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Bonné R, Marshall IPG, Bjerg JJ, Marzocchi U, Manca J, Nielsen LP, Aiyer K. Interaction of living cable bacteria with carbon electrodes in bioelectrochemical systems. Appl Environ Microbiol 2024; 90:e0079524. [PMID: 39082847 PMCID: PMC11337825 DOI: 10.1128/aem.00795-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
Cable bacteria are filamentous bacteria that couple the oxidation of sulfide in sediments to the reduction of oxygen via long-distance electron transport over centimeter distances through periplasmic wires. However, the capability of cable bacteria to perform extracellular electron transfer to acceptors, such as electrodes, has remained elusive. In this study, we demonstrate that living cable bacteria actively move toward electrodes in different bioelectrochemical systems. Carbon felt and carbon fiber electrodes poised at +200 mV attracted live cable bacteria from the sediment. When the applied potential was switched off, cable bacteria retracted from the electrode. qPCR and scanning electron microscopy corroborated this finding and revealed cable bacteria in higher abundance present on the electrode surface compared with unpoised controls. These experiments raise new possibilities to study metabolism of cable bacteria and cultivate them in bioelectrochemical devices for bioelectronic applications, such as biosensing and bioremediation. IMPORTANCE Extracellular electron transfer is a metabolic function associated with electroactive bacteria wherein electrons are exchanged with external electron acceptors or donors. This feature has enabled the development of several applications, such as biosensing, carbon capture, and energy recovery. Cable bacteria are a unique class of long, filamentous microbes that perform long-distance electron transport in freshwater and marine sediments. In this study, we demonstrate the attraction of cable bacteria toward carbon electrodes and demonstrate their potential electroactivity. This finding enables electronic control and monitoring of the metabolism of cable bacteria and may, in turn, aid in the development of bioelectronic applications.
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Affiliation(s)
- Robin Bonné
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Ugo Marzocchi
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Department of Biology, Center for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
| | - Jean Manca
- X-LAB, Hasselt University, Agoralaan, Diepenbeek, Belgium
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Kartik Aiyer
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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2
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Gao Y, Zhou Y, Ji X, Graham AJ, Dundas CM, Miniel Mahfoud IE, Tibbett BM, Tan B, Partipilo G, Dodabalapur A, Rivnay J, Keitz BK. A hybrid transistor with transcriptionally controlled computation and plasticity. Nat Commun 2024; 15:1598. [PMID: 38383505 PMCID: PMC10881478 DOI: 10.1038/s41467-024-45759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Organic electrochemical transistors (OECTs) are ideal devices for translating biological signals into electrical readouts and have applications in bioelectronics, biosensing, and neuromorphic computing. Despite their potential, developing programmable and modular methods for living systems to interface with OECTs has proven challenging. Here we describe hybrid OECTs containing the model electroactive bacterium Shewanella oneidensis that enable the transduction of biological computations to electrical responses. Specifically, we fabricated planar p-type OECTs and demonstrated that channel de-doping is driven by extracellular electron transfer (EET) from S. oneidensis. Leveraging this mechanistic understanding and our ability to control EET flux via transcriptional regulation, we used plasmid-based Boolean logic gates to translate biological computation into current changes within the OECT. Finally, we demonstrated EET-driven changes to OECT synaptic plasticity. This work enables fundamental EET studies and OECT-based biosensing and biocomputing systems with genetically controllable and modular design elements.
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Affiliation(s)
- Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuchen Zhou
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
| | - Xudong Ji
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Austin J Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Ismar E Miniel Mahfoud
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Bailey M Tibbett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Benjamin Tan
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ananth Dodabalapur
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
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3
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Shi XC, Wang K, Xue M, Mao W, Xu K, Tremblay PL, Zhang T. Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens. CHEMOSPHERE 2024; 350:141177. [PMID: 38211787 DOI: 10.1016/j.chemosphere.2024.141177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5-20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.
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Affiliation(s)
- Xiao-Chen Shi
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, 528437, PR China
| | - Kefan Wang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Miao Xue
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Weijia Mao
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Kai Xu
- Center for Material Research and Analysis, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
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4
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Gemünde A, Gail J, Holtmann D. Anodic Respiration of Vibrio natriegens in a Bioelectrochemical System. CHEMSUSCHEM 2023; 16:e202300181. [PMID: 37089008 DOI: 10.1002/cssc.202300181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Vibrio natriegens promises to be a new standard biotechnological working organism since it grows extraordinarily fast, its productivity surpasses E. coli by far, and genomic tools are getting readily available. Recent studies provided insights into its extracellular electron transfer pathway, revealing it to be similar to other well-known electroactive organisms. Therefore, we aimed to show for the first time that V. natriegens donates electrons from its metabolism to an electrode by direct contact as well as via an artificial redox mediator. Our results demonstrate current densities up to 196 μA cm-2 using an artificial mediator. Via direct electron transfer, 6.6 μA cm-2 were achieved within the first 24 h of cultivation. In the mediated system, mainly formate, acetate, and succinate were produced from glucose. These findings favor V. natriegens over established electroactive organisms due to its superior electron-transfer capabilities combined with an outstanding metabolism.
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Affiliation(s)
- André Gemünde
- Institute of Bioprocess Engineering and Pharmaceutical Technology and Competence Centre for Sustainable Engineering and Environmental Systems, University of Applied Sciences Mittelhessen, 35390, Gießen, Germany
| | - Jonas Gail
- Institute of Bioprocess Engineering and Pharmaceutical Technology and Competence Centre for Sustainable Engineering and Environmental Systems, University of Applied Sciences Mittelhessen, 35390, Gießen, Germany
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology and Competence Centre for Sustainable Engineering and Environmental Systems, University of Applied Sciences Mittelhessen, 35390, Gießen, Germany
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5
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Gao Y, Zhou Y, Ji X, Graham AJ, Dundas CM, Mahfoud IEM, Tibbett BM, Tan B, Partipilo G, Dodabalapur A, Rivnay J, Keitz BK. A Hybrid Transistor with Transcriptionally Controlled Computation and Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553547. [PMID: 37645977 PMCID: PMC10462107 DOI: 10.1101/2023.08.16.553547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Organic electrochemical transistors (OECTs) are ideal devices for translating biological signals into electrical readouts and have applications in bioelectronics, biosensing, and neuromorphic computing. Despite their potential, developing programmable and modular methods for living systems to interface with OECTs has proven challenging. Here we describe hybrid OECTs containing the model electroactive bacterium Shewanella oneidensis that enable the transduction of biological computations to electrical responses. Specifically, we fabricated planar p-type OECTs and demonstrated that channel de-doping is driven by extracellular electron transfer (EET) from S. oneidensis. Leveraging this mechanistic understanding and our ability to control EET flux via transcriptional regulation, we used plasmid-based Boolean logic gates to translate biological computation into current changes within the OECT. Finally, we demonstrated EET-driven changes to OECT synaptic plasticity. This work enables fundamental EET studies and OECT-based biosensing and biocomputing systems with genetically controllable and modular design elements.
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Affiliation(s)
- Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuchen Zhou
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Xudong Ji
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Austin J. Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christopher M. Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismar E. Miniel Mahfoud
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Bailey M. Tibbett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Benjamin Tan
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ananth Dodabalapur
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
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6
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Bird LJ, Mickol RL, Eddie BJ, Thakur M, Yates MD, Glaven SM. Marinobacter: A case study in bioelectrochemical chassis evaluation. Microb Biotechnol 2023; 16:494-506. [PMID: 36464922 PMCID: PMC9948230 DOI: 10.1111/1751-7915.14170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/08/2022] Open
Abstract
The junction of bioelectrochemical systems and synthetic biology opens the door to many potentially groundbreaking technologies. When developing these possibilities, choosing the correct chassis organism can save a great deal of engineering effort and, indeed, can mean the difference between success and failure. Choosing the correct chassis for a specific application requires a knowledge of the metabolic potential of the candidate organisms, as well as a clear delineation of the traits, required in the application. In this review, we will explore the metabolic and electrochemical potential of a single genus, Marinobacter. We will cover its strengths, (salt tolerance, biofilm formation and electrochemical potential) and weaknesses (insufficient characterization of many strains and a less developed toolbox for genetic manipulation) in potential synthetic electromicrobiology applications. In doing so, we will provide a roadmap for choosing a chassis organism for bioelectrochemical systems.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Rebecca L. Mickol
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Brian J. Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
- College of Science, George Mason UniversityFairfaxVirginiaUSA
| | - Matthew D. Yates
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research LaboratoryWashingtonDistrict of ColumbiaUSA
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7
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Li X, Liang Y, Wang Z, Yao Y, Chen X, Shao A, Lu L, Dang H. Isolation and Characterization of a Novel Vibrio natriegens—Infecting Phage and Its Potential Therapeutic Application in Abalone Aquaculture. BIOLOGY 2022; 11:biology11111670. [PMID: 36421384 PMCID: PMC9687132 DOI: 10.3390/biology11111670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Phage-based pathogen control (i.e., phage therapy) has received increasing scientific attention to reduce and prevent the emergence, transmission, and detrimental effects of antibiotic resistance. In the current study, multidrug-resistant Vibrio natriegens strain AbY-1805 was isolated and tentatively identified as a pathogen causing the death of juvenile Pacific abalones (Haliotis discus hannai Ino). In order to apply phage therapy, instead of antibiotics, to treat and control V. natriegens infections in marine aquaculture environments, a lytic phage, vB_VnaS-L3, was isolated. It could effectively infect V. natriegens AbY-1805 with a short latent period (40 min) and high burst size (~890 PFU/cell). Treatment with vB_VnaS-L3 significantly reduced the mortality of juvenile abalones and maintained abalone feeding capacity over a 40-day V. natriegens challenge experiment. Comparative genomic and phylogenetic analyses suggested that vB_VnaS-L3 was a novel marine Siphoviridae-family phage. Furthermore, vB_VnaS-L3 had a narrow host range, possibly specific to the pathogenic V. natriegens strains. It also exhibited viability at a wide range of pH, temperature, and salinity. The short latent period, large burst size, high host specificity, and broad environmental adaptation suggest that phage vB_VnaS-L3 could potentially be developed as an alternative antimicrobial for the control and prevention of marine animal infections caused by pathogenic V. natriegens.
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Affiliation(s)
- Xuejing Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Zhenhua Wang
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai 264316, China
| | - Yanyan Yao
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai 264316, China
| | - Xiaoli Chen
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai 264316, China
| | - Anran Shao
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai 264316, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai 264316, China
- Correspondence: (L.L.); (H.D.)
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (L.L.); (H.D.)
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8
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Electrochemical Enrichment and Isolation of Electrogenic Bacteria from 0.22 µm Filtrate. Microorganisms 2022; 10:microorganisms10102051. [PMID: 36296327 PMCID: PMC9611719 DOI: 10.3390/microorganisms10102051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/30/2022] [Accepted: 10/16/2022] [Indexed: 11/23/2022] Open
Abstract
Ultramicrobacteria (UMB) that can pass through a 0.22 µm filter are attractive because of their novelty and diversity. However, isolating UMB has been difficult because of their symbiotic or parasitic lifestyles in the environment. Some UMB have extracellular electron transfer (EET)-related genes, suggesting that these symbionts may grow on an electrode surface independently. Here, we attempted to culture from soil samples bacteria that passed through a 0.22 µm filter poised with +0.2 V vs. Ag/AgCl and isolated Cellulomonas sp. strain NTE-D12 from the electrochemical reactor. A phylogenetic analysis of the 16S rRNA showed 97.9% similarity to the closest related species, Cellulomonas algicola, indicating that the strain NTE-D12 is a novel species. Electrochemical and genomic analyses showed that the strain NTE-D12 generated the highest current density compared to that in the three related species, indicating the presence of a unique electron transfer system in the strain. Therefore, the present study provides a new isolation scheme for cultivating and isolating novel UMB potentially with a symbiotic relationship associated with interspecies electron transfer.
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9
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Jain A, Kalb MJ, Gralnick JA. Reconstructing electron transfer components from an Fe(II) oxidizing bacterium. Microbiology (Reading) 2022; 168. [DOI: 10.1099/mic.0.001240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neutrophilic Fe(II) oxidizing bacteria play an important role in biogeochemical processes and have also received attention for multiple technological applications. These micro-organisms are thought to couple their metabolism with extracellular electron transfer (EET) while oxidizing Fe(II) as electron donor outside the cell. Sideroxydans lithotrophicus ES-1 is a freshwater chemolithoautotrophic Fe(II) oxidizing bacterium that is challenging to culture and not yet genetically tractable. Analysis of the S. lithotrophicus ES-1 genome predicts multiple EET pathways, which are proposed to be involved in Fe(II) oxidation, but not yet validated. Here we expressed components of two of the proposed EET pathways, including the Mto and Slit_0867–0870 PCC3 pathways, from S. lithotrophicus ES-1 into
Aeromonas hydrophila
, an established model EET organism. We demonstrate that combinations of putative inner membrane and periplasmic components from the Mto and Slit_0867–0870 PCC3 pathways partially complemented EET activity in
Aeromonas
mutants lacking native components. Our results provide evidence for electron transfer functionality and interactions of inner membrane and periplasmic components from the Mto and Slit_0867–0870 PCC3 pathways. Based on these findings, we suggest that EET in S. lithotrophicus ES-1 could be more complicated than previously considered and raises questions regarding directionality of these electron transfer pathways.
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Affiliation(s)
- Abhiney Jain
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
| | - Madison J. Kalb
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota — Twin Cities, St. Paul, MN 55108, USA
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10
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Meng W, Zhang Y, Ma L, Lü C, Xu P, Ma C, Gao C. Non-Sterilized Fermentation of 2,3-Butanediol with Seawater by Metabolic Engineered Fast-Growing Vibrio natriegens. Front Bioeng Biotechnol 2022; 10:955097. [PMID: 35903792 PMCID: PMC9315368 DOI: 10.3389/fbioe.2022.955097] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Sustainable and environment-friendly microbial fermentation processes have been developed to produce numerous chemicals. However, the high energy input required for sterilization and substantial fresh water consumption restrict the economic feasibility of traditional fermentation processes. To address these problems, Vibrio natriegens, a promising microbial chassis with low nutritional requirements, high salt tolerance and rapid growth rate can be selected as the host for chemical production. In this study, V. natriegens was metabolic engineered to produce 2,3-butanediol (2,3-BD), an important platform chemical, through non-sterilized fermentation with seawater-based minimal medium after expressing a 2,3-BD synthesis cluster and deleting two byproduct encoding genes. Under optimized fermentative conditions, 41.27 g/L 2,3-BD was produced with a productivity of 3.44 g/L/h and a yield of 0.39 g/g glucose by recombinant strain V. natriegensΔfrdAΔldhA-pETRABC. This study confirmed the feasibility of non-sterilized fermentation using seawater to replace freshwater and other valuable chemicals may also be produced through metabolic engineering of the emerging synthetic biology chassis V. natriegens.
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Affiliation(s)
- Wensi Meng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yongjia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Liting Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Chao Gao,
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11
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Abel AJ, Hilzinger JM, Arkin AP, Clark DS. Systems-informed genome mining for electroautotrophic microbial production. Bioelectrochemistry 2022; 145:108054. [DOI: 10.1016/j.bioelechem.2022.108054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
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12
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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13
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Aiyer K, Doyle LE. Capturing the signal of weak electricigens: a worthy endeavour. Trends Biotechnol 2021; 40:564-575. [PMID: 34696916 DOI: 10.1016/j.tibtech.2021.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/15/2022]
Abstract
Recently several non-traditional electroactive microorganisms have been discovered. These can be considered weak electricigens; microorganisms that typically rely on soluble electron acceptors and donors in their lifecycle but are also capable of extracellular electron transfer (EET), resulting in either a low, unreliable, or otherwise unexpected current. These unanticipated electroactive microorganisms represent a new chapter in electromicrobiology and have important medical, environmental, and biotechnological relevance. As such, it is essential to continue the momentum of their discovery. However, their study poses unique challenges due to their low current output. Capturing their signal necessitates novel approaches including unconventional electrode choice, the use of sensitive electrochemical techniques, and modifications of conventional experiments that use bioelectrochemical systems (BES).
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Affiliation(s)
- Kartik Aiyer
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, G5WV+9H9, Hauz Khas, New Delhi, Delhi 110016, India
| | - Lucinda E Doyle
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, G5WV+9H9, Hauz Khas, New Delhi, Delhi 110016, India.
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14
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Blombach B, Grünberger A, Centler F, Wierckx N, Schmid J. Exploiting unconventional prokaryotic hosts for industrial biotechnology. Trends Biotechnol 2021; 40:385-397. [PMID: 34482995 DOI: 10.1016/j.tibtech.2021.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Developing cost-efficient biotechnological processes is a major challenge in replacing fossil-based industrial production processes. The remarkable progress in genetic engineering ensures efficient and fast tailoring of microbial metabolism for a wide range of bioconversions. However, improving intrinsic properties such as tolerance, handling, growth, and substrate consumption rates is still challenging. At the same time, synthetic biology tools are becoming easier applicable and transferable to nonmodel organisms. These trends have resulted in the exploitation of new and unconventional microbial systems with sophisticated properties, which render them promising hosts for the bio-based industry. Here, we highlight the metabolic and cellular capabilities of representative prokaryotic newcomers and discuss the potential and drawbacks of these hosts for industrial application.
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Affiliation(s)
- Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany; SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | | | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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15
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Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol 2021; 20:5-19. [PMID: 34316046 DOI: 10.1038/s41579-021-00597-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 02/03/2023]
Abstract
Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China. .,Department of Microbiology, University of Massachusetts, Amherst, MA, USA. .,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.,Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA
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16
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Metabolic engineering of Vibrio natriegens. Essays Biochem 2021; 65:381-392. [PMID: 33835156 PMCID: PMC8314017 DOI: 10.1042/ebc20200135] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022]
Abstract
Vibrio natriegens is emerging as a promising host for biotechnology which is basically due to the remarkable intrinsic properties such as the exceptionally high growth and substrate consumption rates. The facultatively anaerobic marine bacterium possesses a versatile metabolism, is able to utilize a variety of substrates as carbon and energy sources and is easy to handle in the lab. These features initiated the rapid development of genetic tools and resulted in extensive engineering of production strains in the past years. Although recent examples illustrate the potential of V. natriegens for biotechnology, a comprehensive understanding of the metabolism and its regulation is still lacking but essential to exploit the full potential of this bacterium. In this review, we summarize the current knowledge on the physiological traits and the genomic organization, provide an overview of the available genetic engineering tools and recent advances in metabolic engineering of V. natriegens. Finally, we discuss the obstacles which have to be overcome in order to establish V. natriegens as industrial production host.
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17
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Boedicker JQ, Gangan M, Naughton K, Zhao F, Gralnick JA, El-Naggar MY. Engineering Biological Electron Transfer and Redox Pathways for Nanoparticle Synthesis. Bioelectricity 2021; 3:126-135. [PMID: 34476388 DOI: 10.1089/bioe.2021.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many species of bacteria are naturally capable of types of electron transport not observed in eukaryotic cells. Some species live in environments containing heavy metals not typically encountered by cells of multicellular organisms, such as arsenic, cadmium, and mercury, leading to the evolution of enzymes to deal with these environmental toxins. Bacteria also inhabit a variety of extreme environments, and are capable of respiration even in the absence of oxygen as a terminal electron acceptor. Over the years, several of these exotic redox and electron transport pathways have been discovered and characterized in molecular-level detail, and more recently synthetic biology has begun to utilize these pathways to engineer cells capable of detecting and processing a variety of metals and semimetals. One such application is the biologically controlled synthesis of nanoparticles. This review will introduce the basic concepts of bacterial metal reduction, summarize recent work in engineering bacteria for nanoparticle production, and highlight the most cutting-edge work in the characterization and application of bacterial electron transport pathways.
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Affiliation(s)
- James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Manasi Gangan
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Kyle Naughton
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Fengjie Zhao
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA.,Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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18
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Fan J, Xiao Y, Quick M, Yang Y, Sun Z, Javitch JA, Zhou X. Crystal structures of LeuT reveal conformational dynamics in the outward-facing states. J Biol Chem 2021; 296:100609. [PMID: 33811858 PMCID: PMC8105300 DOI: 10.1016/j.jbc.2021.100609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023] Open
Abstract
The neurotransmitter:sodium symporter (NSS) homolog LeuT from Aquifex aeolicus has proven to be a valuable model for studying the transport mechanism of the NSS family. Crystal structures have captured LeuT in key conformations visited during the transport cycle, allowing for the construction of a nearly complete model of transport, with much of the conformational dynamics studied by computational simulations. Here, we report crystal structures of LeuT representing new intermediate conformations between the outward-facing open and occluded states. These structures, combined with binding and accessibility studies, reveal details of conformational dynamics that can follow substrate binding at the central substrate binding site (S1) of LeuT in outward-facing states, suggesting a potential competition for direction between the outward-open and outward-occluded states at this stage during substrate transport. Our structures further support an intimate interplay between the protonation state of Glu290 and binding of Na1 that may ultimately regulate the outward-open-to-occluded transition.
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Affiliation(s)
- Jianjun Fan
- Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Xiao
- Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Matthias Quick
- Division of Molecular Therapeutics, New York State Psychiatric Institute, Columbia University, New York, New York, USA; Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yuwei Yang
- Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ziyi Sun
- Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Jonathan A Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, Columbia University, New York, New York, USA; Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA; Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA.
| | - Xiaoming Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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19
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Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria. mBio 2021; 13:e0290421. [PMID: 35100867 PMCID: PMC8805035 DOI: 10.1128/mbio.02904-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.
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