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Sitara A, Hocq R, Horvath J, Pflügl S. Industrial biotechnology goes thermophilic: Thermoanaerobes as promising hosts in the circular carbon economy. BIORESOURCE TECHNOLOGY 2024; 408:131164. [PMID: 39069138 DOI: 10.1016/j.biortech.2024.131164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Transitioning away from fossil feedstocks is imperative to mitigate climate change, and necessitates the utilization of renewable, alternative carbon and energy sources to foster a circular carbon economy. In this context, lignocellulosic biomass and one-carbon compounds emerge as promising feedstocks that could be renewably upgraded by thermophilic anaerobes (thermoanaerobes) via gas fermentation or consolidated bioprocessing to value-added products. In this review, the potential of thermoanaerobes for cost-efficient, effective and sustainable bioproduction is discussed. Metabolic and bioprocess engineering approaches are reviewed to draw a comprehensive picture of current developments and future perspectives for the conversion of renewable feedstocks to chemicals and fuels of interest. Selected bioprocessing scenarios are outlined, offering practical insights into the applicability of thermoanaerobes at a large scale. Collectively, the potential advantages of thermoanaerobes regarding process economics could facilitate an easier transition towards sustainable bioprocesses with renewable feedstocks.
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Affiliation(s)
- Angeliki Sitara
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria; Christian Doppler Laboratory for Optimized Expression of Carbohydrate-active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria; CIRCE Biotechnologie GmbH, Kerpengasse 125, 1210 Vienna, Austria
| | - Josef Horvath
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria; Christian Doppler Laboratory for Optimized Expression of Carbohydrate-active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria; Christian Doppler Laboratory for Optimized Expression of Carbohydrate-active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria.
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Bae J, Park C, Jung H, Jin S, Cho BK. Harnessing acetogenic bacteria for one-carbon valorization toward sustainable chemical production. RSC Chem Biol 2024; 5:812-832. [PMID: 39211478 PMCID: PMC11353040 DOI: 10.1039/d4cb00099d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/06/2024] [Indexed: 09/04/2024] Open
Abstract
The pressing climate change issues have intensified the need for a rapid transition towards a bio-based circular carbon economy. Harnessing acetogenic bacteria as biocatalysts to convert C1 compounds such as CO2, CO, formate, or methanol into value-added multicarbon chemicals is a promising solution for both carbon capture and utilization, enabling sustainable and green chemical production. Recent advances in the metabolic engineering of acetogens have expanded the range of commodity chemicals and biofuels produced from C1 compounds. However, producing energy-demanding high-value chemicals on an industrial scale from C1 substrates remains challenging because of the inherent energetic limitations of acetogenic bacteria. Therefore, overcoming this hurdle is necessary to scale up the acetogenic C1 conversion process and realize a circular carbon economy. This review overviews the acetogenic bacteria and their potential as sustainable and green chemical production platforms. Recent efforts to address these challenges have focused on enhancing the ATP and redox availability of acetogens to improve their energetics and conversion performances. Furthermore, promising technologies that leverage low-cost, sustainable energy sources such as electricity and light are discussed to improve the sustainability of the overall process. Finally, we review emerging technologies that accelerate the development of high-performance acetogenic bacteria suitable for industrial-scale production and address the economic sustainability of acetogenic C1 conversion. Overall, harnessing acetogenic bacteria for C1 valorization offers a promising route toward sustainable and green chemical production, aligning with the circular economy concept.
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Affiliation(s)
- Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Chanho Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Hyunwoo Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology Daejeon 34141 Republic of Korea
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3
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Moon J, Poehlein A, Daniel R, Müller V. Redirecting electron flow in Acetobacterium woodii enables growth on CO and improves growth on formate. Nat Commun 2024; 15:5424. [PMID: 38926344 PMCID: PMC11208171 DOI: 10.1038/s41467-024-49680-5] [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: 01/04/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Anaerobic, acetogenic bacteria are well known for their ability to convert various one-carbon compounds, promising feedstocks for a future, sustainable biotechnology, to products such as acetate and biofuels. The model acetogen Acetobacterium woodii can grow on CO2, formate or methanol, but not on carbon monoxide, an important industrial waste product. Since hydrogenases are targets of CO inhibition, here, we genetically delete the two [FeFe] hydrogenases HydA2 and HydBA in A. woodii. We show that the ∆hydBA/hydA2 mutant indeed grows on CO and produces acetate, but only after a long adaptation period. SNP analyzes of CO-adapted cells reveal a mutation in the HycB2 subunit of the HydA2/HydB2/HydB3/Fdh-containing hydrogen-dependent CO2 reductase (HDCR). We observe an increase in ferredoxin-dependent CO2 reduction and vice versa by the HDCR in the absence of the HydA2 module and speculate that this is caused by the mutation in HycB2. In addition, the CO-adapted ∆hydBA/hydA2 mutant growing on formate has a final biomass twice of that of the wild type.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, Germany.
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Koubaa M. Integrated Biorefinery for a Next-Generation Methanization Process Focusing on Volatile Fatty Acid Valorization: A Critical Review. Molecules 2024; 29:2477. [PMID: 38893350 PMCID: PMC11173433 DOI: 10.3390/molecules29112477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
This review addresses the critical issue of a rapidly increasing worldwide waste stream and the need for sustainable management. The paper proposes an integrated transformation toward a next-generation methanization process, which leads not only to treating waste but also to converting it into higher value compounds and greener energy. Although the current and commonly used anaerobic digestion process is useful for biogas production, it presents limitations of resource exploitation and some negative environmental impacts. Focusing on the acidogenic stage in waste stream processing, the paper discusses the recent strategies to enhance the recovery of volatile fatty acids (VFAs). These acids serve as precursors for synthesizing a variety of biochemicals and biofuels, offering higher value products than solely energy recovery and soil fertilizers. Additionally, the importance of recycling the fermentation residues back into the biorefinery process is highlighted. This recycling not only generates additional VFAs but also contributes to generating clean energy, thereby enhancing the overall sustainability and efficiency of the waste management system. Moreover, the review discusses the necessity to integrate life cycle assessment (LCA) and techno-economic analysis (TEA) to evaluate the environmental impacts, sustainability, and processing costs of the proposed biorefinery.
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Affiliation(s)
- Mohamed Koubaa
- Université de Technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Centre de Recherche Royallieu-CS 60319, 60203 Compiègne Cedex, France
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Niu C, Zhao X, Shi D, Ying Y, Wu M, Lai CY, Guo J, Hu S, Liu T. Bioreduction of chromate in a syngas-based membrane biofilm reactor. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134195. [PMID: 38581872 DOI: 10.1016/j.jhazmat.2024.134195] [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: 01/02/2024] [Revised: 03/07/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
This study leveraged synthesis gas (syngas), a renewable resource attainable through the gasification of biowaste, to achieve efficient chromate removal from water. To enhance syngas transfer efficiency, a membrane biofilm reactor (MBfR) was employed. Long-term reactor operation showed a stable and high-level chromate removal efficiency > 95%, yielding harmless Cr(III) precipitates, as visualised by scanning electron microscopy and energy dispersive X-ray analysis. Corresponding to the short hydraulic retention time of 0.25 days, a high chromate removal rate of 80 µmol/L/d was attained. In addition to chromate reduction, in situ production of volatile fatty acids (VFAs) by gas fermentation was observed. Three sets of in situ batch tests and two groups of ex situ batch tests jointly unravelled the mechanisms, showing that biological chromate reduction was primarily driven by VFAs produced from in situ syngas fermentation, whereas hydrogen originally present in the syngas played a minor role. 16 S rRNA gene amplicon sequencing has confirmed the enrichment of syngas-fermenting bacteria (such as Sporomusa), who performed in situ gas fermentation leading to the synthesis of VFAs, and organics-utilising bacteria (such as Aquitalea), who utilised VFAs to drive chromate reduction. These findings, combined with batch assays, elucidate the pathways orchestrating synergistic interactions between fermentative microbial cohorts and chromate-reducing microorganisms. The findings facilitate the development of cost-effective strategies for groundwater and drinking water remediation and present an alternative application scenario for syngas.
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Affiliation(s)
- Chenkai Niu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Xinyu Zhao
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Danting Shi
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong Special Administrative Region of China
| | - Yifeng Ying
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Chun-Yu Lai
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong Special Administrative Region of China.
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García-Casado S, Muñoz R, Lebrero R. Enrichment of a mixed syngas-converting culture for volatile fatty acids and methane production. BIORESOURCE TECHNOLOGY 2024; 400:130646. [PMID: 38556063 DOI: 10.1016/j.biortech.2024.130646] [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: 01/21/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/02/2024]
Abstract
The present study evaluated the production potential of CH4, carboxylic acids and alcohols from a mixed culture enriched using synthetic syngas. The influence of syngas concentration on the microbial community and products productivity and selectivity was investigated. The results demonstrated the enrichment of a mesophilic mixed culture capable of converting CO and H2 mainly to CH4 and acetate, along with butyrate. The selectivity values showed that acetate production was enhanced during the first cycle in all conditions tested (up to 20 %), while CH4 was the main product generated during following cycles. Concretely, CH4 selectivity remained unaffected by syngas concentration, reaching a stable value of 41.6 ± 2.0 %. On the other hand, butyrate selectivity was only representative at the highest syngas concentration and lower pH values (26.1 ± 5.8 %), where the H2 consumption was completely inhibited. Thus, pH was identified as a key parameter for both butyrate synthesis and the development of hydrogenotrophic activity.
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Affiliation(s)
- Silvia García-Casado
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Raquel Lebrero
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain.
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7
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Cui W, Wei Y, Ji N. Global trends of waste-to-energy (WtE) technologies in carbon neutral perspective: Bibliometric analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115913. [PMID: 38198897 DOI: 10.1016/j.ecoenv.2023.115913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/07/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Waste-to-energy (WtE) technology is at the forefront of low-carbon municipal solid waste (MSW) treatment. MSW has been favoured by researchers in recent years due to its high potential to dispose of resources with WtE technology, which contributes to the carbon neutrality goal. However, there is a lack of research that integrates MSW WtE treatment from a global perspective and explores its future direction. Bibliometric methods are widely used because of their advantages in qualitative and quantitative literature information analysis. A comprehensive search was conducted in the Web of Science (WOS) Core Collection database, covering the period from 1990-2022, resulting in the collection of 702 articles. Subsequently, bibliometric software such as CiteSpace, VOSviewer, and Bibliometrix, were jointly employed for co-occurrence, co-citation, and cluster analyses, providing an in-depth qualitative and quantitative analysis of the research hotspots and development trends of WtE technology for MSW treatment. The research findings indicate a rapid growth in studies on carbon emission reduction through WtE technology for MSW treatment since 2015, with these related articles accounting for 50% of articles. Globally, China, the United States, Italy, and other countries were active research regions, with Chinese research institutions making the largest contributions. However, contributions from developing countries are limited. Furthermore, this study systematically elaborates on the research hotspots in this field. Finally, this study identified some frontier research hotspots and directions. Research on WtE technology primarily focuses on technological methods and policy management, particularly from the carbon neutrality perspective, emphasis WtE technology sustainability in reducing carbon emissions and achieving carbon neutrality goals. Promoting the use of assisted decision-making models in the MSW management process, and focusing on the conversion of food waste into valuable energy. It is hoped that these research directions will provide new ideas for the balanced and rapid development of WtE technology.
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Affiliation(s)
- Wenjing Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yuan Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Ningning Ji
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Zaplana T, Miele S, Tolonen AC. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. Front Bioeng Biotechnol 2024; 11:1324396. [PMID: 38239921 PMCID: PMC10794557 DOI: 10.3389/fbioe.2023.1324396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
The Lachnospiraceae is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of Lachnospiraceae metabolize abundant, low-cost feedstocks such as lignocellulose and carbon dioxide into value-added chemicals. Others are among the dominant species of the human colon and animal rumen, where they ferment dietary fiber to promote healthy gut and immune function. Here, we summarize recent studies of the physiology, cultivation, and genetics of Lachnospiraceae, highlighting their wide substrate utilization and metabolic products with industrial applications. We examine studies of these bacteria as Live Biotherapeutic Products (LBPs), focusing on in vivo disease models and clinical studies using them to treat infection, inflammation, metabolic syndrome, and cancer. We discuss key research areas including elucidation of intra-specific diversity and genetic modification of candidate strains that will facilitate the exploitation of Lachnospiraceae in industry and medicine.
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Affiliation(s)
| | | | - Andrew C. Tolonen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry, Université Paris-Saclay, Evry, France
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Mariën Q, Regueira A, Ganigué R. Steerable isobutyric and butyric acid production from CO 2 and H 2 by Clostridium luticellarii. Microb Biotechnol 2024; 17:e14321. [PMID: 37649327 PMCID: PMC10832561 DOI: 10.1111/1751-7915.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 09/01/2023] Open
Abstract
Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.
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Affiliation(s)
- Quinten Mariën
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
| | - Alberte Regueira
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
- CRETUS, Department of Chemical EngineeringUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGhentBelgium
- Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE)GhentBelgium
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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11
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François JM. Progress advances in the production of bio-sourced methionine and its hydroxyl analogues. Biotechnol Adv 2023; 69:108259. [PMID: 37734648 DOI: 10.1016/j.biotechadv.2023.108259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.
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Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, 31077 Toulouse, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, 31077 Toulouse, France.
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12
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Trischler R, Poehlein A, Daniel R, Müller V. Ethanologenesis from glycerol by the gut acetogen Blautia schinkii. Environ Microbiol 2023; 25:3577-3591. [PMID: 37807918 DOI: 10.1111/1462-2920.16517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The human gut is an anoxic environment that harbours a multitude of microorganisms that not only contribute to food digestion. The microbiome is also involved in malfunctions such as diseases, inflammation processes or development of obesity, but it is also involved in processes that increase the human well-being. Both, the good and the bad, are mediated by fermentation end products of bacterial metabolism, among others. However, despite a steadily growing knowledge of 'who lives out there', little in known of 'what do they do out there'. The genus Blautia is commonly found in the gut and associated with human well-being, but the exploration of their metabolic potential has just started. We demonstrate that B. schinkii grows on glycerol by producing acetate and ethanol. Transcriptome studies and biochemical analyses revealed a glycerol dehydrogenase and dihydroxyacetone kinase that funnel the substrate into glycolysis. Consequently, cells also grew on dihydroxyacetone. Cells could be adapted to grow at high (up to 1.5 M) glycerol concentrations but then only ethanol was formed. Ethanol production from glycerol is not only of relevance for the human host but also for potential bioindustrial production of bioethanol from waste glycerol.
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Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - A Poehlein
- Georg August University Göttingen, Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Göttingen, Germany
| | - R Daniel
- Georg August University Göttingen, Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
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Höfele F, Schoch T, Oberlies C, Dürre P. Heterologous Production of Isopropanol Using Metabolically Engineered Acetobacterium woodii Strains. Bioengineering (Basel) 2023; 10:1381. [PMID: 38135972 PMCID: PMC10741115 DOI: 10.3390/bioengineering10121381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The depletion of fossil fuel resources and the CO2 emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to metabolize CO or CO2 (+H2) via the Wood-Ljungdahl pathway. As isopropanol is widely used in a variety of industrial branches, it is advantageous to find a fossil-independent production process. In this study, Acetobacterium woodii was employed to produce isopropanol via plasmid-based expression of the enzymes thiolase A, CoA-transferase, acetoacetate decarboxylase and secondary alcohol dehydrogenase. An examination of the enzymes originating from different organisms led to a maximum isopropanol production of 5.64 ± 1.08 mM using CO2 + H2 as the carbon and energy source. To this end, the genes thlA (encoding thiolase A) and ctfA/ctfB (encoding CoA-transferase) of Clostridium scatologenes, adc (encoding acetoacetate decarboxylase) originating from C. acetobutylicum and sadH (encoding secondary alcohol dehydrogenase) of C. beijerinckii DSM 6423 were employed. Since bottlenecks in the isopropanol production pathway are known, optimization of the strain was investigated, resulting in a 2.5-fold increase in isopropanol concentration.
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Affiliation(s)
- Franziska Höfele
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, 89081 Ulm, Germany
| | - Teresa Schoch
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
| | - Catarina Oberlies
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany (C.O.); (P.D.)
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14
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Kurt E, Qin J, Williams A, Zhao Y, Xie D. Perspectives for Using CO 2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering (Basel) 2023; 10:1357. [PMID: 38135948 PMCID: PMC10740661 DOI: 10.3390/bioengineering10121357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.
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Affiliation(s)
- Elif Kurt
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Alexandria Williams
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Youbo Zhao
- Physical Sciences Inc., 20 New England Business Ctr., Andover, MA 01810, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
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15
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Karekar SC, Seiple T, Ahring BK, Fuller C. Assessing feasible H 2-CO 2 sources in the US as Feedstocks for Sustainable Aviation Fuel Precursors: Acetic Acid and Ethanol Production via Hydrogenotrophic Pathways. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118641. [PMID: 37549637 DOI: 10.1016/j.jenvman.2023.118641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/02/2023] [Accepted: 07/15/2023] [Indexed: 08/09/2023]
Abstract
The environmental impact of carbon dioxide emissions is significant, and research is focused on mitigating these emissions and developing eco-friendly technologies in line with green chemistry principles. Waste-to-energy technologies play a crucial role in converting waste into renewable energy and valuable biofuels and bioproducts. This study specifically explores the utilization of waste gas emissions, particularly carbon dioxide, from various sources in the United States for the production of sustainable aviation fuel (SAF) precursors, such as ethanol and acetic acid. The study categorizes and quantifies the volumes of carbon dioxide emissions into three types: non-biogenic, biogenic, and biogenic emissions from ethanol production facilities. Stoichiometric calculations are applied to compare the amounts of carbon dioxide from each category with the available hydrogen production capacity, determining if sufficient hydrogen is present for converting carbon dioxide into SAF precursors. The study reveals two key findings. Firstly, there is a significant reserve of carbon dioxide, approximately 1648 million metric tons per year (MMTy), combining all three categories, which would require a substantial increase of approximately 35-40 times in the existing hydrogen production capacity of 4.988 MMTy. This increased hydrogen production has the potential to yield approximately 1067.82 MMTy of acetic acid and 189.19 MMTy of ethanol annually. Secondly, upon analyzing the quality and application of the three sources of carbon dioxide with the currently available hydrogen production capacity, it is found that biogenic carbon dioxide from ethanol plants is the most suitable choice for immediate production of SAF precursors. This would theoretically result in an annual production of 1.36 MMTy of ethanol and 1.772 MMTy of acetic acid. The other two sources of carbon dioxide can be considered potential reserves for future utilization when additional hydrogen production facilities are established. The study provides a foundation for assessing the aggregation potential required for acetic acid and ethanol production. By optimizing the use of waste gases as raw materials, the study not only enables the production of SAF precursors but also contributes to the passive reduction of greenhouse gas emissions.
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Affiliation(s)
- Supriya C Karekar
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Tri-Cities, 2710, Crimson Way, Richland, WA, 99354, USA; Biological Systems Engineering, L.J. Smith Hall, Washington State University, Pullman, WA, 99164, USA
| | - Timonthy Seiple
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Birgitte K Ahring
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Tri-Cities, 2710, Crimson Way, Richland, WA, 99354, USA; Biological Systems Engineering, L.J. Smith Hall, Washington State University, Pullman, WA, 99164, USA; The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99163, USA
| | - Corinne Fuller
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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16
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Yu J, Park MJ, Lee J, Kwon SJ, Lim JK, Lee HS, Kang SG, Lee JH, Kwon KK, Kim YJ. Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria. Front Microbiol 2023; 14:1279544. [PMID: 37933250 PMCID: PMC10625859 DOI: 10.3389/fmicb.2023.1279544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h-1) and 200 mM formate (0.34 h-1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.
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Affiliation(s)
- Jihyun Yu
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Mi-Jeong Park
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Joungmin Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Soo Jae Kwon
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae Kyu Lim
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung-Hyun Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
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17
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Laura M, Jo P. No acetogen is equal: Strongly different H 2 thresholds reflect diverse bioenergetics in acetogenic bacteria. Environ Microbiol 2023; 25:2032-2040. [PMID: 37209014 DOI: 10.1111/1462-2920.16429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Acetogens share the capacity to convert H2 and CO2 into acetate for energy conservation (ATP synthesis). This reaction is attractive for applications, such as gas fermentation and microbial electrosynthesis. Different H2 partial pressures prevail in these distinctive applications (low concentrations during microbial electrosynthesis [<40 Pa] vs. high concentrations with gas fermentation [>9%]). Strain selection thus requires understanding of how different acetogens perform under different H2 partial pressures. Here, we determined the H2 threshold (H2 partial pressure at which acetogenesis halts) for eight different acetogenic strains under comparable conditions. We found a three orders of magnitude difference between the lowest and highest H2 threshold (6 ± 2 Pa for Sporomusa ovata vs. 1990 ± 67 Pa for Clostridium autoethanogenum), while Acetobacterium strains had intermediate H2 thresholds. We used these H2 thresholds to estimate ATP gains, which ranged from 0.16 to 1.01 mol ATP per mol acetate (S. ovata vs. C. autoethanogenum). The experimental H2 thresholds thus suggest strong differences in the bioenergetics of acetogenic strains and possibly also in their growth yields and kinetics. We conclude that no acetogen is equal and that a good understanding of their differences is essential to select the most optimal strain for different biotechnological applications.
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Affiliation(s)
- Munoz Laura
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Philips Jo
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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18
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Elisiário MP, Van Hecke W, De Wever H, Noorman H, Straathof AJJ. Acetic acid, growth rate, and mass transfer govern shifts in CO metabolism of Clostridium autoethanogenum. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12670-6. [PMID: 37410136 PMCID: PMC10390632 DOI: 10.1007/s00253-023-12670-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Syngas fermentation is a leading microbial process for the conversion of carbon monoxide, carbon dioxide, and hydrogen to valuable biochemicals. Clostridium autoethanogenum stands as a model organism for this process, showcasing its ability to convert syngas into ethanol industrially with simultaneous fixation of carbon and reduction of greenhouse gas emissions. A deep understanding on the metabolism of this microorganism and the influence of operational conditions on fermentation performance is key to advance the technology and enhancement of production yields. In this work, we studied the individual impact of acetic acid concentration, growth rate, and mass transfer rate on metabolic shifts, product titres, and rates in CO fermentation by C. autoethanogenum. Through continuous fermentations performed at a low mass transfer rate, we measured the production of formate in addition to acetate and ethanol. We hypothesise that low mass transfer results in low CO concentrations, leading to reduced activity of the Wood-Ljungdahl pathway and a bottleneck in formate conversion, thereby resulting in the accumulation of formate. The supplementation of the medium with exogenous acetate revealed that undissociated acetic acid concentration increases and governs ethanol yield and production rates, assumedly to counteract the inhibition by undissociated acetic acid. Since acetic acid concentration is determined by growth rate (via dilution rate), mass transfer rate, and working pH, these variables jointly determine ethanol production rates. These findings have significant implications for process optimisation as targeting an optimal undissociated acetic acid concentration can shift metabolism towards ethanol production. KEY POINTS: • Very low CO mass transfer rate leads to leaking of intermediate metabolite formate. • Undissociated acetic acid concentration governs ethanol yield on CO and productivity. • Impact of growth rate, mass transfer rate, and pH were considered jointly.
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Affiliation(s)
- Marina P Elisiário
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629HZ, Delft, The Netherlands
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400, Mol, Belgium
| | - Wouter Van Hecke
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400, Mol, Belgium
| | - Heleen De Wever
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400, Mol, Belgium
| | - Henk Noorman
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629HZ, Delft, The Netherlands
- Royal DSM, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Adrie J J Straathof
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629HZ, Delft, The Netherlands.
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19
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Herzog J, Mook A, Utesch T, Bengelsdorf FR, Zeng AP. Lactate based caproate production with Clostridium drakei and process control of Acetobacterium woodii via lactate dependent in situ electrolysis. Front Bioeng Biotechnol 2023; 11:1212044. [PMID: 37425355 PMCID: PMC10327822 DOI: 10.3389/fbioe.2023.1212044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
Syngas fermentation processes with acetogens represent a promising process for the reduction of CO2 emissions alongside bulk chemical production. However, to fully realize this potential the thermodynamic limits of acetogens need to be considered when designing a fermentation process. An adjustable supply of H2 as electron donor plays a key role in autotrophic product formation. In this study an anaerobic laboratory scale continuously stirred tank reactor was equipped with an All-in-One electrode allowing for in-situ H2 generation via electrolysis. Furthermore, this system was coupled to online lactate measurements to control the co-culture of a recombinant lactate-producing Acetobacterium woodii strain and a lactate-consuming Clostridium drakei strain to produce caproate. When C. drakei was grown in batch cultivations with lactate as substrate, 1.6 g·L-1 caproate were produced. Furthermore, lactate production of the A. woodii mutant strain could manually be stopped and reinitiated by controlling the electrolysis. Applying this automated process control, lactate production of the A. woodii mutant strain could be halted to achieve a steady lactate concentration. In a co-culture experiment with the A. woodii mutant strain and the C. drakei strain, the automated process control was able to dynamically react to changing lactate concentrations and adjust H2 formation respectively. This study confirms the potential of C. drakei as medium chain fatty acid producer in a lactate-mediated, autotrophic co-cultivation with an engineered A. woodii strain. Moreover, the monitoring and control strategy presented in this study reinforces the case for autotrophically produced lactate as a transfer metabolite in defined co-cultivations for value-added chemical production.
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Affiliation(s)
- Jan Herzog
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Alexander Mook
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, Ulm, Germany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Frank R. Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, Ulm University, Ulm, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
- Synthetic Biology and Bioengineering Lab, School of Science, Westlake University, Hangzhou, China
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20
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Poulalier-Delavelle M, Baker JP, Millard J, Winzer K, Minton NP. Endogenous CRISPR/Cas systems for genome engineering in the acetogens Acetobacterium woodii and Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1213236. [PMID: 37425362 PMCID: PMC10328091 DOI: 10.3389/fbioe.2023.1213236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Acetogenic bacteria can play a major role in achieving Net Zero through their ability to convert CO2 into industrially relevant chemicals and fuels. Full exploitation of this potential will be reliant on effective metabolic engineering tools, such as those based on the Streptococcus pyogenes CRISPR/Cas9 system. However, attempts to introduce cas9-containing vectors into Acetobacterium woodii were unsuccessful, most likely as a consequence of Cas9 nuclease toxicity and the presence of a recognition site for an endogenous A. woodii restriction-modification (R-M) system in the cas9 gene. As an alternative, this study aims to facilitate the exploitation of CRISPR/Cas endogenous systems as genome engineering tools. Accordingly, a Python script was developed to automate the prediction of protospacer adjacent motif (PAM) sequences and used to identify PAM candidates of the A. woodii Type I-B CRISPR/Cas system. The identified PAMs and the native leader sequence were characterized in vivo by interference assay and RT-qPCR, respectively. Expression of synthetic CRISPR arrays, consisting of the native leader sequence, direct repeats, and adequate spacer, along with an editing template for homologous recombination, successfully led to the creation of 300 bp and 354 bp in-frame deletions of pyrE and pheA, respectively. To further validate the method, a 3.2 kb deletion of hsdR1 was also generated, as well as the knock-in of the fluorescence-activating and absorption-shifting tag (FAST) reporter gene at the pheA locus. Homology arm length, cell density, and the amount of DNA used for transformation were found to significantly impact editing efficiencies. The devised workflow was subsequently applied to the Type I-B CRISPR/Cas system of Clostridium autoethanogenum, enabling the generation of a 561 bp in-frame deletion of pyrE with 100% editing efficiency. This is the first report of genome engineering of both A. woodii and C. autoethanogenum using their endogenous CRISPR/Cas systems.
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Affiliation(s)
| | | | | | | | - Nigel P. Minton
- *Correspondence: Margaux Poulalier-Delavelle, ; Nigel P. Minton,
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21
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Boto ST, Bardl B, Harnisch F, Rosenbaum MA. Microbial electrosynthesis with Clostridium ljungdahlii benefits from hydrogen electron mediation and permits a greater variety of products. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2023; 25:4375-4386. [PMID: 37288452 PMCID: PMC10243432 DOI: 10.1039/d3gc00471f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/21/2023] [Indexed: 06/09/2023]
Abstract
Microbial electrosynthesis (MES) is a very promising technology addressing the challenge of carbon dioxide recycling into organic compounds, which might serve as building blocks for the (bio)chemical industry. However, poor process control and understanding of fundamental aspects such as the microbial extracellular electron transfer (EET) currently limit further developments. In the model acetogen Clostridium ljungdahlii, both direct and indirect electron consumption via hydrogen have been proposed. However, without clarification neither targeted development of the microbial catalyst nor process engineering of MES are possible. In this study, cathodic hydrogen is demonstrated to be the dominating electron source for C. ljungdahlii at electroautotrophic MES allowing for superior growth and biosynthesis, compared to previously reported MES using pure cultures. Hydrogen availability distinctly controlled an either planktonic- or biofilm-dominated lifestyle of C. ljungdahlii. The most robust operation yielded higher planktonic cell densities in a hydrogen mediated process, which demonstrated the uncoupling of growth and biofilm formation. This coincided with an increase of metabolic activity, acetate titers, and production rates (up to 6.06 g L-1 at 0.11 g L-1 d-1). For the first time, MES using C. ljungdahlii was also revealed to deliver other products than acetate in significant amounts: here up to 0.39 g L-1 glycine or 0.14 g L-1 ethanolamine. Hence, a deeper comprehension of the electrophysiology of C. ljungdahlii was shown to be key for designing and improving bioprocess strategies in MES research.
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Affiliation(s)
- Santiago T Boto
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI) Jena Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena Germany
| | - Bettina Bardl
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI) Jena Germany
| | - Falk Harnisch
- UFZ - Helmholtz-Centre for Environmental Research GmbH, Department of Environmental Microbiology Permoserstraße 15 04318 Leipzig Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI) Jena Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena Germany
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22
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Ale Enriquez F, Ahring BK. Strategies to overcome mass transfer limitations of hydrogen during anaerobic gaseous fermentations: A comprehensive review. BIORESOURCE TECHNOLOGY 2023; 377:128948. [PMID: 36963702 DOI: 10.1016/j.biortech.2023.128948] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Fermentation of gaseous substrates such as carbon dioxide (CO2) has emerged as a sustainable approach for transforming greenhouse gas emissions into renewable fuels and biochemicals. CO2 fermentations are catalyzed by hydrogenotrophic methanogens and homoacetogens, these anaerobic microorganisms selectively reduce CO2 using hydrogen (H2) as electron donor. However, H2 possesses low solubility in liquid media leading to slow mass transport, limiting the reaction rates of CO2 reduction. Solving the problems of mass transport of H2 could boost the advance of technologies for valorizing industrial CO2-rich streams, like biogas or syngas. The application could further be extended to combustion flue gases or even atmospheric CO2. In this work, an overview of strategies for overcoming H2 mass transport limitations during methanogenic and acetogenic fermentation of H2 and CO2 is presented. The potential for using these strategies in future full-scale facilities and the knowledge gaps for these applications are discussed in detail.
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Affiliation(s)
- Fuad Ale Enriquez
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, USA; The Gene and Linda Voiland School of Chemical and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Birgitte K Ahring
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, USA; The Gene and Linda Voiland School of Chemical and Bioengineering, Washington State University, Pullman, WA 99164, USA; Biological Systems Engineering Department, L.J. Smith Hall, Washington State University, Pullman, WA 99164, USA.
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23
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Henry GBL, Awedem Wobiwo F, Isenborghs A, Nicolay T, Godin B, Stenuit BA, Gerin PA. A specific H 2/CO 2 consumption molar ratio of 3 as a signature for the chain elongation of carboxylates from brewer's spent grain acidogenesis. Front Bioeng Biotechnol 2023; 11:1165197. [PMID: 37324420 PMCID: PMC10267453 DOI: 10.3389/fbioe.2023.1165197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Brewer's spent grain (BSG) is an undervalorized organic feedstock residue composed of fermentable macromolecules, such as proteins, starch, and residual soluble carbohydrates. It also contains at least 50% (as dry weight) of lignocellulose. Methane-arrested anaerobic digestion is one of the promising microbial technologies to valorize such complex organic feedstock into value-added metabolic intermediates, such as ethanol, H2, and short-chain carboxylates (SCC). Under specific fermentation conditions, these intermediates can be microbially transformed into medium-chain carboxylates through a chain elongation pathway. Medium-chain carboxylates are of great interest as they can be used as bio-based pesticides, food additives, or components of drug formulations. They can also be easily upgraded by classical organic chemistry into bio-based fuels and chemicals. This study investigates the production potential of medium-chain carboxylates driven by a mixed microbial culture in the presence of BSG as an organic substrate. Because the conversion of complex organic feedstock to medium-chain carboxylates is limited by the electron donor content, we assessed the supplementation of H2 in the headspace to improve the chain elongation yield and increase the production of medium-chain carboxylates. The supply of CO2 as a carbon source was tested as well. The additions of H2 alone, CO2 alone, and both H2 and CO2 were compared. The exogenous supply of H2 alone allowed CO2 produced during acidogenesis to be consumed and nearly doubled the medium-chain carboxylate production yield. The exogenous supply of CO2 alone inhibited the whole fermentation. The supplementation of both H2 and CO2 allowed a second elongation phase when the organic feedstock was exhausted, which increased the medium-chain carboxylate production by 285% compared to the N2 reference condition. Carbon- and electron-equivalent balances, and the stoichiometric ratio of 3 observed for the consumed H2/CO2, suggest an H2- and CO2-driven second elongation phase, converting SCC to medium-chain carboxylates without an organic electron donor. The thermodynamic assessment confirmed the feasibility of such elongation.
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Affiliation(s)
- Grégoire B. L. Henry
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Florent Awedem Wobiwo
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Arnaud Isenborghs
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Thomas Nicolay
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Bruno Godin
- Walloon Agricultural Research Center (CRA-W), Valorization of Agricultural Products Department, Gembloux, Belgium
| | - Benoit A. Stenuit
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Patrick A. Gerin
- Laboratory of Bioengineering and Biorefining, Earth and Life Institute—Applied Microbiology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
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Sieborg MU, Ottosen LDM, Kofoed MVW. Enhanced process control of trickle-bed reactors for biomethanation by vertical profiling directed by hydrogen microsensor monitoring. BIORESOURCE TECHNOLOGY 2023:129242. [PMID: 37263445 DOI: 10.1016/j.biortech.2023.129242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
Biomethanation is an emerging Power-to-X technology enabling CO2 valorisation to produce biomethane using renewable H2. A promising reactor for facilitating biomethanation is the trickle bed reactor (TBR), however, these bioreactors are conventionally operated with a black-box approach, where the system is solely described by the input and output characteristics. This study employed a novel approach for process surveillance of internal dynamics in TBRs by installing multiple H2 microsensors along its vertical axis. The H2 microsensor monitoring was demonstrated for 135 days in a TBR integrated into a full-scale biogas plant. Despite achieving an overall CH4 productivity of 12.6 L L-1 d-1, the vertical positioning of microsensors revealed a clear zonation with CH4 productivity zones reaching 54.8 L L-1 d-1 and enabled early warning detection of deteriorating process performance days before detecting it in the product gas. Thus, vertically positioned microsensors present a promising solution for securing process stability.
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Affiliation(s)
- Mads Ujarak Sieborg
- Department of Biological and Chemical Engineering, Aarhus University, Hangøvej 2, DK-8200 Aarhus N., Denmark
| | - Lars Ditlev Mørck Ottosen
- Department of Biological and Chemical Engineering, Aarhus University, Hangøvej 2, DK-8200 Aarhus N., Denmark; The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, DK-8000, Denmark
| | - Michael Vedel Wegener Kofoed
- Department of Biological and Chemical Engineering, Aarhus University, Hangøvej 2, DK-8200 Aarhus N., Denmark; The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, DK-8000, Denmark.
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25
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Xu S, Qiao W, Wang Z, Fu X, Liu Z, Shi S. Exploiting a heterologous construction of the 3-hydroxypropionic acid carbon fixation pathway with mesaconate as an indicator in Saccharomyces cerevisiae. BIORESOUR BIOPROCESS 2023; 10:33. [PMID: 38647598 PMCID: PMC10991142 DOI: 10.1186/s40643-023-00652-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/14/2023] [Indexed: 04/25/2024] Open
Abstract
The 3-Hydroxypropionic acid (3-HP) pathway is one of the six known natural carbon fixation pathways, in which the carbon species used is bicarbonate. It has been considered to be the most suitable pathway for aerobic CO2 fixation among the six natural carbon fixation pathways. Mesaconate is a high value-added derivative in the 3-HP pathway and can be used as a co-monomer to produce fire-retardant materials and hydrogels. In this study, we use mesaconate as a reporting compound to evaluate the construction and optimization of the sub-part of the 3-HP pathway in Saccharomyces cerevisiae. Combined with fine-tuning of the malonyl-CoA reductase (MCR-C and MCR-N) expression level and optimization of 3-Hydroxypropionyl-CoA synthase, the 3-HP sub-pathway was optimized using glucose or ethanol as the substrate, with the productions of mesaconate reaching 90.78 and 61.2 mg/L, respectively.
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Affiliation(s)
- Shijie Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Weibo Qiao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zuanwen Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoying Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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26
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Parera Olm I, Sousa DZ. Upgrading dilute ethanol to odd-chain carboxylic acids by a synthetic co-culture of Anaerotignum neopropionicum and Clostridium kluyveri. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:83. [PMID: 37194097 DOI: 10.1186/s13068-023-02336-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Dilute ethanol streams generated during fermentation of biomass or syngas can be used as feedstocks for the production of higher value products. In this study, we describe a novel synthetic microbial co-culture that can effectively upgrade dilute ethanol streams to odd-chain carboxylic acids (OCCAs), specifically valerate and heptanoate. The co-culture consists of two strict anaerobic microorganisms: Anaerotignum neopropionicum, a propionigenic bacterium that ferments ethanol, and Clostridium kluyveri, well-known for its chain-elongating metabolism. In this co-culture, A. neopropionicum grows on ethanol and CO2 producing propionate and acetate, which are then utilised by C. kluyveri for chain elongation with ethanol as the electron donor. RESULTS A co-culture of A. neopropionicum and C. kluyveri was established in serum bottles with 50 mM ethanol, leading to the production of valerate (5.4 ± 0.1 mM) as main product of ethanol-driven chain elongation. In a continuous bioreactor supplied with 3.1 g ethanol L-1 d-1, the co-culture exhibited high ethanol conversion (96.6%) and produced 25% (mol/mol) valerate, with a steady-state concentration of 8.5 mM and a rate of 5.7 mmol L-1 d-1. In addition, up to 6.5 mM heptanoate was produced at a rate of 2.9 mmol L-1 d-1. Batch experiments were also conducted to study the individual growth of the two strains on ethanol. A. neopropionicum showed the highest growth rate when cultured with 50 mM ethanol (μmax = 0.103 ± 0.003 h-1) and tolerated ethanol concentrations of up to 300 mM. Cultivation experiments with C. kluyveri showed that propionate and acetate were used simultaneously for chain elongation. However, growth on propionate alone (50 mM and 100 mM) led to a 1.8-fold reduction in growth rate compared to growth on acetate. Our results also revealed sub-optimal substrate use by C. kluyveri during odd-chain elongation, where excessive ethanol was oxidised to acetate. CONCLUSIONS This study highlights the potential of synthetic co-cultivation in chain elongation processes to target the production of OCCAs. Furthermore, our findings shed light on to the metabolism of odd-chain elongation by C. kluyveri.
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Affiliation(s)
- Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
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27
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Puiman L, Almeida Benalcázar E, Picioreanu C, Noorman HJ, Haringa C. Downscaling Industrial-Scale Syngas Fermentation to Simulate Frequent and Irregular Dissolved Gas Concentration Shocks. Bioengineering (Basel) 2023; 10:bioengineering10050518. [PMID: 37237589 DOI: 10.3390/bioengineering10050518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
In large-scale syngas fermentation, strong gradients in dissolved gas (CO, H2) concentrations are very likely to occur due to locally varying mass transfer and convection rates. Using Euler-Lagrangian CFD simulations, we analyzed these gradients in an industrial-scale external-loop gas-lift reactor (EL-GLR) for a wide range of biomass concentrations, considering CO inhibition for both CO and H2 uptake. Lifeline analyses showed that micro-organisms are likely to experience frequent (5 to 30 s) oscillations in dissolved gas concentrations with one order of magnitude. From the lifeline analyses, we developed a conceptual scale-down simulator (stirred-tank reactor with varying stirrer speed) to replicate industrial-scale environmental fluctuations at bench scale. The configuration of the scale-down simulator can be adjusted to match a broad range of environmental fluctuations. Our results suggest a preference for industrial operation at high biomass concentrations, as this would strongly reduce inhibitory effects, provide operational flexibility and enhance the product yield. The peaks in dissolved gas concentration were hypothesized to increase the syngas-to-ethanol yield due to the fast uptake mechanisms in C. autoethanogenum. The proposed scale-down simulator can be used to validate such results and to obtain data for parametrizing lumped kinetic metabolic models that describe such short-term responses.
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Affiliation(s)
- Lars Puiman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Eduardo Almeida Benalcázar
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Cristian Picioreanu
- Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Henk J Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
- Royal DSM, Alexander Fleminglaan 1, 2613 Delft, The Netherlands
| | - Cees Haringa
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
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Takemura K, Kato J, Kato S, Fujii T, Wada K, Iwasaki Y, Aoi Y, Matsushika A, Morita T, Murakami K, Nakashimada Y. Enhancing acetone production from H 2 and CO 2 using supplemental electron acceptors in an engineered Moorella thermoacetica. J Biosci Bioeng 2023:S1389-1723(23)00112-3. [PMID: 37100649 DOI: 10.1016/j.jbiosc.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 04/02/2023] [Indexed: 04/28/2023]
Abstract
Acetogens grow autotrophically and use hydrogen (H2) as the energy source to fix carbon dioxide (CO2). This feature can be applied to gas fermentation, contributing to a circular economy. A challenge is the gain of cellular energy from H2 oxidation, which is substantially low, especially when acetate formation coupled with ATP production is diverted to other chemicals in engineered strains. Indeed, an engineered strain of the thermophilic acetogen Moorella thermoacetica that produces acetone lost autotrophic growth on H2 and CO2. We aimed to recover autotrophic growth and enhance acetone production, in which ATP production was assumed to be a limiting factor, by supplementing with electron acceptors. Among the four selected electron acceptors, thiosulfate and dimethyl sulfoxide (DMSO) enhanced both bacterial growth and acetone titers. DMSO was the most effective and was further analyzed. We showed that DMSO supplementation enhanced intracellular ATP levels, leading to increased acetone production. Although DMSO is an organic compound, it functions as an electron acceptor, not a carbon source. Thus, supplying electron acceptors is a potential strategy to complement the low ATP production caused by metabolic engineering and to improve chemical production from H2 and CO2.
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Affiliation(s)
- Kaisei Takemura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Junya Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Tatsuya Fujii
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Keisuke Wada
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yuki Iwasaki
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Yoshiteru Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akinori Matsushika
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan; National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Tomotake Morita
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Katsuji Murakami
- National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan.
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Lo J, Wu C, Humphreys JR, Yang B, Jiang Z, Wang X, Maness P, Tsesmetzis N, Xiong W. Thermodynamic and Kinetic Modeling Directs Pathway Optimization for Isopropanol Production in a Gas-Fermenting Bacterium. mSystems 2023; 8:e0127422. [PMID: 36971551 PMCID: PMC10134883 DOI: 10.1128/msystems.01274-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Highly efficient bioproduction from gaseous substrates (e.g., hydrogen and carbon oxides) will require systematic optimization of the host microbes. To date, the rational redesign of gas-fermenting bacteria is still in its infancy, due in part to the lack of quantitative and precise metabolic knowledge that can direct strain engineering.
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30
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Philp J. Bioeconomy and net-zero carbon: lessons from Trends in Biotechnology, volume 1, issue 1. Trends Biotechnol 2023; 41:307-322. [PMID: 36272819 DOI: 10.1016/j.tibtech.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Many biotechnology applications tend to be for low production volumes and relatively high-value products such as insulin and vaccines. More difficult to perfect at scale are bioprocesses for high-volume products with lower value, especially if the target product is a reduced chemical such as a solvent or a plastic. Historically, industrial microbiology succeeded under special circumstances when fossil feedstocks were either unavailable or expensive. Inevitably, as these circumstances relaxed, bioprocesses struggled to compete with petrochemistry. Why try to compete? Fossil resources will be phased out in the coming decades in the struggle with climate change. To reach net-zero carbon by 2050 will require all sectors to transition, not only energy and transportation. This may herald a new opportunity for industrial bioprocesses with much better tools.
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Affiliation(s)
- Jim Philp
- Organization for Economic Cooperation and Development (OECD), Paris, France.
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31
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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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32
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Noroozi K, Jarboe LR. Strategic nutrient sourcing for biomanufacturing intensification. J Ind Microbiol Biotechnol 2023; 50:kuad011. [PMID: 37245065 PMCID: PMC10549214 DOI: 10.1093/jimb/kuad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
The successful design of economically viable bioprocesses can help to abate global dependence on petroleum, increase supply chain resilience, and add value to agriculture. Specifically, bioprocessing provides the opportunity to replace petrochemical production methods with biological methods and to develop novel bioproducts. Even though a vast range of chemicals can be biomanufactured, the constraints on economic viability, especially while competing with petrochemicals, are severe. There have been extensive gains in our ability to engineer microbes for improved production metrics and utilization of target carbon sources. The impact of growth medium composition on process cost and organism performance receives less attention in the literature than organism engineering efforts, with media optimization often being performed in proprietary settings. The widespread use of corn steep liquor as a nutrient source demonstrates the viability and importance of "waste" streams in biomanufacturing. There are other promising waste streams that can be used to increase the sustainability of biomanufacturing, such as the use of urea instead of fossil fuel-intensive ammonia and the use of struvite instead of contributing to the depletion of phosphate reserves. In this review, we discuss several process-specific optimizations of micronutrients that increased product titers by twofold or more. This practice of deliberate and thoughtful sourcing and adjustment of nutrients can substantially impact process metrics. Yet the mechanisms are rarely explored, making it difficult to generalize the results to other processes. In this review, we will discuss examples of nutrient sourcing and adjustment as a means of process improvement. ONE-SENTENCE SUMMARY The potential impact of nutrient adjustments on bioprocess performance, economics, and waste valorization is undervalued and largely undercharacterized.
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Affiliation(s)
- Kimia Noroozi
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
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Moreira JPC, Heap JT, Alves JI, Domingues L. Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:24. [PMID: 36788587 PMCID: PMC9930230 DOI: 10.1186/s13068-023-02259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Developing new bioprocesses to produce chemicals and fuels with reduced production costs will greatly facilitate the replacement of fossil-based raw materials. In most fermentation bioprocesses, the feedstock usually represents the highest cost, which becomes the target for cost reduction. Additionally, the biorefinery concept advocates revenue growth from the production of several compounds using the same feedstock. Taken together, the production of bio commodities from low-cost gas streams containing CO, CO2, and H2, obtained from the gasification of any carbon-containing waste streams or off-gases from heavy industry (steel mills, processing plants, or refineries), embodies an opportunity for affordable and renewable chemical production. To achieve this, by studying non-model autotrophic acetogens, current limitations concerning low growth rates, toxicity by gas streams, and low productivity may be overcome. The Acetobacterium wieringae strain JM is a novel autotrophic acetogen that is capable of producing acetate and ethanol. It exhibits faster growth rates on various gaseous compounds, including carbon monoxide, compared to other Acetobacterium species, making it potentially useful for industrial applications. The species A. wieringae has not been genetically modified, therefore developing a genetic engineering method is important for expanding its product portfolio from gas fermentation and overall improving the characteristics of this acetogen for industrial demands. RESULTS This work reports the development and optimization of an electrotransformation protocol for A. wieringae strain JM, which can also be used in A. wieringae DSM 1911, and A. woodii DSM 1030. We also show the functionality of the thiamphenicol resistance marker, catP, and the functionality of the origins of replication pBP1, pCB102, pCD6, and pIM13 in all tested Acetobacterium strains, with transformation efficiencies of up to 2.0 × 103 CFU/μgDNA. Key factors affecting electrotransformation efficiency include OD600 of cell harvesting, pH of resuspension buffer, the field strength of the electric pulse, and plasmid amount. Using this method, the acetone production operon from Clostridium acetobutylicum was efficiently introduced in all tested Acetobacterium spp., leading to non-native biochemical acetone production via plasmid-based expression. CONCLUSIONS A. wieringae can be electrotransformed at high efficiency using different plasmids with different replication origins. The electrotransformation procedure and tools reported here unlock the genetic and metabolic manipulation of the biotechnologically relevant A. wieringae strains. For the first time, non-native acetone production is shown in A. wieringae.
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Affiliation(s)
- João P. C. Moreira
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - John T. Heap
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
| | - Joana I. Alves
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal. .,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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Danchin A, Huang JD. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience. Environ Microbiol 2023; 25:64-78. [PMID: 36045561 DOI: 10.1111/1462-2920.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Jian Dong Huang
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
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Velvizhi G, Nair R, Goswami C, Arumugam SK, Shetti NP, Aminabhavi TM. Carbon credit reduction: A techno-economic analysis of "drop-in" fuel production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120507. [PMID: 36341830 DOI: 10.1016/j.envpol.2022.120507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/07/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The current study elucidates the fundamentals of technical, financial, and environmental viability of the processes used for sustainable "drop-in" fuel generation. At present, the price of producing "drop-in" fuels is around two times as costly (5-6 USD/gallon) as the cost of fossil fuels (3 USD/gallon), especially when using second-generation feedstocks. Hence, this necessitates a comprehensive techno-economic understanding of the current technologies with respect to "drop-in"-fuel. This entitles technical-economic viability, and environmental sustainability to make the processes involved commercially viable. In this context, the present review addresses unique contrasts among the various processes involved in "drop-in" fuel production. Furthermore, principles and process flow of techno-economic analysis as well as environmental implications in terms of reduced carbon footprint and carbon credit are elucidated to discuss fundamentals of techno-economic analysis in terms of capital and operational expenditure, revenue, simulation, cash flow analysis, mass and energy balances with respect to evidence-based practices. Case specific techno-economic studies with current developments in this field of research with emphasis on software tools viz., Aspen Plus, Aspen HYSIS, Aspen Plus Economic Analyser (APEC) Aspen Icarus Process Evaluator (AIPE) are also highlighted. The study also emphasis on the carbon foot print of biofuels and its carbon credits (Carbon Offset Credits (COCs) and Carbon Reduction Credits (CRCs)) by leveraging a deep technical and robust business-oriented insights about the techno-economic analysis (TEA) exclusively for the biofuel production.
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Affiliation(s)
- G Velvizhi
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | - Rishika Nair
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | - Chandamita Goswami
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, India
| | | | - Nagaraj P Shetti
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, India; University Center for Research & Development (UCRD), Chandigarh University, Mohali, Punjab, 140413, India
| | - Tejraj M Aminabhavi
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, India; University Center for Research & Development (UCRD), Chandigarh University, Mohali, Punjab, 140413, India.
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36
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Rostain W, Zaplana T, Boutard M, Baum C, Tabuteau S, Sanitha M, Ramya M, Guss A, Ettwiller L, Tolonen AC. Tuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRi. ACS Synth Biol 2022; 11:4077-4088. [PMID: 36427328 PMCID: PMC9765743 DOI: 10.1021/acssynbio.2c00385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/27/2022]
Abstract
Control of gene expression is fundamental to cell engineering. Here we demonstrate a set of approaches to tune gene expression in Clostridia using the model Clostridium phytofermentans. Initially, we develop a simple benchtop electroporation method that we use to identify a set of replicating plasmids and resistance markers that can be cotransformed into C. phytofermentans. We define a series of promoters spanning a >100-fold expression range by testing a promoter library driving the expression of a luminescent reporter. By insertion of tet operator sites upstream of the reporter, its expression can be quantitatively altered using the Tet repressor and anhydrotetracycline (aTc). We integrate these methods into an aTc-regulated dCas12a system with which we show in vivo CRISPRi-mediated repression of reporter and fermentation genes in C. phytofermentans. Together, these approaches advance genetic transformation and experimental control of gene expression in Clostridia.
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Affiliation(s)
- William Rostain
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
| | - Tom Zaplana
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
| | - Magali Boutard
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
| | - Chloé Baum
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
- New
England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Sibylle Tabuteau
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
| | - Mary Sanitha
- Molecular
Genetics Laboratory, Department of Genetic Engineering, College of
Engineering and Technology, SRM Institute
of Science and Technology, SRM Nagar, Kattankulathur-603 203, TN, India
| | - Mohandass Ramya
- Molecular
Genetics Laboratory, Department of Genetic Engineering, College of
Engineering and Technology, SRM Institute
of Science and Technology, SRM Nagar, Kattankulathur-603 203, TN, India
| | - Adam Guss
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038, United States
| | - Laurence Ettwiller
- New
England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Andrew C. Tolonen
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 91057 Évry, France
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Mengers HG, Guntermann N, Graf von Westarp W, Jupke A, Klankermayer J, Blank LM, Leitner W, Rother D. Three Sides of the Same Coin: Combining Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hendrik G. Mengers
- RWTH Aachen University Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt Worringerweg 1 52074 Aachen Germany
| | - Nils Guntermann
- RWTH Aachen University Institute of Macromolecular Chemistry – ITMC Worringerweg 2 52074 Aachen Germany
| | - William Graf von Westarp
- RWTH Aachen University Fluid Process Engineering – AVT.FVT Forckenbeckstraße 51 52074 Aachen Germany
| | - Andreas Jupke
- RWTH Aachen University Fluid Process Engineering – AVT.FVT Forckenbeckstraße 51 52074 Aachen Germany
| | - Jürgen Klankermayer
- RWTH Aachen University Institute of Macromolecular Chemistry – ITMC Worringerweg 2 52074 Aachen Germany
| | - Lars M. Blank
- RWTH Aachen University Institute of Applied Microbiology – iAMB, Aachen Biology and Biotechnology – ABBt Worringerweg 1 52074 Aachen Germany
| | - Walter Leitner
- RWTH Aachen University Institute of Macromolecular Chemistry – ITMC Worringerweg 2 52074 Aachen Germany
- Max Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mülheim a. d. Ruhr Germany
| | - Dörte Rother
- Forschungzentrum Jülich GmbH Institute of Bio- and Geosciences: Biotechnology Wilhelm-Johnen-Straße 52425 Jülich Germany
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Xie D. Continuous biomanufacturing with microbes - upstream progresses and challenges. Curr Opin Biotechnol 2022; 78:102793. [PMID: 36088736 DOI: 10.1016/j.copbio.2022.102793] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.
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Affiliation(s)
- Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States.
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Singh HB, Kang MK, Kwon M, Kim SW. Developing methylotrophic microbial platforms for a methanol-based bioindustry. Front Bioeng Biotechnol 2022; 10:1050740. [PMID: 36507257 PMCID: PMC9727194 DOI: 10.3389/fbioe.2022.1050740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Methanol, a relatively cheap and renewable single-carbon feedstock, has gained considerable attention as a substrate for the bio-production of commodity chemicals. Conventionally produced from syngas, along with emerging possibilities of generation from methane and CO2, this C1 substrate can serve as a pool for sequestering greenhouse gases while supporting a sustainable bio-economy. Methylotrophic organisms, with the inherent ability to use methanol as the sole carbon and energy source, are competent candidates as platform organisms. Accordingly, methanol bioconversion pathways have been an attractive target for biotechnological and bioengineering interventions in developing microbial cell factories. This review summarizes the recent advances in methanol-based production of various bulk and value-added chemicals exploiting the native and synthetic methylotrophic organisms. Finally, the current challenges and prospects of streamlining these methylotrophic platforms are discussed.
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Affiliation(s)
- Hawaibam Birla Singh
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Min-Kyoung Kang
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Moonhyuk Kwon
- Division of Life Science, ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
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Kim S, Jang YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO 2. Microb Cell Fact 2022; 21:231. [PMCID: PMC9636797 DOI: 10.1186/s12934-022-01962-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO2) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO2 is still too low for commercialization. Results Here, we engineer the carbon fixation metabolism to improve CO2 utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO2—fixing metabolism and PHB production were investigated. Conclusions The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01962-7.
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Affiliation(s)
- Soyoung Kim
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Yong Jae Jang
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Sun-Mi Lee
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Kyoung Heon Kim
- grid.222754.40000 0001 0840 2678Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ja Kyong Ko
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
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41
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SimDFBA: A framework for bioprocess simulation and development. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.108073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Cui X, Ma Q, Duan M, Xu H, Liang M, Wei Y. Effects of fishmeal replacement by Clostridium autoethanogenum protein on the growth, digestibility, serum free amino acid and gene expression related to protein metabolism of obscure pufferfish (Takifugu obscurus). Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Perret L, Lacerda de Oliveira Campos B, Herrera Delgado K, Zevaco TA, Neumann A, Sauer J. CO
x
Fixation to Elementary Building Blocks: Anaerobic Syngas Fermentation vs. Chemical Catalysis. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lukas Perret
- Karlsruhe Institute of Technology Institute of Catalysis Research and Technology 76344 Eggenstein-Leopoldshafen Germany
| | | | - Karla Herrera Delgado
- Karlsruhe Institute of Technology Institute of Catalysis Research and Technology 76344 Eggenstein-Leopoldshafen Germany
| | - Thomas A. Zevaco
- Karlsruhe Institute of Technology Institute of Catalysis Research and Technology 76344 Eggenstein-Leopoldshafen Germany
| | - Anke Neumann
- Karlsruhe Institute of Technology Institute of Process Engineering in Life Sciences 2 – Technical Biology 76131 Karlsruhe Germany
| | - Jörg Sauer
- Karlsruhe Institute of Technology Institute of Catalysis Research and Technology 76344 Eggenstein-Leopoldshafen Germany
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44
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O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas. Nat Catal 2022. [DOI: 10.1038/s41929-022-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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Carruthers DN, Lee TS. Translating advances in microbial bioproduction to sustainable biotechnology. Front Bioeng Biotechnol 2022; 10:968437. [PMID: 36082166 PMCID: PMC9445250 DOI: 10.3389/fbioe.2022.968437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Advances in synthetic biology have radically changed our ability to rewire microorganisms and significantly improved the scalable production of a vast array of drop-in biopolymers and biofuels. The success of a drop-in bioproduct is contingent on market competition with petrochemical analogues and weighted upon relative economic and environmental metrics. While the quantification of comparative trade-offs is critical for accurate process-level decision making, the translation of industrial ecology to synthetic biology is often ambiguous and assessment accuracy has proven challenging. In this review, we explore strategies for evaluating industrial biotechnology through life cycle and techno-economic assessment, then contextualize how recent developments in synthetic biology have improved process viability by expanding feedstock availability and the productivity of microbes. By juxtaposing biological and industrial constraints, we highlight major obstacles between the disparate disciplines that hinder accurate process evaluation. The convergence of these disciplines is crucial in shifting towards carbon neutrality and a circular bioeconomy.
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Affiliation(s)
- David N. Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- *Correspondence: Taek Soon Lee,
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47
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A comparative evaluation of machine learning algorithms for predicting syngas fermentation outcomes. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hengsbach JN, Sabel-Becker B, Ulber R, Holtmann D. Microbial electrosynthesis of methane and acetate—comparison of pure and mixed cultures. Appl Microbiol Biotechnol 2022; 106:4427-4443. [PMID: 35763070 PMCID: PMC9259517 DOI: 10.1007/s00253-022-12031-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
Abstract The electrochemical process of microbial electrosynthesis (MES) is used to drive the metabolism of electroactive microorganisms for the production of valuable chemicals and fuels. MES combines the advantages of electrochemistry, engineering, and microbiology and offers alternative production processes based on renewable raw materials and regenerative energies. In addition to the reactor concept and electrode design, the biocatalysts used have a significant influence on the performance of MES. Thus, pure and mixed cultures can be used as biocatalysts. By using mixed cultures, interactions between organisms, such as the direct interspecies electron transfer (DIET) or syntrophic interactions, influence the performance in terms of productivity and the product range of MES. This review focuses on the comparison of pure and mixed cultures in microbial electrosynthesis. The performance indicators, such as productivities and coulombic efficiencies (CEs), for both procedural methods are discussed. Typical products in MES are methane and acetate, therefore these processes are the focus of this review. In general, most studies used mixed cultures as biocatalyst, as more advanced performance of mixed cultures has been seen for both products. When comparing pure and mixed cultures in equivalent experimental setups a 3-fold higher methane and a nearly 2-fold higher acetate production rate can be achieved in mixed cultures. However, studies of pure culture MES for methane production have shown some improvement through reactor optimization and operational mode reaching similar performance indicators as mixed culture MES. Overall, the review gives an overview of the advantages and disadvantages of using pure or mixed cultures in MES. Key points • Undefined mixed cultures dominate as inoculums for the MES of methane and acetate, which comprise a high potential of improvement • Under similar conditions, mixed cultures outperform pure cultures in MES • Understanding the role of single species in mixed culture MES is essential for future industrial applications
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Affiliation(s)
- Jan-Niklas Hengsbach
- Department of Mechanical and Process Engineering, Institute of Bioprocess Engineering, Technical University Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Björn Sabel-Becker
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, Technische Hochschule Mittelhessen, 35390, Giessen, Germany
| | - Roland Ulber
- Department of Mechanical and Process Engineering, Institute of Bioprocess Engineering, Technical University Kaiserslautern, 67663, Kaiserslautern, Germany.
| | - Dirk Holtmann
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, Technische Hochschule Mittelhessen, 35390, Giessen, Germany
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Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation. Microbiol Spectr 2022; 10:e0101922. [PMID: 35735976 PMCID: PMC9431212 DOI: 10.1128/spectrum.01019-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus Clostridium (C. autoethanogenum, C. ljungdahlii, C. carboxidivorans, C. drakei, C. scatologenes, C. coskatii, C. ragsdalei, C. sp. AWRP) to systematically identify their intriguingly diversified hydrogenases’ repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits’ characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases. IMPORTANCE Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus Clostridium are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases’ functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases’ level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.
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Onyeaka H, Ekwebelem OC. A review of recent advances in engineering bacteria for enhanced CO 2 capture and utilization. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2022; 20:4635-4648. [PMID: 35755182 PMCID: PMC9207427 DOI: 10.1007/s13762-022-04303-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Carbon dioxide (CO2) is emitted into the atmosphere due to some anthropogenic activities, such as the combustion of fossil fuels and industrial output. As a result, fears about catastrophic global warming and climate change have intensified. In the face of these challenges, conventional CO2 capture technologies are typically ineffective, dangerous, and contribute to secondary pollution in the environment. Biological systems for CO2 conversion, on the other hand, provide a potential path forward owing to its high application selectivity and adaptability. Moreover, many bacteria can use CO2 as their only source of carbon and turn it into value-added products. The purpose of this review is to discuss recent significant breakthroughs in engineering bacteria to utilize CO2 and other one-carbon compounds as substrate. In the same token, the paper also summarizes and presents aspects such as microbial CO2 fixation pathways, engineered bacteria involved in CO2 fixation, up-to-date genetic and metabolic engineering approaches for CO2 fixation, and promising research directions for the production of value-added products from CO2. This review's findings imply that using biological systems like modified bacteria to manage CO2 has the added benefit of generating useful industrial byproducts like biofuels, pharmaceutical compounds, and bioplastics. The major downside, from an economic standpoint, thus far has been related to methods of cultivation. However, thanks to genetic engineering approaches, this can be addressed by large production yields. As a result, this review aids in the knowledge of various biological systems that can be used to construct a long-term CO2 mitigation technology at an industrial scale, in this instance bacteria-based CO2capture/utilization technology.
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Affiliation(s)
- H. Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - O. C. Ekwebelem
- Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001 Nigeria
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