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Li Y, Cao M, Gupta VK, Wang Y. Metabolic engineering strategies to enable microbial electrosynthesis utilization of CO 2: recent progress and challenges. Crit Rev Biotechnol 2024; 44:352-372. [PMID: 36775662 DOI: 10.1080/07388551.2023.2167065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/17/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
Microbial electrosynthesis (MES) is a promising technology that mainly utilizes microbial cells to convert CO2 into value-added chemicals using electrons provided by the cathode. However, the low electron transfer rate is a solid bottleneck hindering the further application of MES. Thus, as an effective strategy, genetic tools play a key role in MES for enhancing the electron transfer rate and diversity of production. We describe a set of genetic strategies based on fundamental characteristics and current successes and discuss their functional mechanisms in driving microbial electrocatalytic reactions to fully comprehend the roles and uses of genetic tools in MES. This paper also analyzes the process of nanomaterial application in extracellular electron transfer (EET). It provides a technique that combines nanomaterials and genetic tools to increase MES efficiency, because nanoparticles have a role in the production of functional genes in EET although genetic tools can subvert MES, it still has issues with difficult transformation and low expression levels. Genetic tools remain one of the most promising future strategies for advancing the MES process despite these challenges.
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Affiliation(s)
- Yixin Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen, China
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Edinburgh, UK
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
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2
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [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: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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3
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Jones S, Santini JM. Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms. Essays Biochem 2023; 67:685-699. [PMID: 37449416 PMCID: PMC10427800 DOI: 10.1042/ebc20220257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.
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Affiliation(s)
- Sarah Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, U.K
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
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4
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Huang J, Yang J, Han M, Wang B, Sun X, Jiang H. Microbial carbon fixation and its influencing factors in saline lake water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162922. [PMID: 36933719 DOI: 10.1016/j.scitotenv.2023.162922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (14C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L-1 h-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L-1 h-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China.
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5
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Naderi A, Kakavandi B, Giannakis S, Angelidaki I, Rezaei Kalantary R. Putting the electro-bugs to work: A systematic review of 22 years of advances in bio-electrochemical systems and the parameters governing their performance. ENVIRONMENTAL RESEARCH 2023; 229:115843. [PMID: 37068722 DOI: 10.1016/j.envres.2023.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Wastewater treatment using bioelectrochemical systems (BESs) can be considered as a technology finding application in versatile areas such as for renewable energy production and simultaneous reducing environmental problems, biosensors, and bioelectrosynthesis. This review paper reports and critically discusses the challenges, and advances in bio-electrochemical studies in the 21st century. To sum and critically analyze the strides of the last 20+ years on the topic, this study first provides a comprehensive analysis on the structure, performance, and application of BESs, which include Microbial Fuel Cells (MFCs), Microbial Electrolysis Cells (MECs) and Microbial Desalination Cells (MDCs). We focus on the effect of various parameters, such as electroactive microbial community structure, electrode material, configuration of bioreactors, anode unit volume, membrane type, initial COD, co-substrates and the nature of the input wastewater in treatment process and the amount of energy and fuel production, with the purpose of showcasing the modes of operation as a guide for future studies. The results of this review show that the BES have great potential in reducing environmental pollution, purifying saltwater, and producing energy and fuel. At a larger scale, it aspires to facilitate the path of achieving sustainable development and practical application of BES in real-world scenarios.
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Affiliation(s)
- Azra Naderi
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kakavandi
- Research Center for Health, Safety and Environment, Alborz University of Medical Sciences, Karaj, Iran; Department of Environmental Health Engineering, Alborz University of Medical Sciences, Karaj, Iran
| | - Stefanos Giannakis
- Universidad Politécnica de Madrid, E.T.S. de Ingenieros de Caminos, Canales y Puertos, Departamento de Ingeniería Civil: Hidráulica, Energía y Medio Ambiente, Environment, Coast and Ocean Research Laboratory (ECOREL-UPM), C/Profesor Aranguren, s/n, ES-28040, Madrid, Spain
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Roshanak Rezaei Kalantary
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran.
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6
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Shen J, Liu Y, Qiao L. Photodriven Chemical Synthesis by Whole-Cell-Based Biohybrid Systems: From System Construction to Mechanism Study. ACS APPLIED MATERIALS & INTERFACES 2023; 15:6235-6259. [PMID: 36702806 DOI: 10.1021/acsami.2c19528] [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: 06/18/2023]
Abstract
By simulating natural photosynthesis, the desirable high-value chemical products and clean fuels can be sustainably generated with solar energy. Whole-cell-based photosensitized biohybrid system, which innovatively couples the excellent light-harvesting capacity of semiconductor materials with the efficient catalytic ability of intracellular biocatalysts, is an appealing interdisciplinary creature to realize photodriven chemical synthesis. In this review, we summarize the constructed whole-cell-based biohybrid systems in different application fields, including carbon dioxide fixation, nitrogen fixation, hydrogen production, and other chemical synthesis. Moreover, we elaborate the charge transfer mechanism studies of representative biohybrids, which can help to deepen the current understanding of the synergistic process between photosensitizers and microorganisms, and provide schemes for building novel biohybrids with less electron transfer resistance, advanced productive efficiency, and functional diversity. Further exploration in this field has the prospect of making a breakthrough on the biotic-abiotic interface that will provide opportunities for multidisciplinary research.
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Affiliation(s)
- Jiayuan Shen
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Yun Liu
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
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7
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Potysz A, Binkowski ŁJ, Kierczak J, Rattner BA. Drivers of Pb, Sb and As release from spent gunshot in wetlands: Enhancement by organic matter and native microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159121. [PMID: 36183763 DOI: 10.1016/j.scitotenv.2022.159121] [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: 06/23/2022] [Revised: 09/02/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
In many countries the use of lead-based ammunition is prevalent, and results in exposure and poisoning of waterfowl and other species of birds. In waterfowl hunting areas large quantities of spent shot may be deposited in wetland and terrestrial habitats. These pellets can undergo transformations, which are influenced by various abiotic and biotic factors. In addition to lead (Pb), other elements like antimony (Sb) and arsenic (As) can be leached from Pb shot into the environment. In vitro simulations that included organic matter and microorganisms were utilized to examine elemental leaching from gunshot. We found that leaching efficiency was the greatest in solutions rich in organic matter derived from artificial root exudates (2.69 % for Pb, 1.16 % for Sb, 1.83 % for As), while leaching efficiency was considerably lower in river water (0.04 %). In vitro simulations containing native microorganisms also exhibited greater leaching efficiency (0.49 % for Pb, 0.52 % for Sb, 1.32 % for As) than in ultrapure deionized water and river water. Surface alterations in gunshot included the formation of a weathering crust and secondary phases dominated by carbonates. Spent gunshot is a source of Pb, Sb and As in wetlands that could affect aquatic ecosystems.
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Affiliation(s)
- Anna Potysz
- University of Wrocław, Institute of Geological Sciences, Pl. M. Borna 9, 50-204 Wrocław, Poland
| | - Łukasz J Binkowski
- Pedagogical University of Krakow, Institute of Biology, Podchorążych 2, 30-084 Kraków, Poland.
| | - Jakub Kierczak
- University of Wrocław, Institute of Geological Sciences, Pl. M. Borna 9, 50-204 Wrocław, Poland
| | - Barnett A Rattner
- U.S. Geological Survey, Eastern Ecological Science Center, Beltsville, MD, USA
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8
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In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent. THE ISME JOURNAL 2023; 17:12-20. [PMID: 36151459 PMCID: PMC9751133 DOI: 10.1038/s41396-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
Abstract
Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.
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9
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Chen Y, Li X, Liu T, Li F, Sun W, Young LY, Huang W. Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158068. [PMID: 35987227 DOI: 10.1016/j.scitotenv.2022.158068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO3, and Fe3(PO4)2 as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d-1) was obtained in the FeCO3 tubes, and cells grown in the Fe3(PO4)2 tubes yielded maximum assimilation amounts of 13C-NaHCO3 of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.
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Affiliation(s)
- Yating Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu 610207, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, 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, 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, China.
| | - Weimin Sun
- 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, China
| | - Lily Y Young
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales. mSphere 2022; 7:e0022322. [PMID: 36069437 PMCID: PMC9599434 DOI: 10.1128/msphere.00223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.
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11
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Edel M, Philipp LA, Lapp J, Reiner J, Gescher J. Electron transfer of extremophiles in bioelectrochemical systems. Extremophiles 2022; 26:31. [PMID: 36222927 PMCID: PMC9556394 DOI: 10.1007/s00792-022-01279-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022]
Abstract
The interaction of bacteria and archaea with electrodes is a relatively new research field which spans from fundamental to applied research and influences interdisciplinary research in the fields of microbiology, biochemistry, biotechnology as well as process engineering. Although a substantial understanding of electron transfer processes between microbes and anodes and between microbes and cathodes has been achieved in mesophilic organisms, the mechanisms used by microbes under extremophilic conditions are still in the early stages of discovery. Here, we review our current knowledge on the biochemical solutions that evolved for the interaction of extremophilic organisms with electrodes. To this end, the available knowledge on pure cultures of extremophilic microorganisms has been compiled and the study has been extended with the help of bioinformatic analyses on the potential distribution of different electron transfer mechanisms in extremophilic microorganisms.
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Affiliation(s)
- Miriam Edel
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Laura-Alina Philipp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Jonas Lapp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Johannes Reiner
- Karlsruhe Institute of Technology, Engler-Bunte-Institute, Karlsruhe, Germany
| | - Johannes Gescher
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany.
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12
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Shono N, Ito M, Umezawa A, Sakata K, Li A, Kikuchi J, Ito K, Nakamura R. Tracing and regulating redox homeostasis of model benthic ecosystems for sustainable aquaculture in coastal environments. Front Microbiol 2022; 13:907703. [PMID: 36033891 PMCID: PMC9399343 DOI: 10.3389/fmicb.2022.907703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Abstract
Aquaculture in coastal environments has an increasingly important role in the world’s food supply; however, the accumulation of organic compounds on seafloors due to overfeeding adversely affects benthic ecosystems. To assess the ecological resilience of aquafarms to nutrient influx, we investigated the redox homeostasis of benthic ecosystems using a marine oligochaete as a model benthic organism in aquaculture fields. Real-time monitoring of the redox potential of a model benthic ecosystem constructed in an electrochemical reactor allowed evaluation of the homeostatic response of the system to nutrient addition. Although the detrimental effects of overfeeding were confirmed by irreversible potential changes in the sediment, redox homeostasis was reinforced through a cooperative relationship between oligochaetes and sediment microorganisms. Specifically, the oligochaetes exhibited reversible changes in metabolism and body position in response to dynamic changes in the sediment potential between −300 and 500 mV, thereby promoting the decomposition of organic compounds. The potential-dependent changes in metabolism and body position were reproduced by artificially manipulating the sediment potential in electrochemical reactors. Given the importance of benthic animals in sustaining coastal ecosystems, the electrochemical monitoring and physiologic regulation of marine oligochaetes could offer an intriguing approach toward sustainable aquaculture.
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Affiliation(s)
- Nobuaki Shono
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Mana Ito
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Japan
| | - Akio Umezawa
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Kenji Sakata
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ailong Li
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Katsutoshi Ito
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Japan
- *Correspondence: Katsutoshi Ito,
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Ryuhei Nakamura,
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13
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Azemtsop Matanfack G, Taubert M, Reilly-Schott V, Küsel K, Rösch P, Popp J. Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D 2O Labeling. Anal Chem 2022; 94:7759-7766. [PMID: 35608509 DOI: 10.1021/acs.analchem.1c04097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO2) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D2O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D2O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Vincent Reilly-Schott
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
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14
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Lovley DR. Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations. BIORESOURCE TECHNOLOGY 2022; 345:126553. [PMID: 34906705 DOI: 10.1016/j.biortech.2021.126553] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H2 as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H2 is actually the electron donor supporting growth has not been rigorously excluded.
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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 110819, China; Department of Microbiology and Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
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15
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Harnessing electrical-to-biochemical conversion for microbial synthesis. Curr Opin Biotechnol 2022; 75:102687. [PMID: 35104718 DOI: 10.1016/j.copbio.2022.102687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/18/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022]
Abstract
Electrical-to-biochemical conversion (E2BC) drives cell metabolism for biosynthesis and has become a promising way to realize green biomanufacturing. This review discusses the following aspects: 1. the natural E2BC processes and their underlying E2BC mechanism; 2. development of artificial E2BC for tunable microbial electrosynthesis; 3. design of electrobiochemical systems using self-powered, light-assisted, and nano-biohybrid approaches; 4. synthetic biology methods for efficient microbial electrosynthesis. This review also compares E2BC with electrocatalysis-biochemical conversion (EC2BC), as both strategies may lead to future carbon negative green biomanufacturing.
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16
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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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17
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Yamada S, Suzuki Y, Kouzuma A, Watanabe K. Development of a CRISPR interference system for selective gene knockdown in Acidithiobacillus ferrooxidans. J Biosci Bioeng 2021; 133:105-109. [PMID: 34865958 DOI: 10.1016/j.jbiosc.2021.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus ferrooxidans is an iron-oxidizing chemolithotroph used for bioleaching of precious metals and is also regarded as a potential host for bioelectrochemical production of value-added chemicals. Despite its industrial utility, however, it is difficult to genetically engineer A. ferrooxidans due to low transformation and recombination efficiencies. Here, we developed a clustered regularly interspaced short palindromic repeats interference (CRISPRi) system that can selectively repress the expression of a target gene in A. ferrooxidans. The mutated gene encoding a nuclease-deactivated Cas9 protein was cloned into the broad-host-range plasmid pBBR1-MCS2, and the applicability of the CRISPRi system was examined using the nitrogenase nifH gene as a knockdown target. Introduction of the CRISPRi plasmid into A. ferrooxidans resulted in decreased nifH transcription and retarded cell growth in the absence of nitrogen sources, demonstrating that the CRISPRi system altered the phenotype of this bacterium via selective gene knockdown. We suggest that the CRISPRi system developed in this study provides an efficient technique for constructing A. ferrooxidans knockdown mutants that are useful for the genetic dissection of this bacterium.
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Affiliation(s)
- Shohei Yamada
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yusuke Suzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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18
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Zhang YT, Zhang Y, Peng L. Electrochemical fluorescence microscopy reveals insignificant long-range extracellular electron transfer in Shewanella oneidensis anodic processes. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Massazza D, Robledo AJ, Rodriguez Simón CN, Busalmen JP, Bonanni S. Energetics, electron uptake mechanisms and limitations of electroautotrophs growing on biocathodes - A review. BIORESOURCE TECHNOLOGY 2021; 342:125893. [PMID: 34537530 DOI: 10.1016/j.biortech.2021.125893] [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: 07/17/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Electroautotrophs are microorganisms that can take the electrons needed for energy generation, CO2 fixation and other metabolic reactions from a polarized electrode. They have been the focus of intense research for its application in wastewater treatment, bioelectrosynthetic processes and hydrogen generation. As a general trend, current densities produced by the electron uptake of these microorganisms are low, limiting their applicability at large scale. In this work, the electron uptake mechanisms that may operate in electroautotrophs are reviewed, aiming at finding possible causes for this low performance. Biomass yields, growth rates and electron uptake rates observed when these microorganisms use chemical electron donors are compared with those typically obtained with electrodes, to explore limitations and advantages inherent to the electroautotrophic metabolism. Also, the factors affecting biofilm development are analysed to show how interfacial interactions condition bacterial adhesion, biofilm growth and electrons uptake. Finally, possible strategies to overcome these limitations are described.
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Affiliation(s)
- Diego Massazza
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Alejandro Javier Robledo
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Carlos Norberto Rodriguez Simón
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Juan Pablo Busalmen
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina
| | - Sebastián Bonanni
- División Ingeniería de Interfases y Bioprocesos, INTEMA (Conicet, Universidad Nacional de Mar del Plata), Av. Colón 10850, Mar del Plata 7600, Argentina.
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20
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Valorisation of CO2 into Value-Added Products via Microbial Electrosynthesis (MES) and Electro-Fermentation Technology. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040291] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial electrocatalysis reckons on microbes as catalysts for reactions occurring at electrodes. Microbial fuel cells and microbial electrolysis cells are well-known in this context; both prefer the oxidation of organic and inorganic matter for producing electricity. Notably, the synthesis of high energy-density chemicals (fuels) or their precursors by microorganisms using bio-cathode to yield electrical energy is called Microbial Electrosynthesis (MES), giving an exceptionally appealing novel way for producing beneficial products from electricity and wastewater. This review accentuates the concept, importance and opportunities of MES, as an emerging discipline at the nexus of microbiology and electrochemistry. Production of organic compounds from MES is considered as an effective technique for the generation of various beneficial reduced end-products (like acetate and butyrate) as well as in reducing the load of CO2 from the atmosphere to mitigate the harmful effect of greenhouse gases in global warming. Although MES is still an emerging technology, this method is not thoroughly known. The authors have focused on MES, as it is the next transformative, viable alternative technology to decrease the repercussions of surplus carbon dioxide in the environment along with conserving energy.
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21
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Pillot G, Amin Ali O, Davidson S, Shintu L, Combet-Blanc Y, Godfroy A, Bonin P, Liebgott PP. Evolution of Thermophilic Microbial Communities from a Deep-Sea Hydrothermal Chimney under Electrolithoautotrophic Conditions with Nitrate. Microorganisms 2021; 9:microorganisms9122475. [PMID: 34946077 PMCID: PMC8705573 DOI: 10.3390/microorganisms9122475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on electrotrophic enrichment with nitrate as electron acceptor. The biofilm density, community composition, production of organic compounds, and electrical consumption were monitored by FISH confocal microscopy, qPCR, metabarcoding, NMR, and potentiostat measurements. A statistical analysis by PCA showed the correlation between the different parameters (qPCR, organic compounds, and electron acceptors) in three distinct temporal phases. In our conditions, the Archaeoglobales have been shown to play a key role in the development of the community as the first colonizers on the cathode and the first producers of organic compounds, which are then used as an organic source by heterotrophs. Finally, through subcultures of the community, we showed the development of a greater biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal contexts, where energy sources are transient and unstable.
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Affiliation(s)
- Guillaume Pillot
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
| | - Oulfat Amin Ali
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
| | - Sylvain Davidson
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
| | - Laetitia Shintu
- Aix Marseille Université, CNRS Centrale Marseille, iSm2, 13284 Marseille, France;
| | - Yannick Combet-Blanc
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, CNRS, IFREMER, 29280 Plouzané, France;
| | - Patricia Bonin
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
| | - Pierre-Pol Liebgott
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France; (G.P.); (O.A.A.); (S.D.); (Y.C.-B.); (P.B.)
- Correspondence:
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22
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Ye J, Hu A, Ren G, Chen M, Zhou S, He Z. Biophotoelectrochemistry for renewable energy and environmental applications. iScience 2021; 24:102828. [PMID: 34368649 PMCID: PMC8326206 DOI: 10.1016/j.isci.2021.102828] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Biophotoelectrochemistry (BPEC) is an interdisciplinary research field and combines bioelectrochemistry and photoelectrochemistry through the utilization of the catalytic abilities of biomachineries and light harvesters to accomplish the production of energy or chemicals driven by solar energy. The BPEC process may act as a new approach for sustainable green chemistry and waste minimization. This review provides the state-of-the-art introduction of BPEC basics and systems, with a focus on light harvesters and biocatalysts, configurations, photoelectron transfer mechanisms, and the potential applications in energy and environment. Several examples of BPEC applications are discussed including H2 production, CO2 reduction, chemical synthesis, pollution control, and biogeochemical cycle of elements. The challenges about BPEC systems are identified and potential solutions are proposed. The review aims to encourage further research of BPEC toward development of practical BPEC systems for energy and environmental applications.
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Affiliation(s)
- Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhen He
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Pillot G, Amin Ali O, Davidson S, Shintu L, Godfroy A, Combet-Blanc Y, Bonin P, Liebgott PP. Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions. Sci Rep 2021; 11:14782. [PMID: 34285254 PMCID: PMC8292307 DOI: 10.1038/s41598-021-94135-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culturing, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.
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Affiliation(s)
- Guillaume Pillot
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Oulfat Amin Ali
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Sylvain Davidson
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Anne Godfroy
- IFREMER, CNRS, Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes-UMR6197, Ifremer, Centre de Brest CS10070, Plouzané, France
| | - Yannick Combet-Blanc
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Patricia Bonin
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France
| | - Pierre-Pol Liebgott
- Aix Marseille Université, Université de Toulon, IRD, CNRS, MIO UM 110, 13288, Marseille Cedex 09, France.
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24
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Chin K, Pasalic J, Hermis N, Barge LM. Chemical Gardens as Electrochemical Systems: In Situ Characterization of Simulated Prebiotic Hydrothermal Vents by Impedance Spectroscopy. Chempluschem 2021; 85:2619-2628. [PMID: 33270995 DOI: 10.1002/cplu.202000600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/17/2020] [Indexed: 11/05/2022]
Abstract
In an early earth or planetary chimney systems, hydrothermal fluid chemistry and flow durations play a large role in the chimney's ability to drive electrochemical reactions for the origin of life. We performed continuous electrochemical impedance spectroscopy (EIS) characterization on inorganic membranes representing prebiotic hydrothermal chimney vents in natural seafloor systems, by incorporating an electrode array into a chimney growth experiment. Localized potential and capacitances profiles in the chimney reveal a dynamic system where redox processes are driven by transport phenomena, increasing rapidly due to disequilibrium until achieving equilibrium at about 100 mV and 1000 μF/cm2 . The impedance in the chimney interior is three orders of magnitude lower (100 Ohms/cm2 vs 100 KOhms/cm2 ) than at the ocean or the ocean/chimney interface. The calculated peak dissipation factor (DF) values are more than ten times higher (40.0 vs 3.0) and also confirm the elevated chemical reactivity in the chimney interior.
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Affiliation(s)
- Keith Chin
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Jasmina Pasalic
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Ninos Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
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25
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Chacon-Baca E, Santos A, Sarmiento AM, Luís AT, Santisteban M, Fortes JC, Dávila JM, Diaz-Curiel JM, Grande JA. Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain. ASTROBIOLOGY 2021; 21:443-463. [PMID: 33351707 DOI: 10.1089/ast.2019.2164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.
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Affiliation(s)
- Elizabeth Chacon-Baca
- Departamento de Geología, Facultad de Ciencias de la Tierra, Universidad Autónoma de Nuevo Léon (UANL), Linares, México
| | - Ana Santos
- Department of Applied Geosciences, CCTH-Science and Technology Research Centre, University of Huelva, Huelva, Spain
- Applied Geosciences Research Group (RNM276), Departamento de Ciencias de la Tierra, Facultad de Ciencias Experimentales, Universidad de Huelva, Huelva, Spain
| | - Aguasanta Miguel Sarmiento
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Ana Teresa Luís
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- GeoBioTec Research Unit, Department of Geosciences, University of Aveiro, Aveiro, Portugal
| | - Maria Santisteban
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Juan Carlos Fortes
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - José Miguel Dávila
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Jesus M Diaz-Curiel
- Departamento de Geología, Escuela Técnica Superior de Ingenieros de Minas, Madrid, Spain
| | - Jose Antonio Grande
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
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26
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Asplund-Samuelsson J, Hudson EP. Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes. PLoS Comput Biol 2021; 17:e1008742. [PMID: 33556078 PMCID: PMC7895386 DOI: 10.1371/journal.pcbi.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Elton P. Hudson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
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27
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Rimboud M, Barakat M, Achouak W, Bergel A, Délia ML. Oxygen-reducing microbial cathodes in hypersaline electrolyte. BIORESOURCE TECHNOLOGY 2021; 319:124165. [PMID: 33039843 DOI: 10.1016/j.biortech.2020.124165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Hypersaline electrolytes offer a way to boost the development of microbial fuel cells by overcoming the issue due to the low conductivity of the usual media. Efficient halotolerant bioanodes have already been designed but O2-reducing cathodes remain a strong bottleneck. Here, O2-reducing biocathodes were designed by using salt marsh sediment as the inoculum and a hypersaline media (45 g/L NaCl) of high conductivity (10.4 S m-1). Current density up to 2.2 A m-2 was reached from potential of +0.2 V/SCE. The efficiency of the biocathodes was correlated to the presence of Gammaproteobacteria strain(s) related to Thiohalobacter thiocyanaticus, which were considerably enriched in the best performing biocathodes. This work opens up new perspectives to overcome the O2 reduction issue in hypersaline MFCs by designing efficient halotolerant microbial cathodes and pointing out the strains that should now be focused to improve them.
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Affiliation(s)
- Mickaël Rimboud
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France
| | - Mohamed Barakat
- Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements Extrêmes (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille Université, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements Extrêmes (LEMIRE), BIAM, UMR 7265, CEA-CNRS-Aix Marseille Université, CEA Cadarache, 13108 Saint Paul Lez Durance, France
| | - Alain Bergel
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France
| | - Marie-Line Délia
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Allée Emile Monso, 31432 Toulouse, France.
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28
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Deng X, Saito J, Kaksonen A, Okamoto A. Enhancement of cell growth by uncoupling extracellular electron uptake and oxidative stress production in sediment sulfate-reducing bacteria. ENVIRONMENT INTERNATIONAL 2020; 144:106006. [PMID: 32795748 DOI: 10.1016/j.envint.2020.106006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial extracellular electron uptake (EEU) from solid electron donors has critical implications for microbial energy acquisition in energy-limited environments as well as electrochemical microbial technologies. Although EEU supplies sufficient energy to support cellular growth, additional soluble electron donors are required for most microbes to grow on electrode surfaces. Here, we demonstrated that the minimization of exogenous and endogenous oxidative stress greatly enhanced the growth rate of the sediment EEU-capable sulfate-reducing bacterium Desulfovibrio ferrophilus IS5 on an electrode without the addition of a soluble electron donor. Single-cell activity analysis by nanoscale secondary ion mass spectrometry showed that the metabolic activity of IS5 cells on the electrode was significantly enhanced following incubation in an H-type reactor, which was configured to reduce the exposure of cells to the potential oxidative stress source of the Pt counter electrode (CE). Additionally, the highest metabolic activity was observed at an electrode potential of -0.4 V (versus the standard hydrogen electrode), where electron uptake rate was not at peak. Compared to a single-chamber reactor, incubation in an H-type reactor at -0.4 V shortened the cell doubling time by 50-fold, which resulted in sufficient anabolism for cell replication (15N/Ntotal > 50%). The production of strongly oxidizing species at the CE was confirmed by X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry analyses. Transcriptome analysis revealed overexpression of antioxidative genes in cells incubated at a potential with higher current production. These results suggested that higher levels of endogenous oxidative species were produced by a more reduced electron-transport chain from trace amounts of oxygen in the reactor, thereby lowering cell activity. In conclusion, EEU may enable sediment microbes to undergo enhanced cell growth and to find niches on minerals under anaerobic energy-limited conditions, where oxidative stress is much less likely to be present.
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Affiliation(s)
- Xiao Deng
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan; CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia
| | - Junki Saito
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan
| | - Anna Kaksonen
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, 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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29
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Gupta D, Guzman MS, Bose A. Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications. ACTA ACUST UNITED AC 2020; 47:863-876. [DOI: 10.1007/s10295-020-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Abstract
Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
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Affiliation(s)
- Dinesh Gupta
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| | - Michael S Guzman
- grid.250008.f 0000 0001 2160 9702 Biosciences and Biotechnology Division Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA USA
| | - Arpita Bose
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
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30
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Guardia AE, Beligni MV, Cortéz N, Busalmen J. Electrochemistry of R. palustris Azul during phototrophic growth. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Altermann E, Hickey WJ. Grand Challenges in Microbiotechnology: Through the Prism of Microbiotechnology. Front Microbiol 2020; 11:430. [PMID: 32265872 PMCID: PMC7099634 DOI: 10.3389/fmicb.2020.00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Eric Altermann
- AgResearch, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - William J Hickey
- Department of Soil Science, University of Wisconsin, Madison, WI, United States
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32
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From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst. ISME JOURNAL 2020; 14:1125-1140. [PMID: 31996786 DOI: 10.1038/s41396-020-0595-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 11/08/2022]
Abstract
Coupling microbial electrosynthesis to renewable energy sources can provide a promising future technology for carbon dioxide conversion. However, this technology suffers from a limited number of suitable biocatalysts, resulting in a narrow product range. Here, we present the characterization of the first thermoacidophilic electroautotrophic community using chronoamperometric, metagenomic, and 13C-labeling analyses. The cathodic biofilm showed current consumption of up to -80 µA cm-2 over a period of 90 days (-350 mV vs. SHE). Metagenomic analyses identified members of the genera Moorella, Desulfofundulus, Thermodesulfitimonas, Sulfolobus, and Acidianus as potential primary producers of the biofilm, potentially thriving via an interspecies sulfur cycle. Hydrogenases seem to be key for cathodic electron uptake. An isolation campaign led to a pure culture of a Knallgas bacterium from this community. Growth of this organism on cathodes led to increasing reductive currents over time. Transcriptomic analyses revealed a distinct gene expression profile of cells grown at a cathode. Moreover, pressurizable flow cells combined with optical coherence tomography allowed an in situ observation of cathodic biofilm growth. Autotrophic growth was confirmed via isotope analysis. As a natural polyhydroxybutyrate (PHB) producer, this novel species, Kyrpidia spormannii, coupled the production of PHB to CO2 fixation on cathode surfaces.
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33
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Li X, Ding L, Yuan H, Li X, Zhu Y. Identification of potential electrotrophic microbial community in paddy soils by enrichment of microbial electrolysis cell biocathodes. J Environ Sci (China) 2020; 87:411-420. [PMID: 31791514 DOI: 10.1016/j.jes.2019.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Electrotrophs are microbes that can receive electrons directly from cathode in a microbial electrolysis cell (MEC). They not only participate in organic biosynthesis, but also be crucial in cathode-based bioremediation. However, little is known about the electrotrophic community in paddy soils. Here, the putative electrotrophs were enriched by cathodes of MECs constructed from five paddy soils with various properties using bicarbonate as an electron acceptor, and identified by 16S rRNA-gene based Illumina sequencing. The electrons were gradually consumed on the cathodes, and 25%-45% of which were recovered to reduce bicarbonate to acetic acid during MEC operation. Firmicutes was the dominant bacterial phylum on the cathodes, and Bacillus genus within this phylum was greatly enriched and was the most abundant population among the detected putative electrotrophs for almost all soils. Furthermore, several other members of Firmicutes and Proteobacteria may also participate in electrotrophic process in different soils. Soil pH, amorphous iron and electrical conductivity significantly influenced the putative electrotrophic bacterial community, which explained about 33.5% of the community structural variation. This study provides a basis for understanding the microbial diversity of putative electrotrophs in paddy soils, and highlights the importance of soil properties in shaping the community of putative electrotrophs.
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Affiliation(s)
- Xiaomin Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjun Ding
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China.
| | - Haiyan Yuan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongguan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road, No. 1799, Jimei District, Xiamen 361021, China
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34
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Rimboud M, Achouak W. Electroautotrophy of Thioalkalivibrio nitratireducens. Bioelectrochemistry 2019; 126:48-55. [DOI: 10.1016/j.bioelechem.2018.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
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35
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Guzman MS, Rengasamy K, Binkley MM, Jones C, Ranaivoarisoa TO, Singh R, Fike DA, Meacham JM, Bose A. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat Commun 2019; 10:1355. [PMID: 30902976 PMCID: PMC6430793 DOI: 10.1038/s41467-019-09377-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/07/2019] [Indexed: 01/06/2023] Open
Abstract
Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. EEU is performed by prevalent phototrophic bacterial genera, but the electron transfer pathways and the physiological electron sinks are poorly understood. Here we show that electrons enter the photosynthetic electron transport chain during EEU in the phototrophic bacterium Rhodopseudomonas palustris TIE-1. Cathodic electron flow is also correlated with a highly reducing intracellular redox environment. We show that reducing equivalents are used for carbon dioxide (CO2) fixation, which is the primary electron sink. Deletion of the genes encoding ruBisCO (the CO2-fixing enzyme of the Calvin-Benson-Bassham cycle) leads to a 90% reduction in EEU. This work shows that phototrophs can directly use solid-phase conductive substances for electron transfer, energy transduction, and CO2 fixation. Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. Here, Guzman et al. show that electrons enter the photosynthetic electron transport chain and are used for CO2 fixation during EEU in a phototrophic bacterium.
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Affiliation(s)
- Michael S Guzman
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Karthikeyan Rengasamy
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael M Binkley
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Clive Jones
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | | | - Rajesh Singh
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - J Mark Meacham
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Institute of Materials Science Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Arpita Bose
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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36
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Logan BE, Rossi R, Ragab A, Saikaly PE. Electroactive microorganisms in bioelectrochemical systems. Nat Rev Microbiol 2019; 17:307-319. [DOI: 10.1038/s41579-019-0173-x] [Citation(s) in RCA: 546] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Ooka H, McGlynn SE, Nakamura R. Electrochemistry at Deep‐Sea Hydrothermal Vents: Utilization of the Thermodynamic Driving Force towards the Autotrophic Origin of Life. ChemElectroChem 2019. [DOI: 10.1002/celc.201801432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
| | - Shawn E. McGlynn
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
- Blue Marble Space Institute of Science Seattle, WA USA
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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38
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Gao Y, Trueman BF, Stoddart AK, Gagnon GA. Understanding the Impact of Extracellular Polymeric Substances on Lead Release in Drinking Water Systems. ACS OMEGA 2018; 3:14824-14832. [PMID: 30555991 PMCID: PMC6289567 DOI: 10.1021/acsomega.8b02363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 05/16/2023]
Abstract
Lead release in a lead (Pb, anode)-iron oxide (α-Fe2O3, cathode) galvanic system was studied under the influence of synthetic extracellular polymeric substances (sEPS). Sodium alginate, bovine serum albumin (BSA), and cytochrome c represented extracellular polysaccharides, proteins, and electrochemically active components, respectively. Microbiologically influenced corrosion was investigated using sEPS and pelleted and resuspended Pseudomonas aeruginosa cells. Relative to the anaerobic inorganic control, Pb release increased by 156, 202, and 198 μg/L when sEPS was present on the cathode side at 200 mg/L (100 mg/L alginate + 100 mg/L BSA), 400 mg/L (200 mg/L alginate + 200 mg/L BSA), and 200 mg/L with 123.84 mg/L cytochrome c, respectively, under anaerobic conditions. When the cathode was aerated, Pb release increased by 75, 260, and -71 μg/L under the aforementioned conditions, all relative to the aerated inorganic control. When sEPS was instead present on the anode side, sEPS caused localized corrosion on Pb and resulted in higher Pb release than predicted by electric current. P. aeruginosa generally enhanced corrosion; when cells were dosed in the anode side, part of the oxidized Pb was immobilized by cells or organic compounds adhered to the electrodes.
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39
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Tanaka K, Yokoe S, Igarashi K, Takashino M, Ishikawa M, Hori K, Nakanishi S, Kato S. Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath). Front Microbiol 2018; 9:2905. [PMID: 30555443 PMCID: PMC6281684 DOI: 10.3389/fmicb.2018.02905] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 11/24/2022] Open
Abstract
Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria.
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Affiliation(s)
- Kenya Tanaka
- Graduate School of Engineering Science, Osaka University, Toyonaka, Japan
| | - Sho Yokoe
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Masahito Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shuji Nakanishi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
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40
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Deng X, Okamoto A. Electrode Potential Dependency of Single-Cell Activity Identifies the Energetics of Slow Microbial Electron Uptake Process. Front Microbiol 2018; 9:2744. [PMID: 30483241 PMCID: PMC6243204 DOI: 10.3389/fmicb.2018.02744] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Electrochemical measurements have been widely applied to study microbial extracellular electron transport processes. However, because electrochemistry detects not only microbial electron transport but also other reactions, background signals comparable to or larger than microbial ones hamper the identification of microbial electrochemical properties. This problem is crucial especially for the detection of electron uptake processes by slow-growing microbes in low-energy subsurface sediments, as the environmental samples contain electrochemically active humus and mineral particles. In this study, we report a cell-specific stable isotope analysis to quantify the electrode potential dependency of anabolic activity in individual cells for identifying the electron uptake energetics of slow-growing bacteria. Followed by the incubation of Desulfovibrio ferrophilus IS5 cells with isotopic 15N-ammonium as the sole N source on electrodes poised at potentials of -0.2, -0.3, -0.4, and -0.5 V [vs. standard hydrogen electrode (SHE)], we conducted nanoscale secondary ion mass spectroscopy (NanoSIMS) to quantify 15N assimilation in more than 100 individual cells on the electrodes. We observed significant 15N assimilation at potentials of -0.4 and more 15N assimilation at -0.5 V, which is consistent with the onset potential for electron uptake via outer-membrane cytochromes (OMCs). The activation of cell energy metabolism was further examined by transcriptome analysis. Our results showed a novel methodology to study microbial electron uptake energetics. The results also serve as the first direct evidence that energy acquisition is coupled to the electron uptake process in sulfate-reducing bacteria that are ubiquitous in the subsurface environments, with implications on the electron-fueled subsurface biosphere hypothesis and other microbial processes, such as anaerobic iron corrosion and anaerobic methane oxidation.
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Affiliation(s)
- Xiao Deng
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan.,International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan.,Center for Functional Sensor and Actuator, National Institute for Materials Science, Tsukuba, Japan
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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
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Barge LM, Krause FC, Jones JP, Billings K, Sobron P. Geoelectrodes and Fuel Cells for Simulating Hydrothermal Vent Environments. ASTROBIOLOGY 2018; 18:1147-1158. [PMID: 30106308 DOI: 10.1089/ast.2017.1707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gradients generated in hydrothermal systems provide a significant source of free energy for chemosynthetic life and may play a role in present-day habitability on ocean worlds. Electron/proton/ion gradients, particularly in the context of hydrothermal chimney structures, may also be relevant to the origins of life on Earth. Hydrothermal vents are similar in some ways to typical fuel cell devices: redox/pH gradients between seawater and hydrothermal fluid are analogous to the fuel cell oxidant and fuel reservoirs; the porous chimney wall is analogous to a separator or ion-exchange membrane and is also a conductive path for electrons; and the hydrothermal minerals are analogous to electrode catalysts. The modular and scalable characteristics of fuel cell systems make for a convenient planetary geology test bed in which geologically relevant components may be assembled and investigated in a controlled simulation environment. We have performed fuel cell experiments and electrochemical studies to better understand the catalytic potential of seafloor minerals and vent chimneys, using samples from a black smoker vent chimney as an initial demonstration. In a fuel cell with Na+-conducting Nafion® membranes and liquid fuel/oxidant reservoirs (simulating the vent environment), the black smoker mineral catalyst in the membrane electrode assembly was effective in reducing O2 and oxidizing sulfide. In a H2/O2 polymer electrolyte membrane (PEM) fuel cell with H+-conducting Nafion membranes, the black smoker catalyst was effective in reducing O2 but not in oxidizing H2. These fuel cell experiments accurately simulated the redox reactions that could occur in a geological setting with this particular catalyst, and also tested whether the minerals are sufficiently active to replace a commercial fuel cell catalyst. Similar experiments with other geocatalysts could be utilized to test which redox reactions could be driven in other hydrothermal systems, including hypothesized vent systems on other worlds.
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Affiliation(s)
- Laura M Barge
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Frederick C Krause
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - John-Paul Jones
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Keith Billings
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Pablo Sobron
- 2 Carl Sagan Center, SETI Institute , Mountain View, California
- 3 Impossible Sensing , St. Louis, Missouri
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Chong GW, Karbelkar AA, El-Naggar MY. Nature's conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion? Curr Opin Chem Biol 2018; 47:7-17. [PMID: 30015234 DOI: 10.1016/j.cbpa.2018.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022]
Abstract
Microorganisms can acquire energy from the environment by extending their electron transport chains to external solid electron donors or acceptors. This process, known as extracellular electron transfer (EET), is now being heavily pursued for wiring microbes to electrodes in bioelectrochemical renewable energy technologies. Recent studies highlight the crucial role of multi-heme cytochromes in facilitating biotic-abiotic EET both for cellular electron export and uptake. Here we explore progress in understanding the range and function of these biological electron conduits in the context of fuel-to-electricity and electricity-to-bioproduct conversion. We also highlight emerging topics, including the role of multi-heme cytochromes in inter-species electron transfer and in inspiring the design and synthesis of a new generation of protein-based bioelectronic components.
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Affiliation(s)
- Grace W Chong
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Amruta A Karbelkar
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA
| | - Mohamed Y El-Naggar
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA; Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA.
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44
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Yamamoto M, Nakamura R, Takai K. Deep-Sea Hydrothermal Fields as Natural Power Plants. ChemElectroChem 2018. [DOI: 10.1002/celc.201800394] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Masahiro Yamamoto
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka 273-0061 Japan
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute; Tokyo Institute of Technology; 2-12-1-IE-1, Ookayama, Meguro-ku Tokyo 152-8550 Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka 273-0061 Japan
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Zhang S, Yan L, Xing W, Chen P, Zhang Y, Wang W. Acidithiobacillus ferrooxidans and its potential application. Extremophiles 2018; 22:563-579. [PMID: 29696439 DOI: 10.1007/s00792-018-1024-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
The widely distributed Acidithiobacillus ferrooxidans (A. ferrooxidans) lives in extremely acidic conditions by fixing CO2 and nitrogen, and by obtaining energy from Fe2+ oxidation with either downhill or uphill electron transfer pathway and from reduced sulfur oxidation. A. ferrooxidans exists as different genomovars and its genome size is 2.89-4.18 Mb. The chemotactic movement of A. ferrooxidans is regulated by quorum sensing. A. ferrooxidans shows weak magnetotaxis due to formation of 15-70 nm magnetite magnetosomes with surface functional groups. The room- and low-temperature magnetic features of A. ferrooxidans are different from other magnetotactic bacteria. A. ferrooxidans has potential for removing sulfur from solids and gases, metals recycling from metal-bearing ores, electric wastes and sludge, biochemical production synthesizing, and metal workpiece machining.
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Affiliation(s)
- Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University (HBAU), 5 Xinfeng Road, Daqing High-Tech Industrial Development Zone, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University (HBAU), 5 Xinfeng Road, Daqing High-Tech Industrial Development Zone, Daqing, 163319, Heilongjiang, People's Republic of China.
| | - Weijia Xing
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University (HBAU), 5 Xinfeng Road, Daqing High-Tech Industrial Development Zone, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, People's Republic of China
| | - Yu Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University (HBAU), 5 Xinfeng Road, Daqing High-Tech Industrial Development Zone, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University (HBAU), 5 Xinfeng Road, Daqing High-Tech Industrial Development Zone, Daqing, 163319, Heilongjiang, People's Republic of China
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Chin KB, Chi I, Pasalic J, Huang CK, Barge LM. An introductory study using impedance spectroscopy technique with polarizable microelectrode for amino acids characterization. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:045108. [PMID: 29716330 DOI: 10.1063/1.5020076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Portable, low power, yet ultra-sensitive life detection instrumentations are vital to future astrobiology flight programs at NASA. In this study, initial attempts to characterize amino acids in an aqueous environment by electrochemical impedance spectroscopy (EIS) using polarizable (blocking) electrodes in order to establish a means of detection via their electrical properties. Seven amino acids were chosen due to their scientific importance in demonstrating sensitivity levels in the range of part per billion concentration. Albeit more challenging in real systems of analyst mixtures, we found individual amino acids in aqueous environment do exhibit some degree of chemical and physical uniqueness to warrant characterization by EIS. The polar amino acids (Asp, Glu, and His) exhibited higher electrochemical activity than the non-polar amino acids (Ala, Gly, Val, and Leu). The non-polar amino acids (Gly and Ala) also exhibited unique electrical properties which appeared to be more dependent on physical characteristics such as molecular weight and structure. At concentrations above 1 mM where the amino acids play a more dominant transport role within the water, the conductivity was found to be more sensitive to concentrations. At lower concentrations <1 mM, however, the polar amino acid solution conductivity remained constant, suggesting poor chemical activity with water. As revealed by equivalent circuit modeling, the relaxation times showed a 1-2 order of magnitude difference between polar and non-polar amino acids. The pseudo-capacitance from EIS measurements on sample mixtures containing salt water and individual amino acids revealed the possibility for improvement in amino acid selectivity using gold nanoporous surface enhanced electrodes. This work establishes important methodologies for characterizing amino acids using EIS combined with microscale electrodes, supporting the case for instrumentation development for life detection and origin of life programs.
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Affiliation(s)
- K B Chin
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - I Chi
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - J Pasalic
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - C-K Huang
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
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Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev 2018; 42:205-231. [PMID: 29177446 PMCID: PMC5972617 DOI: 10.1093/femsre/fux056] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors. mBio 2018; 9:mBio.02203-17. [PMID: 29487241 PMCID: PMC5829830 DOI: 10.1128/mbio.02203-17] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH2) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH2 under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited. The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important implications for how microorganisms persist in energy-limited environments, such as reduced sediments under changing redox conditions. From an applied perspective, this work has important implications for microbially catalyzed processes on electrodes, particularly with regard to understanding models of cellular conversion of electrons from cathodes to microbially synthesized products.
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Deng X, Dohmae N, Nealson KH, Hashimoto K, Okamoto A. Multi-heme cytochromes provide a pathway for survival in energy-limited environments. SCIENCE ADVANCES 2018; 4:eaao5682. [PMID: 29464208 PMCID: PMC5815863 DOI: 10.1126/sciadv.aao5682] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/12/2018] [Indexed: 05/22/2023]
Abstract
Bacterial reduction of oxidized sulfur species (OSS) is critical for energy production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has been considered as a major energy source for bacterial respiration. We identified outer-membrane cytochromes (OMCs) that are broadly conserved in sediment OSS-respiring bacteria and enable cells to directly use electrons from insoluble minerals via extracellular electron transport. Biochemical, transcriptomic, and microscopic analyses revealed that the identified OMCs were highly expressed on the surface of cells and nanofilaments in response to electron donor limitation. This electron uptake mechanism provides sufficient but minimum energy to drive the reduction of sulfate and other OSS. These results suggest a widespread mechanism for survival of OSS-respiring bacteria via electron uptake from solid minerals in energy-poor marine sediments.
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Affiliation(s)
- Xiao Deng
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kenneth H. Nealson
- Department of Earth and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kazuhito Hashimoto
- Interfacial Energy Conversion Group, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Akihiro Okamoto
- Interfacial Energy Conversion Group, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Corresponding author.
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Cabrol NA. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures. ASTROBIOLOGY 2018; 18:1-27. [PMID: 29252008 PMCID: PMC5779243 DOI: 10.1089/ast.2017.1756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 05/09/2023]
Abstract
Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.
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