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Feliu-Paradeda L, Puig S, Bañeras L. Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans. Sci Rep 2023; 13:20073. [PMID: 37973932 PMCID: PMC10654501 DOI: 10.1038/s41598-023-47007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.
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Affiliation(s)
- Laura Feliu-Paradeda
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Carrer Maria Aurèlia Capmany 40, 17003, Girona, Spain
| | - Sebastià Puig
- LEQUiA, Institute of the Environment, University of Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Lluis Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Carrer Maria Aurèlia Capmany 40, 17003, Girona, Spain.
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2
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Bäumler M, Burgmaier V, Herrmann F, Mentges J, Schneider M, Ehrenreich A, Liebl W, Weuster-Botz D. Continuous Production of Ethanol, 1-Butanol and 1-Hexanol from CO with a Synthetic Co-Culture of Clostridia Applying a Cascade of Stirred-Tank Bioreactors. Microorganisms 2023; 11:microorganisms11041003. [PMID: 37110426 PMCID: PMC10144111 DOI: 10.3390/microorganisms11041003] [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: 03/14/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Syngas fermentation with clostridial co-cultures is promising for the conversion of CO to alcohols. A CO sensitivity study with Clostridium kluyveri monocultures in batch operated stirred-tank bioreactors revealed total growth inhibition of C. kluyveri already at 100 mbar CO, but stable biomass concentrations and ongoing chain elongation at 800 mbar CO. On/off-gassing with CO indicated a reversible inhibition of C. kluyveri. A continuous supply of sulfide led to increased autotrophic growth and ethanol formation by Clostridium carboxidivorans even at unfavorable low CO concentrations. Based on these results, a continuously operated cascade of two stirred-tank reactors was established with a synthetic co-culture of both Clostridia. An amount of 100 mbar CO and additional sulfide supply enabled growth and chain elongation in the first bioreactor, whereas 800 mbar CO resulted in an efficient reduction of organic acids and de-novo synthesis of C2-C6 alcohols in the second reactor. High alcohol/acid ratios of 4.5-9.1 (w/w) were achieved in the steady state of the cascade process, and the space-time yields of the alcohols produced were improved by factors of 1.9-5.3 compared to a batch process. Further improvement of continuous production of medium chain alcohols from CO may be possible by applying less CO-sensitive chain-elongating bacteria in co-cultures.
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Affiliation(s)
- Miriam Bäumler
- Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Veronika Burgmaier
- Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Fabian Herrmann
- Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Julian Mentges
- Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
| | - Martina Schneider
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Armin Ehrenreich
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Dirk Weuster-Botz
- Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, 85748 Garching, Germany
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3
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Mittermeier F, Bäumler M, Arulrajah P, García Lima JDJ, Hauke S, Stock A, Weuster‐Botz D. Artificial microbial consortia for bioproduction processes. Eng Life Sci 2023; 23:e2100152. [PMID: 36619879 PMCID: PMC9815086 DOI: 10.1002/elsc.202100152] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO2 through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.
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Affiliation(s)
- Fabian Mittermeier
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Miriam Bäumler
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Prasika Arulrajah
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | | | - Sebastian Hauke
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Anna Stock
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Dirk Weuster‐Botz
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
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4
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Bäumler M, Herrmann F, Burgmaier V, Mentges J, Schneider M, Ehrenreich A, Liebl W, Weuster-Botz D. Autotrophic alcohol production with a synthetic co‐culture of
Clostridium carboxidivorans
and
Clostridium kluyveri. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202255155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M. Bäumler
- Technical University of Munich TUM School of Engineering and Design, Institute of Biochemical Engineering Boltzmannstr. 15 85748 Garching Germany
| | - F. Herrmann
- Technical University of Munich TUM School of Engineering and Design, Institute of Biochemical Engineering Boltzmannstr. 15 85748 Garching Germany
| | - V. Burgmaier
- Technical University of Munich TUM School of Engineering and Design, Institute of Biochemical Engineering Boltzmannstr. 15 85748 Garching Germany
| | - J. Mentges
- Technical University of Munich TUM School of Engineering and Design, Institute of Biochemical Engineering Boltzmannstr. 15 85748 Garching Germany
| | - M. Schneider
- Technical University of Munich TUM School of Life Sciences, Chair of Microbiology Emil-Ramann-Str. 4 85354 Freising Germany
| | - A. Ehrenreich
- Technical University of Munich TUM School of Life Sciences, Chair of Microbiology Emil-Ramann-Str. 4 85354 Freising Germany
| | - W. Liebl
- Technical University of Munich TUM School of Life Sciences, Chair of Microbiology Emil-Ramann-Str. 4 85354 Freising Germany
| | - D. Weuster-Botz
- Technical University of Munich TUM School of Engineering and Design, Institute of Biochemical Engineering Boltzmannstr. 15 85748 Garching Germany
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Herzog J, Mook A, Guhl L, Bäumler M, Beck MH, Weuster‐Botz D, Bengelsdorf FR, Zeng A. Novel synthetic co-culture of Acetobacterium woodii and Clostridium drakei using CO 2 and in situ generated H 2 for the production of caproic acid via lactic acid. Eng Life Sci 2022; 23:e2100169. [PMID: 36619880 PMCID: PMC9815077 DOI: 10.1002/elsc.202100169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 01/11/2023] Open
Abstract
Acetobacterium woodii is known to produce mainly acetate from CO2 and H2, but the production of higher value chemicals is desired for the bioeconomy. Using chain-elongating bacteria, synthetic co-cultures have the potential to produce longer-chained products such as caproic acid. In this study, we present first results for a successful autotrophic co-cultivation of A. woodii mutants and a Clostridium drakei wild-type strain in a stirred-tank bioreactor for the production of caproic acid from CO2 and H2 via the intermediate lactic acid. For autotrophic lactate production, a recombinant A. woodii strain with a deleted Lct-dehydrogenase complex, which is encoded by the lctBCD genes, and an inserted D-lactate dehydrogenase (LdhD) originating from Leuconostoc mesenteroides, was used. Hydrogen for the process was supplied using an All-in-One electrode for in situ water electrolysis. Lactate concentrations as high as 0.5 g L-1 were achieved with the AiO-electrode, whereas 8.1 g L-1 lactate were produced with direct H2 sparging in a stirred-tank bioreactor. Hydrogen limitation was identified in the AiO process. However, with cathode surface area enlargement or numbering-up of the electrode and on-demand hydrogen generation, this process has great potential for a true carbon-negative production of value chemicals from CO2.
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Affiliation(s)
- Jan Herzog
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Alexander Mook
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
| | - Lotta Guhl
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Miriam Bäumler
- Department of Energy and Process EngineeringChair of Biochemical EngineeringTechnical University of MunichTUM School of Engineering and DesignGarchingGermany
| | - Matthias H. Beck
- Institute of Microbiology and BiotechnologyUlm UniversityUlmGermany
| | - Dirk Weuster‐Botz
- Department of Energy and Process EngineeringChair of Biochemical EngineeringTechnical University of MunichTUM School of Engineering and DesignGarchingGermany
| | | | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
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Bäumler M, Schneider M, Ehrenreich A, Liebl W, Weuster-Botz D. Synthetic co-culture of autotrophic Clostridium carboxidivorans and chain elongating Clostridium kluyveri monitored by flow cytometry. Microb Biotechnol 2021; 15:1471-1485. [PMID: 34669248 PMCID: PMC9049614 DOI: 10.1111/1751-7915.13941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 01/21/2023] Open
Abstract
Syngas fermentation with acetogens is known to produce mainly acetate and ethanol efficiently. Co-cultures with chain elongating bacteria making use of these products are a promising approach to produce longer-chain alcohols. Synthetic co-cultures with identical initial cell concentrations of Clostridium carboxidivorans and Clostridium kluyveri were studied in batch-operated stirred-tank bioreactors with continuous CO/CO2 -gassing and monitoring of the cell counts of both clostridia by flow cytometry after fluorescence in situ hybridization (FISH-FC). At 800 mbar CO, chain elongation activity was observed at pH 6.0, although growth of C. kluyveri was restricted. Organic acids produced by C. kluyveri were reduced by C. carboxidivorans to the corresponding alcohols butanol and hexanol. This resulted in a threefold increase in final butanol concentration and enabled hexanol production compared with a mono-culture of C. carboxidivorans. At 100 mbar CO, growth of C. kluyveri was improved; however, the capacity of C. carboxidivorans to form alcohols was reduced. Because of the accumulation of organic acids, a constant decay of C. carboxidivorans was observed. The measurement of individual cell concentrations in co-culture established in this study may serve as an effective tool for knowledge-based identification of optimum process conditions for enhanced formation of longer-chain alcohols by clostridial co-cultures.
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Affiliation(s)
- Miriam Bäumler
- Institute of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany
| | - Martina Schneider
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 4, Freising, Germany
| | - Armin Ehrenreich
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 4, Freising, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 4, Freising, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany
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