I Hochbaum
- Department of Materials Science & Engineering, University of California, Irvine, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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Thermodynamic and functional characterization of the periplasmic triheme cytochrome PpcA from Geobacter metallireducens. Biochem J 2018; 475:2861-2875. [PMID: 30072494 DOI: 10.1042/bcj20180457] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 12/29/2022]
Abstract
The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular electron acceptors, including pollutants or electrode surfaces for current production in microbial fuel cells. For these reasons, G. metallireducens are of interest for practical biotechnological applications. The use of such electron acceptors relies on a mechanism that permits electrons to be transferred to the cell exterior. The cytochrome PpcA from G. metallireducens is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron transfer from the cytoplasmic donors to the extracellular acceptors. Using NMR and visible spectroscopic techniques, a detailed thermodynamic characterization of PpcA was obtained, including the determination of the heme reduction potentials and their redox and redox-Bohr interactions. These parameters revealed unique features for PpcA from G. metallireducens compared with other triheme cytochromes from different microorganisms, namely the less negative heme reduction potentials and concomitant functional working potential ranges. It was also shown that the order of oxidation of the hemes is pH-independent, but the protein is designed to couple e-/H+ transfer exclusively at physiological pH.
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Biochemical and functional insights on the triheme cytochrome PpcA from Geobacter metallireducens. Arch Biochem Biophys 2018; 644:8-16. [PMID: 29486160 DOI: 10.1016/j.abb.2018.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 02/07/2023]
Abstract
G. metallireducens bacterium has highly versatile respiratory pathways that provide the microorganism an enormous potential for many biotechnological applications. However, little is known about the structural and functional properties of its electron transfer components. In this work, the periplasmic cytochrome PpcA from G. metallireducens was studied in detail for the first time using complementary biophysical techniques, including UV-visible, CD and NMR spectroscopy. The results obtained showed that PpcA contains three low-spin c-type heme groups with His-His axial coordination, a feature also observed for its homologue in G. sulfurreducens. However, despite the high sequence homology between the two cytochromes, important structural and functional differences were observed. The comparative analysis of the backbone, side chain and heme substituents NMR signals revealed differences in the relative orientation of the hemes I and III. In addition, redox titrations followed by visible spectroscopy showed that the redox potential values for PpcA from G. metallireducens (-78 and -93 mV at pH 7 and 8, respectively) are considerably less negative. Overall, this study provides biochemical and biophysical data of a key cytochrome from G. metallireducens, paving the way to understand the extracellular electron transfer mechanisms in these bacteria.
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Ying X, Guo K, Chen W, Gu Y, Shen D, Zhou Y, Liang Y, Wang Y, Wang M, Feng H. The impact of electron donors and anode potentials on the anode-respiring bacteria community. Appl Microbiol Biotechnol 2017; 101:7997-8005. [PMID: 28944402 DOI: 10.1007/s00253-017-8518-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/15/2017] [Accepted: 09/04/2017] [Indexed: 01/13/2023]
Abstract
Both anode potentials and substrates can affect the process of biofilm formation in bioelectrochemical systems, but it is unclear who primarily determine the anode-respiring bacteria (ARB) community structure and composition. To address this issue, we divided microbial electrolysis cells (MECs) into groups, feeding them with different substrates and culturing them at various potentials. Non-turnover cyclic voltammetry indicated that the extracellular electron transfer components were uniform when feeding acetate, because the same oxidation peaks occurred at - 0.36 ± 0.01 and - 0.17 ± 0.01 V (vs. Ag/AgCl). Illumina MiSeq sequencing revealed that the dominating ARB was Geobacter, which did not change with different potentials. When the MECs were cultured with sucrose and mixed substrates, oxidation peak P3 (- 0.29 ± 0.015 V) occurred at potentials of - 0.29 and 0.01 V. This may be because of the appearance of Unclassified_AKYG597. In addition, oxidation peak P4 (- 0.99 ± 0.01 V) occurred at high and low potentials (0.61 and - 0.45 V, respectively), and the maximum current densities were far below those of the middle potentials. Illumina MiSeq sequencing showed that fermentation microorganisms (Lactococcus and Sphaerochaeta) dominated the biofilms. Consequently, substrate primarily determined the dominating ARB, and Geobacter invariably dominated the acetate-fed biofilms with potentials changed. Conversely, different potentials mainly affected fermentable substrate-fed biofilms, with dominating ARB turning into Unclassified_AKYG59.
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Affiliation(s)
- Xianbin Ying
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Kun Guo
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wei Chen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yuan Gu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yuyang Zhou
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yuxiang Liang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yanfeng Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China. .,Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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Fonseca BM, Tien M, Rivera M, Shi L, Louro RO. Efficient and selective isotopic labeling of hemes to facilitate the study of multiheme proteins. Biotechniques 2012; 52:000113859. [PMID: 26307249 DOI: 10.2144/000113859] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 04/02/2012] [Indexed: 11/23/2022] Open
Abstract
Specific isotopic labeling of hemes provides a unique opportunity to characterize the structure and function of heme-proteins. Unfortunately, current methods do not allow efficient labeling in high yields of multiheme cytochromes c, which are of great biotechnological interest. Here, a method for production of recombinant multiheme cytochromes c in Escherichia coli with isotopically labeled hemes is reported. A small tetraheme cytochrome of 12 kDa from Shewanella oneidensis MR-1 was used to demonstrate the method, achieving a production of 4 mg pure protein per liter. This method achieves, in a single step, efficient expression and incorporation of hemes isotopically labeled in specific atom positions adequate for spectroscopic characterization of these complex heme proteins. It is, furthermore, of general application to heme proteins, opening new possibilities for the characterization of this important class of proteins.
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Affiliation(s)
- Bruno M Fonseca
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mario Rivera
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Liang Shi
- Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 380] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
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