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Liu Y, Zhou X, Wang T, Luo A, Jia Z, Pan X, Cai W, Sun M, Wang X, Wen Z, Zhou G. Genetic algorithm-based semisupervised convolutional neural network for real-time monitoring of Escherichia coli fermentation of recombinant protein production using a Raman sensor. Biotechnol Bioeng 2024; 121:1583-1595. [PMID: 38247359 DOI: 10.1002/bit.28661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
As a non-destructive sensing technique, Raman spectroscopy is often combined with regression models for real-time detection of key components in microbial cultivation processes. However, achieving accurate model predictions often requires a large amount of offline measurement data for training, which is both time-consuming and labor-intensive. In order to overcome the limitations of traditional models that rely on large datasets and complex spectral preprocessing, in addition to the difficulty of training models with limited samples, we have explored a genetic algorithm-based semi-supervised convolutional neural network (GA-SCNN). GA-SCNN integrates unsupervised process spectral labeling, feature extraction, regression prediction, and transfer learning. Using only an extremely small number of offline samples of the target protein, this framework can accurately predict protein concentration, which represents a significant challenge for other models. The effectiveness of the framework has been validated in a system of Escherichia coli expressing recombinant ProA5M protein. By utilizing the labeling technique of this framework, the available dataset for glucose, lactate, ammonium ions, and optical density at 600 nm (OD600) has been expanded from 52 samples to 1302 samples. Furthermore, by introducing a small component of offline detection data for recombinant proteins into the OD600 model through transfer learning, a model for target protein detection has been retrained, providing a new direction for the development of associated models. Comparative analysis with traditional algorithms demonstrates that the GA-SCNN framework exhibits good adaptability when there is no complex spectral preprocessing. Cross-validation results confirm the robustness and high accuracy of the framework, with the predicted values of the model highly consistent with the offline measurement results.
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Affiliation(s)
- Yuan Liu
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Xiaotian Zhou
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Teng Wang
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Key Laboratory of Enze Biomass and Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - An Luo
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Zhaojun Jia
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Xingquan Pan
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Weiqi Cai
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Mengge Sun
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Xuezhong Wang
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Key Laboratory of Enze Biomass and Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Zhenguo Wen
- Department of Pharmaceutical Engineering, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Key Laboratory of Enze Biomass and Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
| | - Guangzheng Zhou
- Beijing Key Laboratory of Enze Biomass and Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
- Beijing Institute of Petrochemical Technology, College of New Materials and Chemical Engineering, Beijing, China
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2
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Wan S, Lai M, Gao X, Zhou M, Yang S, Li Q, Li F, Xia L, Tan Y. Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities. Synth Syst Biotechnol 2024; 9:19-25. [PMID: 38205027 PMCID: PMC10776380 DOI: 10.1016/j.synbio.2023.12.001] [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: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Excessive mining and utilization fossil fuels has led to drastic environmental consequences, which will contribute to global warming and cause further climate change with severe consequences for the human population. The magnitude of these challenges requires several approaches to develop sustainable alternatives for chemicals and fuels production. In this context, biological processes, mainly microbial fermentation, have gained particular interest. For example, autotrophic gas-fermenting acetogenic bacteria are capable of converting CO, CO2 and H2 into biomass and multiple metabolites through Wood-Ljungdahl pathway, which can be exploited for large-scale fermentation processes to sustainably produce bulk biochemicals and biofuels (e.g. acetate and ethanol) from syngas. Clostridium autoethanogenum is one representative of these chemoautotrophic bacteria and considered as the model for the gas fermentation. Recently, the development of synthetic biology toolbox for this strain has enabled us to study and genetically improve their metabolic capability in gas fermentation. In this review, we will summarize the recent progress involved in the understanding of physiological mechanism and strain engineering for C. autoethanogenum, and provide our perspectives on the future development about the basic biology and engineering biology of this strain.
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Affiliation(s)
- Sai Wan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Mingchi Lai
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinyu Gao
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Mingxin Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Fuli Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Lin Xia
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Yang Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
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3
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Perret L, Boukis N, Sauer J. Synthesis gas fermentation at high cell density: How pH and hydrogen partial pressure affect productivity and product ratio in continuous fermentation. BIORESOURCE TECHNOLOGY 2024; 391:129894. [PMID: 37866768 DOI: 10.1016/j.biortech.2023.129894] [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: 08/30/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
For the first time, syngas fermentation was operated continuously with total cell retention and process pressures up to 4barg in long-term runs of up to 3000 hours. Throughout this time, the process was stable. The measured data have shown that hydrogen uptake and ethanol space-time yield are highest at a slightly reduced pH of 5.7 compared to pH5.9. Even lower pH values lead to higher acetic acid to ethanol product ratios, while C2space-time yields remain constant. Increasing the hydrogen partial pressure to 1.52bar resulted in a significant increase in hydrogen uptake rate and ethanol formation. An ethanol space-time yield of 10mmolL-1h-1 was short-term achieved, being the highest space-time yield measured to date for the wild type of C. ljungdahlii. Hydrogen uptake above a theoretical equilibrium concentration of [Formula: see text] is significantly reduced, indicating an inhibition of an enzymatic reaction.
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Affiliation(s)
- Lukas Perret
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany.
| | - Nikolaos Boukis
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany
| | - Jörg Sauer
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Baden-Wurttemberg, Germany
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4
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Kolasinliler G, Aagre MM, Akkale C, Kaya HB. The use of CRISPR-Cas-based systems in bacterial cell factories. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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5
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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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6
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Hu L, Guo S, Wang B, Fu R, Fan D, Jiang M, Fei Q, Gonzalez R. Bio-valorization of C1 gaseous substrates into bioalcohols: Potentials and challenges in reducing carbon emissions. Biotechnol Adv 2022; 59:107954. [DOI: 10.1016/j.biotechadv.2022.107954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
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7
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He Y, Lens PNL, Veiga MC, Kennes C. Enhanced Ethanol Production From Carbon Monoxide by Enriched Clostridium Bacteria. Front Microbiol 2021; 12:754713. [PMID: 34777310 PMCID: PMC8585497 DOI: 10.3389/fmicb.2021.754713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide (CO)-metabolizing Clostridium spp. were enriched from the biomass of a butanol-producing reactor. After six successive biomass transfers, ethanol production reached as much as 11.8 g/L with minor accumulation of acetic acid, under intermittent gas feeding conditions and over a wide pH range of 6.45-4.95. The molar ratio of ethanol to acetic acid exceeded 1.7 after the lag phase of 11 days and reached its highest value of 8.6 during the fermentation process after 25 days. Although butanol production was not significantly enhanced in the enrichment, the biomass was able to convert exogenous butyric acid (3.2 g/L) into butanol with nearly 100% conversion efficiency using CO as reducing power. This suggested that inhibition of butanol production from CO was caused by the lack of natural butyric acid production, expectedly induced by unsuitable pH values due to initial acidification resulting from the acetic acid production. The enriched Clostridium population also converted glucose to formic, acetic, propionic, and butyric acids in batch tests with daily pH adjustment to pH 6.0. The Clostridium genus was enriched with its relative abundance significantly increasing from 7% in the inoculum to 94% after five successive enrichment steps. Unidentified Clostridium species showed a very high relative abundance, reaching 73% of the Clostridium genus in the enriched sludge (6th transfer).
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Affiliation(s)
- Yaxue He
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of A Coruña (UDC), A Coruña, Spain.,National University of Ireland Galway, Galway, Ireland
| | - Piet N L Lens
- National University of Ireland Galway, Galway, Ireland
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of A Coruña (UDC), A Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of A Coruña (UDC), A Coruña, Spain
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8
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Dhakal N, Acharya B. Syngas Fermentation for the Production of Bio-Based Polymers: A Review. Polymers (Basel) 2021; 13:polym13223917. [PMID: 34833218 PMCID: PMC8618084 DOI: 10.3390/polym13223917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/21/2022] Open
Abstract
Increasing environmental awareness among the general public and legislators has driven this modern era to seek alternatives to fossil-derived products such as fuel and plastics. Addressing environmental issues through bio-based products driven from microbial fermentation of synthetic gas (syngas) could be a future endeavor, as this could result in both fuel and plastic in the form of bioethanol and polyhydroxyalkanoates (PHA). Abundant availability in the form of cellulosic, lignocellulosic, and other organic and inorganic wastes presents syngas catalysis as an interesting topic for commercialization. Fascination with syngas fermentation is trending, as it addresses the limitations of conventional technologies like direct biochemical conversion and Fischer–Tropsch’s method for the utilization of lignocellulosic biomass. A plethora of microbial strains is available for syngas fermentation and PHA production, which could be exploited either in an axenic form or in a mixed culture. These microbes constitute diverse biochemical pathways supported by the activity of hydrogenase and carbon monoxide dehydrogenase (CODH), thus resulting in product diversity. There are always possibilities of enzymatic regulation and/or gene tailoring to enhance the process’s effectiveness. PHA productivity drags the techno-economical perspective of syngas fermentation, and this is further influenced by syngas impurities, gas–liquid mass transfer (GLMT), substrate or product inhibition, downstream processing, etc. Product variation and valorization could improve the economical perspective and positively impact commercial sustainability. Moreover, choices of single-stage or multi-stage fermentation processes upon product specification followed by microbial selection could be perceptively optimized.
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9
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Safo L, Abdelrazig S, Grosse-Honebrink A, Millat T, Henstra AM, Norman R, Thomas NR, Winzer K, Minton NP, Kim DH, Barrett DA. Quantitative Bioreactor Monitoring of Intracellular Bacterial Metabolites in Clostridium autoethanogenum Using Liquid Chromatography-Isotope Dilution Mass Spectrometry. ACS OMEGA 2021; 6:13518-13526. [PMID: 34095647 PMCID: PMC8173575 DOI: 10.1021/acsomega.0c05588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/03/2021] [Indexed: 05/05/2023]
Abstract
We report a liquid chromatography-isotope dilution mass spectrometry method for the simultaneous quantification of 131 intracellular bacterial metabolites of Clostridium autoethanogenum. A comprehensive mixture of uniformly 13C-labeled internal standards (U-13C IS) was biosynthesized from the closely related bacterium Clostridium pasteurianum using 4% 13C-glucose as a carbon source. The U-13C IS mixture combined with 12C authentic standards was used to validate the linearity, precision, accuracy, repeatability, limits of detection, and quantification for each metabolite. A robust-fitting algorithm was employed to reduce the weight of the outliers on the quantification data. The metabolite calibration curves were linear with R 2 ≥ 0.99, limits of detection were ≤1.0 μM, limits of quantification were ≤10 μM, and precision/accuracy was within RSDs of 15% for all metabolites. The method was subsequently applied for the daily monitoring of the intracellular metabolites of C. autoethanogenum during a CO gas fermentation over 40 days as part of a study to optimize biofuel production. The concentrations of the metabolites were estimated at steady states of different pH levels using the robust-fitting mathematical approach, and we demonstrate improved accuracy of results compared to conventional regression. Metabolic pathway analysis showed that reactions of the incomplete (branched) tricarboxylic acid "cycle" were the most affected pathways associated with the pH shift in the bioreactor fermentation of C. autoethanogenum and the concomitant changes in ethanol production.
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Affiliation(s)
- Laudina Safo
- Centre
for Analytical Bioscience, Advanced Materials and Healthcare Technologies
Division, School of Pharmacy, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | - Salah Abdelrazig
- Centre
for Analytical Bioscience, Advanced Materials and Healthcare Technologies
Division, School of Pharmacy, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | | | - Thomas Millat
- Clostridia
Research Group, BBSRC/EPSCR Synthetic Biology Research Centre (SBRC),
Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Anne M. Henstra
- Clostridia
Research Group, BBSRC/EPSCR Synthetic Biology Research Centre (SBRC),
Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Rupert Norman
- Clostridia
Research Group, BBSRC/EPSCR Synthetic Biology Research Centre (SBRC),
Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Neil R. Thomas
- Biodiscovery
Institute, School of Chemistry, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | - Klaus Winzer
- Clostridia
Research Group, BBSRC/EPSCR Synthetic Biology Research Centre (SBRC),
Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- Clostridia
Research Group, BBSRC/EPSCR Synthetic Biology Research Centre (SBRC),
Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Dong-Hyun Kim
- Centre
for Analytical Bioscience, Advanced Materials and Healthcare Technologies
Division, School of Pharmacy, University
of Nottingham, Nottingham NG7 2RD, U.K.
| | - David A. Barrett
- Centre
for Analytical Bioscience, Advanced Materials and Healthcare Technologies
Division, School of Pharmacy, University
of Nottingham, Nottingham NG7 2RD, U.K.
- . Phone: +44(0)115 9515062
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10
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e Silva MPGDC, Miranda JCDC. Exergy efficiency of thermochemical syngas-to-ethanol production plants. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04526-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Abstract
This work presents exergy analyses applied in four different conceptual second-generation ethanol production processes through a thermochemical route using catalysts based on Molybdenum (P-1), Copper (P-2), and Rhodium (P-3 and P-4), aiming to assess their exergetic efficiencies. The results show that the conceptual processes have satisfactory exergy efficiencies in both cases, when compared among themselves and when compared with other processes reported in literature. The processes’ efficiency for P-1, P-2, P-3 and P-4 were, respectively, 52.4%, 41.4%, 43.7% and 48.9%. The reactors were the sections in which exergy destruction was more significant, due to the exothermic reactions and mixing points (where streams with different temperatures were mixed). Such results show the potential of thermochemical ethanol production, besides opening the possibilities of process improvement.
Graphic abstract
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11
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He Y, Cassarini C, Lens PNL. Bioethanol Production From H 2/CO 2 by Solventogenesis Using Anaerobic Granular Sludge: Effect of Process Parameters. Front Microbiol 2021; 12:647370. [PMID: 33790882 PMCID: PMC8006448 DOI: 10.3389/fmicb.2021.647370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/15/2021] [Indexed: 11/23/2022] Open
Abstract
CO2 fermentation by biocatalysis is a promising route for the sustainable production of valuable chemicals and fuels, such as acetic acid and ethanol. Considering the important role of environmental parameters on fermentation processes, granular sludge from an industrial anaerobic wastewater treatment system was tested as inoculum for ethanol production from H2/CO2 at psychrophilic (18°C), submesophilic (25°C), and mesophilic (30°C) temperatures. The highest acetic acid and ethanol production was obtained at 25°C with a final concentration of 29.7 and 8.8 mM, respectively. The presence of bicarbonate enhanced acetic acid production 3.0 ∼ 4.1-fold, while inhibiting ethanol production. The addition of 0.3 g/L glucose induced butyric acid production (3.7 mM), while 5.7 mM ethanol was produced at the end of the incubation at pH 4 with glucose. The addition of 10 μM W enhanced ethanol production up to 3.8 and 7.0-fold compared to, respectively, 2 μM W addition and the control. The addition of 2 μM Mo enhanced ethanol production up to 8.1- and 5.4-fold compared to, respectively, 10 μM Mo and the control. This study showed that ethanol production from H2/CO2 conversion using granular sludge as the inoculum can be optimized by selecting the operational temperature and by trace metal addition.
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Affiliation(s)
- Yaxue He
- National University of Ireland Galway, Galway, Ireland
| | | | - Piet N L Lens
- National University of Ireland Galway, Galway, Ireland
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12
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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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13
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Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture. mSystems 2021; 6:6/1/e01325-20. [PMID: 33622858 PMCID: PMC8573953 DOI: 10.1128/msystems.01325-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum-evolved H2 and through acquisition of C. acetobutylicum-native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community.IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.
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Rojas MDPA, Zaiat M, González ER, De Wever H, Pant D. Enhancing the gas–liquid mass transfer during microbial electrosynthesis by the variation of CO2 flow rate. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Watanabe K, Perez CMT, Kitahori T, Hata K, Aoi M, Takahashi H, Sakuma T, Okamura Y, Nakashimada Y, Yamamoto T, Matsuyama K, Mayuzumi S, Aki T. Improvement of fatty acid productivity of thraustochytrid, Aurantiochytrium sp. by genome editing. J Biosci Bioeng 2020; 131:373-380. [PMID: 33386277 DOI: 10.1016/j.jbiosc.2020.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/12/2023]
Abstract
Thraustochytrid strains belonging to the genus Aurantiochytrium accumulate significant amounts of lipids including polyunsaturated fatty acids and carotenoids and, therefore, are expected to be used for industrial production of various valuable materials. Although various efforts such as chemical mutagenesis and homologous gene recombination have been made to improve lipid productivity of Aurantiochytrium species, low specificity and efficiency in the conventional methods hinder the research progress. Here, we attempted to apply a genome editing technology, the CRISPR-Cas9 system as an alternative molecular breeding technique for Aurantiochytrium species to accelerate the metabolic engineering. The efficiency of specific gene knock-in by the homologous recombination increased more than 10-folds by combining the CRISPR-Cas9 system. As a result of disrupting the genes associated with β-oxidation of fatty acids by the improved method, the genome edited strains with higher fatty acid productivity were isolated, demonstrating for the first time that the CRISPR-Cas9 system was effective for molecular breeding of the strains in the genus Aurantiochytrium to improve lipid productivity.
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Affiliation(s)
- Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Charose Marie Ting Perez
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tomoki Kitahori
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Kosuke Hata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Masato Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tetsushi Sakuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | | | - Shinzo Mayuzumi
- Idemitsu Kosan Co., Ltd., 1280 Kami-izumi, Sodegaura, Chiba 299-0293, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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Syngas Derived from Lignocellulosic Biomass Gasification as an Alternative Resource for Innovative Bioprocesses. Processes (Basel) 2020. [DOI: 10.3390/pr8121567] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A hybrid system based on lignocellulosic biomass gasification and syngas fermentation represents a second-generation biorefinery approach that is currently in the development phase. Lignocellulosic biomass can be gasified to produce syngas, which is a gas mixture consisting mainly of H2, CO, and CO2. The major challenge of biomass gasification is the syngas’s final quality. Consequently, the development of effective syngas clean-up technologies has gained increased interest in recent years. Furthermore, the bioconversion of syngas components has been intensively studied using acetogenic bacteria and their Wood–Ljungdahl pathway to produce, among others, acetate, ethanol, butyrate, butanol, caproate, hexanol, 2,3-butanediol, and lactate. Nowadays, syngas fermentation appears to be a promising alternative for producing commodity chemicals in comparison to fossil-based processes. Research studies on syngas fermentation have been focused on process design and optimization, investigating the medium composition, operating parameters, and bioreactor design. Moreover, metabolic engineering efforts have been made to develop genetically modified strains with improved production. In 2018, for the first time, a syngas fermentation pilot plant from biomass gasification was built by LanzaTech Inc. in cooperation with Aemetis, Inc. Future research will focus on coupling syngas fermentation with additional bioprocesses and/or on identifying new non-acetogenic microorganisms to produce high-value chemicals beyond acetate and ethanol.
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Evaluation of Media Components and Process Parameters in a Sensitive and Robust Fed-Batch Syngas Fermentation System with Clostridium ljungdahlii. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6020061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fermentation of synthesis gas, or syngas, by acetogenic bacteria can help in transitioning from a fossil-fuel-based to a renewable bioeconomy. The main fermentation products of Clostridium ljungdahlii, one of such microorganisms, are acetate and ethanol. A sensitive, robust and reproducible system was established for C. ljungdahlii syngas fermentation, and several process parameters and medium components (pH, gas flow, cysteine and yeast extract) were investigated to assess its impact on the fermentation outcomes, as well as real time gas consumption. Moreover, a closed carbon balance could be achieved with the data obtained. This system is a valuable tool to detect changes in the behavior of the culture. It can be applied for the screening of strains, gas compositions or media components, for a better understanding of the physiology and metabolic regulation of acetogenic bacteria. Here, it was shown that neither yeast extract nor cysteine was a limiting factor for cell growth since their supplementation did not have a noticeable impact on product formation or overall gas consumption. By combining the lowering of both the pH and the gas flow after 24 h, the highest ethanol to acetate ratio was achieved, but with the caveat of lower productivity.
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Thi HN, Park S, Li H, Kim YK. Medium Compositions for the Improvement of Productivity in Syngas Fermentation with Clostridium autoethanogenum. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0428-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Cantos-Parra E, Ramió-Pujol S, Colprim J, Puig S, Bañeras L. Specific detection of "Clostridium autoethanogenum", Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples. FEMS Microbiol Lett 2019; 365:5062789. [PMID: 30084932 DOI: 10.1093/femsle/fny191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.
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Affiliation(s)
- Ester Cantos-Parra
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Campus Montilivi, Carrer Maria Aurèlia Capmany, 40, E-17003 Girona, Catalonia, Spain
| | - Sara Ramió-Pujol
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Campus Montilivi, Carrer Maria Aurèlia Capmany, 40, E-17003 Girona, Catalonia, Spain.,GoodGut, Centre d'Empreses Giroemprèn, Parc Científic i Tecnològic UdG, Carrer Pic de Peguera, 11, E-17003 Girona, Catalonia, Spain
| | - Jesús Colprim
- LEQUiA, Institute of the Environment. University of Girona, Campus Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Sebastià Puig
- LEQUiA, Institute of the Environment. University of Girona, Campus Montilivi, Carrer Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Lluís Bañeras
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Campus Montilivi, Carrer Maria Aurèlia Capmany, 40, E-17003 Girona, Catalonia, Spain
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Yasin M, Jang N, Lee M, Kang H, Aslam M, Bazmi AA, Chang IS. Bioreactors, gas delivery systems and supporting technologies for microbial synthesis gas conversion process. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100207] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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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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22
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Norman RO, Millat T, Schatschneider S, Henstra AM, Breitkopf R, Pander B, Annan FJ, Piatek P, Hartman HB, Poolman MG, Fell DA, Winzer K, Minton NP, Hodgman C. Genome‐scale model of
C. autoethanogenum
reveals optimal bioprocess conditions for high‐value chemical production from carbon monoxide. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2018.5003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Rupert O.J. Norman
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- School of BiosciencesUniversity of NottinghamSutton Bonington Campus, Sutton BoningtonLeicestershireLE12 5RDUK
| | - Thomas Millat
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Sarah Schatschneider
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- Evonik Nutrition and Care GmbHKantstr. 233798Halle‐KinsbeckGermany
| | - Anne M. Henstra
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Ronja Breitkopf
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Bart Pander
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Florence J. Annan
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Pawel Piatek
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Hassan B. Hartman
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
- Public Health England61 Colindale AvenueLondonNW9 5EQUK
| | - Mark G. Poolman
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - David A. Fell
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Klaus Winzer
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Nigel P. Minton
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Charlie Hodgman
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- School of BiosciencesUniversity of NottinghamSutton Bonington Campus, Sutton BoningtonLeicestershireLE12 5RDUK
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Liebal UW, Blank LM, Ebert BE. CO 2 to succinic acid - Estimating the potential of biocatalytic routes. Metab Eng Commun 2018; 7:e00075. [PMID: 30197864 PMCID: PMC6127376 DOI: 10.1016/j.mec.2018.e00075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/07/2018] [Accepted: 06/25/2018] [Indexed: 11/26/2022] Open
Abstract
Microbial carbon dioxide assimilation and conversion to chemical platform molecules has the potential to be developed as economic, sustainable processes. The carbon dioxide assimilation can proceed by a variety of natural pathways and recently even synthetic CO2 fixation routes have been designed. Early assessment of the performance of the different carbon fixation alternatives within biotechnological processes is desirable to evaluate their potential. Here we applied stoichiometric metabolic modeling based on physiological and process data to evaluate different process variants for the conversion of C1 carbon compounds to the industrial relevant platform chemical succinic acid. We computationally analyzed the performance of cyanobacteria, acetogens, methylotrophs, and synthetic CO2 fixation pathways in Saccharomyces cerevisiae in terms of production rates, product yields, and the optimization potential. This analysis provided insight into the economic feasibility and allowed to estimate the future industrial applicability by estimating overall production costs. With reported, or estimated data of engineered or wild type strains, none of the simulated microbial succinate production processes showed a performance allowing competitive production. The main limiting factors were identified as gas and photon transfer and metabolic activities whereas metabolic network structure was not restricting. In simulations with optimized parameters most process alternatives reached economically interesting values, hence, represent promising alternatives to sugar-based fermentations.
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Affiliation(s)
| | - Lars M. Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
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Li X, Griffin D, Li X, Henson MA. Incorporating hydrodynamics into spatiotemporal metabolic models of bubble column gas fermentation. Biotechnol Bioeng 2018; 116:28-40. [PMID: 30267585 DOI: 10.1002/bit.26848] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 08/02/2018] [Accepted: 09/27/2018] [Indexed: 11/12/2022]
Abstract
Gas fermentation has emerged as a technologically and economically attractive option for producing renewable fuels and chemicals from carbon monoxide (CO) rich waste streams. LanzaTech has developed a proprietary strain of the gas fermentating acetogen Clostridium autoethanogenum as a microbial platform for synthesizing ethanol, 2,3-butanediol, and other chemicals. Bubble column reactor technology is being developed for the large-scale production, motivating the investigation of multiphase reactor hydrodynamics. In this study, we combined hydrodynamics with a genome-scale reconstruction of C. autoethanogenum metabolism and multiphase convection-dispersion equations to compare the performance of bubble column reactors with and without liquid recycle. For both reactor configurations, hydrodynamics was predicted to diminish bubble column performance with respect to CO conversion, biomass production, and ethanol production when compared with bubble column models in which the gas phase was modeled as ideal plug flow plus axial dispersion. Liquid recycle was predicted to be advantageous by increasing CO conversion, biomass production, and ethanol and 2,3-butanediol production compared with the non-recycle reactor configuration. Parametric studies performed for the liquid recycle configuration with two-phase hydrodynamics showed that increased CO feed flow rates (more gas supply), smaller CO gas bubbles (more gas-liquid mass transfer), and shorter column heights (more gas per volume of liquid per time) favored ethanol production over acetate production. Our computational results demonstrate the power of combining cellular metabolic models and two-phase hydrodynamics for simulating and optimizing gas fermentation reactors.
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Affiliation(s)
- Xiangan Li
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts
| | | | | | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts
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25
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Acedos MG, Santos VE, Garcia-Ochoa F. Resting cells isobutanol production by Shimwellia blattae (p424IbPSO): Influence of growth culture conditions. Biotechnol Prog 2018; 34:1073-1080. [PMID: 30281946 DOI: 10.1002/btpr.2705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
Abstract
Isobutanol is a promising gasoline additive and could even be a potential substitute used directly as combustible. In this work, the production of isobutanol from glucose by Shimwellia blattae (p424IbPSO) in resting cell cultures is studied. This production has two stages, involving a resting cell phase that has not been studied before. The cell growth was carried out under different operating conditions: temperature and medium composition (YE, ammonium, and IPTG concentrations), looking for the highest isobutanol production. Moreover, the cells were collected at three different growth times checking their isobutanol production capacity. The best operating conditions have been determined as: 30°C of temperature, a medium containing 1.5 g L-1 YE and 1.4 g L-1 of ammonium as nitrogen sources, adding 0.5 mM IPTG as inducer. The cells collected at early growth times are significantly more active. The use of S. blattae (p424IbPSO) in resting cells is a good strategy for the production of isobutanol from glucose yielding better results than in batch growth cultures, a yield of 60% attainment of theoretical maximum yield is obtained under optimal conditions. In addition, it has been demonstrated that if the cells are cultured at higher temperatures and with high IPTG concentrations, inclusion bodies are formed in the cytoplasm inhibiting the isobutanol production in the resting cell stage.
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Affiliation(s)
- Miguel G Acedos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Victoria E Santos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Felix Garcia-Ochoa
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
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26
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Progress towards platform chemical production using Clostridium autoethanogenum. Biochem Soc Trans 2018; 46:523-535. [DOI: 10.1042/bst20170259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/02/2018] [Accepted: 03/12/2018] [Indexed: 01/28/2023]
Abstract
Since 2013, there has been an explosion in the number of research articles published on Clostridium autoethanogenum, an acetogen capable of producing platform chemicals such as ethanol and 2,3-butanediol from greenhouse gases. However, no review focusing solely on C. autoethanogenum has appeared in the literature. This review outlines the research conducted into this organism in three broad categories (Enzymology, Genetics, and Systems Biology) and suggestions for future research are offered.
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27
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Chen J, Daniell J, Griffin D, Li X, Henson MA. Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.10.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Continuous Ethanol Production from Synthesis Gas by Clostridium ragsdalei in a Trickle-Bed Reactor. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Direct bioethanol production from wheat straw using xylose/glucose co-fermentation by co-culture of two recombinant yeasts. ACTA ACUST UNITED AC 2017; 44:453-464. [DOI: 10.1007/s10295-016-1893-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
Abstract
To achieve a cost-effective bioconversion of lignocellulosic materials, a novel xylose/glucose co-fermentation process by co-culture of cellulose-utilizing recombinant Saccharomyces cerevisiae (S. cerevisiae) and xylan-utilizing recombinant Pichia pastoris (P. pastoris) was developed, in which ethanol was produced directly from wheat straw without additional hydrolytic enzymes. Recombinant S. cerevisiae coexpressing three types of cellulase and recombinant P. pastoris coexpressing two types of xylanase were constructed, respectively. All cellulases and xylanases were successfully expressed and similar extracellular activity was demonstrated. The maximum ethanol concentration of 32.6 g L−1 with the yield 0.42 g g−1 was achieved from wheat straw corresponding to 100 g L−1 of total sugar after 80 h co-fermentation, which corresponds to 82.6% of the theoretical yield. These results demonstrate that the direct and efficient ethanol production from lignocellulosic materials is accomplished by simultaneous saccharification (cellulose and hemicellulose) and co-fermentation (glucose and xylose) with the co-culture of the two recombinant yeasts.
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Production of chemicals from C1 gases (CO, CO2) by Clostridium carboxidivorans. World J Microbiol Biotechnol 2017; 33:43. [DOI: 10.1007/s11274-016-2188-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
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Liew F, Henstra AM, Kӧpke M, Winzer K, Simpson SD, Minton NP. Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metab Eng 2017; 40:104-114. [PMID: 28111249 PMCID: PMC5367853 DOI: 10.1016/j.ymben.2017.01.007] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/01/2016] [Accepted: 01/19/2017] [Indexed: 01/27/2023]
Abstract
Gas fermentation using acetogenic bacteria such as Clostridium autoethanogenum offers an attractive route for production of fuel ethanol from industrial waste gases. Acetate reduction to acetaldehyde and further to ethanol via an aldehyde: ferredoxin oxidoreductase (AOR) and alcohol dehydrogenase has been postulated alongside the classic pathway of ethanol formation via a bi-functional aldehyde/alcohol dehydrogenase (AdhE). Here we demonstrate that AOR is critical to ethanol formation in acetogens and inactivation of AdhE led to consistently enhanced autotrophic ethanol production (up to 180%). Using ClosTron and allelic exchange mutagenesis, which was demonstrated for the first time in an acetogen, we generated single mutants as well as double mutants for both aor and adhE isoforms to confirm the role of each gene. The aor1+2 double knockout strain lost the ability to convert exogenous acetate, propionate and butyrate into the corresponding alcohols, further highlighting the role of these enzymes in catalyzing the thermodynamically unfavourable reduction of carboxylic acids into alcohols. 180% improvement in C. autoethanogenum ethanol production via metabolic engineering. Confirmed role of AOR in autotrophic ethanol production of acetogens. Generated both aor and adhE mutants of C. autoethanogenum.. Demonstrated allelic exchange mutagenesis for stable deletions in acetogens. Inactivation of adhE and aor2, but not aor1, improves autotrophic ethanol production.
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Affiliation(s)
- Fungmin Liew
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK; LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Michael Kӧpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK.
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Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Appl Microbiol Biotechnol 2016; 101:1615-1630. [PMID: 27866253 DOI: 10.1007/s00253-016-7978-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO2. Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites. Failed attempts to grow OTA1 autotrophically suggested that one or both of these mutated genes prevented acetyl-CoA synthesis from CO/CO2, demonstrating that its activity was required for autotrophic growth by C. ljungdahlii. An inoperable Wood-Ljungdahl pathway resulted in higher CO2 and ethanol yields and lower biomass and acetate yields compared to WT for multiple growth conditions including heterotrophic and mixotrophic conditions. The two other SNPs identified in the C. ljungdahlii OTA1 genome were in genes coding for transcriptional regulators (CLJU_c09320 and CLJU_c18110) and were found to be responsible for deregulated expression of co-localized arginine catabolism and 2-deoxy-D-ribose catabolism genes. Growth medium supplementation experiments suggested that increased arginine metabolism and 2-deoxy-D-ribose were likely to have minor effects on biomass and fermentation product yields. In addition, in silico flux balance analysis simulating mixotrophic and heterotrophic conditions showed no change in flux to ethanol when flux through HemL was changed whereas limited flux through AcsA increased the ethanol flux for both simulations. In characterizing the effects of the SNPs identified in the C. ljungdahlii OTA1 genome, a non-autotrophic hyper ethanol-producing strain of C. ljungdahlii was identified that has utility for further physiology and strain performance studies and as a biocatalyst for industrial applications.
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Affiliation(s)
- Jason M Whitham
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mark J Schulte
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Duke University, Durham, NC, 27710, USA
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mari S Chinn
- Department of Biological and Agricultural Engineering, North Carolina State University, 277 Weaver Labs, Campus Box 7625, Raleigh, NC, 27695-7625, USA
| | - Michael C Flickinger
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Joel J Pawlak
- Department of Forest Biomaterials, North Carolina State University, 2028C Biltmore Hall, Campus Box 8001, Raleigh, NC, 27695-8001, USA
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA.
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Molitor B, Richter H, Martin ME, Jensen RO, Juminaga A, Mihalcea C, Angenent LT. Carbon recovery by fermentation of CO-rich off gases - Turning steel mills into biorefineries. BIORESOURCE TECHNOLOGY 2016; 215:386-396. [PMID: 27095410 DOI: 10.1016/j.biortech.2016.03.094] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 05/08/2023]
Abstract
Technological solutions to reduce greenhouse gas (GHG) emissions from anthropogenic sources are required. Heavy industrial processes, such as steel making, contribute considerably to GHG emissions. Fermentation of carbon monoxide (CO)-rich off gases with wild-type acetogenic bacteria can be used to produce ethanol, acetate, and 2,3-butanediol, thereby, reducing the carbon footprint of heavy industries. Here, the processes for the production of ethanol from CO-rich off gases are discussed and a perspective on further routes towards an integrated biorefinery at a steel mill is given. Recent achievements in genetic engineering as well as integration of other biotechnology platforms to increase the product portfolio are summarized. Already, yields have been increased and the portfolio of products broadened. To develop a commercially viable process, however, the extraction from dilute product streams is a critical step and alternatives to distillation are discussed. Finally, another critical step is waste(water) treatment with the possibility to recover resources.
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Affiliation(s)
- Bastian Molitor
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States
| | - Hanno Richter
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States
| | - Michael E Martin
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | - Rasmus O Jensen
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | - Alex Juminaga
- LanzaTech, 8045 Lamon Avenue, Suite 400, Skokie, IL 60077, United States
| | | | - Largus T Angenent
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, United States.
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Lee SH, Yun EJ, Kim J, Lee SJ, Um Y, Kim KH. Biomass, strain engineering, and fermentation processes for butanol production by solventogenic clostridia. Appl Microbiol Biotechnol 2016; 100:8255-71. [PMID: 27531513 DOI: 10.1007/s00253-016-7760-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022]
Abstract
Butanol is considered an attractive biofuel and a commercially important bulk chemical. However, economical production of butanol by solventogenic clostridia, e.g., via fermentative production of acetone-butanol-ethanol (ABE), is hampered by low fermentation performance, mainly as a result of toxicity of butanol to microorganisms and high substrate costs. Recently, sugars from marine macroalgae and syngas were recognized as potent carbon sources in biomass feedstocks that are abundant and do not compete for arable land with edible crops. With the aid of systems metabolic engineering, many researchers have developed clostridial strains with improved performance on fermentation of these substrates. Alternatively, fermentation strategies integrated with butanol recovery processes such as adsorption, gas stripping, liquid-liquid extraction, and pervaporation have been designed to increase the overall titer of butanol and volumetric productivity. Nevertheless, for economically feasible production of butanol, innovative strategies based on recent research should be implemented. This review describes and discusses recent advances in the development of biomass feedstocks, microbial strains, and fermentation processes for butanol production.
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Affiliation(s)
- Sang-Hyun Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology and Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.
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Schulte MJ, Wiltgen J, Ritter J, Mooney CB, Flickinger MC. A high gas fraction, reduced power, syngas bioprocessing method demonstrated with a Clostridium ljungdahlii OTA1 paper biocomposite. Biotechnol Bioeng 2016; 113:1913-23. [PMID: 26927418 DOI: 10.1002/bit.25966] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/02/2016] [Accepted: 02/21/2016] [Indexed: 01/30/2023]
Abstract
We propose a novel approach to continuous bioprocessing of gases. A miniaturized, coated-paper strip, high gas fraction, biocomposite absorber has been developed using slowly shaken horizontal anaerobic tubes. Concentrated Clostridium ljungdahlii OTA1 was used as a model system. These gas absorbers demonstrate elevated CO mass transfer with low power input, reduced liquid requirements, elevated substrate consumption, and increased product secretion compared to shaken suspended cells. Concentrated OTA1 cell paste was coated by extrusion onto chromatography paper. The immobilized system shows high, constant reactivity immediately upon rehydration. Cell adhesion was by adsorption to the cellulose fibers; visualized by SEM. The C. ljungdahlii OTA1 coated paper mounted above the liquid level absorbs CO and H2 from a model syngas secreting acetate with minimal ethanol. At 100 rpm shaking speed (7.7 Wm(-3) ) the optimal cell loading is 6.5 gDCW m(-2) to maintain high CO absorbing reactivity without the cells coming off of the paper into the liquid phase. Reducing the medium volume from 10 mL to 4 mL (15% of tube volume) did not decrease CO reactivity. The reduced liquid volume increased secreted product concentration by 80%. The specific CO consumption by paper biocomposites was higher at all shaking frequencies <100 rpm than suspended cells under identical incubation conditions. At 25 rpm the biocomposite outperforms suspended cells for CO absorption by 2.5-fold, with an estimated power reduction of 97% over the power input at 100 rpm. The estimated minimum kL a for miniaturized biocomposite gas-absorbers is ∼100 h(-1) , 10 to 10(4) less power input than other syngas fermentation systems reported in the literature at similar kL a. Specific consumption rates in a biocomposite were ∼14 mmol gDCW-1 h(-1) . This work intensified CO absorption and reactivity by 14-fold to 94 mmol CO m(-2) h(-1) over previous C. ljungdahlii OTA1 work by our group. Specific acetate production rates were 23 mM h(-1) or 46 mmol m(-2) h(-1) . The specific rates and apparent kL a scaled linearly with biocomposite coating area. Biotechnol. Bioeng. 2016;113: 1913-1923. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Mark J Schulte
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, 27695
| | - Jeff Wiltgen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, 27695
| | - John Ritter
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, 27695
| | - Charles B Mooney
- Analytical Instrumentation Facility, North Carolina State University, Raleigh, North Carolina
| | - Michael C Flickinger
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, 27695. .,Golden-LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina, 27695.
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Glycerol acts as alternative electron sink during syngas fermentation by thermophilic anaerobe Moorella thermoacetica. J Biosci Bioeng 2016; 121:268-73. [DOI: 10.1016/j.jbiosc.2015.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 01/03/2023]
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Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesman A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genomics 2015; 16:1085. [PMID: 26692227 PMCID: PMC4687164 DOI: 10.1186/s12864-015-2287-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022] Open
Abstract
Background Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence. Results We performed next generation sequencing using Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum and observed 243 single nucleotide discrepancies when compared to the published finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions. These variations were confirmed by Sanger sequencing and subsequent analysis suggested that the discrepancies were sequencing errors in the published genome not true single nucleotide polymorphisms. This was corroborated by the observation that over 90 % occurred within homopolymer regions of greater than 4 nucleotides in length. It was also observed that many genes containing these sequencing errors were annotated in the published closed genome as encoding proteins containing frameshift mutations (18 instances) or were annotated despite the coding frame containing stop codons, which if genuine, would severely hinder the organism’s ability to survive. Furthermore, we have completed a comprehensive manual curation to reduce errors in the annotation that occur through serial use of automated annotation pipelines in related species. As a result, different functions were assigned to gene products or previous functional annotations rejected because of missing evidence in various occasions. Conclusions We present a revised manually curated full genome sequence for Clostridium autoethanogenum DSM10061, which provides reliable information for genome-scale models that rely heavily on the accuracy of annotation, and represents an important step towards the manipulation and metabolic modelling of this industrially relevant acetogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2287-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher M Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Samantha McLean
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | | | - Thomas Millat
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Florence J Annan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Ronja Breitkopf
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Bart Pander
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Pawel Piatek
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Peter Rowe
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | | | - Craig Woods
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Rupert Norman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
| | - Alexander Goesman
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
| | - Charlie Hodgman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - David Barrett
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Neil R Thomas
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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Willrodt C, Hoschek A, Bühler B, Schmid A, Julsing MK. Decoupling production from growth by magnesium sulfate limitation boosts de novo limonene production. Biotechnol Bioeng 2015; 113:1305-14. [PMID: 26574166 DOI: 10.1002/bit.25883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/08/2015] [Indexed: 01/23/2023]
Abstract
The microbial production of isoprenoids has recently developed into a prime example for successful bottom-up synthetic biology or top-down systems biology strategies. Respective fermentation processes typically rely on growing recombinant microorganisms. However, the fermentative production of isoprenoids has to compete with cellular maintenance and growth for carbon and energy. Non-growing but metabolically active E. coli cells were evaluated in this study as alternative biocatalyst configurations to reduce energy and carbon loss towards biomass formation. The use of non-growing cells in an optimized fermentation medium resulted in more than fivefold increased specific limonene yields on cell dry weight and glucose, as compared to the traditional growing-cell-approach. Initially, the stability of the resting-cell activity was limited. This instability was overcome via the optimization of the minimal fermentation medium enabling high and stable limonene production rates for up to 8 h and a high specific yield of ≥50 mg limonene per gram cell dry weight. Omitting MgSO4 from the fermentation medium was very promising to prohibit growth and allow high productivities. Applying a MgSO4 -limitation also improved limonene formation by growing cells during non-exponential growth involving a reduced biomass yield on glucose and a fourfold increase in specific limonene yields on biomass as compared to non-limited cultures. The control of microbial growth via the medium composition was identified as a key but yet underrated strategy for efficient isoprenoid production. Biotechnol. Bioeng. 2016;113: 1305-1314. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Christian Willrodt
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.,Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Anna Hoschek
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.
| | - Mattijs K Julsing
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
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Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl Environ Microbiol 2015; 81:8379-91. [PMID: 26431975 DOI: 10.1128/aem.02491-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Clostridium ljungdahlii is an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and that C. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism of C. ljungdahlii and provides new genetic targets to generate C. ljungdahlii strains that produce more ethanol and are more tolerant to syngas contaminants.
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Martin ME, Richter H, Saha S, Angenent LT. Traits of selectedClostridiumstrains for syngas fermentation to ethanol. Biotechnol Bioeng 2015; 113:531-9. [DOI: 10.1002/bit.25827] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 08/23/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Michael E. Martin
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
| | - Hanno Richter
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
| | - Surya Saha
- Boyce Thompson Institute for Plant Research; 533 Tower Road; Ithaca New York 14853
| | - Largus T. Angenent
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
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Ramió-Pujol S, Ganigué R, Bañeras L, Colprim J. How can alcohol production be improved in carboxydotrophic clostridia? Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Sun W, Xiao F, Wei Z, Cui F, Yu L, Yu S, Zhou Q. Non-sterile and buffer-free bioconversion of glucose to 2-keto-gluconic acid by using Pseudomonas fluorescens AR4 free resting cells. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abubackar HN, Veiga MC, Kennes C. Ethanol and acetic acid production from carbon monoxide in a Clostridium strain in batch and continuous gas-fed bioreactors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:1029-43. [PMID: 25608591 PMCID: PMC4306909 DOI: 10.3390/ijerph120101029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/31/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
Abstract
The effect of different sources of nitrogen as well as their concentrations on the bioconversion of carbon monoxide to metabolic products such as acetic acid and ethanol by Clostridium autoethanogenum was studied. In a first set of assays, under batch conditions, either NH4Cl, trypticase soy broth or yeast extract (YE) were used as sources of nitrogen. The use of YE was found statistically significant (p < 0.05) on the product spectrum in such batch assays. In another set of experiments, three bioreactors were operated with continuous CO supply, in order to estimate the effect of running conditions on products and biomass formation. The bioreactors were operated under different conditions, i.e., EXP1 (pH = 5.75, YE 1g/L), EXP2 (pH = 4.75, YE 1 g/L) and EXP3 (pH = 5.75, YE 0.2 g/L). When compared to EXP2 and EXP3, it was found that EXP1 yielded the maximum biomass accumulation (302.4 mg/L) and products concentrations, i.e., acetic acid (2147.1 mg/L) and ethanol (352.6 mg/L). This can be attributed to the fact that the higher pH and higher YE concentration used in EXP1 stimulated cell growth and did, consequently, also enhance metabolite production. However, when ethanol is the desired end-product, as a biofuel, the lower pH used in EXP2 was more favourable for solventogenesis and yielded the highest ethanol/acetic acid ratio, reaching a value of 0.54.
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Affiliation(s)
- Haris Nalakath Abubackar
- Chemical Engineering Laboratory, Faculty of Sciences, University of La Coruña, Rúa da Fraga 10, 15008 La Coruña, Spain.
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences, University of La Coruña, Rúa da Fraga 10, 15008 La Coruña, Spain.
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences, University of La Coruña, Rúa da Fraga 10, 15008 La Coruña, Spain.
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Zomorrodi AR, Islam MM, Maranas CD. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol 2014; 3:247-57. [PMID: 24742179 DOI: 10.1021/sb4001307] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Most microbial communities change with time in response to changes and/or perturbations in environmental conditions. Temporal variations in interspecies metabolic interactions within these communities can significantly affect their structure and function. Here, we introduce d-OptCom, an extension of the OptCom procedure, for the dynamic metabolic modeling of microbial communities. It enables capturing the temporal dynamics of biomass concentration of the community members and extracellular concentration of the shared metabolites, while integrating species- and community-level fitness functions. The applicability of d-OptCom was demonstrated by modeling the dynamic co-growth of auxotrophic mutant pairs of E. coli and by computationally assessing the dynamics and composition of a uranium-reducing community comprised of Geobacter sulfurreducens, Rhodoferax ferrireducens, and Shewanella oneidensis. d-OptCom was also employed to examine the impact of lactate vs acetate addition on the relative abundance of uranium-reducing species. These studies highlight the importance of simultaneously accounting for both species- and community-level fitness functions when modeling microbial communities, and demonstrate that the incorporation of uptake kinetic information can substantially improve the prediction of interspecies flux trafficking. Overall, this study paves the way for the dynamic multi-level and multi-objective analysis of microbial ecosystems.
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Affiliation(s)
- Ali R. Zomorrodi
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad Mazharul Islam
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Lactose-inducible system for metabolic engineering of Clostridium ljungdahlii. Appl Environ Microbiol 2014; 80:2410-6. [PMID: 24509933 DOI: 10.1128/aem.03666-13] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The development of tools for genetic manipulation of Clostridium ljungdahlii has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for C. ljungdahlii, the possibility of adapting a lactose-inducible system for gene expression, previously reported for Clostridium perfringens, was investigated. The plasmid pAH2, originally developed for C. perfringens with a gusA reporter gene, functioned as an effective lactose-inducible system in C. ljungdahlii. Lactose induction of C. ljungdahlii containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of adhE1 30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of adhE1 in a strain in which adhE1 and the adhE1 homolog adhE2 had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of adhE2 similarly failed to restore ethanol production, suggesting that adhE1 is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.
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Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Köpke M. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:40. [PMID: 24655715 PMCID: PMC4022347 DOI: 10.1186/1754-6834-7-40] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/19/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. RESULTS A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. CONCLUSIONS Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.
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Affiliation(s)
- Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Sagar Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | | | | | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Empirical predictive modelling of poly-ɛ-lysine biosynthesis in resting cells of Streptomyces noursei. Food Sci Biotechnol 2013. [DOI: 10.1007/s10068-014-0027-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Grishko VV, Tarasova EV, Ivshina IB. Biotransformation of betulin to betulone by growing and resting cells of the actinobacterium Rhodococcus rhodochrous IEGM 66. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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