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Xu P, Liu H, Liu C, Zhu G. Syntrophic methane production from volatile fatty acids: Focus on interspecies electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174410. [PMID: 38960157 DOI: 10.1016/j.scitotenv.2024.174410] [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: 03/22/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Methane is a renewable biomass energy source produced via anaerobic digestion (AD). Interspecies electron transfer (IET) between methanogens and syntrophic bacteria is crucial for mitigating energy barriers in this process. Understanding IET is essential for enhancing the efficiency of syntrophic methanogenesis in anaerobic digestion. Interspecies electron transfer mechanisms include interspecies H2/formate transfer, direct interspecies electron transfer (DIET), and electron-shuttle-mediated transfer. This review summarizes the mechanisms, developments, and research gaps in IET pathways. Interspecies H2/formate transfer requires strict control of low H2 partial pressure and involves complex enzymatic reactions. In contrast, DIET enhances the electron transfer efficiency and process stability. Conductive materials and key microorganisms can be modulated to stimulate the DIET. Electron shuttles (ES) allow microorganisms to interact with extracellular electron acceptors without direct contact; however, their efficiency depends on various factors. Future studies should elucidate the key functional groups, metabolic pathways, and regulatory mechanisms of IET to guide the optimization of AD processes for efficient renewable energy production.
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Affiliation(s)
- Panhui Xu
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Haichen Liu
- Shanghai Investigation, Design & Research Institute Co., Ltd., 200080, China
| | - Chong Liu
- The 101 Research Institute, Ministry of Civil Affairs of the People's Republic of China, Beijing 100070, China.
| | - Gefu Zhu
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
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2
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Shi X, Liang Y, Wen G, Evlashin SA, Fedorov FS, Ma X, Feng Y, Zheng J, Wang Y, Shi J, Liu Y, Zhu W, Guo P, Kim BH. Review of cathodic electroactive bacteria: Species, properties, applications and electron transfer mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174332. [PMID: 38950630 DOI: 10.1016/j.scitotenv.2024.174332] [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: 02/06/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
Cathodic electroactive bacteria (C-EAB) which are capable of accepting electrons from solid electrodes provide fresh avenues for pollutant removal, biosensor design, and electrosynthesis. This review systematically summarized the burgeoning applications of the C-EAB over the past decade, including 1) removal of nitrate, aromatic derivatives, and metal ions; 2) biosensing based on biocathode; 3) electrosynthesis of CH4, H2, organic carbon, NH3, and protein. In addition, the mechanisms of electron transfer by the C-EAB are also classified and summarized. Extracellular electron transfer and interspecies electron transfer have been introduced, and the electron transport mechanism of typical C-EAB, such as Shewanella oneidensis MR-1, has been combed in detail. By bringing to light this cutting-edge area of the C-EAB, this review aims to stimulate more interest and research on not only exploring great potential applications of these electron-accepting bacteria, but also developing steady and scalable processes harnessing biocathodes.
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Affiliation(s)
- Xinxin Shi
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yutong Liang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Gang Wen
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Stanislav A Evlashin
- Center for Materials Technologies, Skolkovo Institute of Science and Technology, the territory of the Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1, Moscow 121205, Russia
| | - Fedor S Fedorov
- Center for Photonic Science and Engineering, Skolkovo Institute of Science and Technology, the territory of the Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1, Moscow 121205, Russia
| | - Xinyue Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Junjie Zheng
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yixing Wang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Julian Shi
- Xi'an Institute for Innovative Earth Environment Research, Xi'an 710061, China
| | - Yang Liu
- Shaanxi Land Engineering Construction Group Co., Ltd, Xi'an 710061, China
| | - Weihuang Zhu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Pengfei Guo
- School of Civil Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Byung Hong Kim
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China; Korea Institute of Science & Technology, Seongbug-ku, Seoul 02792, Republic of Korea
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3
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Kong Z, Wang H, Wang H, Man S, Yan Q. Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics. WATER RESEARCH 2024; 262:122132. [PMID: 39053208 DOI: 10.1016/j.watres.2024.122132] [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: 05/02/2024] [Revised: 07/10/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm², would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.
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Affiliation(s)
- Ziang Kong
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - He Wang
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Han Wang
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China
| | - Shuaishuai Man
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Qun Yan
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215011, China.
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4
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Li Y, Yang B, Kong Y, Tao Y, Zhao Z, Li Y, Zhang Y. Correlation between intracellular electron transfer and gene expression for electrically conductive pili in electroactive bacteria during anaerobic digestion with ethanol. WATER RESEARCH 2024; 265:122307. [PMID: 39180955 DOI: 10.1016/j.watres.2024.122307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/24/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Ethanol feeding has been widely documented as an economical and effective strategy for establishing direct interspecies electron transfer (DIET) during anaerobic digestion. However, the mechanisms involved are still unclear, especially on correlation between intracellular electron transfer in electroactive bacteria and their gene expression for electrically conductive pili (e-pili), the most essential electrical connection component for DIET. Upon cooling from room temperature, the conductivity of digester aggregates with ethanol exponentially increased by an order of magnitude (from 45.5 to 125.4 μS/cm), whereas which with its metabolites (acetaldehyde [from 40.5 to 54.4 μS/cm] or acetate [from 32.1 to 50.4 μS/cm]) did not increase significantly. In addition, the digester aggregates only with ethanol were observed with a strong dependence of conductivity on pH. Metagenomic and metatranscriptomic analysis showed that Desulfovibrio desulfuricans was the most dominant and metabolically active bacterium that contained and highly expressed the genes for e-pili. Abundance of genes encoding the total type IV pilus assembly proteins (6.72E-04 vs 1.24E-03, P < 0.05), PilA that determined the conductive properties (2.22E-04 vs 2.44E-04, P > 0.05), and PilB that proceeded the polymerization of pilin (1.56E-04 vs 3.52E-03, P < 0.05) with ethanol was lower than that with acetaldehyde. However, transcript abundance of these genes with ethanol was generally higher than that with acetaldehyde. In comparison to acetaldehyde, ethanol increased the transcript abundance of genes encoding the key enzymes involved in NADH/NAD+ transformation on complex I and ATP synthesis on complex V in intracellular electron transport chain. The improvement of intracellular electron transfer in D. desulfuricans suggested that electrons were intracellularly energized with high energy to activate e-pili during DIET.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bowen Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yaohui Kong
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yang Tao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yang Li
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin 124221, China.
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China; School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin 124221, China
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Yoshizu D, Shimizu S, Tsuchiya M, Tomita K, Kouzuma A, Watanabe K. Isolation of Electrochemically Active Bacteria from an Anaerobic Digester Treating Food Waste and Their Characterization. Microorganisms 2024; 12:1645. [PMID: 39203487 PMCID: PMC11356707 DOI: 10.3390/microorganisms12081645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Studies have used anaerobic-digester sludge and/or effluent as inocula for bioelectrochemical systems (BESs), such as microbial fuel cells (MFCs), for power generation, while limited studies have isolated and characterized electrochemically active bacteria (EAB) that inhabit anaerobic digesters. In the present work, single-chamber MFCs were operated using the anaerobic-digester effluent as the sole source of organics and microbes, and attempts were made to isolate EAB from anode biofilms in MFCs by repeated anaerobic cultivations on agar plates. Red colonies were selected from those grown on the agar plates, resulting in the isolation of three phylogenetically diverse strains affiliated with the phyla Bacillota, Campylobacterota and Deferribacterota. All these strains are capable of current generation in pure-culture BESs, while they exhibit different electrochemical properties as assessed by cyclic voltammetry. The analyses of their cell-free extracts show that cytochromes are abundantly present in their cells, suggesting their involvement in current generation. The results suggest that anaerobic digesters harbor diverse EAB, and it would be of interest to examine their ecological niches in anaerobic digestion.
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Affiliation(s)
- Daichi Yoshizu
- Laboratory of Bioenergy Science and Technology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (D.Y.); (S.S.); (K.T.); (A.K.)
- J &T Recycling Corporation, Yokohama 230-0044, Japan;
| | - Soranosuke Shimizu
- Laboratory of Bioenergy Science and Technology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (D.Y.); (S.S.); (K.T.); (A.K.)
| | - Miyu Tsuchiya
- J &T Recycling Corporation, Yokohama 230-0044, Japan;
| | - Keisuke Tomita
- Laboratory of Bioenergy Science and Technology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (D.Y.); (S.S.); (K.T.); (A.K.)
| | - Atsushi Kouzuma
- Laboratory of Bioenergy Science and Technology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (D.Y.); (S.S.); (K.T.); (A.K.)
| | - Kazuya Watanabe
- Laboratory of Bioenergy Science and Technology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (D.Y.); (S.S.); (K.T.); (A.K.)
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6
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Giangeri G, Tsapekos P, Gaspari M, Ghofrani-Isfahani P, Hong Lin MKT, Treu L, Kougias P, Campanaro S, Angelidaki I. Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16399-16413. [PMID: 37862709 PMCID: PMC10620991 DOI: 10.1021/acs.est.3c05948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023]
Abstract
It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.
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Affiliation(s)
- Ginevra Giangeri
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Panagiotis Tsapekos
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Maria Gaspari
- Department
of Hydraulics, Soil Science and Agricultural Engineering, Faculty
of Agriculture, Aristotle University of
Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Parisa Ghofrani-Isfahani
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Marie Karen Tracy Hong Lin
- National
Centre for Nano Fabrication and Characterization, Technical University of Denmark, Kgs, DK-2800 Lyngby, Denmark
| | - Laura Treu
- Department
of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
| | - Panagiotis Kougias
- Hellenic
Agricultural Organization Dimitra, Soil
and Water Resources Institute, Thermi, GR-54124 Thessaloniki, Greece
| | - Stefano Campanaro
- Department
of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
| | - Irini Angelidaki
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Mohammad Mirsoleimani Azizi S, Zakaria BS, Haffiez N, Kumar A, Ranjan Dhar B. Pilot-scale investigation of conductive carbon cloth amendment for enhancing high-solids anaerobic digestion and mitigating antibiotic resistance. BIORESOURCE TECHNOLOGY 2023; 385:129411. [PMID: 37394042 DOI: 10.1016/j.biortech.2023.129411] [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: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
This study examined the effectiveness of introducing conductive carbon cloth into a pilot-scale high-solids anaerobic digestion (HSAD) system. Adding carbon cloth increased methane production by 22 % and improved the maximum methane production rate by 39 %. Microbial community characterization indicated a possible direct interspecies electron transfer-based syntrophic association among microbes. Using carbon cloth also enhanced microbial richness, diversity, and evenness. Carbon cloth effectively reduced the total abundance of antibiotic resistance genes (ARGs) by 44.6 %, mainly by inhibiting horizontal gene transfer, as shown by the significant decrease in the relative abundance of integron genes (particularly intl1). The multivariate analysis further demonstrated strong correlations of intl1 with most of the targeted ARGs. These findings suggest that carbon cloth amendment can promote efficient methane production and attenuate the spread of ARGs in HSAD systems.
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Affiliation(s)
| | - Basem S Zakaria
- Civil and Environmental Engineering, University of Alberta, Edmonton, AB, Canada
| | - Nervana Haffiez
- Civil and Environmental Engineering, University of Alberta, Edmonton, AB, Canada
| | - Amit Kumar
- Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Bipro Ranjan Dhar
- Civil and Environmental Engineering, University of Alberta, Edmonton, AB, Canada.
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Ao Z, Li Y, Li Y, Zhao Z, Zhang Y. Facilitating direct interspecies electron transfer in anaerobic digestion via speeding up transmembrane transport of electrons and CO 2 reduction in methanogens by Na + adjustment. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 170:252-260. [PMID: 37729842 DOI: 10.1016/j.wasman.2023.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/08/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The possibility of facilitating direct interspecies electron transfer (DIET) in anaerobic digestion with different concentrations of NaCl was explored. Additional NaCl at 2 or 4 g/L strengthened anaerobic digestion to resist the high-organic loading rate impacts, whereas the higher concentrations of NaCl (6 or 8 g/L) suppressed methanogenesis. Additional MgCl2 with the same ion strength as NaCl at 2 g/L had no effect on performances. Additional NaCl at 2 or 4 g/L dramatically increased the abundance of Methanosarcina species (20.7%/23.4% vs 8.6%) and stimulated the growth of Sphaerochaeta and Petrimonas species that could transfer electrons to the soluble Fe(III) or elemental sulfur. Electrochemical evidences showed that, additional NaCl at 2 or 4 g/L increased capacitances and decreased charge transfer resistances of Methanosarcina-dominant communities. Metagenomic evidences showed that, additional NaCl at 2 or 4 g/L increased the abundance of genes that encoded the type IV pilus assembly proteins (1.98E-04/1.87E-04 vs 1.85E-04) and cytochrome c-like proteins (5.51E-04/5.60E-04 vs 5.31E-04). In addition, additional NaCl at 2 or 4 g/L increased the abundance of genes for methanophenazine (MP)/MPH2 transformation (1.04E-05/1.24E-05 vs 8.06E-06) and CO2 reduction (1.64E-03/1.86E-03 vs 1.06E-03), suggesting a rapid transmembrane transport of electrons and CO2 reduction in methanogens. Both processes were closely associated with F420/F420H2 transformation that required ATP. Additional NaCl at 2 or 4 g/L increased the yield of ATP (256.0/249.3 vs 231.8 nmol/L) that might promote F420/F420H2 transformation in methanogens, which overcame the thermodynamic limitations of combining electrons with protons for the reduction of CO2 to methane and facilitated DIET.
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Affiliation(s)
- Zhipeng Ao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yang Li
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Abstract
Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.
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Affiliation(s)
- J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
| | - D R Bond
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA; ,
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10
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Smith JA, Holmes DE, Woodard TL, Li Y, Liu X, Wang LY, Meier D, Schwarz IA, Lovley DR. Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer. Microbiol Spectr 2023; 11:e0094123. [PMID: 37650614 PMCID: PMC10580878 DOI: 10.1128/spectrum.00941-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/02/2023] [Indexed: 09/01/2023] Open
Abstract
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.
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Affiliation(s)
- Jessica A. Smith
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Yang Li
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - David Meier
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
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Song B, Wang Z, Wang L, Wang Q, Li J, Song M, Ali J, Wang Y, Glebov EM, Zhuang X. In Situ Enhanced Yields of Microbial Nanowires: The Key Role of Environmental Stress. ACS Biomater Sci Eng 2023. [PMID: 37146257 DOI: 10.1021/acsbiomaterials.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The conductive microbial nanowires of Geobacter sulfurreducens serve as a model for long-range extracellular electron transfer (EET), which is considered a revolutionary "green" nanomaterial in the fields of bioelectronics, renewable energy, and bioremediation. However, there is no efficient pathway to induce microorganisms to express a large amount of microbial nanowires. Here, several strategies have been used to successfully induce the expression of microbial nanowires. Microbial nanowire expression was closely related to the concentration of electron acceptors. The microbial nanowire was around 17.02 μm in length, more than 3 times compared to its own length. The graphite electrode was used as an alternative electron acceptor by G. sulfurreducens, which obtained a fast start-up time of 44 h in microbial fuel cells (MFCs). Meanwhile, Fe(III) citrate-coated sugarcane carbon and biochar were prepared to test the applicability of these strategies in the actual microbial community. The unsatisfied EET efficiency between c-type cytochrome and extracellular insoluble electron receptors promoted the expression of microbial nanowires. Hence, microbial nanowires were proposed to be an effective survival strategy for G. sulfurreducens to cope with various environmental stresses. Based on this top-down strategy of artificially constructed microbial environmental stress, this study is of great significance for exploring more efficient methods to induce microbial nanowires expression.
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Affiliation(s)
- Bo Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qi Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450003, China
| | - Jiaxin Li
- Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang 110819, China
| | - Manjiao Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jafar Ali
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Evgeni M Glebov
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, 3 Institutskaya Str., Novosibirsk 630090, Russian Federation
- Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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12
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Römling U. Is biofilm formation intrinsic to the origin of life? Environ Microbiol 2023; 25:26-39. [PMID: 36655713 PMCID: PMC10086821 DOI: 10.1111/1462-2920.16179] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 01/21/2023]
Abstract
Biofilms are multicellular, often surface-associated, communities of autonomous cells. Their formation is the natural mode of growth of up to 80% of microorganisms living on this planet. Biofilms refractory towards antimicrobial agents and the actions of the immune system due to their tolerance against multiple environmental stresses. But how did biofilm formation arise? Here, I argue that the biofilm lifestyle has its foundation already in the fundamental, surface-triggered chemical reactions and energy preserving mechanisms that enabled the development of life on earth. Subsequently, prototypical biofilm formation has evolved and diversified concomitantly in composition, cell morphology and regulation with the expansion of prokaryotic organisms and their radiation by occupation of diverse ecological niches. This ancient origin of biofilm formation thus mirrors the harnessing environmental conditions that have been the rule rather than the exception in microbial life. The subsequent emergence of the association of microbes, including recent human pathogens, with higher organisms can be considered as the entry into a nutritional and largely stress-protecting heaven. Nevertheless, basic mechanisms of biofilm formation have surprisingly been conserved and refunctionalized to promote sustained survival in new environments.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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13
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Guberman-Pfeffer MJ. Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire. J Phys Chem B 2022; 126:10083-10097. [PMID: 36417757 PMCID: PMC9743091 DOI: 10.1021/acs.jpcb.2c06822] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨Hmn⟩), reaction free energies (ΔGmn), reorganization energies (λmn), and activation energies (Ea) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔGmn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.
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Affiliation(s)
- Matthew J. Guberman-Pfeffer
- Department
of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, Connecticut06510, United States,Microbial
Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut06516, United States,
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14
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Holmes DE, Zhou J, Smith JA, Wang C, Liu X, Lovley DR. Different outer membrane c-type cytochromes are involved in direct interspecies electron transfer to Geobacter or Methanosarcina species. MLIFE 2022; 1:272-286. [PMID: 38818222 PMCID: PMC10989804 DOI: 10.1002/mlf2.12037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 06/01/2024]
Abstract
Direct interspecies electron transfer (DIET) may be most important in methanogenic environments, but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with G. sulfurreducens reducing fumarate was compared with G. metallireducens grown in coculture with diverse Methanosarcina. The transcriptome of G. metallireducens cocultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface c-type cytochromes, differed from those of G. metallireducens cocultured with M. acetivorans or M. subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable. Cocultures with c-type cytochrome deletion mutant strains, ∆Gmet_0930, ∆Gmet_0557 and ∆Gmet_2896, never became established with G. sulfurreducens but adapted to grow with all three Methanosarcina. Two porin-cytochrome complexes, PccF and PccG, were important for DIET; however, PccG was more important for growth with Methanosarcina. Unlike cocultures with G. sulfurreducens and M. acetivorans, electrically conductive pili were not needed for growth with M. barkeri. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface c-type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron-accepting partner on the physiology of the electron-donating DIET partner.
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Affiliation(s)
- Dawn E. Holmes
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Physical and Biological ScienceWestern New England UniversitySpringfieldMassachusettsUSA
| | - Jinjie Zhou
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Jessica A. Smith
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Biomolecular SciencesCentral Connecticut State UniversityNew BritainConnecticutUSA
| | - Caiqin Wang
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of EnvironmentZhejiang University of TechnologyHangzhouChina
| | - Xinying Liu
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of Environmental Science and EngineeringBeijing Forestry UniversityBeijingChina
| | - Derek R. Lovley
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
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15
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Zhu R, Zhang Y, Zou H, Zheng Y, Guo RB, Fu SF. Understanding the mechanisms behind enhanced anaerobic digestion of corn straw by humic acids. BIORESOURCE TECHNOLOGY 2022; 359:127454. [PMID: 35697261 DOI: 10.1016/j.biortech.2022.127454] [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: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Humic acids (HAs) are abundant on earth, yet their effects on anaerobic digestion (AD) of cellulosic substrate are not fully uncovered. The effects of HAs on AD of corn straw and the mechanisms behind were analyzed in this study. Results showed that the effects of HAs on methane yield were closely related to the total solids (TS) content. At relative high TS content of 5.0%, HAs benefited AD process by increasing 13.8% of methane yield, accelerating methane production rate by 43% and shortening lag phase time by 37.5%. Microbial community analysis indicated that HAs increased the relative abundance of syntrophic bacteria (Syntrophomonadaceae and Synergistaceae), facilitating the degradation of volatile fatty acids. HAs might act as electron shuttles to directly transfer electrons to hydrogenotrophic methanogens for CO2 reduction to CH4. This study provides a simple and efficient strategy to facilitate the AD of cellulosic substrate by HAs addition.
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Affiliation(s)
- Rong Zhu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506, United States.
| | - Yun Zhang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Hua Zou
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506, United States
| | - Rong-Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China
| | - Shan-Fei Fu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China.
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16
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Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
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17
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Li Y, Liang L, Sun C, Wang Z, Yu Q, Zhao Z, Zhang Y. Glycol/glycerol-fed electrically conductive aggregates suggest a mechanism of stimulating direct interspecies electron transfer in methanogenic digesters. WATER RESEARCH 2022; 217:118448. [PMID: 35430471 DOI: 10.1016/j.watres.2022.118448] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
The possibility of stimulating direct interspecies electron transfer (DIET) within aggregates of methanogenic digesters respectively with ethanol, glycol, and glycerol as a primary substrate was investigated to better understand the mechanisms of alcohol compounds stimulating DIET. Aggregates fed with ethanol, glycol, and glycerol were electrically conductive (10.4-19.4 uS/cm), with a temperature dependence of metallic-like conductivity. Close examination of transmission electron microscope images observed the potential interspecies connected networks assembled by filaments within these aggregates. Further investigations via metatranscriptomics found that, genes for electrically conductive pili (e-pili) (Log2FPKM, 9.39-10.96) and c-type cytochromes (8.90-9.64) were highly expressed within aggregates. Glycerol-fed aggregates exhibited the highest gene expression for e-pili, while glycol-fed aggregates exhibited the highest gene expression for c-type cytochromes. Methanothrix species were dominant and metabolically active within aggregates. Genes encoding the enzymes involved in carbon dioxide reduction were highly expressed in Methanothrix species, suggesting that they participated in DIET. In addition, transcript abundance of genes encoding alcohol dehydrogenase and NADH-quinone oxidoreductase in alcohol dehydrogenation closely associated with NADH/NAD+ transformation within glycol- and glycerol-fed aggregates was generally higher than that within ethanol-fed aggregates. These results, and the fact that NADH/NAD+ transformation was very linked to the ATP synthesis complex that further supported the formation of extracellular electrical connection components, e-pili and membrane-bound multi-heme c-type cytochromes (MHCs), provided a possibility that alcohol compounds comprised of hydroxy groups could stimulate DIET and more hydroxy groups comprised were better for this stimulation.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Lianfu Liang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Cheng Sun
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhenxin Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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18
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Lovley DR. On the Existence of Pilin-Based Microbial Nanowires. Front Microbiol 2022; 13:872610. [PMID: 35733974 PMCID: PMC9207759 DOI: 10.3389/fmicb.2022.872610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
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19
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Choi S. Electrogenic Bacteria Promise New Opportunities for Powering, Sensing, and Synthesizing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107902. [PMID: 35119203 DOI: 10.1002/smll.202107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Considerable research efforts into the promises of electrogenic bacteria and the commercial opportunities they present are attempting to identify potential feasible applications. Metabolic electrons from the bacteria enable electricity generation sufficient to power portable or small-scale applications, while the quantifiable electric signal in a miniaturized device platform can be sensitive enough to monitor and respond to changes in environmental conditions. Nanomaterials produced by the electrogenic bacteria can offer an innovative bottom-up biosynthetic approach to synergize bacterial electron transfer and create an effective coupling at the cell-electrode interface. Furthermore, electrogenic bacteria can revolutionize the field of bioelectronics by effectively interfacing electronics with microbes through extracellular electron transfer. Here, these new directions for the electrogenic bacteria and their recent integration with micro- and nanosystems are comprehensively discussed with specific attention toward distinct applications in the field of powering, sensing, and synthesizing. Furthermore, challenges of individual applications and strategies toward potential solutions are provided to offer valuable guidelines for practical implementation. Finally, the perspective and view on how the use of electrogenic bacteria can hold immeasurable promise for the development of future electronics and their applications are presented.
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Affiliation(s)
- Seokheun Choi
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, NY, 13902, USA
- Center for Research in Advanced Sensing Technologies & Environmental Sustainability, State University of New York at Binghamton, Binghamton, NY, 13902, USA
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20
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Sharma R, Kumari R, Pant D, Malaviya P. Bioelectricity generation from human urine and simultaneous nutrient recovery: Role of Microbial Fuel Cells. CHEMOSPHERE 2022; 292:133437. [PMID: 34973250 DOI: 10.1016/j.chemosphere.2021.133437] [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: 07/09/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Urine is a 'valuable waste' that can be exploited to generate bioelectricity and recover key nutrients for producing NPK-rich biofertilizers. In recent times, improved and innovative waste management technologies have emerged to manage the rapidly increasing environmental pollution and to accomplish the goal of sustainable development. Microbial fuel cells (MFCs) have attracted the attention of environmentalists worldwide to treat human urine and produce power through bioelectrochemical reactions in presence of electroactive bacteria growing on the anode. The bacteria break down the complex organic matter present in urine into simpler compounds and release the electrons which flow through an external circuit generating current at the cathode. Many other useful products are harvested at the end of the process. So, in this review, an attempt has been made to synthesize the information on MFCs fuelled with urine to generate bioelectricity and recover value-added resources (nutrients), and their modifications to enhance productivity. Moreover, configuration and mode of system operation, and factors enhancing the performance of MFCs have been also presented.
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Affiliation(s)
- Rozi Sharma
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Rekha Kumari
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Pant
- Separation & Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, 2400, Belgium
| | - Piyush Malaviya
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India.
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21
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Abstract
In this Quick guide, Derek Lovley introduces microbial nanowires-conductive extracellular appendages made by some bacteria and archaea.
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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 01003, USA.
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22
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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: 26] [Impact Index Per Article: 13.0] [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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23
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Timmis K, Hallsworth JE. The darkest microbiome-a post-human biosphere. Microb Biotechnol 2022; 15:176-185. [PMID: 34843168 PMCID: PMC8719803 DOI: 10.1111/1751-7915.13976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
Microbial technology is exceptional among human activities and endeavours in its range of applications that benefit humanity, even exceeding those of chemistry. What is more, microbial technologists are among the most creative scientists, and the scope of the field continuously expands as new ideas and applications emerge. Notwithstanding this diversity of applications, given the dire predictions for the fate of the surface biosphere as a result of current trajectories of global warming, the future of microbial biotechnology research must have a single purpose, namely to help secure the future of life on Earth. Everything else will, by comparison, be irrelevant. Crucially, microbes themselves play pivotal roles in climate (Cavicchioli et al., Nature Revs Microbiol 17: 569-586, 2019). To enable realization of their full potential in humanity's effort to survive, development of new and transformative global warming-relevant technologies must become the lynchpin of microbial biotechnology research and development. As a consequence, microbial biotechnologists must consider constraining their usual degree of freedom, and re-orienting their focus towards planetary-biosphere exigences. And they must actively seek alliances and synergies with others to get the job done as fast as humanly possible; they need to enthusiastically embrace and join the global effort, subordinating where necessary individual aspirations to the common good (the amazing speed with which new COVID-19 diagnostics and vaccines were developed and implemented demonstrates what is possible given creativity, singleness of purpose and funding). In terms of priorities, some will be obvious, others less so, with some only becoming revealed after dedicated effort yields new insights/opens new vistas. We therefore refrain from developing a priority list here. Rather, we consider what is likely to happen to the Earth's biosphere if we (and the rest of humanity) fail to rescue it. We do so with the aim of galvanizing the formulation and implementation of strategic and financial science policy decisions that will maximally stimulate the development of relevant new microbial technologies, and maximally exploit available technologies, to repair existing environmental damage and mitigate against future deterioration.
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Affiliation(s)
- Kenneth Timmis
- Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
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24
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Liang D, Liu X, Woodard TL, Holmes DE, Smith JA, Nevin KP, Feng Y, Lovley DR. Extracellular Electron Exchange Capabilities of Desulfovibrio ferrophilus and Desulfopila corrodens. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16195-16203. [PMID: 34748326 DOI: 10.1021/acs.est.1c04071] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbial extracellular electron transfer plays an important role in diverse biogeochemical cycles, metal corrosion, bioelectrochemical technologies, and anaerobic digestion. Evaluation of electron uptake from pure Fe(0) and stainless steel indicated that, in contrast to previous speculation in the literature, Desulfovibrio ferrophilus and Desulfopila corrodens are not able to directly extract electrons from solid-phase electron-donating surfaces. D. ferrophilus grew with Fe(III) as the electron acceptor, but Dp. corrodens did not. D. ferrophilus reduced Fe(III) oxide occluded within porous alginate beads, suggesting that it released a soluble electron shuttle to promote Fe(III) oxide reduction. Conductive atomic force microscopy revealed that the D. ferrophilus pili are electrically conductive and the expression of a gene encoding an aromatics-rich putative pilin was upregulated during growth on Fe(III) oxide. The expression of genes for multi-heme c-type cytochromes was not upregulated during growth with Fe(III) as the electron acceptor, and genes for a porin-cytochrome conduit across the outer membrane were not apparent in the genome. The results suggest that D. ferrophilus has adopted a novel combination of strategies to enable extracellular electron transport, which may be of biogeochemical and technological significance.
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Affiliation(s)
- Dandan Liang
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Trevor L Woodard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119-2612, United States
| | - Jessica A Smith
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut 06053-2490, United States
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
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25
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Generation of High Current Densities in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor. Microbiol Spectr 2021; 9:e0087721. [PMID: 34585977 PMCID: PMC8557921 DOI: 10.1128/spectrum.00877-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacter sulfurreducens is commonly employed as a model for the study of extracellular electron transport mechanisms in the Geobacter species. Deletion of pilB, which is known to encode the pilus assembly motor protein for type IV pili in other bacteria, has been proposed as an effective strategy for evaluating the role of electrically conductive pili (e-pili) in G. sulfurreducens extracellular electron transfer. In those studies, the inhibition of e-pili expression associated with pilB deletion was not demonstrated directly but was inferred from the observation that pilB deletion mutants produced lower current densities than wild-type cells. Here, we report that deleting pilB did not diminish current production. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are expressed heterologously from the G. sulfurreducens pilin gene in Escherichia coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing a pilin monomer with a His tag continued to express His tag-labeled filaments when pilB was deleted. These results suggest that a reinterpretation of the results of previous studies on G. sulfurreducens pilB deletion strains may be necessary. IMPORTANCE Geobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes, such as the reduction of Fe(III) oxides in soils and sediments, bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity, direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments, and metal corrosion. Elucidating the phenotypes associated with gene deletions is an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that we cannot replicate the key phenotype reported for a gene deletion that has been central to the development of models for long-range electron transport in G. sulfurreducens.
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26
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McCuskey SR, Chatsirisupachai J, Zeglio E, Parlak O, Panoy P, Herland A, Bazan GC, Nguyen TQ. Current Progress of Interfacing Organic Semiconducting Materials with Bacteria. Chem Rev 2021; 122:4791-4825. [PMID: 34714064 DOI: 10.1021/acs.chemrev.1c00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial bioelectronics require interfacing microorganisms with electrodes. The resulting abiotic/biotic platforms provide the basis of a range of technologies, including energy conversion and diagnostic assays. Organic semiconductors (OSCs) provide a unique strategy to modulate the interfaces between microbial systems and external electrodes, thereby improving the performance of these incipient technologies. In this review, we explore recent progress in the field on how OSCs, and related materials capable of charge transport, are being used within the context of microbial systems, and more specifically bacteria. We begin by examining the electrochemical communication modes in bacteria and the biological basis for charge transport. Different types of synthetic organic materials that have been designed and synthesized for interfacing and interrogating bacteria are discussed next, followed by the most commonly used characterization techniques for evaluating transport in microbial, synthetic, and hybrid systems. A range of applications is subsequently examined, including biological sensors and energy conversion systems. The review concludes by summarizing what has been accomplished so far and suggests future design approaches for OSC bioelectronics materials and technologies that hybridize characteristic properties of microbial and OSC systems.
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Affiliation(s)
- Samantha R McCuskey
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Jirat Chatsirisupachai
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Erica Zeglio
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden
| | - Onur Parlak
- Dermatology and Venereology Division, Department of Medicine(Solna), Karolinska Institute, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Patchareepond Panoy
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Anna Herland
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Guillermo C Bazan
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Thuc-Quyen Nguyen
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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27
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Scarborough MJ, Lawson CE, DeCola AC, Gois IM. Microbiomes for sustainable biomanufacturing. Curr Opin Microbiol 2021; 65:8-14. [PMID: 34700205 DOI: 10.1016/j.mib.2021.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Matthew James Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States.
| | - Christopher Evan Lawson
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Amy Camille DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ian Mateus Gois
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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28
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Mao Z, Cheng S, Sun Y, Lin Z, Li L, Yu Z. Enhancing stability and resilience of electromethanogenesis system by acclimating biocathode with intermittent step-up voltage. BIORESOURCE TECHNOLOGY 2021; 337:125376. [PMID: 34116281 DOI: 10.1016/j.biortech.2021.125376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Electromethanogenesis (EMG) system could efficiently convert CO2 to CH4 by using excess renewable electricity. However, the fluctuation and interruption of renewable electricity will adversely affect the biocathode and therefore the CH4 production of the EMG system. In this work, a novel biocathode acclimation strategy with intermittent step-up voltage (ISUV) was proposed to improve the stability and resilience of the EMG system against the unstable input of renewable power. Compared with the intermittent application of constant voltage (IACV), the ISUV increased the rate of CH4 production by 11.7 times with the improvement of the stability and resilience by 56% and 500%, respectively. Morphology and microflora structure analysis revealed that the biofilm enriched with ISUV exhibited a compact microflora structure with high-density cells and nanowires interconnected. This study provided a novel effective strategy to regulate the biofilm structure and enhance the performance of the EMG system.
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Affiliation(s)
- Zhengzhong Mao
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Shaoan Cheng
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China.
| | - Yi Sun
- Powerchina Huadong Engineering Corporation Limited, Hangzhou 311122, PR China
| | - Zhufan Lin
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Longxin Li
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Zhen Yu
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
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29
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Nanosecond heme-to-heme electron transfer rates in a multiheme cytochrome nanowire reported by a spectrally unique His/Met-ligated heme. Proc Natl Acad Sci U S A 2021; 118:2107939118. [PMID: 34556577 PMCID: PMC8488605 DOI: 10.1073/pnas.2107939118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/29/2022] Open
Abstract
Multiheme cytochromes have been identified as essential proteins for electron exchange between bacterial enzymes and redox substrates outside of the cell. In microbiology, these proteins contribute to efficient energy storage and conversion. For biotechnology, multiheme cytochromes contribute to the production of green fuels and electricity. Furthermore, these proteins inspire the design of molecular-scale electronic devices. Here, we report exceptionally high rates of heme-to-heme electron transfer in a multiheme cytochrome. We expect similarly high rates, among the highest reported for ground-state electron transfer in biology, in other multiheme cytochromes as the close-packed hemes adopt similar configurations despite very different amino acid sequences and protein folds. Proteins achieve efficient energy storage and conversion through electron transfer along a series of redox cofactors. Multiheme cytochromes are notable examples. These proteins transfer electrons over distance scales of several nanometers to >10 μm and in so doing they couple cellular metabolism with extracellular redox partners including electrodes. Here, we report pump-probe spectroscopy that provides a direct measure of the intrinsic rates of heme–heme electron transfer in this fascinating class of proteins. Our study took advantage of a spectrally unique His/Met-ligated heme introduced at a defined site within the decaheme extracellular MtrC protein of Shewanella oneidensis. We observed rates of heme-to-heme electron transfer on the order of 109 s−1 (3.7 to 4.3 Å edge-to-edge distance), in good agreement with predictions based on density functional and molecular dynamics calculations. These rates are among the highest reported for ground-state electron transfer in biology. Yet, some fall 2 to 3 orders of magnitude below the Moser–Dutton ruler because electron transfer at these short distances is through space and therefore associated with a higher tunneling barrier than the through-protein tunneling scenario that is usual at longer distances. Moreover, we show that the His/Met-ligated heme creates an electron sink that stabilizes the charge separated state on the 100-μs time scale. This feature could be exploited in future designs of multiheme cytochromes as components of versatile photosynthetic biohybrid assemblies.
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30
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Liu X, Walker DJF, Nonnenmann SS, Sun D, Lovley DR. Direct Observation of Electrically Conductive Pili Emanating from Geobacter sulfurreducens. mBio 2021; 12:e0220921. [PMID: 34465020 PMCID: PMC8406130 DOI: 10.1128/mbio.02209-21] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Geobacter sulfurreducens is a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport in G. sulfurreducens. However, it has recently been reported that G. sulfurreducens does not express e-pili and that filaments comprised of multi-heme c-type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90% of the filaments emanating from wild-type cells had a diameter (3 nm) and conductance consistent with previous reports of e-pili harvested from G. sulfurreducens or heterologously expressed in Escherichia coli from the G. sulfurreducens pilin gene. The remaining 10% of filaments had a morphology consistent with filaments comprised of the c-type cytochrome OmcS. A strain expressing a modified pilin gene designed to yield poorly conductive pili expressed 90% filaments with a 3-nm diameter, but greatly reduced conductance, further indicating that the 3-nm diameter conductive filaments in the wild-type strain were e-pili. A strain in which genes for five of the most abundant outer-surface c-type cytochromes, including OmcS, were deleted yielded only 3-nm-diameter filaments with the same conductance as in the wild type. These results demonstrate that e-pili are the most abundant conductive filaments expressed by G. sulfurreducens, consistent with previous functional studies demonstrating the need for e-pili for long-range extracellular electron transfer. IMPORTANCE Electroactive microbes have significant environmental impacts, as well as applications in bioenergy and bioremediation. The composition, function, and even existence of electrically conductive pili (e-pili) has been one of the most contentious areas of investigation in electromicrobiology, in part because e-pili offer a mechanism for long-range electron transport that does not involve the metal cofactors common in much of biological electron transport. This study demonstrates that e-pili are abundant filaments emanating from Geobacter sulfurreducens, which serves as a model for long-range extracellular electron transfer in direct interspecies electron transfer, dissimilatory metal reduction, microbe-electrode exchange, and corrosion caused by direct electron uptake from Fe(0). The methods described in this study provide a simple strategy for evaluating the distribution of conductive filaments throughout the microbial world with an approach that avoids artifactual production and/or enrichment of filaments that may not be physiologically relevant.
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Affiliation(s)
- Xinying Liu
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - David J. F. Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Stephen S. Nonnenmann
- Institute for Applied Life Sciences, university of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Department of Mechanical and Industrial Engineering, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Dezhi Sun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, university of Massachusetts—Amherst, Amherst, Massachusetts, USA
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31
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Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol 2021; 20:5-19. [PMID: 34316046 DOI: 10.1038/s41579-021-00597-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 02/03/2023]
Abstract
Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China. .,Department of Microbiology, University of Massachusetts, Amherst, MA, USA. .,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.,Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA
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32
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Abstract
Extracellular electron transfer (EET) is an important biological process in microbial physiology as found in dissimilatory metal oxidation/reduction and interspecies electron transfer in syntrophy in natural environments. EET also plays a critical role in microorganisms relevant to environmental biotechnology in metal-contaminated areas, metal corrosion, bioelectrochemical systems, and anaerobic digesters. Geobacter species exist in a diversity of natural and artificial environments. One of the outstanding features of Geobacter species is the capability of direct EET with solid electron donors and acceptors, including metals, electrodes, and other cells. Therefore, Geobacter species are pivotal in environmental biogeochemical cycles and biotechnology applications. Geobacter sulfurreducens, a representative Geobacter species, has been studied for direct EET as a model microorganism. G. sulfurreducens employs electrically conductive pili (e-pili) and c-type cytochromes for the direct EET. The biological function and electronics applications of the e-pili have been reviewed recently, and this review focuses on the cytochromes. Geobacter species have an unusually large number of cytochromes encoded in their genomes. Unlike most other microorganisms, Geobacter species localize multiple cytochromes in each subcellular fraction, outer membrane, periplasm, and inner membrane, as well as in the extracellular space, and differentially utilize these cytochromes for EET with various electron donors and acceptors. Some of the cytochromes are functionally redundant. Thus, the EET in Geobacter is complicated. Geobacter coordinates the cytochromes with other cellular components in the elaborate EET system to flourish in the environment.
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Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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33
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Jarrell KF, Albers SV, Machado JNDS. A comprehensive history of motility and Archaellation in Archaea. FEMS MICROBES 2021; 2:xtab002. [PMID: 37334237 PMCID: PMC10117864 DOI: 10.1093/femsmc/xtab002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 08/24/2023] Open
Abstract
Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Sonja-Verena Albers
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
| | - J Nuno de Sousa Machado
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
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34
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Lekbach Y, Liu T, Li Y, Moradi M, Dou W, Xu D, Smith JA, Lovley DR. Microbial corrosion of metals: The corrosion microbiome. Adv Microb Physiol 2021; 78:317-390. [PMID: 34147188 DOI: 10.1016/bs.ampbs.2021.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe0 oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe0 oxidation. Microbes can consume H2 abiotically generated from the oxidation of Fe0. Microbial H2 removal makes continued Fe0 oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe0 oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H2 as the electron carrier between Fe0 and cells. Direct Fe0-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe0 oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.
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Affiliation(s)
- Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Tao Liu
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, China
| | - Yingchao Li
- Beijing Key Laboratory of Failure, Corrosion and Protection of Oil/Gas Facility Materials, College of New Energy and Materials, China University of Petroleum-Beijing, Beijing, China
| | - Masoumeh Moradi
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Wenwen Dou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China.
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, CT, United States
| | - Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China; Department of Microbiology, University of Massachusetts, Amherst, MA, United States.
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35
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Kappler A, Bryce C, Mansor M, Lueder U, Byrne JM, Swanner ED. An evolving view on biogeochemical cycling of iron. Nat Rev Microbiol 2021; 19:360-374. [PMID: 33526911 DOI: 10.1038/s41579-020-00502-7] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 01/23/2023]
Abstract
Biogeochemical cycling of iron is crucial to many environmental processes, such as ocean productivity, carbon storage, greenhouse gas emissions and the fate of nutrients, toxic metals and metalloids. Knowledge of the underlying processes involved in iron cycling has accelerated in recent years along with appreciation of the complex network of biotic and abiotic reactions dictating the speciation, mobility and reactivity of iron in the environment. Recent studies have provided insights into novel processes in the biogeochemical iron cycle such as microbial ammonium oxidation and methane oxidation coupled to Fe(III) reduction. They have also revealed that processes in the biogeochemical iron cycle spatially overlap and may compete with each other, and that oxidation and reduction of iron occur cyclically or simultaneously in many environments. This Review discusses these advances with particular focus on their environmental consequences, including the formation of greenhouse gases and the fate of nutrients and contaminants.
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Affiliation(s)
- Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany.
| | - Casey Bryce
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Muammar Mansor
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Ulf Lueder
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Elizabeth D Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, USA
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36
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Puvača N, de Llanos Frutos R. Antimicrobial Resistance in Escherichia coli Strains Isolated from Humans and Pet Animals. Antibiotics (Basel) 2021; 10:69. [PMID: 33450827 PMCID: PMC7828219 DOI: 10.3390/antibiotics10010069] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Throughout scientific literature, we can find evidence that antimicrobial resistance has become a big problem in the recent years on a global scale. Public healthcare systems all over the world are faced with a great challenge in this respect. Obviously, there are many bacteria that can cause infections in humans and animals alike, but somehow it seems that the greatest threat nowadays comes from the Enterobacteriaceae members, especially Escherichia coli. Namely, we are witnesses to the fact that the systems that these bacteria developed to fight off antibiotics are the strongest and most diverse in Enterobacteriaceae. Our great advantage is in understanding the systems that bacteria developed to fight off antibiotics, so these can help us understand the connection between these microorganisms and the occurrence of antibiotic-resistance both in humans and their pets. Furthermore, unfavorable conditions related to the ease of E. coli transmission via the fecal-oral route among humans, environmental sources, and animals only add to the problem. For all the above stated reasons, it is evident that the epidemiology of E. coli strains and resistance mechanisms they have developed over time are extremely significant topics and all scientific findings in this area will be of vital importance in the fight against infections caused by these bacteria.
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Affiliation(s)
- Nikola Puvača
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
- Department of Engineering Management in Biotechnology, Faculty of Economics and Engineering Management in Novi Sad, University Business Academy in Novi Sad, Cvećarska 2, 21000 Novi Sad, Serbia
| | - Rosa de Llanos Frutos
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
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37
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Lovley DR, Yao J. Intrinsically Conductive Microbial Nanowires for 'Green' Electronics with Novel Functions. Trends Biotechnol 2021; 39:940-952. [PMID: 33419586 DOI: 10.1016/j.tibtech.2020.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Intrinsically conductive protein nanowires, microbially produced from inexpensive, renewable feedstocks, are a sustainable alternative to traditional nanowire electronic materials, which require high energy inputs and hazardous conditions/chemicals for fabrication and can be highly toxic. Pilin-based nanowires can be tailored for specific functions via the design of synthetic pilin genes to tune wire conductivity or introduce novel functionalities. Other microbially produced nanowire options for electronics may include cytochrome wires, curli fibers, and the conductive fibers of cable bacteria. Proof-of-concept protein nanowire electronics that have been successfully demonstrated include biomedical sensors, neuromorphic devices, and a device that generates electricity from ambient humidity. Further development of applications will require interdisciplinary teams of engineers, biophysicists, and synthetic biologists.
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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, University of Massachusetts, Amherst, MA, USA; Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
| | - Jun Yao
- Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA; Department of Electrical and Computer Engineering, University of Massachusetts, Amherst, MA, USA; Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
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Zhao Z, Li Y, Zhang Y, Lovley DR. Sparking Anaerobic Digestion: Promoting Direct Interspecies Electron Transfer to Enhance Methane Production. iScience 2020; 23:101794. [PMID: 33294801 PMCID: PMC7695907 DOI: 10.1016/j.isci.2020.101794] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Anaerobic digestion was one of the first bioenergy strategies developed, yet the interactions of the microbial community that is responsible for the production of methane are still poorly understood. For example, it has only recently been recognized that the bacteria that oxidize organic waste components can forge electrical connections with methane-producing microbes through biologically produced, protein-based, conductive circuits. This direct interspecies electron transfer (DIET) is faster than interspecies electron exchange via diffusive electron carriers, such as H2. DIET is also more resilient to perturbations such as increases in organic load inputs or toxic compounds. However, with current digester practices DIET rarely predominates. Improvements in anaerobic digestion associated with the addition of electrically conductive materials have been attributed to increased DIET, but experimental verification has been lacking. This deficiency may soon be overcome with improved understanding of the diversity of microbes capable of DIET, which is leading to molecular tools for determining the extent of DIET. Here we review the microbiology of DIET, suggest molecular strategies for monitoring DIET in anaerobic digesters, and propose approaches for re-engineering digester design and practices to encourage DIET.
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Affiliation(s)
- Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Yang Li
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Derek R. Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang 110819, China
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA
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