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Valero A, Petrash DA, Kuchenbuch A, Korth B. Enriching electroactive microorganisms from ferruginous lake waters - Mind the sulfate reducers! Bioelectrochemistry 2024; 157:108661. [PMID: 38340618 DOI: 10.1016/j.bioelechem.2024.108661] [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: 08/15/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Electroactive microorganisms are pivotal players in mineral transformation within redox interfaces characterized by pronounced oxygen and dissolved metal gradients. Yet, their systematic cultivation from such environments remains elusive. Here, we conducted an anodic enrichment using anoxic ferruginous waters from a post-mining lake as inoculum. Weak electrogenicity (j = ∼5 µA cm-2) depended on electroactive planktonic cells rather than anodic biofilms, with a preference for formate as electron donor. Addition of yeast extract decreased the lag phase but did not increase current densities. The enriched bacterial community varied depending on the substrate composition but mainly comprised of sulfate- and nitrate-reducing bacteria (e.g., Desulfatomaculum spp. and Stenotrophomonas spp.). A secondary enrichment strategy resulted in different bacterial communities composed of iron-reducing (e.g., Klebsiella spp.) and fermentative bacteria (e.g., Paeniclostridium spp.). Secondary electron microscopy and energy-dispersive X-ray spectroscopy results indicate the precipitation of sulfur- and iron-rich organomineral aggregates at the anode surface, presumably impeding current production. Our findings indicate that (i) anoxic waters containing geogenically derived metals can be used to enrich weak electricigens, and (ii) it is necessary to specifically inhibit sulfate reducers. Otherwise, sulfate reducers tend to dominate over EAM during cultivation, which can lead to anode passivation due to biomineralization.
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Affiliation(s)
- Astolfo Valero
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Daniel A Petrash
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Environmental Geochemistry and Biogeochemistry, Czech Geological Survey, Prague, Czech Republic
| | - Anne Kuchenbuch
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Benjamin Korth
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany.
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Wan S, Lai M, Gao X, Zhou M, Yang S, Li Q, Li F, Xia L, Tan Y. Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities. Synth Syst Biotechnol 2024; 9:19-25. [PMID: 38205027 PMCID: PMC10776380 DOI: 10.1016/j.synbio.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Excessive mining and utilization fossil fuels has led to drastic environmental consequences, which will contribute to global warming and cause further climate change with severe consequences for the human population. The magnitude of these challenges requires several approaches to develop sustainable alternatives for chemicals and fuels production. In this context, biological processes, mainly microbial fermentation, have gained particular interest. For example, autotrophic gas-fermenting acetogenic bacteria are capable of converting CO, CO2 and H2 into biomass and multiple metabolites through Wood-Ljungdahl pathway, which can be exploited for large-scale fermentation processes to sustainably produce bulk biochemicals and biofuels (e.g. acetate and ethanol) from syngas. Clostridium autoethanogenum is one representative of these chemoautotrophic bacteria and considered as the model for the gas fermentation. Recently, the development of synthetic biology toolbox for this strain has enabled us to study and genetically improve their metabolic capability in gas fermentation. In this review, we will summarize the recent progress involved in the understanding of physiological mechanism and strain engineering for C. autoethanogenum, and provide our perspectives on the future development about the basic biology and engineering biology of this strain.
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Affiliation(s)
- Sai Wan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Mingchi Lai
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinyu Gao
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Mingxin Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Fuli Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Lin Xia
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Yang Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
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Su R, Fu H, Ding L, Fu B, He S, Ma H, Hu H, Ren H. Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system. BIORESOURCE TECHNOLOGY 2024; 393:130028. [PMID: 37977494 DOI: 10.1016/j.biortech.2023.130028] [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: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.
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Affiliation(s)
- Runhua Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Huimin Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Su He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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Flaiz M, Poehlein A, Wilhelm W, Mook A, Daniel R, Dürre P, Bengelsdorf FR. Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering. Microb Cell Fact 2024; 23:24. [PMID: 38233843 PMCID: PMC10795377 DOI: 10.1186/s12934-024-02301-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The genus Eubacterium is quite diverse and includes several acetogenic strains capable of fermenting C1-substrates into valuable products. Especially, Eubacterium limosum and closely related strains attract attention not only for their capability to ferment C1 gases and liquids, but also due to their ability to produce butyrate. Apart from its well-elucidated metabolism, E. limosum is also genetically accessible, which makes it an interesting candidate to be an industrial biocatalyst. RESULTS In this study, we examined genomic, phylogenetic, and physiologic features of E. limosum and the closest related species E. callanderi as well as E. maltosivorans. We sequenced the genomes of the six Eubacterium strains 'FD' (DSM 3662T), 'Marburg' (DSM 3468), '2A' (DSM 2593), '11A' (DSM 2594), 'G14' (DSM 107592), and '32' (DSM 20517) and subsequently compared these with previously available genomes of the E. limosum type strain (DSM 20543T) as well as the strains 'B2', 'KIST612', 'YI' (DSM 105863T), and 'SA11'. This comparison revealed a close relationship between all eleven Eubacterium strains, forming three distinct clades: E. limosum, E. callanderi, and E. maltosivorans. Moreover, we identified the gene clusters responsible for methanol utilization as well as genes mediating chain elongation in all analyzed strains. Subsequent growth experiments revealed that strains of all three clades can convert methanol and produce acetate, butyrate, and hexanoate via reverse β-oxidation. Additionally, we used a harmonized electroporation protocol and successfully transformed eight of these Eubacterium strains to enable recombinant plasmid-based expression of the gene encoding the fluorescence-activating and absorption shifting tag (FAST). Engineered Eubacterium strains were verified regarding their FAST-mediated fluorescence at a single-cell level using a flow cytometry approach. Eventually, strains 'FD' (DSM 3662T), '2A' (DSM 2593), '11A' (DSM 2594), and '32' (DSM 20517) were genetically engineered for the first time. CONCLUSION Strains of E. limosum, E. callanderi, and E. maltosivorans are outstanding candidates as biocatalysts for anaerobic C1-substrate conversion into valuable biocommodities. A large variety of strains is genetically accessible using a harmonized electroporation protocol, and FAST can serve as a reliable fluorescent reporter protein to characterize genetically engineered cells. In total eleven strains have been assigned to distinct clades, providing a clear and updated classification. Thus, the description of respective Eubacterium species has been emended, improved, aligned, and is requested to be implemented in respective databases.
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Affiliation(s)
- Maximilian Flaiz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Wiebke Wilhelm
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Alexander Mook
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Ulm, Germany.
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5
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Keller NS, Lüders K, Hornbruch G, Birnstengel S, Vogt C, Ebert M, Kallies R, Dahmke A, Richnow HH. Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:333-341. [PMID: 38117480 PMCID: PMC10785757 DOI: 10.1021/acs.est.3c04340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.
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Affiliation(s)
- Nina S. Keller
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Klas Lüders
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Götz Hornbruch
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Susann Birnstengel
- Department
of Monitoring & Exploration Technologies, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Markus Ebert
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - René Kallies
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Andreas Dahmke
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Hans H. Richnow
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Isodetect
GmbH, Deutscher Platz
5b, 04103 Leipzig, Germany
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6
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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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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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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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9
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [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: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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10
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Moon J, Schubert A, Poehlein A, Daniel R, Müller V. A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:339-351. [PMID: 37150590 PMCID: PMC10472528 DOI: 10.1111/1758-2229.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Schubert
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
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11
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Katsyv A, Essig M, Bedendi G, Sahin S, Milton RD, Müller V. Characterization of ferredoxins from the thermophilic, acetogenic bacterium Thermoanaerobacter kivui. FEBS J 2023; 290:4107-4125. [PMID: 37074156 DOI: 10.1111/febs.16801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 04/19/2023] [Indexed: 04/20/2023]
Abstract
A major electron carrier involved in energy and carbon metabolism in the acetogenic model organism Thermoanaerobacter kivui is ferredoxin, an iron-sulfur-containing, electron-transferring protein. Here, we show that the genome of T. kivui encodes four putative ferredoxin-like proteins (TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530). All four genes were cloned, a His-tag encoding sequence was added and the proteins were produced from a plasmid in T. kivui. The purified proteins had an absorption peak at 430 nm typical for ferredoxins. The determined iron-sulfur content is consistent with the presence of two predicted [4Fe4S] clusters in TKV_c09620 and TKV_c19530 or one predicted [4Fe4S] cluster in TKV_c16450 and TKV_c10420 respectively. The reduction potential (Em ) for TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530 was determined to be -386 ± 4 mV, -386 ± 2 mV, -559 ± 10 mV and -557 ± 3 mV, respectively. TKV_c09620 and TKV_c16450 served as electron carriers for different oxidoreductases from T. kivui. Deletion of the ferredoxin genes led to only a slight reduction of growth on pyruvate or autotrophically on H2 + CO2 . Transcriptional analysis revealed that TKV_c09620 was upregulated in a ΔTKV_c16450 mutant and vice versa TKV_c16450 in a ΔTKV_c09620 mutant, indicating that TKV_c09620 and TKV_c16450 can replace each other. In sum, our data are consistent with the hypothesis that TKV_c09620 and TKV_c16450 are ferredoxins involved in autotrophic and heterotrophic metabolism of T. kivui.
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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
| | - Melanie Essig
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Giada Bedendi
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Selmihan Sahin
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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12
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Moon J, Waschinger LM, Müller V. Lactate formation from fructose or C1 compounds in the acetogen Acetobacterium woodii by metabolic engineering. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12637-7. [PMID: 37417977 PMCID: PMC10390620 DOI: 10.1007/s00253-023-12637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
Anaerobic, acetogenic bacteria are promising biocatalysts for a sustainable bioeconomy since they capture and convert carbon dioxide to acetic acid. Hydrogen is an intermediate in acetate formation from organic as well as C1 substrates. Here, we analyzed mutants of the model acetogen Acetobacterium woodii in which either one of the two hydrogenases or both together were genetically deleted. In resting cells of the double mutant, hydrogen formation from fructose was completely abolished and carbon was redirected largely to lactate. The lactate/fructose and lactate/acetate ratios were 1.24 and 2.76, respectively. We then tested for lactate formation from methyl groups (derived from glycine betaine) and carbon monoxide. Indeed, also under these conditions lactate and acetate were formed in equimolar amounts with a lactate/acetate ratio of 1.13. When the electron-bifurcating lactate dehydrogenase/ETF complex was genetically deleted, lactate formation was completely abolished. These experiments demonstrate the capability of A. woodii to produce lactate from fructose but also from promising C1 substrates, methyl groups and carbon monoxide. This adds an important milestone towards generation of a value chain leading from CO2 to value-added compounds. KEY POINTS: • Resting cells of the ΔhydBA/hdcr mutant of Acetobacterium woodii produced lactate from fructose or methyl groups + CO • Lactate formation from methyl groups + CO was completely abolished after deletion of lctBCD • Metabolic engineering of a homoacetogen to lactate formation gives a potential for industrial applications.
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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, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
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13
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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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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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15
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Wood JC, Gonzalez-Garcia RA, Daygon D, Talbo G, Plan MR, Marcellin E, Virdis B. Characterisation of acetogen formatotrophic potential using Eubacterium limosum. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12600-6. [PMID: 37272938 DOI: 10.1007/s00253-023-12600-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023]
Abstract
Formate is a promising energy carrier that could be used to transport renewable electricity. Some acetogenic bacteria, such as Eubacterium limosum, have the native ability to utilise formate as a sole substrate for growth, which has sparked interest in the biotechnology industry. However, formatotrophic metabolism in E. limosum is poorly understood, and a system-level characterisation in continuous cultures is yet to be reported. Here, we present the first steady-state dataset for E. limosum formatotrophic growth. At a defined dilution rate of 0.4 d-1, there was a high specific uptake rate of formate (280 ± 56 mmol/gDCW/d; gDCW = gramme dry cell weight); however, most carbon went to CO2 (150 ± 11 mmol/gDCW/d). Compared to methylotrophic growth, protein differential expression data and intracellular metabolomics revealed several key features of formate metabolism. Upregulation of phosphotransacetylase (Pta) appears to be a futile attempt of cells to produce acetate as the major product. Instead, a cellular energy limitation resulted in the accumulation of intracellular pyruvate and upregulation of pyruvate formate ligase (Pfl) to convert formate to pyruvate. Therefore, metabolism is controlled, at least partially, at the protein expression level, an unusual feature for an acetogen. We anticipate that formate could be an important one-carbon substrate for acetogens to produce chemicals rich in pyruvate, a metabolite generally in low abundance during syngas growth. KEY POINTS: First Eubacterium limosum steady-state formatotrophic growth omics dataset High formate specific uptake rate, however carbon dioxide was the major product Formate may be the cause of intracellular stress and biofilm formation.
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Affiliation(s)
- Jamin C Wood
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - R Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Dara Daygon
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Gert Talbo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia.
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16
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Frolov EN, Elcheninov AG, Gololobova AV, Toshchakov SV, Novikov AA, Lebedinsky AV, Kublanov IV. Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium. Front Microbiol 2023; 14:1185739. [PMID: 37250036 PMCID: PMC10213532 DOI: 10.3389/fmicb.2023.1185739] [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: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
One of the important current issues of bioenergetics is the establishment of the thermodynamic limits of life. There is still no final understanding of what is the minimum value of the energy yield of a reaction that is sufficient to be used by an organism (the so-called "biological quantum of energy"). A reasonable model for determination of the minimal energy yield would be microorganisms capable of living on low-energy substrates, such as acetogenic prokaryotes. The most prominent metabolic feature of acetogens is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates, which is hardly competitive in environments. Most probably, that is why only facultative autotrophic acetogens have been known so far. Here, we describe the first obligately autotrophic acetogenic bacterium Aceticella autotrophica gen. nov., sp. nov., strain 3443-3AcT. Phylogenetically, the new genus falls into a monophyletic group of heterotrophic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, and Caldanaerobacter (hereinafter referred to as TTC group), where the sole acetogenic representative has so far been the facultatively autotrophic Thermoanaerobacter kivui. A. autotrophica and T. kivui both are acetogens employing energy-converting hydrogenase (Ech-acetogens) that are likely to have inherited the acetogenesis capacity vertically from common ancestor. However, their acetogenic machineries have undergone different adjustments by gene replacements due to horizontal gene transfers from different donors. Obligate autotrophy of A. autotrophica is associated with the lack of many sugar transport systems and carbohydrate catabolism enzymes that are present in other TTC group representatives, including T. kivui.
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Affiliation(s)
- Evgenii N. Frolov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G. Elcheninov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra V. Gololobova
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Andrei A. Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, Moscow, Russia
| | - Alexander V. Lebedinsky
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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17
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Moon J, Schubert A, Waschinger LM, Müller V. Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis. THE ISME JOURNAL 2023:10.1038/s41396-023-01411-2. [PMID: 37061584 DOI: 10.1038/s41396-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Methyl groups are abundant in anoxic environments and their utilization as carbon and energy sources by microorganisms involves oxidation of the methyl groups to CO2, followed by transfer of the electrons to an acceptor. In acetogenic bacteria, the electron acceptor is CO2 that is reduced to enzyme bound carbon monoxide, the precursor of the carboxyl group in acetate. Here, we describe the generation of a mutant of the acetogen Acetobacterium woodii in which the last step in methyl group oxidation, formate oxidation to CO2 catalyzed by the HDCR enzyme, has been genetically deleted. The mutant grew on glycine betaine as methyl group donor, and in contrast to the wild type, formed formate alongside acetate, in a 1:2 ratio, demonstrating that methyl group oxidation stopped at the level of formate and reduced electron carriers were reoxidized by CO2 reduction to acetate. In the presence of the alternative electron acceptor caffeate, CO2 was no longer reduced to acetate, formate was the only product and all the carbon went to formate. Apparently, acetogenesis was not required to sustain formatogenic growth. This is the first demonstration of a genetic reprogramming of an acetogen into a formatogen that grows by homoformatogenesis from methyl groups. Formate production from methyl groups is not only of biotechnological interest but also for the mechanism of electron transfer in syntrophic interactions in anoxic environments.
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Affiliation(s)
- Jimyung Moon
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Schubert
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany.
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18
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Recent Applications and Strategies to Enhance Performance of Electrochemical Reduction of CO2 Gas into Value-Added Chemicals Catalyzed by Whole-Cell Biocatalysts. Processes (Basel) 2023. [DOI: 10.3390/pr11030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Carbon dioxide (CO2) is one of the major greenhouse gases that has been shown to cause global warming. Decreasing CO2 emissions plays an important role to minimize the impact of climate change. The utilization of CO2 gas as a cheap and sustainable source to produce higher value-added chemicals such as formic acid, methanol, methane, and acetic acid has been attracting much attention. The electrochemical reduction of CO2 catalyzed by whole-cell biocatalysts is a promising process for the production of value-added chemicals because it does not require costly enzyme purification steps and the supply of exogenous cofactors such as NADH. This study covered the recent applications of the diversity of microorganisms (pure cultures such as Shewanella oneidensis MR1, Sporomusa species, and Clostridium species and mixed cultures) as whole-cell biocatalysts to produce a wide range of value-added chemicals including methane, carboxylates (e.g., formate, acetate, butyrate, caproate), alcohols (e.g., ethanol, butanol), and bioplastics (e.g., Polyhydroxy butyrate). Remarkably, this study provided insights into the molecular levels of the proteins/enzymes (e.g., formate hydrogenases for CO2 reduction into formate and electron-transporting proteins such as c-type cytochromes) of microorganisms which are involved in the electrochemical reduction of CO2 into value-added chemicals for the suitable application of the microorganism in the chemical reduction of CO2 and enhancing the catalytic efficiency of the microorganisms toward the reaction. Moreover, this study provided some strategies to enhance the performance of the reduction of CO2 to produce value-added chemicals catalyzed by whole-cell biocatalysts.
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19
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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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20
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Zhao R, Dong W, Yang C, Jiang W, Tian J, Gu Y. Formate as a supplementary substrate facilitates sugar metabolism and solvent production by Clostridium beijerinckii NCIMB 8052. Synth Syst Biotechnol 2023; 8:196-205. [PMID: 36824491 PMCID: PMC9941364 DOI: 10.1016/j.synbio.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Microbial utilization and conversion of organic one-carbon compounds, such as formate and methanol that can be easily produced from CO2, has emerged as an attractive approach for biorefinery. In this study, we discovered Clostridium beijerinckii NCIMB 8052, a typical solventogenic Clostridium strain, to be a native formate-utilizing bacterium. 13C isotope analysis showed that formate could be metabolized via both assimilation and dissimilation pathways in C. beijerinckii NCIMB 8052. Notably, the use of formate as the supplementary substrate by this strain could significantly enhance its glucose consumption and ABE (acetone-butanol-ethanol) production, largely due to the up-regulation of genes responsible for glycolysis and glucose transport under formate stress. Based on these findings, we further improved formate tolerance of C. beijerinckii NCIMB 8052 by adaptive laboratory evolution, generating an evolved strain Cbei-FA01. The Cbei-FA01 strain could produce 23.0 g/L of ABE solvents using glucose and formate as dual substrates, ∼50% higher than that of the wild-type strain under the same condition. Moreover, such a promotion effect of formate on ABE production by Cbei-FA01 was also observed in fermenting a glucose-xylose mixture. This work reveals a previously unreported role of formate in biological ABE production, providing a new approach to utilize this one-carbon source.
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Affiliation(s)
- Ran Zhao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenyue Dong
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China,Corresponding author. 300 Fenglin Road, Shanghai, 200032, China.
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China,Corresponding author.
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21
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Ricci L, Seifert A, Bernacchi S, Fino D, Pirri CF, Re A. Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production. Microb Biotechnol 2022; 16:218-237. [PMID: 36464980 PMCID: PMC9871533 DOI: 10.1111/1751-7915.14172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022] Open
Abstract
Carbon dioxide (CO2 ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H2 -dependent CO2 gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO2 as sole carbon feedstock and H2 as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO2 into C1 products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO2 abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.
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Affiliation(s)
- Luca Ricci
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | | | | | - Debora Fino
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | - Candido Fabrizio Pirri
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
| | - Angela Re
- Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly,Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTurinItaly
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22
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Burger Y, Schwarz FM, Müller V. Formate-driven H2 production by whole cells of Thermoanaerobacter kivui. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:48. [PMID: 35545791 PMCID: PMC9097184 DOI: 10.1186/s13068-022-02147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/26/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.
Results
In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.
Conclusions
The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.
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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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Abstract
Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water-rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
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Abstract
Acetogenic bacteria are a group of strictly anaerobic bacteria that make a living from acetate formation from two molecules of CO2 via the Wood-Ljungdahl pathway (WLP). The free energy change of this reaction is very small and allows the synthesis of only a fraction of an ATP. How this pathway is coupled to energy conservation has been an enigma since its discovery ~90 years ago. Here, we describe an electron transport chain in the cytochrome- and quinone-containing acetogen Sporomusa ovata that leads from molecular hydrogen as an electron donor to an intermediate of the WLP, methylenetetrahydrofolate (methylene-tetrahydrofolate [THF]), as an electron acceptor. The catalytic site of the hydrogenase is periplasmic and likely linked cytochrome b to the membrane. We provide evidence that the MetVF-type methylenetetrahydrofolate reductase is linked proteins MvhD and HdrCBA to the cytoplasmic membrane. Membrane preparations catalyzed the H2-dependent reduction of methylene-THF to methyl-THF. In our model, a transmembrane electrochemical H+ gradient is established by both scalar and vectorial protons that leads to the synthesis of 0.5 mol ATP/mol methylene-THF by a H+-F1Fo ATP synthase. This H2- and methylene-THF-dependent electron transport chain may be present in other cytochrome-containing acetogens as well and represents a third way of chemiosmotic energy conservation in acetogens, but only in addition to the well-established respiratory enzymes Rnf and Ech. IMPORTANCE Acetogenic bacteria grow by making acetate from CO2 and are considered the first life forms on Earth since they couple CO2 reduction to the conservation of energy. How this is achieved has been an enigma ever since. Recently, two respiratory enzymes, a ferredoxin:NAD+ oxidoreductase (Rnf) and a ferredoxin:H+ oxidoreductase (Ech), have been found in cytochrome-free acetogenic model bacteria. However, some acetogens contain cytochromes in addition, and there has been a long-standing assumption of a cytochrome-containing electron transport chain in those acetogens. Here, we provide evidence for a respiratory chain in Sporomusa ovata that has a cytochrome-containing hydrogenase as the electron donor and a methylenetetrahydrofolate reductase as the terminal electron acceptor. This is the third way of chemiosmotic energy conservation found in acetogens.
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Stark C, Münßinger S, Rosenau F, Eikmanns BJ, Schwentner A. The Potential of Sequential Fermentations in Converting C1 Substrates to Higher-Value Products. Front Microbiol 2022; 13:907577. [PMID: 35722332 PMCID: PMC9204031 DOI: 10.3389/fmicb.2022.907577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Today production of (bulk) chemicals and fuels almost exclusively relies on petroleum-based sources, which are connected to greenhouse gas release, fueling climate change. This increases the urgence to develop alternative bio-based technologies and processes. Gaseous and liquid C1 compounds are available at low cost and often occur as waste streams. Acetogenic bacteria can directly use C1 compounds like CO, CO2, formate or methanol anaerobically, converting them into acetate and ethanol for higher-value biotechnological products. However, these microorganisms possess strict energetic limitations, which in turn pose limitations to their potential for biotechnological applications. Moreover, efficient genetic tools for strain improvement are often missing. However, focusing on the metabolic abilities acetogens provide, they can prodigiously ease these technological disadvantages. Producing acetate and ethanol from C1 compounds can fuel via bio-based intermediates conversion into more energy-demanding, higher-value products, by deploying aerobic organisms that are able to grow with acetate/ethanol as carbon and energy source. Promising new approaches have become available combining these two fermentation steps in sequential approaches, either as separate fermentations or as integrated two-stage fermentation processes. This review aims at introducing, comparing, and evaluating the published approaches of sequential C1 fermentations, delivering a list of promising organisms for the individual fermentation steps and giving an overview of the existing broad spectrum of products based on acetate and ethanol. Understanding of these pioneering approaches allows collecting ideas for new products and may open avenues toward making full use of the technological potential of these concepts for establishment of a sustainable biotechnology.
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Affiliation(s)
- Christina Stark
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Sini Münßinger
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Bernhard J. Eikmanns,
| | - Andreas Schwentner
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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27
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Lee H, Bae J, Jin S, Kang S, Cho BK. Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization. Front Microbiol 2022; 13:865168. [PMID: 35615514 PMCID: PMC9124964 DOI: 10.3389/fmicb.2022.865168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood–Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.
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Affiliation(s)
- Hyeonsik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangrak Jin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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28
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Trischler R, Roth J, Sorbara MT, Schlegel X, Müller V. A functional Wood-Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae, Blautia luti and beyond. Environ Microbiol 2022; 24:3111-3123. [PMID: 35466558 DOI: 10.1111/1462-2920.16029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Species of the genus Blautia are typical inhabitants of the human gut and considered as beneficial gut microbes. However, their role in the gut microbiome and their metabolic features are poorly understood. Blautia schinkii was described as an acetogenic bacterium, characterized by a functional Wood-Ljungdahl pathway (WLP) of acetogenesis from H2 + CO2 . Here we report that two relatives, Blautia luti and Blautia wexlerae do not grow on H2 + CO2 . Inspection of the genome sequence revealed all genes of the WLP except genes encoding a formate dehydrogenase and an electron-bifurcating hydrogenase. Enzyme assays confirmed this prediction. Accordingly, resting cells neither converted H2 + CO2 nor H2 + HCOOH + CO2 to acetate. Carbon monoxide is an intermediate of the WLP and substrate for many acetogens. B. luti and B. wexlerae had an active CO dehydrogenase and resting cells performed acetogenesis from HCOOH + CO2 + CO, demonstrating a functional WLP. Bioinformatic analyses revealed that many Blautia strains as well as other gut acetogens lack formate dehydrogenases and hydrogenases. Thus, the use of formate instead of H2 + CO2 as an interspecies hydrogen and electron carrier seems to be more common in the gut microbiome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Jennifer Roth
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Matthew T Sorbara
- Department Molecular and Cellular Biology, University of Guelph, Ontario, N1G 2W1, Canada
| | - Xenia Schlegel
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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29
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Litty D, Kremp F, Müller V. One substrate, many fates: different ways of methanol utilization in the acetogen Acetobacterium woodii. Environ Microbiol 2022; 24:3124-3133. [PMID: 35416389 DOI: 10.1111/1462-2920.16011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/28/2022]
Abstract
Acetogenic bacteria such as Acetobacterium woodii use the Wood-Ljungdahl pathway (WLP) for fixation of CO2 and energy conservation. This pathway enables conversion of diverse substrates to the main product of acetogenesis, acetate. Methyl group containing substrates such as methanol or methylated compounds, derived from pectin, are abundant in the environment and a source for CO2 . Methyl groups enter the WLP at the level of methyltetrahydrofolic acid (methyl-THF). For methyl transfer from methanol to THF a substrate specific methyltransferase system is required. In this study, we used genetic methods to identify mtaBC2A (Awo_c22760- Awo_c22740) as the methanol specific methyltransferase system of A. woodii. After methyl transfer, methyl-THF serves as carbon and/or electron- source and the respiratory Rnf complex is required for redox homeostasis if methanol+CO2 is the substrate. Resting cells fed with methanol+CO2 , indeed converted methanol to acetate in a 4:3 stoichiometry. When methanol was fed in combination with other electron sources such as H2 + CO2 or CO, methanol was converted Rnf-independently and the methyl group was condensed with CO to build acetate. When fed in combination with alternative electron sinks such as caffeate methanol was oxidized only and resulting electrons were used for non-acetogenic growth. These different pathways for the conversion of methyl-group containing substrates enable acetogens to adapt to various ecological niches and to syntrophic communities. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dennis Litty
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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30
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A synthetic bacterial microcompartment as production platform for pyruvate from formate and acetate. Proc Natl Acad Sci U S A 2022; 119:2201330119. [PMID: 35217629 PMCID: PMC8892506 DOI: 10.1073/pnas.2201330119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Autotrophic lactate production from H2 + CO2 using recombinant and fluorescent FAST-tagged Acetobacterium woodii strains. Appl Microbiol Biotechnol 2022; 106:1447-1458. [PMID: 35092454 PMCID: PMC8882112 DOI: 10.1007/s00253-022-11770-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
AbstractLactate has various uses as industrial platform chemical, poly-lactic acid precursor or feedstock for anaerobic co-cultivations. The aim of this study was to construct and characterise Acetobacterium woodii strains capable of autotrophic lactate production. Therefore, the lctBCD genes, encoding the native Lct dehydrogenase complex, responsible for lactate consumption, were knocked out. Subsequently, a gene encoding a d-lactate dehydrogenase (LDHD) originating from Leuconostoc mesenteroides was expressed in A. woodii, either under the control of the anhydrotetracycline-inducible promoter Ptet or under the lactose-inducible promoter PbgaL. Moreover, LDHD was N-terminally fused to the oxygen-independent fluorescence-activating and absorption-shifting tag (FAST) and expressed in respective A. woodii strains. Cells that produced the LDHD fusion protein were capable of lactate production of up to 18.8 mM in autotrophic batch experiments using H2 + CO2 as energy and carbon source. Furthermore, cells showed a clear and bright fluorescence during exponential growth, as well as in the stationary phase after induction, mediated by the N-terminal FAST. Flow cytometry at the single-cell level revealed phenotypic heterogeneities for cells expressing the FAST-tagged LDHD fusion protein. This study shows that FAST provides a new reporter tool to quickly analyze gene expression over the course of growth experiments of A. woodii. Consequently, fluorescence-based reporters allow for faster and more targeted optimization of production strains.Key points
•Autotrophic lactate production was achieved with A. woodii.
•FAST functions as fluorescent marker protein in A. woodii.
•Fluorescence measurements on single-cell level revealed population heterogeneity.
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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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