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Tokunou Y, Tongu H, Kogure Y, Okamoto A, Toyofuku M, Nomura N. Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4670-4679. [PMID: 38411077 DOI: 10.1021/acs.est.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.
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Affiliation(s)
- Yoshihide Tokunou
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Ibaraki 305-0044, Japan
| | - Hiromasa Tongu
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Yugo Kogure
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Akihiro Okamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Ibaraki 305-0044, Japan
- School of Chemical Sciences and Engineering, Hokkaido University, 13 Kita, 8 Nishi, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8577, Japan
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Long X, Tokunou Y, Okamoto A. Mechano-control of Extracellular Electron Transport Rate via Modification of Inter-heme Coupling in Bacterial Surface Cytochrome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7421-7430. [PMID: 37079493 DOI: 10.1021/acs.est.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial outer-membrane multi-heme cytochromes (OMCs) mediate extracellular electron transport (EET). While heme alignment dictates the rate of EET, control of inter-heme coupling in a single OMC remains challenging, especially in intact cells. Given that OMCs diffuse and collide without aggregation on the cell surface, the overexpression of OMCs could increase such mechanical stress to impact the OMCs' protein structure. Here, the heme coupling is modified via mechanical interactions among OMCs by controlling their concentrations. Employment of whole-cell circular dichroism (CD) spectra of genetically engineered Escherichia coli reveals that the OMC concentration significantly impacts the molar CD and redox property of OMCs, resulting in a 4-fold change of microbial current production. The overexpression of OMCs increased the conductive current across the biofilm on an interdigitated electrode, indicating that a higher concentration of OMCs causes more lateral inter-protein electron hopping via collision on the cell surface. The present study would open a novel strategy to increase microbial current production by mechanically enhancing the inter-heme coupling.
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Affiliation(s)
- Xizi Long
- School of the Key Laboratory of Typical Environmental Pollution and Health Hazards of Hunan Province, School of Basic Medicine, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Yoshihide Tokunou
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kitaku, Sapporo, Hokkaido 060-8628, Japan
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Abstract
Extracellular electron transfer (EET) is a process via which certain microorganisms, such as bacteria, exchange electrons with extracellular materials by creating an electrical link across their membranes. EET has been studied for the reactions on solid materials such as minerals and electrodes with implication in geobiology and biotechnology. EET-capable bacteria exhibit broad phylogenetic diversity, and some are found in environments with various types of electron acceptors/donors not limited to electrodes or minerals. Oxygen has also been shown to serve as the terminal electron acceptor for EET of Pseudomonas aeruginosa and Faecalibacterium prausnitzii. However, the physiological significance of such oxygen-terminating EETs, as well as the mechanisms underlying them, remain unclear. In order to understand the physiological advantage of oxygen-terminating EET and its link with energy metabolism, in this review, we compared oxygen-terminating EET with aerobic respiration, fermentation, and electrode-terminating EET. We also summarized benefits and limitations of oxygen-terminating EET in a biofilm setting, which indicate that EET capability enables bacteria to create a niche in the anoxic zone of aerobic biofilms, thereby remodeling bacterial metabolic activities in biofilms.
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Then A, Ewald J, Söllner N, Cooper RE, Küsel K, Ibrahim B, Schuster S. Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211553. [PMID: 35620008 PMCID: PMC9115035 DOI: 10.1098/rsos.211553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe3+)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe2+)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe2+-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe3+-reducing/Fe2+-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe3+ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe2+ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe3+ reduction rate than longer periods.
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Affiliation(s)
- Andre Then
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Natalie Söllner
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Rebecca E. Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bashar Ibrahim
- Centre for Applied Mathematics and Bioinformatics, and Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
- European Virus Bioinformatics Center, Leutragraben 1 07743 Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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Deng X, Luo D, Okamoto A. Defined and unknown roles of conductive nanoparticles for the enhancement of microbial current generation: A review. BIORESOURCE TECHNOLOGY 2022; 350:126844. [PMID: 35158034 DOI: 10.1016/j.biortech.2022.126844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The ability of various bacteria to make use of solid substrates through extracellular electron transfer (EET) or extracellular electron uptake (EEU) has enabled the development of valuable biotechnologies such as microbial fuel cells (MFCs) and microbial electrosynthesis (MES). It is common practice to use metallic and semiconductive nanoparticles (NPs) for microbial current enhancement. However, the effect of NPs is highly variable between systems, and there is no clear guideline for effectively increasing the current generation. In the present review, the proposed mechanisms for enhancing current production in MFCs and MES are summarized, and the critical factors for NPs to enhance microbial current generation are discussed. Implications for microbially induced iron corrosion, where iron sulfide NPs are proposed to enhance the rate of EEU, photochemically driven MES, and several future research directions to further enhance microbial current generation, are also discussed.
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Affiliation(s)
- Xiao Deng
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Dan Luo
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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Springthorpe SK, Keitz BK. Extraction of Au(III) by Microbially Reduced Metal-Organic Frameworks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9078-9088. [PMID: 34292745 PMCID: PMC9307060 DOI: 10.1021/acs.langmuir.1c01180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gold is a critical resource in the jewelry and electronics industries and is facing increased consumer demand. Accordingly, methods for its extraction from waste effluents and environmental water sources have been sought to supplement existing mining infrastructure. Redox-mediated treatments, such as Fe(II)-based platforms, offer promise for precipitating soluble Au(III). We hypothesized that microbial generation of Fe(II) in the presence of sorbent metal-organic frameworks could capitalize on the advantages of both biological- and chemical-driven extraction approaches. Toward this aim, we tested Au(III) removal by Shewanella oneidensis cultured with Fe(III)-based materials (ferrihydrite, Fe-BTC, MIL-100, or MIL-127). Across all tested materials, S. oneidensis generated the highest levels of redox-active Fe(II) (1.99 ± 0.27 mM) when cultured with MIL-127 as a respiratory substrate in a bicarbonate-buffered medium. This translated into superior Au(III) removal performance in terms of both removal rate and capacity (k = 2.55 ± 0.60 h-1; Q = 183 mg g-1). Unlike other materials tested, MIL-127 also maintained cell viability following repeated Au(III) challenges, enabling the regeneration of Fe(II) in the framework. Together, these effects facilitated the treatment of multiple cycles of Au(III) by S. oneidensis-reduced MIL-127. Overall, this work demonstrates that microbial generation of Fe(II) can facilitate the removal of Au(III), augmenting purely adsorptive platforms. Given the biological and chemical modularity of our system, our results suggest that future optimizations to microbial Fe(II) generation may offer promise for improving Au(III) extraction processes.
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Affiliation(s)
- Sarah K Springthorpe
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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Hu S, Wu Y, Li F, Shi Z, Ma C, Liu T. Fulvic Acid-Mediated Interfacial Reactions on Exposed Hematite Facets during Dissimilatory Iron Reduction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6139-6150. [PMID: 33974438 DOI: 10.1021/acs.langmuir.1c00124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Although the dual role of natural organic matter (NOM) as an electron shuttle and an electron donor for dissimilatory iron (Fe) reduction has been extensively investigated, the underlying interfacial interactions between various exposed facets and NOM are poorly understood. In this study, fulvic acid (FA), as typical NOM, was used and its effect on the dissimilatory reduction of hematite {001} and {100} by Shewanella putrefaciens CN-32 was investigated. FA accelerates the bioreduction rates of hematite {001} and {100}, where the rate of hematite {100} is lower than that of hematite {001}. Secondary Fe minerals were not observed, but the HR-TEM images reveal significant defects. The ATR-FTIR results demonstrate that facet-dependent binding mainly occurs via surface complexation between the surface iron atoms and carboxyl groups of NOM. The spectroscopic and mass spectrometry analyses suggest that organic compounds with large molecular weight, highly aromatic and unsaturated structures, and lower H/C ratios are easily adsorbed on Fe oxides or decomposed by bacteria in FA-hematite {001} treatment after iron reduction. Due to the metabolic processes of cells, a significant number of compounds with higher H/C and medium O/C ratios appear. The Tafel curves show that hematite {100} possessed higher resistance (4.1-2.6 Ω) than hematite {001} (3.5-2.2 Ω) at FA concentrations ranging from 0 to 500 mg L-1, indicating that hematite {100} is less conductive during the electron transfer from reduced FA or cells to Fe oxides than hematite {001}. Overall, the discrepancy in the iron bioreduction of two exposed facets is attributed to both the different electrochemical activities of the Fe oxides and the different impacts on the properties and composition of OM. Our findings shed light on the molecular mechanisms of mutual interactions between FA and Fe oxides with various facets.
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Affiliation(s)
- Shiwen Hu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou, Guangdong 510006, P. R. China
| | - Yundang Wu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
| | - Zhenqing Shi
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou, Guangdong 510006, P. R. China
| | - Chao Ma
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 300072, P. R. China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, P. R. China
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Matsuda N, Okabe H, Nagamura T, Nakano K. Direct Electron Transfer Reaction of Cytochrome c Immobilized on a Bare ITO Electrode. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Naoki Matsuda
- Sensing System Research Center, AIST, 807-1 Shukumachi, Tosu, Saga 841-0052, Japan
| | - Hirotaka Okabe
- Sensing System Research Center, AIST, 807-1 Shukumachi, Tosu, Saga 841-0052, Japan
| | - Toshihiko Nagamura
- Sensing System Research Center, AIST, 807-1 Shukumachi, Tosu, Saga 841-0052, Japan
| | - Koji Nakano
- Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Takahara A. Preface to the Interfaces and Biology 1: Mechanobiology Special Issue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7333-7334. [PMID: 31181916 DOI: 10.1021/acs.langmuir.9b01206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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