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Tang M, Zhen X, Zhao G, Wu S, Hua W, Qiang J, Yanling C, Wang W. The metabolic pathways of carbon assimilation and polyhydroxyalkanoate production by Rhodospirillum rubrum in response to different atmospheric fermentation. PLoS One 2024; 19:e0306222. [PMID: 39046963 PMCID: PMC11268599 DOI: 10.1371/journal.pone.0306222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024] Open
Abstract
The purple nonsulfur bacteria, Rhodospirillum rubrum, is recognized as a potential strain for PHAs bioindustrial processes since they can assimilate a broad range of carbon sources, such as syngas, to allow reduction of the production costs. In this study, we comparatively analyzed the biomass and PHA formation behaviors of R. rubrum under 100% CO and 50% CO gas atmosphere and found that pure CO promoted the PHA synthesis (PHA content up to 23.3% of the CDW). Hydrogen addition facilitated the uptake and utilization rates of CO and elevated 3-HV monomers content (molar proportion of 3-HV up to 9.2% in the presence of 50% H2). To elucidate the genetic events culminating in the CO assimilation process, we performed whole transcriptome analysis of R. rubrum grown under 100% CO or 50% CO using RNA sequencing. Transcriptomic analysis indicated different CO2 assimilation strategy was triggered by the presence of H2, where the CBB played a minor role. An increase in BCAA biosynthesis related gene abundance was observed under 50% CO condition. Furthermore, we detected the α-ketoglutarate (αKG) synthase, converting fumarate to αKG linked to the αKG-derived amino acids synthesis, and series of threonine-dependent isoleucine synthesis enzymes were significantly induced. Collectively, our results suggested that those amino acid synthesis pathways represented a key way for carbon assimilation and redox potential maintenance by R. rubrum growth under syngas condition, which could partly replace the PHA production and affect its monomer composition in copolymers. Finally, a fed-batch fermentation of the R. rubrum in a 3-l bioreactor was carried out and proved H2 addition indeed increased the PHA accumulation rate, yielding 20% ww-1 PHA production within six days.
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Affiliation(s)
- Manyu Tang
- Biochemical Engineering College, Beijing Union University, Beijing, China
| | - Xin Zhen
- Biochemical Engineering College, Beijing Union University, Beijing, China
| | - Guoqiang Zhao
- Biochemical Engineering College, Beijing Union University, Beijing, China
| | - Shuang Wu
- Biochemical Engineering College, Beijing Union University, Beijing, China
- Beijing Key Laboratory of Biomass Waste Resource Utilization, Beijing, China
| | - Wei Hua
- Biochemical Engineering College, Beijing Union University, Beijing, China
- Beijing Key Laboratory of Biomass Waste Resource Utilization, Beijing, China
| | - Jingwen Qiang
- Biochemical Engineering College, Beijing Union University, Beijing, China
| | - Cheng Yanling
- Biochemical Engineering College, Beijing Union University, Beijing, China
- Beijing Key Laboratory of Biomass Waste Resource Utilization, Beijing, China
| | - Wanqing Wang
- Biochemical Engineering College, Beijing Union University, Beijing, China
- Beijing Key Laboratory of Biomass Waste Resource Utilization, Beijing, China
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Zhao J, Ma H, Gao M, Qian D, Wang Q, Shiung Lam S. Advancements in Medium-Chain fatty acids production through chain Elongation: Key mechanisms and innovative solutions for overcoming Rate-Limiting steps. BIORESOURCE TECHNOLOGY 2024:131133. [PMID: 39033828 DOI: 10.1016/j.biortech.2024.131133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024]
Abstract
The depletion of fossil fuels has prompted an urgent search for alternative chemicals from renewable sources. Current technology in medium chain fatty acids (MCFAs) production though chain elongation (CE) is becoming increasingly sustainable, hence the motivation for this review, which provides the detailed description, insights and analysis of the metabolic pathways, substrates type, inoculum and fermentation process. The main rate-limiting steps of microbial MCFAs production were comprehensively revealed and the corresponding innovative solutions were also critically evaluated. Innovative strategies such as substrate pretreatment, electrochemical regulation, product separation, fermentation parameter optimization, and electroactive additives have shown significant advantages in overcoming the rate-limiting steps. Furthermore, novel regulatory strategies such as quorum sensing and electronic bifurcation are expected to further increase the MCFAs yield. Finally, the techno-economic analysis was carried out, and the future research focuses were also put forward.
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Affiliation(s)
- Jihua Zhao
- Department of Environmental Science and Engineering, University of Science and Technology, Beijing, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Hongzhi Ma
- Department of Environmental Science and Engineering, University of Science and Technology, Beijing, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China; Xinjiang Key Laboratory of Clean Conversion and High Value Utilization of Biomass Resources, School of Resource and Environmental Science, Yili Normal University, Yining 835000, China.
| | - Ming Gao
- Department of Environmental Science and Engineering, University of Science and Technology, Beijing, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Dayi Qian
- Department of Environmental Science and Engineering, University of Science and Technology, Beijing, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China; Xinjiang Key Laboratory of Clean Conversion and High Value Utilization of Biomass Resources, School of Resource and Environmental Science, Yili Normal University, Yining 835000, China
| | - Qunhui Wang
- Department of Environmental Science and Engineering, University of Science and Technology, Beijing, Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Center for Global Health Research (CGHR), Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
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Llorente M, Tejedor‐Sanz S, Berná A, Manchón C, Esteve‐Núñez A. Novel electrochemical strategies for the microbial conversion of CO 2 into biomass and volatile fatty acids using a fluid-like bed electrode in a three-phase reactor. Microb Biotechnol 2024; 17:e14383. [PMID: 38231155 PMCID: PMC10832540 DOI: 10.1111/1751-7915.14383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/18/2024] Open
Abstract
Microbial electrosynthesis (MES) constitutes a bioelectrochemical process where bacteria uptake electrons extracellularly from a polarized electrode to incorporate them into their anabolic metabolism. However, the efficiency of current MES reactor designs can be lower than expected due to limitations regarding electron transfer and mass transport. One of the most promising bioreactor configurations to overcome these bottlenecks is the Microbial Electrochemical Fluidized Bed Reactor (ME-FBR). In this study, microbial CO2 fixation is investigated for the first time in a ME-FBR operated as a 3-phase reactor (solid-liquid-gas). An electroconductive carbon bed, acting as a working electrode, was fluidized with gas and polarized at different potentials (-0.6, -0.8 and -1 V vs. Ag/AgCl) so it could act as an electron donor (biocathode). Under these potentials, CO2 fixation and electron transfer were evaluated. Autotrophic electroactive microorganisms from anaerobic wastewater were enriched in a ME-FBR in the presence of 2-bromoethanosulfonic acid (BES) to inhibit the growth of methanogens. Cyclic voltammetry analysis revealed interaction between the microorganisms and the cathode. Furthermore, volatile fatty acids like propionate, formate and acetate were detected in the culture supernatant. Acetate production had a maximum rate of ca. 1 g L-1 day-1 . Planktonic cell biomass was produced under continuous culture at values as high as ca. 0.7 g L-1 dry weight. Overall, this study demonstrates the feasibility of employing a fluidized electrode with gaseous substrates and electricity as the energy source for generating biomass and carboxylic acids.
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Affiliation(s)
- María Llorente
- Department of Chemical EngineeringUniversidad de AlcaláAlcalá de HenaresMadridSpain
| | - Sara Tejedor‐Sanz
- Department of Chemical EngineeringUniversidad de AlcaláAlcalá de HenaresMadridSpain
| | | | - Carlos Manchón
- Department of Chemical EngineeringUniversidad de AlcaláAlcalá de HenaresMadridSpain
| | - Abraham Esteve‐Núñez
- Department of Chemical EngineeringUniversidad de AlcaláAlcalá de HenaresMadridSpain
- IMDEA WATERAlcalá de HenaresMadridSpain
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Wang W, Zhang Y, Yin TM, Zhao L, Xu XJ, Xing DF, Zhang RC, Lee DJ, Ren NQ, Chen C. Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167142. [PMID: 37722432 DOI: 10.1016/j.scitotenv.2023.167142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Yu Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Tian-Ming Yin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Ruo-Chen Zhang
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China; Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
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Herzog J, Mook A, Utesch T, Bengelsdorf FR, Zeng AP. Lactate based caproate production with Clostridium drakei and process control of Acetobacterium woodii via lactate dependent in situ electrolysis. Front Bioeng Biotechnol 2023; 11:1212044. [PMID: 37425355 PMCID: PMC10327822 DOI: 10.3389/fbioe.2023.1212044] [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: 04/25/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
Syngas fermentation processes with acetogens represent a promising process for the reduction of CO2 emissions alongside bulk chemical production. However, to fully realize this potential the thermodynamic limits of acetogens need to be considered when designing a fermentation process. An adjustable supply of H2 as electron donor plays a key role in autotrophic product formation. In this study an anaerobic laboratory scale continuously stirred tank reactor was equipped with an All-in-One electrode allowing for in-situ H2 generation via electrolysis. Furthermore, this system was coupled to online lactate measurements to control the co-culture of a recombinant lactate-producing Acetobacterium woodii strain and a lactate-consuming Clostridium drakei strain to produce caproate. When C. drakei was grown in batch cultivations with lactate as substrate, 1.6 g·L-1 caproate were produced. Furthermore, lactate production of the A. woodii mutant strain could manually be stopped and reinitiated by controlling the electrolysis. Applying this automated process control, lactate production of the A. woodii mutant strain could be halted to achieve a steady lactate concentration. In a co-culture experiment with the A. woodii mutant strain and the C. drakei strain, the automated process control was able to dynamically react to changing lactate concentrations and adjust H2 formation respectively. This study confirms the potential of C. drakei as medium chain fatty acid producer in a lactate-mediated, autotrophic co-cultivation with an engineered A. woodii strain. Moreover, the monitoring and control strategy presented in this study reinforces the case for autotrophically produced lactate as a transfer metabolite in defined co-cultivations for value-added chemical production.
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Affiliation(s)
- Jan Herzog
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Alexander Mook
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, Ulm, Germany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Frank R. Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, Ulm, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
- Synthetic Biology and Bioengineering Lab, School of Science, Westlake University, Hangzhou, China
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Fernández-Blanco C, Robles-Iglesias R, Naveira-Pazos C, Veiga MC, Kennes C. Production of biofuels from C 1 -gases with Clostridium and related bacteria-Recent advances. Microb Biotechnol 2023; 16:726-741. [PMID: 36661185 PMCID: PMC10034633 DOI: 10.1111/1751-7915.14220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/21/2023] Open
Abstract
Clostridium spp. are suitable for the bioconversion of C1 -gases (e.g., CO2 , CO and syngas) into different bioproducts. These products can be used as biofuels and are reviewed here, focusing on ethanol, butanol and hexanol, mainly. The production of higher alcohols (e.g., butanol and hexanol) has hardly been reviewed. Parameters affecting the optimization of the bioconversion process and bioreactor performance are addressed as well as the pathways involved in these bioconversions. New aspects, such as mixotrophy and sugar versus gas fermentation, are also reviewed. In addition, Clostridia can also produce higher alcohols from the integration of the Wood-Ljungdahl pathway and the reverse ß-oxidation pathway, which has also not yet been comprehensively reviewed. In the latter process, the acetogen uses the reducing power of CO/syngas to reduce C4 or C6 fatty acids, previously produced by a chain elongating microorganism (commonly Clostridium kluyveri), into the corresponding bioalcohol.
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Affiliation(s)
- Carla Fernández-Blanco
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research-Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña, La Coruña, Spain
| | - Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research-Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña, La Coruña, Spain
| | - Cecilia Naveira-Pazos
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research-Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña, La Coruña, Spain
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research-Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña, La Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research-Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña, La Coruña, Spain
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7
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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [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: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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Schulz S, Molitor B, Angenent LT. Acetate augmentation boosts the ethanol production rate and specificity by Clostridium ljungdahlii during gas fermentation with pure carbon monoxide. BIORESOURCE TECHNOLOGY 2023; 369:128387. [PMID: 36435417 DOI: 10.1016/j.biortech.2022.128387] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Recycling waste gases from industry is vital for the transition toward a circular economy. The model microbe Clostridium ljungdahlii reduces carbon from syngas and primarily produces acetate and ethanol. Here, a gas fermentation experiment is presented in chemostats with C. ljungdahlii and pure carbon monoxide (CO) as feedstock while entirely omitting yeast extract. A maximum ethanol production rate of 0.07 ± 0.01 g L-1 h-1 and a maximum average ethanol/acetate ratio of 1.41 ± 0.39 was observed under steady-state conditions. This confirmed that CO as the sole feedstock pushes the metabolism toward more reduced fermentation products. This effect was even more pronounced when 15 mM sodium acetate was added to the feed medium. An ethanol production rate of 0.23 ± 0.01 g L-1 h-1 was achieved, representing an increase of more than 240%. This increase was accompanied by an increase in cell density and selectivity toward ethanol, with a maximum average ethanol/acetate ratio of 92.96 ± 28.39. Oxygen contaminations voided this effect, although the cultures were still able to maintain a stable biomass concentration and ethanol production rate. These findings highlight the potential of CO-fermentation with acetate augmentation and the importance of preventing oxygen contaminations.
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Affiliation(s)
- Sarah Schulz
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Germany; AG Angenent, Max Planck Institute for Biology Tübingen, Max Planck Ring 5, 72076 Tübingen, Germany; Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000 Aarhus C, Denmark; The Novo Nordisk Foundation CO(2) Research Center (CORC), Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark.
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9
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Velvizhi G, Nair R, Goswami C, Arumugam SK, Shetti NP, Aminabhavi TM. Carbon credit reduction: A techno-economic analysis of "drop-in" fuel production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120507. [PMID: 36341830 DOI: 10.1016/j.envpol.2022.120507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/07/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The current study elucidates the fundamentals of technical, financial, and environmental viability of the processes used for sustainable "drop-in" fuel generation. At present, the price of producing "drop-in" fuels is around two times as costly (5-6 USD/gallon) as the cost of fossil fuels (3 USD/gallon), especially when using second-generation feedstocks. Hence, this necessitates a comprehensive techno-economic understanding of the current technologies with respect to "drop-in"-fuel. This entitles technical-economic viability, and environmental sustainability to make the processes involved commercially viable. In this context, the present review addresses unique contrasts among the various processes involved in "drop-in" fuel production. Furthermore, principles and process flow of techno-economic analysis as well as environmental implications in terms of reduced carbon footprint and carbon credit are elucidated to discuss fundamentals of techno-economic analysis in terms of capital and operational expenditure, revenue, simulation, cash flow analysis, mass and energy balances with respect to evidence-based practices. Case specific techno-economic studies with current developments in this field of research with emphasis on software tools viz., Aspen Plus, Aspen HYSIS, Aspen Plus Economic Analyser (APEC) Aspen Icarus Process Evaluator (AIPE) are also highlighted. The study also emphasis on the carbon foot print of biofuels and its carbon credits (Carbon Offset Credits (COCs) and Carbon Reduction Credits (CRCs)) by leveraging a deep technical and robust business-oriented insights about the techno-economic analysis (TEA) exclusively for the biofuel production.
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Affiliation(s)
- G Velvizhi
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | - Rishika Nair
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | - Chandamita Goswami
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | | | - Nagaraj P Shetti
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, India; University Center for Research & Development (UCRD), Chandigarh University, Mohali, Punjab, 140413, India
| | - Tejraj M Aminabhavi
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, India; University Center for Research & Development (UCRD), Chandigarh University, Mohali, Punjab, 140413, India.
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10
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SimDFBA: A framework for bioprocess simulation and development. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.108073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Current Trends in Biological Valorization of Waste-Derived Biomass: The Critical Role of VFAs to Fuel A Biorefinery. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The looming climate and energy crises, exacerbated by increased waste generation, are driving research and development of sustainable resource management systems. Research suggests that organic materials, such as food waste, grass, and manure, have potential for biotransformation into a range of products, including: high-value volatile fatty acids (VFAs); various carboxylic acids; bioenergy; and bioplastics. Valorizing these organic residues would additionally reduce the increasing burden on waste management systems. Here, we review the valorization potential of various sustainably sourced feedstocks, particularly food wastes and agricultural and animal residues. Such feedstocks are often micro-organism-rich and well-suited to mixed culture fermentations. Additionally, we touch on the technologies, mainly biological systems including anaerobic digestion, that are being developed for this purpose. In particular, we provide a synthesis of VFA recovery techniques, which remain a significant technological barrier. Furthermore, we highlight a range of challenges and opportunities which will continue to drive research and discovery within the field. Analysis of the literature reveals growing interest in the development of a circular bioeconomy, built upon a biorefinery framework, which utilizes biogenic VFAs for chemical, material, and energy applications.
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12
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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A Scoping Review on Environmental, Economic, and Social Impacts of the Gasification Processes. ENVIRONMENTS 2022. [DOI: 10.3390/environments9070092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In recent years, computer-based simulations have been used to enhance production processes, and sustainable industrial strategies are increasingly being considered in the manufacturing industry. In order to evaluate the performance of a gasification process, the Life Cycle Thinking (LCT) technique gathers relevant impact assessment tools to offer quantitative indications across different domains. Following the PRISMA guidelines, the present paper undertakes a scoping review of gasification processes’ environmental, economic, and social impacts to reveal how LCT approaches coping with sustainability. This report categorizes the examined studies on the gasification process (from 2017 to 2022) through the lens of LCT, discussing the challenges and opportunities. These studies have investigated a variety of biomass feedstock, assessment strategies and tools, geographical span, bioproducts, and databases. The results show that among LCT approaches, by far, the highest interest belonged to life cycle assessment (LCA), followed by life cycle cost (LCC). Only a few studies have addressed exergetic life cycle assessment (ELCA), life cycle energy assessment (LCEA), social impact assessment (SIA), consequential life cycle assessment (CLCA), and water footprint (WLCA). SimaPro® (PRé Consultants, Netherlands), GaBi® (sphere, USA), and OpenLCA (GreenDelta, Germany) demonstrated the greatest contribution. Uncertainty analysis (Monte Carlo approach and sensitivity analysis) was conducted in almost half of the investigations. Most importantly, the results confirm that it is challenging or impossible to compare the environmental impacts of the gasification process with other alternatives since the results may differ based on the methodology, criteria, or presumptions. While gasification performed well in mitigating negative environmental consequences, it is not always the greatest solution compared to other technologies.
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14
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He Y, Kennes C, Lens PNL. Enhanced solventogenesis in syngas bioconversion: Role of process parameters and thermodynamics. CHEMOSPHERE 2022; 299:134425. [PMID: 35351479 DOI: 10.1016/j.chemosphere.2022.134425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Biofuels, such as ethanol and butanol, obtained from carbon monoxide-rich gas or syngas bioconversion (solventogenesis) are an attractive alternative to traditional fermentation processes with merits of no competition with food production and sustainability. However, there is a lack of comprehensive understanding of some key process parameters and mechanisms enhancing solventogenesis during the fermentation process. This review provides an overview of the current state of the art of the main influencing factors during the syngas fermentation process catalyzed by acetogenic species as well as undefined mixed cultures. The role of syngas pressure, syngas components, fermentation pH, temperature, trace metals, organic compounds and additional materials is overviewed. As a so far hardly considered approach, thermodynamic calculations of the Gibbs free energy of CO conversion to acetic acid, ethanol, butyric acid and butanol under different CO pressures and pH at 25, 33 and 55 °C are also addressed and reviewed. Strategies for enhancing mass transfer and longer carbon chain solvent production are considered as well.
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Affiliation(s)
- Yaxue He
- National University of Ireland Galway, H91 TK33, Galway, Ireland; Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain.
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain
| | - Piet N L Lens
- National University of Ireland Galway, H91 TK33, Galway, Ireland
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15
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Lee H, Bae J, Jin S, Kang S, Cho BK. Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. Front Microbiol 2022; 13:865168. [PMID: 35615514 PMCID: PMC9124964 DOI: 10.3389/fmicb.2022.865168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.
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Affiliation(s)
- Hyeonsik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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16
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Liu C, Ji J, Wu W, Arhin SG, Papadakis VG, Goula MA, Zhang S, Zhang Y, Wang W. Heterogeneous Catalyst–Microbiome Hybrids for Efficient CO-Driven C6 Carboxylic Acid Synthesis via Metabolic Pathway Manipulation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Chao Liu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiacheng Ji
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wanling Wu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Samuel Gyebi Arhin
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Vagelis G. Papadakis
- Department of Environmental Engineering, University of Patras, Agrinio 30100, Greece
| | - Maria A. Goula
- Laboratory of Alternative Fuels and Environmental Catalysis, Department of Chemical Engineering, University of Western Macedonia, Kozani 50100, Greece
| | - Sanpeng Zhang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yi Zhang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wen Wang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
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17
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Calvo DC, Luna HJ, Arango JA, Torres CI, Rittmann BE. Determining global trends in syngas fermentation research through a bibliometric analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 307:114522. [PMID: 35066199 DOI: 10.1016/j.jenvman.2022.114522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Syngas fermentation, in which microorganisms convert H2, CO, and CO2 to acids and alcohols, is a promising alternative for carbon cycling and valorization. The intellectual landscape of the topic was characterized through a bibliometric analysis using a search query (SQ) that included all relevant documents on syngas fermentation available through the Web of Science database up to December 31st, 2021. The SQ was validated with a preliminary analysis in bibliometrix and a review of titles and abstracts of all sources. Although syngas fermentation began in the early 1980s, it grew rapidly beginning in 2008, with 92.5% of total publications and 87.3% of total citations from 2008 to 2021. The field has been steadily moving from fundamentals towards applications, suggesting that the field is maturing scientifically. The greatest number of publications and citations are from the USA, and researchers in China, Germany, and Spain also are highly active. Although collaborations have increased in the past few years, author-cluster analysis shows specialized research domains with little collaboration between groups. Based on topic trends, the main challenges to be address are related to mass-transfer limitations, and researchers are starting to explore mixed cultures, genetic engineering, microbial chain elongation, and biorefineries.
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Affiliation(s)
- Diana C Calvo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, PO Box 85287-3005, USA; Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, PO Box 85287-3005, USA.
| | - Hector J Luna
- Grupo GRESIA, Department of Environmental Engineering, Universidad Antonio Nariño, Bogotá, 110231, Colombia; Environmental and Chemical Technology Group, Department of Chemistry, Federal University of Ouro Preto, Campus University, Campus Universitario, Brazil
| | - Jineth A Arango
- Pontificia Universidad Católica de Valparaíso, Valparaíso, 2362803, Chile.
| | - Cesar I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, PO Box 85287-3005, USA.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, PO Box 85287-3005, USA.
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18
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Abstract
The majority of the genes present in bacterial genomes remain poorly characterized, with up to one-third of those that are protein encoding having no definitive function. Transposon insertion sequencing represents a high-throughput technique that can help rectify this deficiency. The technology, however, can only be realistically applied to those species in which high rates of DNA transfer can be achieved. Here, we have developed a number of approaches that overcome this barrier in the autotrophic species Clostridium autoethanogenum by using a mariner-based transposon system. The inherent instability of such systems in the Escherichia coli conjugation donor due to transposition events was counteracted through the incorporation of a conditionally lethal codA marker on the plasmid backbone. Relatively low frequencies of transformation of the plasmid into C. autoethanogenum were circumvented through the use of a plasmid that is conditional for replication coupled with the routine implementation of an Illumina library preparation protocol that eliminates plasmid-based reads. A transposon library was then used to determine the essential genes needed for growth using carbon monoxide as the sole carbon and energy source. IMPORTANCE Although microbial genome sequences are relatively easily determined, assigning gene function remains a bottleneck. Consequently, relatively few genes are well characterized, leaving the function of many as either hypothetical or entirely unknown. High-throughput transposon sequencing can help remedy this deficiency, but is generally only applicable to microbes with efficient DNA transfer procedures. These exclude many microorganisms of importance to humankind either as agents of disease or as industrial process organisms. Here, we developed approaches to facilitate transposon insertion sequencing in the acetogen Clostridium autoethanogenum, a chassis being exploited to convert single-carbon waste gases CO and CO2 into chemicals and fuels at an industrial scale. This allowed the determination of gene essentiality under heterotrophic and autotrophic growth, providing insights into the utilization of CO as a sole carbon and energy source. The strategies implemented are translatable and will allow others to apply transposon insertion sequencing to other microbes where DNA transfer has until now represented a barrier to progress.
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19
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Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum. Metab Eng 2022; 72:215-226. [DOI: 10.1016/j.ymben.2022.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 12/22/2022]
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20
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Cui Z, Wang Z, Zheng M, Chen T. Advances in biological production of acetoin: a comprehensive overview. Crit Rev Biotechnol 2021; 42:1135-1156. [PMID: 34806505 DOI: 10.1080/07388551.2021.1995319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Acetoin, a high-value-added bio-based platform chemical, is widely used in foods, cosmetics, agriculture, and the chemical industry. It is an important precursor for the synthesis of: 2,3-butanediol, liquid hydrocarbon fuels and heterocyclic compounds. Since the fossil resources are becoming increasingly scarce, biological production of acetoin has received increasing attention as an alternative to chemical synthesis. Although there are excellent reviews on the: application, catabolism and fermentative production of acetoin, little attention has been paid to acetoin production via: electrode-assisted fermentation, whole-cell biocatalysis, and in vitro/cell-free biocatalysis. In this review, acetoin biosynthesis pathways and relevant key enzymes are firstly reviewed. In addition, various strategies for biological acetoin production are summarized including: cell-free biocatalysis, whole-cell biocatalysis, microbial fermentation, and electrode-assisted fermentation. The advantages and disadvantages of the different approaches are discussed and weighed, illustrating the increasing progress toward economical, green and efficient production of acetoin. Additionally, recent advances in acetoin extraction and recovery in downstream processing are also briefly reviewed. Moreover, the current issues and future prospects of diverse strategies for biological acetoin production are discussed, with the hope of realizing the promises of industrial acetoin biomanufacturing in the near future.
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Affiliation(s)
- Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Meiyu Zheng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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21
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Montoya ACV, da Silva Mazareli RC, Delforno TP, Centurion VB, de Oliveira VM, Silva EL, Varesche MBA. New Insights into Controlling Homoacetogenesis in the Co-digestion of Coffee Waste: Effect of Operational Conditions and Characterization of Microbial Communities. Appl Biochem Biotechnol 2021; 194:1458-1478. [PMID: 34739703 DOI: 10.1007/s12010-021-03725-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
In this research batch reactors were operated with coffee processing waste and autochthonous microbial consortium, and a taxonomic and functional analysis was performed for phase I of stabilization of maximum H2 production and for phase II of maximum H2 consumption. During phase I, the reactor's operating conditions were pH 4.84 to 8.18, headspace 33.18% to 66.82%, and pulp and husk from 6.95 to 17.05 g/L. These assays continued for phase II, with initial pH conditions of 5.8-8.1, headspace of 33.18-66.82%, and pulp and husk remaining from phase I. The highest homoacetogenesis was observed in assay 5 with pH 7.7, 40% headspace, and 15 g/L of pulp and husk (initial concentrations of phase I). A relative abundance of Clostridium 41%, Lactobacillus 20% and Acetobacter 14% was observed in phase I. In phase II, there was a change in relative abundance of 21%, 63%, and 1%, respectively, and functional genes involved with autotrophic (formyltetrahydrofolate synthase) and heterotrophic (enolase) homoacetogenesis, butanol (3-hydroxybutyryl-CoA dehydrogenase), and propionic acid (propionate CoA-transferase) were identified. This study provides a new and amplified insight into the physicochemical and microbiological factors, which can be used to propose adequate operational conditions to maximize the bioenergy production and reduce homoacetogenesis in biological reactors.
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Affiliation(s)
- Alejandra Carolina Villa Montoya
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil.
| | - Raissa Cristina da Silva Mazareli
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil
| | | | - Victor Borin Centurion
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), State University of Campinas, Campinas, SP, CEP 13081-970, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), State University of Campinas, Campinas, SP, CEP 13081-970, Brazil
| | - Edson Luiz Silva
- Center of Exact Sciences and Technology, Department of Chemical Engineering, Federal University of São Carlos, São Carlos, SP, CEP 13565-905, Brazil
| | - Maria Bernadete Amâncio Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP, CEP 13563-120, Brazil.
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22
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Multi-Objective Sustainability Optimization of Biomass Residues to Ethanol via Gasification and Syngas Fermentation: Trade-Offs between Profitability, Energy Efficiency, and Carbon Emissions. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work presents a strategy for optimizing the production process of ethanol via integrated gasification and syngas fermentation, a conversion platform of growing interest for its contribution to carbon recycling. The objective functions (minimum ethanol selling price (MESP), energy efficiency, and carbon footprint) were evaluated for the combinations of different input variables in models of biomass gasification, energy production from syngas, fermentation, and ethanol distillation, and a multi-objective genetic algorithm was employed for the optimization of the integrated process. Two types of waste feedstocks were considered, wood residues and sugarcane bagasse, with the former leading to lower MESP and a carbon footprint of 0.93 USD/L and 3 g CO2eq/MJ compared to 1.00 USD/L and 10 g CO2eq/MJ for sugarcane bagasse. The energy efficiency was found to be 32% in both cases. An uncertainty analysis was conducted to determine critical decision variables, which were found to be the gasification zone temperature, the split fraction of the unreformed syngas sent to the combustion chamber, the dilution rate, and the gas residence time in the bioreactor. Apart from the abovementioned objectives, other aspects such as water footprint, ethanol yield, and energy self-sufficiency were also discussed.
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23
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Abstract
Acetogens synthesize acetyl-CoA via the CO2-fixing Wood-Ljungdahl pathway. Despite their ecological and biotechnological importance, their translational regulation of carbon and energy metabolisms remains unclear. Here, we report how carbon and energy metabolisms in the model acetogen Acetobacterium woodii are translationally controlled under different growth conditions. Data integration of genome-scale transcriptomic and translatomic analyses revealed that the acetogenesis genes, including those of the Wood-Ljungdahl pathway and energy metabolism, showed changes in translational efficiency under autotrophic growth conditions. In particular, genes encoding the Wood-Ljungdahl pathway are translated at similar levels to achieve efficient acetogenesis activity under autotrophic growth conditions, whereas genes encoding the carbonyl branch present increased translation levels in comparison to those for the methyl branch under heterotrophic growth conditions. The translation efficiency of genes in the pathways is differentially regulated by 5′ untranslated regions and ribosome-binding sequences under different growth conditions. Our findings provide potential strategies to optimize the metabolism of syngas-fermenting acetogenic bacteria for better productivity. IMPORTANCE Acetogens are capable of reducing CO2 to multicarbon compounds (e.g., ethanol or 2,3-butanediol) via the Wood-Ljungdahl pathway. Given that protein synthesis in bacteria is highly energy consuming, acetogens living at the thermodynamic limit of life are inevitably under translation control. Here, we dissect the translational regulation of carbon and energy metabolisms in the model acetogen Acetobacterium woodii under heterotrophic and autotrophic growth conditions. The latter may be experienced when acetogen is used as a cell factory that synthesizes products from CO2 during the gas fermentation process. We found that the methyl and carbonyl branches of the Wood-Ljungdahl pathway are activated at similar translation levels during autotrophic growth. Translation is mainly regulated by the 5′-untranslated-region structure and ribosome-binding-site sequence. This work reveals novel translational regulation for coping with autotrophic growth conditions and provides the systematic data set, including the transcriptome, translatome, and promoter/5′-untranslated-region bioparts.
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24
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Debabov VG. Acetogens: Biochemistry, Bioenergetics, Genetics, and Biotechnological Potential. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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25
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Wang Q, Al Makishah NH, Li Q, Li Y, Liu W, Sun X, Wen Z, Yang S. Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production. Front Bioeng Biotechnol 2021; 9:661694. [PMID: 34164382 PMCID: PMC8215697 DOI: 10.3389/fbioe.2021.661694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Naief H Al Makishah
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wenzheng Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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26
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Calvo DC, Ontiveros-Valencia A, Krajmalnik-Brown R, Torres CI, Rittmann BE. Carboxylates and alcohols production in an autotrophic hydrogen-based membrane biofilm reactor. Biotechnol Bioeng 2021; 118:2338-2347. [PMID: 33675236 DOI: 10.1002/bit.27745] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023]
Abstract
Microbiological conversion of CO2 into biofuels and/or organic industrial feedstock is an excellent carbon-cycling strategy. Here, autotrophic anaerobic bacteria in the membrane biofilm reactor (MBfR) transferred electrons from hydrogen gas (H2 ) to inorganic carbon (IC) and produced organic acids and alcohols. We systematically varied the H2 -delivery, the IC concentration, and the hydraulic retention time in the MBfR. The relative availability of H2 versus IC was the determining factor for enabling microbial chain elongation (MCE). When the H2 :IC mole ratio was high (>2.0 mol H2 /mol C), MCE was an important process, generating medium-chain carboxylates up to octanoate (C8, 9.1 ± 1.3 mM C and 28.1 ± 4.1 mmol C m-2 d-1 ). Conversely, products with two carbons were the only ones present when the H2 :IC ratio was low (<2.0 mol H2 /mol C), so that H2 was the limiting factor. The biofilm microbial community was enriched in phylotypes most similar to the well-known acetogen Acetobacterium for all conditions tested, but phylotypes closely related with families capable of MCE (e.g., Bacteroidales, Rhodocyclaceae, Alcaligenaceae, Thermoanaerobacteriales, and Erysipelotrichaceae) became important when the H2 :IC ratio was high. Thus, proper management of IC availability and H2 supply allowed control over community structure and function, reflected by the chain length of the carboxylates and alcohols produced in the MBfR.
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Affiliation(s)
- Diana C Calvo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA.,School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Design Annex, Tempe, Arizona, USA
| | - Aura Ontiveros-Valencia
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA.,Department of Environmental Sciences, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA.,School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Design Annex, Tempe, Arizona, USA.,Biodesign Center for Health Through Microbiome, Arizona State University, Tempe, Arizona, USA
| | - Cesar I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA.,School for Engineering of Matter, Transport and Energy, Ira A. Fulton Schools of Engineering, Tempe, Arizona, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA.,School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Design Annex, Tempe, Arizona, USA
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Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Dürre P, Takors R. Identifying and Engineering Bottlenecks of Autotrophic Isobutanol Formation in Recombinant C. ljungdahlii by Systemic Analysis. Front Bioeng Biotechnol 2021; 9:647853. [PMID: 33748092 PMCID: PMC7968104 DOI: 10.3389/fbioe.2021.647853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridium ljungdahlii (C. ljungdahlii, CLJU) is natively endowed producing acetic acid, 2,3-butandiol, and ethanol consuming gas mixtures of CO2, CO, and H2 (syngas). Here, we present the syngas-based isobutanol formation using C. ljungdahlii harboring the recombinant amplification of the "Ehrlich" pathway that converts intracellular KIV to isobutanol. Autotrophic isobutanol production was studied analyzing two different strains in 3-L gassed and stirred bioreactors. Physiological characterization was thoroughly applied together with metabolic profiling and flux balance analysis. Thereof, KIV and pyruvate supply were identified as key "bottlenecking" precursors limiting preliminary isobutanol formation in CLJU[KAIA] to 0.02 g L-1. Additional blocking of valine synthesis in CLJU[KAIA]:ilvE increased isobutanol production by factor 6.5 finally reaching 0.13 g L-1. Future metabolic engineering should focus on debottlenecking NADPH availability, whereas NADH supply is already equilibrated in the current generation of strains.
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Affiliation(s)
- Maria Hermann
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Sandra Weitz
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Alexander Niess
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Frank Robert Bengelsdorf
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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29
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Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Takors R. Electron availability in CO 2 , CO and H 2 mixtures constrains flux distribution, energy management and product formation in Clostridium ljungdahlii. Microb Biotechnol 2020; 13:1831-1846. [PMID: 32691533 PMCID: PMC7533319 DOI: 10.1111/1751-7915.13625] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/14/2020] [Accepted: 06/24/2020] [Indexed: 01/25/2023] Open
Abstract
Acetogens such as Clostridium ljungdahlii can play a crucial role reducing the human CO2 footprint by converting industrial emissions containing CO2 , CO and H2 into valuable products such as organic acids or alcohols. The quantitative understanding of cellular metabolism is a prerequisite to exploit the bacterial endowments and to fine-tune the cells by applying metabolic engineering tools. Studying the three gas mixtures CO2 + H2 , CO and CO + CO2 + H2 (syngas) by continuously gassed batch cultivation experiments and applying flux balance analysis, we identified CO as the preferred carbon and electron source for growth and producing alcohols. However, the total yield of moles of carbon (mol-C) per electrons consumed was almost identical in all setups which underlines electron availability as the main factor influencing product formation. The Wood-Ljungdahl pathway (WLP) showed high flexibility by serving as the key NAD+ provider for CO2 + H2, whereas this function was strongly compensated by the transhydrogenase-like Nfn complex when CO was metabolized. Availability of reduced ferredoxin (Fdred ) can be considered as a key determinant of metabolic control. Oxidation of CO via carbon monoxide dehydrogenase (CODH) is the main route of Fdred formation when CO is used as substrate, whereas Fdred is mainly regenerated via the methyl branch of WLP and the Nfn complex utilizing CO2 + H2 . Consequently, doubled growth rates, highest ATP formation rates and highest amounts of reduced products (ethanol, 2,3-butanediol) were observed when CO was the sole carbon and electron source.
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Affiliation(s)
- Maria Hermann
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Attila Teleki
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Sandra Weitz
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert‐Einstein‐Allee 11Ulm89069Germany
| | - Alexander Niess
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Andreas Freund
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Frank R. Bengelsdorf
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert‐Einstein‐Allee 11Ulm89069Germany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
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30
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Effect of temperature and surfactant on biomass growth and higher-alcohol production during syngas fermentation by Clostridium carboxidivorans P7. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00344-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractHexanol–butanol–ethanol fermentation from syngas by Clostridium carboxidivorans P7 is a promising route for biofuel production. However, bacterial agglomeration in the culture of 37 °C severely hampers the accumulation of biomass and products. To investigate the effect of culture temperature on biomass growth and higher-alcohol production, C. carboxidivorans P7 was cultivated at both constant and two-step temperatures in the range from 25 to 37 °C. Meanwhile, Tween-80 and saponin were screened out from eight surfactants to alleviate agglomeration at 37 °C. The results showed that enhanced higher-alcohol production was contributed mainly by the application of two-step temperature culture rather than the addition of anti-agglomeration surfactants. Furthermore, comparative transcriptome revealed that although 37 °C promoted high expression of genes involved in the Wood–Ljungdahl pathway, genes encoding enzymes catalyzing acyl-condensation reactions associated with higher-alcohol production were highly expressed at 25 °C. This study gained greater insight into temperature-effect mechanism on syngas fermentation by C. carboxidivorans P7.
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31
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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32
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Geinitz B, Hüser A, Mann M, Büchs J. Gas Fermentation Expands the Scope of a Process Network for Material Conversion. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202000086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Bertram Geinitz
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Aline Hüser
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Marcel Mann
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Jochen Büchs
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
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33
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Jeong J, Kim JY, Park B, Choi IG, Chang IS. Genetic engineering system for syngas-utilizing acetogen, Eubacterium limosum KIST612. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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34
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Siebler F, Lapin A, Takors R. Synergistically applying 1-D modeling and CFD for designing industrial scale bubble column syngas bioreactors. Eng Life Sci 2020; 20:239-251. [PMID: 32647503 PMCID: PMC7336164 DOI: 10.1002/elsc.201900132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/08/2020] [Accepted: 01/31/2020] [Indexed: 01/04/2023] Open
Abstract
The reduction of greenhouse gas emissions and future perspectives of circular economy ask for new solutions to produce commodities and fine chemicals. Large-scale bubble columns operated by gaseous substrates such as CO, CO2, and H2 to feed acetogens for product formations could be promising approaches. Valid in silico predictions of large-scale performance are needed to dimension bioreactors properly taking into account biological constraints, too. This contribution deals with the trade-off between sophisticated spatiotemporally resolved large-scale simulations using computationally intensive Euler-Euler and Euler-Lagrange approaches and coarse-grained 1-D models enabling fast performance evaluations. It is shown that proper consideration of gas hold-up is key to predict biological performance. Intrinsic bias of 1-D models can be compensated by reconsideration of Sauter diameters derived from uniquely performed Euler-Lagrange computational fluid dynamics.
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Affiliation(s)
- Flora Siebler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Alexey Lapin
- Stuttgart Research Centre Systems BiologyUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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35
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Klask CM, Kliem-Kuster N, Molitor B, Angenent LT. Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO 2 and H 2, but Results in Stochastic Inhibition Events. Front Microbiol 2020; 11:724. [PMID: 32435236 PMCID: PMC7219301 DOI: 10.3389/fmicb.2020.00724] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The pH-value in fermentation broth is a critical factor for the metabolic flux and growth behavior of acetogens. A decreasing pH level throughout time due to undissociated acetic acid accumulation is anticipated under uncontrolled pH conditions such as in bottle experiments. As a result, the impact of changes in the metabolism (e.g., due to a genetic modification) might remain unclear or even unrevealed. In contrast, pH-controlled conditions can be achieved in bioreactors. Here, we present a self-built, comparatively cheap, and user-friendly multiple-bioreactor system (MBS) consisting of six pH-controlled bioreactors at a 1-L scale. We tested the functionality of the MBS by cultivating the acetogen Clostridium ljungdahlii with CO2 and H2 at steady-state conditions (=chemostat). The experiments (total of 10 bioreactors) were addressing the two questions: (1) does the MBS provide replicable data for gas-fermentation experiments?; and (2) does feeding nitrate influence the product spectrum under controlled pH conditions with CO2 and H2? We applied four different periods in each experiment ranging from pH 6.0 to pH 4.5. On the one hand, our data showed high reproducibility for gas-fermentation experiments with C. ljungdahlii under standard cultivation conditions using the MBS. On the other hand, feeding nitrate as sole N-source improved growth by up to 62% and ethanol production by 2-3-fold. However, we observed differences in growth, and acetate and ethanol production rates between all nitrate bioreactors. We explained the different performances with a pH-buffering effect that resulted from the interplay between undissociated acetic acid production and ammonium production and because of stochastic inhibition events, which led to complete crashes at different operating times.
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Affiliation(s)
- Christian-Marco Klask
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Nicolai Kliem-Kuster
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany.,Max Planck Fellow Groups, Max Planck Institute for Developmental Biology, Tübingen, Germany
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36
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Kang S, Song Y, Jin S, Shin J, Bae J, Kim DR, Lee JK, Kim SC, Cho S, Cho BK. Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide. Front Microbiol 2020; 11:402. [PMID: 32218779 PMCID: PMC7079680 DOI: 10.3389/fmicb.2020.00402] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood–Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.
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Affiliation(s)
- Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering, Hanyang University, Seoul, South Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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37
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Redl S, Poehlein A, Esser C, Bengelsdorf FR, Jensen TØ, Jendresen CB, Tindall BJ, Daniel R, Dürre P, Nielsen AT. Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica. Front Microbiol 2020; 10:3070. [PMID: 32010113 PMCID: PMC6978639 DOI: 10.3389/fmicb.2019.03070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/19/2019] [Indexed: 11/24/2022] Open
Abstract
Fermentation of gases provides a promising opportunity for the production of biochemicals from renewable resources, which has resulted in a growing interest in acetogenic bacteria. Thermophilic organisms provide potential advantages for the fermentation of, e.g., syngas into for example volatile compounds, and the thermophiles Moorella thermoacetica and Moorella thermoautotrophica have become model organisms of acetogenic metabolism. The justification for the recognition of the closely related species M. thermoautotrophica has, however, recently been disputed. In order to expand knowledge on the genus, we have here genome sequenced a total of 12 different M. thermoacetica and M. thermoautotrophica strains. From the sequencing results, it became clear that M. thermoautotrophica DSM 1974T consists of at least two different strains. Two different strains were isolated in Lyngby and Ulm from a DSM 1974T culture obtained from the DSMZ (Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Brunswick, Germany). Phylogenetic analysis revealed a close relationship between all the sequenced genomes, suggesting that the two strains detected in the type strain of the species M. thermoautotrophica could not be distinguished at the species level from M. thermoacetica. Despite genetic similarities, differences in genomic features were observed between the strains. Differences in compounds that can serve as carbon and energy sources for selected strains were also identified. On the contrary, strain DSM 21394, currently still named M. thermoacetica, obviously represents a new Moorella species. In addition, based on genome analysis and comparison M. glycerini NMP, M. stamsii DSM 26217T, and M. perchloratireducens An10 cannot be distinguished at the species level. Thus, this comprehensive analysis provides a significantly increased knowledge of the genetic diversity of Moorella strains.
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Affiliation(s)
- Stephanie Redl
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Carola Esser
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Torbjørn Ø Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christian B Jendresen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Brian J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Brunswick, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Alex T Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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38
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Almeida Benalcázar E, Noorman H, Maciel Filho R, Posada JA. Modeling ethanol production through gas fermentation: a biothermodynamics and mass transfer-based hybrid model for microbial growth in a large-scale bubble column bioreactor. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:59. [PMID: 32231709 PMCID: PMC7102449 DOI: 10.1186/s13068-020-01695-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Ethanol production through fermentation of gas mixtures containing CO, CO2 and H2 has just started operating at commercial scale. However, quantitative schemes for understanding and predicting productivities, yields, mass transfer rates, gas flow profiles and detailed energy requirements have been lacking in literature; such are invaluable tools for process improvements and better systems design. The present study describes the construction of a hybrid model for simulating ethanol production inside a 700 m3 bubble column bioreactor fed with gas of two possible compositions, i.e., pure CO and a 3:1 mixture of H2 and CO2. RESULTS Estimations made using the thermodynamics-based black-box model of microbial reactions on substrate threshold concentrations, biomass yields, as well as CO and H2 maximum specific uptake rates agreed reasonably well with data and observations reported in literature. According to the bioreactor simulation, there is a strong dependency of process performance on mass transfer rates. When mass transfer coefficients were estimated using a model developed from oxygen transfer to water, ethanol productivity reached 5.1 g L-1 h-1; when the H2/CO2 mixture is fed to the bioreactor, productivity of CO fermentation was 19% lower. Gas utilization reached 23 and 17% for H2/CO2 and CO fermentations, respectively. If mass transfer coefficients were 100% higher than those estimated, ethanol productivity and gas utilization may reach 9.4 g L-1 h-1 and 38% when feeding the H2/CO2 mixture at the same process conditions. The largest energetic requirements for a complete manufacturing plant were identified for gas compression and ethanol distillation, being higher for CO fermentation due to the production of CO2. CONCLUSIONS The thermodynamics-based black-box model of microbial reactions may be used to quantitatively assess and consolidate the diversity of reported data on CO, CO2 and H2 threshold concentrations, biomass yields, maximum substrate uptake rates, and half-saturation constants for CO and H2 for syngas fermentations by acetogenic bacteria. The maximization of ethanol productivity in the bioreactor may come with a cost: low gas utilization. Exploiting the model flexibility, multi-objective optimizations of bioreactor performance might reveal how process conditions and configurations could be adjusted to guide further process development.
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Affiliation(s)
- Eduardo Almeida Benalcázar
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Henk Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- DSM Biotechnology Center, A. Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Rubens Maciel Filho
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
| | - John A. Posada
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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39
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Clostridium sp. as Bio-Catalyst for Fuels and Chemicals Production in a Biorefinery Context. Catalysts 2019. [DOI: 10.3390/catal9110962] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Clostridium sp. is a genus of anaerobic bacteria capable of metabolizing several substrates (monoglycerides, diglycerides, glycerol, carbon monoxide, cellulose, and more), into valuable products. Biofuels, such as ethanol and butanol, and several chemicals, such as acetone, 1,3-propanediol, and butyric acid, can be produced by these organisms through fermentation processes. Among the most well-known species, Clostridium carboxidivorans, C. ragsdalei, and C. ljungdahlii can be highlighted for their ability to use gaseous feedstocks (as syngas), obtained from the gasification or pyrolysis of waste material, to produce ethanol and butanol. C. beijerinckii is an important species for the production of isopropanol and butanol, with the advantage of using hydrolysate lignocellulosic material, which is produced in large amounts by first-generation ethanol industries. High yields of 1,3 propanediol by C. butyricum are reported with the use of another by-product from fuel industries, glycerol. In this context, several Clostridium wild species are good candidates to be used as biocatalysts in biochemical or hybrid processes. In this review, literature data showing the technical viability of these processes are presented, evidencing the opportunity to investigate them in a biorefinery context.
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Emerging technologies for the pretreatment of lignocellulosic materials for bio-based products. Appl Microbiol Biotechnol 2019; 104:455-473. [DOI: 10.1007/s00253-019-10158-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
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Syngas-aided anaerobic fermentation for medium-chain carboxylate and alcohol production: the case for microbial communities. Appl Microbiol Biotechnol 2019; 103:8689-8709. [PMID: 31612269 DOI: 10.1007/s00253-019-10086-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023]
Abstract
Syngas fermentation has been successfully implemented in commercial-scale plants and can enable the biochemical conversion of the driest fractions of biomass through synthesis gas (H2, CO2, and CO). The process relies on optimized acetogenic strains able to reach and maintain high productivity of ethanol and acetate. In parallel, microbial communities have shown to be the best choice for the production of valuable medium-chain carboxylates through anaerobic fermentation of biomass, demanding low technical complexity and being able to realize simultaneous hydrolysis of the substrate. Each of the two technologies benefits from different strong points and has different challenges to overcome. This review discusses the rationales for merging these two seemingly disparate technologies by analyzing previous studies and drawing opinions based on the lessons learned from such studies. For keeping the technical demands of the resulting process low, a case is built for using microbial communities instead of pure strains. For that to occur, a shift from conventional syngas-based to "syngas-aided" anaerobic fermentation is suggested. Strategies for tackling the intricacies of working simultaneously with communities and syngas, such as competing pathways, and thermodynamic aspects are discussed as well as the stoichiometry and economic feasibility of the concept. Overall, syngas-aided anaerobic fermentation seems to be a promising concept for the biorefinery of the future. However, the effects of process parameters on microbial interactions have to be understood in greater detail, in order to achieve and sustain feasible medium-chain carboxylate and alcohol productivity.
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Greene J, Daniell J, Köpke M, Broadbelt L, Tyo KE. Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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C1 Compound Biosensors: Design, Functional Study, and Applications. Int J Mol Sci 2019; 20:ijms20092253. [PMID: 31067766 PMCID: PMC6540204 DOI: 10.3390/ijms20092253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 01/25/2023] Open
Abstract
The microbial assimilation of one-carbon (C1) gases is a topic of interest, given that products developed using this pathway have the potential to act as promising substrates for the synthesis of valuable chemicals via enzymatic oxidation or C–C bonding. Despite extensive studies on C1 gas assimilation pathways, their key enzymes have yet to be subjected to high-throughput evolution studies on account of the lack of an efficient analytical tool for C1 metabolites. To address this challenging issue, we attempted to establish a fine-tuned single-cell–level biosensor system constituting a combination of transcription factors (TFs) and several C1-converting enzymes that convert target compounds to the ligand of a TF. This enzymatic conversion broadens the detection range of ligands by the genetic biosensor systems. In this study, we presented new genetic enzyme screening systems (GESSs) to detect formate, formaldehyde, and methanol from specific enzyme activities and pathways, named FA-GESS, Frm-GESS, and MeOH-GESS, respectively. All the biosensors displayed linear responses to their respective C1 molecules, namely, formate (1.0–250 mM), formaldehyde (1.0–50 μM), and methanol (5–400 mM), and they did so with high specificity. Consequently, the helper enzymes, including formaldehyde dehydrogenase and methanol dehydrogenase, were successfully combined to constitute new versatile combinations of the C1-biosensors.
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Making the case for edible microorganisms as an integral part of a more sustainable and resilient food production system. Food Secur 2019. [DOI: 10.1007/s12571-019-00912-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput Biol 2019; 15:e1006848. [PMID: 30845144 PMCID: PMC6430413 DOI: 10.1371/journal.pcbi.1006848] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/22/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.
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Affiliation(s)
- Joanne K. Liu
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Colton Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Mahmoud M. Al-Bassam
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ji-Nu Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Connor Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America
| | - Pieter Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, United States of America
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Vassilev I, Kracke F, Freguia S, Keller J, Krömer JO, Ledezma P, Virdis B. Microbial electrosynthesis system with dual biocathode arrangement for simultaneous acetogenesis, solventogenesis and carbon chain elongation. Chem Commun (Camb) 2019; 55:4351-4354. [DOI: 10.1039/c9cc00208a] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A microbial electrosynthesis cell comprising two biological cathode chambers sharing the same anode compartment is used to promote the production of C2–C4 carboxylic acids and alcohols from carbon dioxide.
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Affiliation(s)
- Igor Vassilev
- Advanced Water Management Centre
- The University of Queensland
- Brisbane
- Australia
| | - Frauke Kracke
- Department of Civil and Environmental Engineering
- Stanford University
- Stanford
- USA
| | - Stefano Freguia
- Advanced Water Management Centre
- The University of Queensland
- Brisbane
- Australia
| | - Jürg Keller
- Advanced Water Management Centre
- The University of Queensland
- Brisbane
- Australia
| | - Jens O. Krömer
- Department for Solar Materials
- Helmholtz Centre for Environmental Research (UFZ)
- Leipzig 04318
- Germany
| | - Pablo Ledezma
- Advanced Water Management Centre
- The University of Queensland
- Brisbane
- Australia
| | - Bernardino Virdis
- Advanced Water Management Centre
- The University of Queensland
- Brisbane
- Australia
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Luo G, Jing Y, Lin Y, Zhang S, An D. A novel concept for syngas biomethanation by two-stage process: Focusing on the selective conversion of syngas to acetate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1194-1200. [PMID: 30248844 DOI: 10.1016/j.scitotenv.2018.07.263] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Thermal gasification of nonrenewable and renewable sources produces syngas, containing CO, H2, CO2 and N2. Anaerobic conversion of syngas to CH4 is a promising way to replace natural gas. However, the high N2 content (>50%) in syngas would result in the low CH4 content in the biogas and CO in syngas also had serious inhibition on methanogens. The present study proposed a two-stage anaerobic process for syngas biomethanation, and syngas was first anaerobically converted to acetate by mixed culture, which could be further converted to methane easily without the negative effects of N2 and CO. The results showed that mesophilic condition was more suitable for the conversion of syngas to acetate compared to thermophilic and ambient conditions at pH 5.5 considering the higher acetate yield and syngas conversion rate. Although CO was efficiently converted at thermophilic condition, it was mostly converted to H2, which was then converted to acetate. CO was much easier to be converted compared to H2. Further study showed that pH 6.5 and 7.5 were optimal for selective conversion of syngas to acetate. The other products including butyrate and ethanol were also detected in relatively higher amounts at pH 4.5 and 9.5. Although pH 5.5 and 8.5 had relatively lower syngas conversion rates compared to pH 6.5 and 7.5, they might inhibit methanogens naturally without adding methane inhibitors. Finally, batch experiments showed that the acetate concentration had obvious inhibition on syngas conversion when the acetate concentration was higher than 2 g/L.
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Affiliation(s)
- Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yuhang Jing
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China
| | - Yujin Lin
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Dong An
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Shin J, Song Y, Jin S, Lee JK, Kim DR, Kim SC, Cho S, Cho BK. Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation. RNA (NEW YORK, N.Y.) 2018; 24:1839-1855. [PMID: 30249742 PMCID: PMC6239172 DOI: 10.1261/rna.068239.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/20/2018] [Indexed: 05/09/2023]
Abstract
Acetogens synthesize acetyl-CoA via CO2 or CO fixation, producing organic compounds. Despite their ecological and industrial importance, their transcriptional and post-transcriptional regulation has not been systematically studied. With completion of the genome sequence of Acetobacterium bakii (4.28-Mb), we measured changes in the transcriptome of this psychrotolerant acetogen in response to temperature variations under autotrophic and heterotrophic growth conditions. Unexpectedly, acetogenesis genes were highly up-regulated at low temperatures under heterotrophic, as well as autotrophic, growth conditions. To mechanistically understand the transcriptional regulation of acetogenesis genes via changes in RNA secondary structures of 5'-untranslated regions (5'-UTR), the primary transcriptome was experimentally determined, and 1379 transcription start sites (TSS) and 1100 5'-UTR were found. Interestingly, acetogenesis genes contained longer 5'-UTR with lower RNA-folding free energy than other genes, revealing that the 5'-UTRs control the RNA abundance of the acetogenesis genes under low temperature conditions. Our findings suggest that post-transcriptional regulation via RNA conformational changes of 5'-UTRs is necessary for cold-adaptive acetogenesis.
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Affiliation(s)
- Jongoh Shin
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoseb Song
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Sangrak Jin
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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Wang HJ, Dai K, Wang YQ, Wang HF, Zhang F, Zeng RJ. Mixed culture fermentation of synthesis gas in the microfiltration and ultrafiltration hollow-fiber membrane biofilm reactors. BIORESOURCE TECHNOLOGY 2018; 267:650-656. [PMID: 30059945 DOI: 10.1016/j.biortech.2018.07.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
The effects of pore sizes on the in-situ utilization of synthesis gas (syngas, H2 and CO) mixed culture fermentation (MCF) in the hollow-fiber membrane biofilm reactor (HfMBR) are not clear. Thus, the ultrafiltration (R1) and microfiltration (R2) HfMBRs were constructed. Syngas was totally consumed within the formed biofilm in R1; contrarily, it accumulated notably in R2. In the batch mode of R1 and R2, volatile fatty acids (VFAs) of acetate, butyrate and caproate were the main metabolites, but the production rate of total VFA in R1 (61.9 mmol-C/(L·d)) was higher than that of R2 (27.6 mmol-C/(L·d)). In the continuous mode, the R1 performance was much better than that of R2, and the biofilm in R2 was even washed out. Furthermore, Clostridium (30.0%) was the main genus in the enriched biofilm of R1, which converted syngas to VFAs. Thus, the ultrafiltration membrane shall be the suitable candidate for syngas MCF.
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Affiliation(s)
- Hua-Jie Wang
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China; School of Environmental and Chemical Engineering, Anhui Vocational and Technical College, Hefei, Anhui 230011, PR China
| | - Kun Dai
- Centre of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yun-Qi Wang
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Hou-Feng Wang
- Centre of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Fang Zhang
- Centre of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Raymond Jianxiong Zeng
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China; Centre of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
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