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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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2
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Heffernan J, Garcia Gonzalez RA, Mahamkali V, McCubbin T, Daygon D, Liu L, Palfreyman R, Harris A, Koepke M, Valgepea K, Nielsen LK, Marcellin E. Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO 2 and H 2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microb Biotechnol 2024; 17:e14452. [PMID: 38568755 PMCID: PMC10990044 DOI: 10.1111/1751-7915.14452] [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: 08/17/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Gas fermentation of CO2 and H2 is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO to ethanol and presents an opportunity for CO2-to-ethanol processes. As we have previously characterized its CO2/H2 chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO2/H2. Seven ALE lineages were generated, all with improved specific growth rates. ALE conducted in the presence of 2% CO along with CO2/H2 generated Evolved lineage D, which showed the highest ethanol titres amongst all the ALE lineages during the fermentation of CO2/H2. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Multi-omics analyses at steady state revealed that Evolved D has widespread proteome and intracellular metabolome changes. However, the uptake and production rates and titres remain unaltered until investigating their maximum dilution rate. Yet, we provide numerous insights into CO2/H2 metabolism via these multi-omics data and link these results to mutations, suggesting novel targets for metabolic engineering in this bacterium.
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Affiliation(s)
- James Heffernan
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - R. Axayactl Garcia Gonzalez
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | - Tim McCubbin
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Dara Daygon
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lian Liu
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Robin Palfreyman
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of TechnologyUniversity of TartuTartuEstonia
| | - Lars Keld Nielsen
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Esteban Marcellin
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
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3
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Barla RJ, Raghuvanshi S, Gupta S. Reforming CO 2 bio-mitigation utilizing Bacillus cereus from hypersaline realms in pilot-scale bubble column bioreactor. Sci Rep 2024; 14:6354. [PMID: 38491100 PMCID: PMC10943127 DOI: 10.1038/s41598-024-56965-8] [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: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
The bubble column reactor of 10 and 20 L capacity was designed to bio-mitigate 10% CO2 (g) with 90% air utilizing thermophilic bacteria (Bacillus cereus SSLMC2). The maximum biomass yield during the growth phase was obtained as 9.14 and 10.78 g L-1 for 10 and 20 L capacity, respectively. The maximum removal efficiency for CO2 (g) was obtained as 56% and 85% for the 10 and 20 L reactors, respectively. The FT-IR and GC-MS examination of the extracellular and intracellular samples identified value-added products such as carboxylic acid, fatty alcohols, and hydrocarbons produced during the process. The total carbon balance for CO2 utilization in different forms confirmed that B. cereus SSLMC2 utilized 1646.54 g C in 10 L and 1587 g of C in 20 L reactor out of 1696.13 g of total carbon feed. The techno-economic assessment established that the capital investment required was $286.21 and $289.08 per reactor run of 11 days and $0.167 and $0.187 per gram of carbon treated for 10 and 20 L reactors, respectively. The possible mechanism pathways for bio-mitigating CO2 (g) by B. cereus SSLMC2 were also presented utilizing the energy reactions. Hence, the work presents the novelty of utilizing thermophilic bacteria and a bubble column bioreactor for CO2 (g) bio-mitigation.
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Affiliation(s)
- Rachael J Barla
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India
| | - Smita Raghuvanshi
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India.
| | - Suresh Gupta
- Faculty Division-1, Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), BITS PILANI, Pilani, 333031, Rajasthan, India
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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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Lv X, Yu W, Zhang C, Ning P, Li J, Liu Y, Du G, Liu L. C1-based biomanufacturing: Advances, challenges and perspectives. BIORESOURCE TECHNOLOGY 2023; 367:128259. [PMID: 36347475 DOI: 10.1016/j.biortech.2022.128259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Baima Future Foods Research Institute, Nanjing 211225, China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chenyang Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Peng Ning
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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Conversion of Syngas from Entrained Flow Gasification of Biogenic Residues with Clostridium carboxidivorans and Clostridium autoethanogenum. FERMENTATION 2022. [DOI: 10.3390/fermentation8090465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Synthesis gas fermentation is a microbial process, which uses anaerobic bacteria to convert CO-rich gases to organic acids and alcohols and thus presents a promising technology for the sustainable production of fuels and platform chemicals from renewable sources. Clostridium carboxidivorans and Clostridium autoethanogenum are two acetogenic bacteria, which have shown their high potential for these processes by their high tolerance toward CO and in the production of industrially relevant products such as ethanol, 1-butanol, 1-hexanol, and 2,3-butanediol. A promising approach is the coupling of gasification of biogenic residues with a syngas fermentation process. This study investigated batch processes with C. carboxidivorans and C. autoethanogenum in fully controlled stirred-tank bioreactors and continuous gassing with biogenic syngas produced by an autothermal entrained flow gasifier on a pilot scale >1200 °C. They were then compared to the results of artificial gas mixtures of pure gases. Because the biogenic syngas contained 2459 ppm O2 from the bottling process after gasification of torrefied wood and subsequent syngas cleaning for reducing CH4, NH3, H2S, NOX, and HCN concentrations, the oxygen in the syngas was reduced to 259 ppm O2 with a Pd catalyst before entering the bioreactor. The batch process performance of C. carboxidivorans in a stirred-tank bioreactor with continuous gassing of purified biogenic syngas was identical to an artificial syngas mixture of the pure gases CO, CO2, H2, and N2 within the estimation error. The alcohol production by C. autoethanogenum was even improved with the purified biogenic syngas compared to reference batch processes with the corresponding artificial syngas mixture. Both acetogens have proven their potential for successful fermentation processes with biogenic syngas, but full carbon conversion to ethanol is challenging with the investigated biogenic syngas.
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Lo J, Humphreys JR, Magnusson L, Wachter B, Urban C, Hebdon SD, Xiong W, Chou KJ, Ching Maness P. Acetogenic production of 3-Hydroxybutyrate using a native 3-Hydroxybutyryl-CoA Dehydrogenase. Front Microbiol 2022; 13:948369. [PMID: 36003933 PMCID: PMC9393629 DOI: 10.3389/fmicb.2022.948369] [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: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
3-Hydroxybutyrate (3HB) is a product of interest as it is a precursor to the commercially produced bioplastic polyhydroxybutyrate. It can also serve as a platform for fine chemicals, medicines, and biofuels, making it a value-added product and feedstock. Acetogens non-photosynthetically fix CO2 into acetyl-CoA and have been previously engineered to convert acetyl-CoA into 3HB. However, as acetogen metabolism is poorly understood, those engineering efforts have had varying levels of success. 3HB, using acetyl-CoA as a precursor, can be synthesized by a variety of different pathways. Here we systematically compare various pathways to produce 3HB in acetogens and discover a native (S)-3-hydroxybutyryl-CoA dehydrogenase, hbd2, responsible for endogenous 3HB production. In conjunction with the heterologous thiolase atoB and CoA transferase ctfAB, hbd2 overexpression improves yields of 3HB on both sugar and syngas (CO/H2/CO2), outperforming the other tested pathways. These results uncovered a previously unknown 3HB production pathway, inform data from prior metabolic engineering efforts, and have implications for future physiological and biotechnological anaerobic research.
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He Y, Kennes C, Lens PNL. Enhanced solventogenesis in syngas bioconversion: Role of process parameters and thermodynamics. CHEMOSPHERE 2022; 299:134425. [PMID: 35351479 DOI: 10.1016/j.chemosphere.2022.134425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Biofuels, such as ethanol and butanol, obtained from carbon monoxide-rich gas or syngas bioconversion (solventogenesis) are an attractive alternative to traditional fermentation processes with merits of no competition with food production and sustainability. However, there is a lack of comprehensive understanding of some key process parameters and mechanisms enhancing solventogenesis during the fermentation process. This review provides an overview of the current state of the art of the main influencing factors during the syngas fermentation process catalyzed by acetogenic species as well as undefined mixed cultures. The role of syngas pressure, syngas components, fermentation pH, temperature, trace metals, organic compounds and additional materials is overviewed. As a so far hardly considered approach, thermodynamic calculations of the Gibbs free energy of CO conversion to acetic acid, ethanol, butyric acid and butanol under different CO pressures and pH at 25, 33 and 55 °C are also addressed and reviewed. Strategies for enhancing mass transfer and longer carbon chain solvent production are considered as well.
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Affiliation(s)
- Yaxue He
- National University of Ireland Galway, H91 TK33, Galway, Ireland; Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain.
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research - Centro de Investigaciones Científicas Avanzadas (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008, La Coruña, Spain
| | - Piet N L Lens
- National University of Ireland Galway, H91 TK33, Galway, Ireland
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Klask CM, Jäger B, Casini I, Angenent LT, Molitor B. Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii. Front Microbiol 2022; 13:887578. [PMID: 35615511 PMCID: PMC9124969 DOI: 10.3389/fmicb.2022.887578] [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: 03/01/2022] [Accepted: 03/31/2022] [Indexed: 11/20/2022] Open
Abstract
For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: (1) the RNF complex-encoding gene cluster rnfCDGEAB; (2) the putative RNF regulator gene rseC; and (3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy, and in addition, contribute to understand the connection of nitrate reduction to energy metabolism.
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Affiliation(s)
- Christian-Marco Klask
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Benedikt Jäger
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Isabella Casini
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Largus T. Angenent
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- *Correspondence: Bastian Molitor,
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10
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Oliveira L, Rückel A, Nordgauer L, Schlumprecht P, Hutter E, Weuster-Botz D. Comparison of Syngas-Fermenting Clostridia in Stirred-Tank Bioreactors and the Effects of Varying Syngas Impurities. Microorganisms 2022; 10:microorganisms10040681. [PMID: 35456733 PMCID: PMC9032146 DOI: 10.3390/microorganisms10040681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
In recent years, syngas fermentation has emerged as a promising means for the production of fuels and platform chemicals, with a variety of acetogens efficiently converting CO-rich gases to ethanol. However, the feasibility of syngas fermentation processes is related to the occurrence of syngas impurities such as NH3, H2S, and NOX. Therefore, the effects of defined additions of NH4+, H2S, and NO3− were studied in autotrophic batch processes with C. autoethanogenum, C. ljungdahlii, and C. ragsdalei while applying continuously gassed stirred-tank bioreactors. Any initial addition of ammonium and nitrate curbed the cell growth of the Clostridia being studied and reduced the final alcohol concentrations. C. ljungdahlii showed the highest tolerance to ammonium and nitrate, whereas C. ragsdalei was even positively influenced by the presence of 0.1 g L−1 H2S. Quantitative goals for the purification of syngas were identified for each of the acetogens studied in the used experimental setup. Syngas purification should in particular focus on the NOX impurities that caused the highest inhibiting effect and maintain the concentrations of NH3 and H2S within an acceptable range (e.g., NH3 < 4560 ppm and H2S < 108 ppm) in order to avoid inhibition through the accumulation of these impurities in the bioreactor.
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Dahle ML, Papoutsakis ET, Antoniewicz MR. 13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions. Metab Eng 2022; 72:161-170. [DOI: 10.1016/j.ymben.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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12
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Heffernan JK, Mahamkali V, Valgepea K, Marcellin E, Nielsen LK. Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Curr Opin Biotechnol 2022; 75:102700. [PMID: 35240422 DOI: 10.1016/j.copbio.2022.102700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/24/2022] [Accepted: 02/05/2022] [Indexed: 12/23/2022]
Abstract
Acetogens harness the Wood-Ljungdahl Pathway, a unique metabolic pathway for C1 capture close to the thermodynamic limit. Gas fermentation using acetogens is already used for CO-to-ethanol conversion at industrial-scale and has the potential to valorise a range of C1 and waste substrates to short-chain and medium-chain carboxylic acids and alcohols. Advances in analytical quantification and metabolic modelling have helped guide industrial gas fermentation designs. Further advances in the measurements of difficult to measure metabolites are required to improve kinetic modelling and understand the regulation of acetogen metabolism. This will help guide future synthetic biology designs needed to realise the full potential of gas fermentation in stimulating a circular bioeconomy.
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Affiliation(s)
- James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vishnu Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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13
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Hoyt KO, Woolston BM. Adapting isotopic tracer and metabolic flux analysis approaches to study C1 metabolism. Curr Opin Biotechnol 2022; 75:102695. [PMID: 35182834 DOI: 10.1016/j.copbio.2022.102695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/20/2022]
Abstract
Single-carbon (C1, or one-carbon) substrates are promising feedstocks for sustainable biofuel and biochemical production. Crucial to the goal of engineering C1-utilizing strains for improved production is a quantitative understanding of the organization, regulation and rates of the reactions that underpin C1 metabolism. 13C Metabolic flux analysis (MFA) is a well-established platform for interrogating these questions with multi-carbon substrates, and uses the differential labeling of metabolites that results from feeding a substrate with position-specific incorporation of 13C in order to infer quantitative fluxes and pathway topology. Adapting isotopic tracer approaches to C1 metabolism, where position-specific substrate labeling is impossible, requires additional experimental considerations. Here we review recent studies that have developed isotopic tracer approaches to overcome the challenge of uniform metabolite labeling and provide quantitative insight into C1 metabolism.
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Affiliation(s)
- Kathryn O Hoyt
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA.
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14
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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15
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Hong Y, Zeng AP. Biosynthesis Based on One-Carbon Mixotrophy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:351-371. [DOI: 10.1007/10_2021_198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Fan YX, Zhang JZ, Zhang Q, Ma XQ, Liu ZY, Lu M, Qiao K, Li FL. Biofuel and chemical production from carbon one industry flux gas by acetogenic bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2021; 117:1-34. [PMID: 34742365 DOI: 10.1016/bs.aambs.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Carbon one industry flux gas generated from fossil fuels, various industrial and domestic waste, as well as lignocellulosic biomass provides an innovative raw material to lead the sustainable development. Through the chemical and biological processing, the gas mixture composed of CO, CO2, and H2, also termed as syngas, is converted to biofuels and high-value chemicals. Here, the syngas fermentation process is elaborated to provide an overview. Sources of syngas are summarized and the influences of impurities on biological fermentation are exhibited. Acetogens and carboxydotrophs are the two main clusters of syngas utilizing microorganisms, their essential characters are presented, especially the energy metabolic scheme with CO, CO2, and H2. Synthetic biology techniques and microcompartment regulation are further discussed and proposed to create a high-efficiency cell factory. Moreover, the influencing factors in fermentation and products in carboxylic acids, alcohols, and others such like polyhydroxyalkanoate and poly-3-hydroxybutyrate are addressed. Biological fermentation from carbon one industry flux gas is a promising alternative, the latest scientific advances are expatiated hoping to inspire more creative transformation.
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Affiliation(s)
- Yi-Xuan Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Zhe Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Quan Zhang
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Zi-Yong Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Kai Qiao
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China.
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Dalian National Laboratory for Clean Energy, Dalian, China.
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17
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Yi J, Huang H, Liang J, Wang R, Liu Z, Li F, Wang S. A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii. Microbiol Spectr 2021; 9:e0095821. [PMID: 34643446 PMCID: PMC8515935 DOI: 10.1128/spectrum.00958-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
The strict anaerobe Clostridium ljungdahlii can ferment CO or H2/CO2 via the Wood-Ljungdahl pathway to acetate, ethanol, and 2,3-butanediol. This ability has attracted considerable interest, since it can be used for syngas fermentation to produce biofuels and biochemicals. However, the key enzyme methylenetetrahydrofolate reductase (MTHFR) in the Wood-Ljungdahl pathway of the strain has not been characterized, and its physiological electron donor is unclear. In this study, we purified the enzyme 46-fold with a benzyl viologen reduction activity of 41.2 U/mg from C. ljungdahlii cells grown on CO. It is composed of two subunits, MetF (31.5 kDa) and MetV (23.5 kDa), and has an apparent molecular mass of 62.2 kDa. The brownish yellow protein contains 0.73 flavin mononucleotide (FMN) and 7.4 Fe, in agreement with the prediction that MetF binds one flavin and MetV binds two [4Fe4S] clusters. It cannot use NAD(P)H as its electron donor or catalyze an electron-bifurcating reaction in combination with ferredoxin as an electron acceptor. The reduced recombinant ferredoxin, flavodoxin, and thioredoxin of C. ljungdahlii can serve as electron donors with specific activities of 91.2, 22.1, and 7.4 U/mg, respectively. The apparent Km values for reduced ferredoxin and flavodoxin were around 1.46 μM and 0.73 μM, respectively. Subunit composition and phylogenetic analysis showed that the enzyme from C. ljungdahlii belongs to MetFV-type MTHFR, which is a heterodimer, and uses reduced ferredoxin as its electron donor. Based on these results, we discuss the energy metabolism of C. ljungdahlii when it grows on CO or H2 plus CO2. IMPORTANCE Syngas, a mixture of CO, CO2, and H2, is the main component of steel mill waste gas and also can be generated by the gasification of biomass and urban domestic waste. Its fermentation to biofuels and biocommodities has attracted attention due to the economic and environmental benefits of this process. Clostridium ljungdahlii is one of the superior acetogens used in the technology. However, the biochemical mechanism of its gas fermentation via the Wood-Ljungdahl pathway is not completely clear. In this study, the key enzyme, methylenetetrahydrofolate reductase (MTHFR), was characterized and found to be a non-electron-bifurcating heterodimer with reduced ferredoxin as its electron donor, representing another example of MetFV-type MTHFR. The findings will form the basis for a deeper understanding of the energy metabolism of syngas fermentation by C. ljungdahlii, which is valuable for developing metabolic engineering strains and efficient syngas fermentation technologies.
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Affiliation(s)
- Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Rufei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Ziyong Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People’s Republic of China
| | - Fuli Li
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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18
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Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria. Extremophiles 2021; 25:413-424. [PMID: 34480656 PMCID: PMC8578096 DOI: 10.1007/s00792-021-01241-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022]
Abstract
Acetogenic bacteria are a polyphyletic group of organisms that fix carbon dioxide under anaerobic, non-phototrophic conditions by reduction of two mol of CO2 to acetyl-CoA via the Wood–Ljungdahl pathway. This pathway also allows for lithotrophic growth with H2 as electron donor and this pathway is considered to be one of the oldest, if not the oldest metabolic pathway on Earth for CO2 reduction, since it is coupled to the synthesis of ATP. How ATP is synthesized has been an enigma for decades, but in the last decade two ferredoxin-dependent respiratory chains were discovered. Those respiratory chains comprise of a cytochrome-free, ferredoxin-dependent respiratory enzyme complex, which is either the Rnf or Ech complex. However, it was discovered already 50 years ago that some acetogens contain cytochromes and quinones, but their role had only a shadowy existence. Here, we review the literature on the characterization of cytochromes and quinones in acetogens and present a hypothesis that they may function in electron transport chains in addition to Rnf and Ech.
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19
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Rückel A, Hannemann J, Maierhofer C, Fuchs A, Weuster-Botz D. Studies on Syngas Fermentation With Clostridium carboxidivorans in Stirred-Tank Reactors With Defined Gas Impurities. Front Microbiol 2021; 12:655390. [PMID: 33936011 PMCID: PMC8081853 DOI: 10.3389/fmicb.2021.655390] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Syngas fermentation processes with acetogenic bacteria like Clostridium carboxidivorans have been proven to be a promising approach for the conversion of CO-rich waste gases into short- and medium-chain alcohols. The challenge of synthesis gas impurities, on the other hand, has always been a major concern for establishing an industrial-scale process, since some of the trace components in waste gases, such as NH3, H2S, and NOx, can have inhibiting or even toxic effects on microbial growth and product formation. Thus, this study aims to identify the effects of the main trace impurities in syngas from gasification of biogenic residues by the supply of defined concentrations of trace impurities to the cultivation medium. Autotrophic gas fermentation studies were performed with C. carboxidivorans in batch-operated fully-controlled stirred-tank bioreactors with continuous gas supply (80% CO and 20% CO2). The syngas components NH3 and H2S had a positive effect on both growth and alcohol formation (ethanol, 1-butanol, and 1-hexanol). The maximum biomass concentration was increased by more than 50%, and the maximum ethanol concentration was more than doubled with 5.0 g L−1 NH4Cl or 1.0 g L−1 H2S provided by the addition of 2.2 g L−1 thioacetamide. The addition of the nitrogen oxide species nitrate and nitrite, on the other hand, reduced biomass growth as well as alcohol concentrations. Already, the supply of 0.1 g L−1 NaNO3 resulted in reduced growth and 25% reduction of the maximum ethanol concentration. The production of the longer chain alcohols 1-butanol and 1-hexanol was reduced as well. All NaNO2 concentrations tested showed a strong toxic effect on the metabolism of C. carboxidivorans, and neither CO consumption nor product formation was observed after addition. As a consequence, NOx components in syngas from the gasification of biogenic residues should be reduced by the gasification process and/or selectively removed from the syngas after gasification.
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Affiliation(s)
- Anton Rückel
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Jens Hannemann
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Carolin Maierhofer
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Alexander Fuchs
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
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20
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Ma X, Zhang G, Li F, Jiao M, Yao S, Chen Z, Liu Z, Zhang Y, Lv M, Liu L. Boosting the Microbial Electrosynthesis of Acetate from CO2 by Hydrogen Evolution Catalysts of Pt Nanoparticles/rGO. Catal Letters 2021. [DOI: 10.1007/s10562-021-03537-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Liang D, He W, Li C, Wang F, Crittenden JC, Feng Y. Remediation of nitrate contamination by membrane hydrogenotrophic denitrifying biofilm integrated in microbial electrolysis cell. WATER RESEARCH 2021; 188:116498. [PMID: 33080455 DOI: 10.1016/j.watres.2020.116498] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Complete biological denitrification is usually restricted in electron donor lacking waters. Hydrogenotrophic denitrification attracts attention for its clean and cost-efficiency advantages. Therein, the hydrogen could be effectively generated by microbial electrolysis cells (MECs) from organic wastes. In this study, a gas diffusion membrane (GDM) integrated MEC (MMEC) was constructed and provided a novel non-polluting approach for nitrate contaminated water remediation, in which the hydrogen was recovered from substrate degradation in anode and diffused across GDM as electron donor for denitrification. The high overall nitrogen removal of 91 ± 0.1%-95 ± 1.9% and 90 ± 1.6%-94 ± 2.2% were respectively achieved in Ti-MMEC and SS-MMEC with titanium and stainless-steel mesh as cathode at all applied voltages (0.4-0.8 V). Decreasing applied voltage from 0.8 to 0.4 V significantly improved the electron utilization efficiency for denitrification from 26 ± 3.6% to 73 ± 0.1% in Ti-MMEC. Integrating MEC with GDM greatly improved TN removal by 40% under applied voltage of 0.8 V. The hydrogenotrophic denitrifiers of Rhodocyclaceae, Paracoccus, and Dethiobacter, dominated in MMECs facilitating TN removal. Functional denitrification related genes including napAB, nirKS, norBC and nosZ predicted by PICRUSt2 based on 16S rRNA gene data demonstrated higher abundance in MMECs.
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Affiliation(s)
- Dandan Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China
| | - Weihua He
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China.
| | - Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China
| | - Fei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China
| | - John C Crittenden
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China; Brook Byers Institute for Sustainable Systems and School of Civil and Environmental Engineering, Georgia Institute of Technology, 828 West Peachtree Street, Atlanta, GA 30332, United States
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, P. R. China.
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22
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Katsyv A, Müller V. Overcoming Energetic Barriers in Acetogenic C1 Conversion. Front Bioeng Biotechnol 2020; 8:621166. [PMID: 33425882 PMCID: PMC7793690 DOI: 10.3389/fbioe.2020.621166] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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23
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Liang B, Zhao Y, Yang J. Recent Advances in Developing Artificial Autotrophic Microorganism for Reinforcing CO 2 Fixation. Front Microbiol 2020; 11:592631. [PMID: 33240247 PMCID: PMC7680860 DOI: 10.3389/fmicb.2020.592631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/21/2020] [Indexed: 11/13/2022] Open
Abstract
With the goal of achieving carbon sequestration, emission reduction and cleaner production, biological methods have been employed to convert carbon dioxide (CO2) into fuels and chemicals. However, natural autotrophic organisms are not suitable cell factories due to their poor carbon fixation efficiency and poor growth rate. Heterotrophic microorganisms are promising candidates, since they have been proven to be efficient biofuel and chemical production chassis. This review first briefly summarizes six naturally occurring CO2 fixation pathways, and then focuses on recent advances in artificially designing efficient CO2 fixation pathways. Moreover, this review discusses the transformation of heterotrophic microorganisms into hemiautotrophic microorganisms and delves further into fully autotrophic microorganisms (artificial autotrophy) by use of synthetic biological tools and strategies. Rapid developments in artificial autotrophy have laid a solid foundation for the development of efficient carbon fixation cell factories. Finally, this review highlights future directions toward large-scale applications. Artificial autotrophic microbial cell factories need further improvements in terms of CO2 fixation pathways, reducing power supply, compartmentalization and host selection.
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Affiliation(s)
- Bo Liang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yukun Zhao
- Pony Testing International Group, Qingdao, China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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24
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Köpke M, Simpson SD. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr Opin Biotechnol 2020; 65:180-189. [DOI: 10.1016/j.copbio.2020.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 02/01/2023]
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25
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Sorokin DY, Diender M, Merkel AY, Koenen M, Bale NJ, Pabst M, Sinninghe Damsté JS, Sousa DZ. Natranaerofaba carboxydovora gen. nov., sp. nov., an extremely haloalkaliphilic CO-utilizing acetogen from a hypersaline soda lake representing a novel deep phylogenetic lineage in the class 'Natranaerobiia'. Environ Microbiol 2020; 23:3460-3476. [PMID: 32955149 PMCID: PMC8359318 DOI: 10.1111/1462-2920.15241] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023]
Abstract
An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class ‘Natranaerobiia’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr‐like operon. The organism obviously relies on Na‐based bioenergetics, since the genome encodes for the Na+‐Rnf complex, Na+‐F1F0 ATPase and Na+‐translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO‐oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands.,Department of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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26
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Evaluation of Media Components and Process Parameters in a Sensitive and Robust Fed-Batch Syngas Fermentation System with Clostridium ljungdahlii. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6020061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fermentation of synthesis gas, or syngas, by acetogenic bacteria can help in transitioning from a fossil-fuel-based to a renewable bioeconomy. The main fermentation products of Clostridium ljungdahlii, one of such microorganisms, are acetate and ethanol. A sensitive, robust and reproducible system was established for C. ljungdahlii syngas fermentation, and several process parameters and medium components (pH, gas flow, cysteine and yeast extract) were investigated to assess its impact on the fermentation outcomes, as well as real time gas consumption. Moreover, a closed carbon balance could be achieved with the data obtained. This system is a valuable tool to detect changes in the behavior of the culture. It can be applied for the screening of strains, gas compositions or media components, for a better understanding of the physiology and metabolic regulation of acetogenic bacteria. Here, it was shown that neither yeast extract nor cysteine was a limiting factor for cell growth since their supplementation did not have a noticeable impact on product formation or overall gas consumption. By combining the lowering of both the pH and the gas flow after 24 h, the highest ethanol to acetate ratio was achieved, but with the caveat of lower productivity.
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27
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Zhang L, Zhao R, Jia D, Jiang W, Gu Y. Engineering Clostridium ljungdahlii as the gas-fermenting cell factory for the production of biofuels and biochemicals. Curr Opin Chem Biol 2020; 59:54-61. [PMID: 32480247 DOI: 10.1016/j.cbpa.2020.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/08/2020] [Accepted: 04/12/2020] [Indexed: 01/08/2023]
Abstract
Clostridium ljungdahlii is a representative autotrophic gas-fermenting acetogen capable of converting CO2 and CO into biomass and multiple metabolites. The carbon fixation and conversion based on C. ljungdahlii have great potential for the sustainable production of bulk biochemicals and biofuels using industrial syngas and waste gases. With substantial recent advances in genetic manipulation tools, it has become possible to study and improve the metabolic capability of C. ljungdahlii in gas fermentation. The product scope of C. ljungdahlii has been expanded through the introduction of heterologous production pathways followed by the modification of native metabolic networks. In addition, progress has been made in understanding the physiological and metabolic mechanisms of this anaerobe, contributing to strain designs for expected phenotypes. In this review, we highlight the latest research progresses regarding C. ljungdahlii and discuss the next steps to comprehensively understand and engineer this bacterium for an improved bacterial gas bioconversion platform.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Dechen Jia
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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Klask CM, Kliem-Kuster N, Molitor B, Angenent LT. Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO 2 and H 2, but Results in Stochastic Inhibition Events. Front Microbiol 2020; 11:724. [PMID: 32435236 PMCID: PMC7219301 DOI: 10.3389/fmicb.2020.00724] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The pH-value in fermentation broth is a critical factor for the metabolic flux and growth behavior of acetogens. A decreasing pH level throughout time due to undissociated acetic acid accumulation is anticipated under uncontrolled pH conditions such as in bottle experiments. As a result, the impact of changes in the metabolism (e.g., due to a genetic modification) might remain unclear or even unrevealed. In contrast, pH-controlled conditions can be achieved in bioreactors. Here, we present a self-built, comparatively cheap, and user-friendly multiple-bioreactor system (MBS) consisting of six pH-controlled bioreactors at a 1-L scale. We tested the functionality of the MBS by cultivating the acetogen Clostridium ljungdahlii with CO2 and H2 at steady-state conditions (=chemostat). The experiments (total of 10 bioreactors) were addressing the two questions: (1) does the MBS provide replicable data for gas-fermentation experiments?; and (2) does feeding nitrate influence the product spectrum under controlled pH conditions with CO2 and H2? We applied four different periods in each experiment ranging from pH 6.0 to pH 4.5. On the one hand, our data showed high reproducibility for gas-fermentation experiments with C. ljungdahlii under standard cultivation conditions using the MBS. On the other hand, feeding nitrate as sole N-source improved growth by up to 62% and ethanol production by 2-3-fold. However, we observed differences in growth, and acetate and ethanol production rates between all nitrate bioreactors. We explained the different performances with a pH-buffering effect that resulted from the interplay between undissociated acetic acid production and ammonium production and because of stochastic inhibition events, which led to complete crashes at different operating times.
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Affiliation(s)
- Christian-Marco Klask
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Nicolai Kliem-Kuster
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany.,Max Planck Fellow Groups, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Heffernan JK, Valgepea K, de Souza Pinto Lemgruber R, Casini I, Plan M, Tappel R, Simpson SD, Köpke M, Nielsen LK, Marcellin E. Enhancing CO 2-Valorization Using Clostridium autoethanogenum for Sustainable Fuel and Chemicals Production. Front Bioeng Biotechnol 2020; 8:204. [PMID: 32292775 PMCID: PMC7135887 DOI: 10.3389/fbioe.2020.00204] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 03/02/2020] [Indexed: 01/02/2023] Open
Abstract
Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO2 and H2 revealed that captured carbon (460 ± 80 mmol/gDCW/day) had a significant distribution to ethanol (54 ± 3 C-mol% with a 2.4 ± 0.3 g/L titer). We were impressed with this initial result, but also observed limitations to biomass concentration and growth rate. Metabolic modeling predicted culture performance and indicated significant metabolic adjustments when compared to fermentation with CO as the carbon source. Moreover, modeling highlighted flux to pyruvate, and subsequently reduced ferredoxin, as a target for improving CO2 and H2 fermentation. Supplementation with a small amount of CO enabled co-utilization with CO2, and enhanced CO2 fermentation performance significantly, while maintaining an industrially relevant product profile. Additionally, the highest specific flux through the Wood-Ljungdahl pathway was observed during co-utilization of CO2 and CO. Furthermore, the addition of CO led to superior CO2-valorizing characteristics (9.7 ± 0.4 g/L ethanol with a 66 ± 2 C-mol% distribution, and 540 ± 20 mmol CO2/gDCW/day). Similar industrial processes are commercial or currently being scaled up, indicating CO-supplemented CO2 and H2 fermentation has high potential for sustainable fuel and chemical production. This work also provides a reference dataset to advance our understanding of CO2 gas fermentation, which can contribute to mitigating climate change.
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Affiliation(s)
- James K. Heffernan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Saint Lucia, QLD, Australia
| | - Kaspar Valgepea
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Saint Lucia, QLD, Australia
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Isabella Casini
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Manuel Plan
- Queensland Node of Metabolomics Australia, The University of Queensland, Saint Lucia, QLD, Australia
| | | | | | | | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Saint Lucia, QLD, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Saint Lucia, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Saint Lucia, QLD, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Saint Lucia, QLD, Australia
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Beck MH, Flaiz M, Bengelsdorf FR, Dürre P. Induced heterologous expression of the arginine deiminase pathway promotes growth advantages in the strict anaerobe Acetobacterium woodii. Appl Microbiol Biotechnol 2019; 104:687-699. [DOI: 10.1007/s00253-019-10248-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023]
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