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Ai S, Wang X, Zhu J, Meng X, Liu Z, Yang F, Cheng K. Microbial community assemblage altered by coprecipitation of artificial humic substances and ferrihydrite: Implications for carbon fixation pathway transformation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:174838. [PMID: 39029757 DOI: 10.1016/j.scitotenv.2024.174838] [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: 04/21/2024] [Revised: 07/10/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
The suppression of soil carbon mineralization has been demonstrated to be effectively facilitated by carbon‑iron interactions, yet the specific mechanisms by which artificial humic substances (A-HS) coupled with ferrihydrite influence this process remain insufficiently explored. This study is to investigate how the A-HS, specifically artificial fulvic acid (A-FA) and artificial humic acid (A-HA), coupled with ferrihydrite, affect carbon mineralization under anaerobic system that simulates paddy flooding conditions. The object is to investigate trends in carbon emissions and to delineate microbial community structure and functional pathways. The findings indicate that A-HA and A-FA substantially reduce CO2 and CH4 emissions, with A-FA having a particularly pronounced effect on carbon fixation, halving CO2 concentrations. The low concentration of Fe(II) observed suggest that A-FA and A-HA impede the dissimilatory iron reduction (DIR) process. Detailed 16S rDNA sequencing and gene prediction analyses reveal changes in microbial community structures and functions, highlighting Methanobacterium as the dominant hydrogenotrophic methanogens. The reductive citric acid cycle, predominantly utilized by Clostridium carboxidivorans, was identified as the principal carbon fixation pathway. This work provides a novel insight into the microbial mechanisms of carbon sequestration and highlights the potential of A-HS in improving soil fertility and contributing to climate change mitigation through enhancing soil carbon storage.
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Affiliation(s)
- Shuang Ai
- College of Engineering, Northeast Agricultural University, Harbin, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Xiaobin Wang
- College of Engineering, Northeast Agricultural University, Harbin, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Jiayu Zhu
- College of Engineering, Northeast Agricultural University, Harbin, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Xianghui Meng
- College of Engineering, Northeast Agricultural University, Harbin, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Zhuqing Liu
- International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China; School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, China.
| | - Fan Yang
- International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China; School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, China.
| | - Kui Cheng
- College of Engineering, Northeast Agricultural University, Harbin, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China.
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2
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Zhang Y, Liang Y, Xiang H, Li P, Zhan D, Ding D, Du S, Ding Y, Liu W, Qiu X, Feng H. Critical impact of pressure regulation on carbon dioxide biosynthesis. BIORESOURCE TECHNOLOGY 2024; 413:131445. [PMID: 39278365 DOI: 10.1016/j.biortech.2024.131445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/03/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
Abstract
Carbon dioxide (CO2) biosynthesis is a promising alternative to traditional chemical synthesis. However, its application in engineering is hampered by poor gas mass transfer rates. Pressurization is an effective method to enhance mass transfer and increase synthesis yield, although the underlying mechanisms remain unclear. This review examines the effects of high pressure on CO2 biosynthesis, elucidating the mechanisms behind yield enhancement from three perspectives: microbial physiological traits, gas mass transfer and synthetic pathways. The critical role of pressurization in improving microbial activity and gas transfer efficiency is emphasized, with particular attention to maintaining pressure within microbial tolerance limits to maximize yield without compromising cell structure integrity.
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Affiliation(s)
- Yanqing Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Yuxiang Liang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Hai Xiang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Pingli Li
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Dongqing Zhan
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Danna Ding
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Shuangwei Du
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yangcheng Ding
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Wen Liu
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Xiawen Qiu
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China.
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3
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Gao YL, Cournoyer JE, De BC, Wallace CL, Ulanov AV, La Frano MR, Mehta AP. Introducing carbon assimilation in yeasts using photosynthetic directed endosymbiosis. Nat Commun 2024; 15:5947. [PMID: 39013857 PMCID: PMC11252298 DOI: 10.1038/s41467-024-49585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Abstract
Conversion of heterotrophic organisms into partially or completely autotrophic organisms is primarily accomplished by extensive metabolic engineering and laboratory evolution efforts that channel CO2 into central carbon metabolism. Here, we develop a directed endosymbiosis approach to introduce carbon assimilation in budding yeasts. Particularly, we engineer carbon assimilating and sugar-secreting photosynthetic cyanobacterial endosymbionts within the yeast cells, which results in the generation of yeast/cyanobacteria chimeras that propagate under photosynthetic conditions in the presence of CO2 and in the absence of feedstock carbon sources like glucose or glycerol. We demonstrate that the yeast/cyanobacteria chimera can be engineered to biosynthesize natural products under the photosynthetic conditions. Additionally, we expand our directed endosymbiosis approach to standard laboratory strains of yeasts, which transforms them into photosynthetic yeast/cyanobacteria chimeras. We anticipate that our studies will have significant implications for sustainable biotechnology, synthetic biology, and experimentally studying the evolutionary adaptation of an additional organelle in yeast.
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Affiliation(s)
- Yang-le Gao
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois, US
| | - Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois, US
| | - Bidhan C De
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois, US
| | - Catherine L Wallace
- The Imaging Technology Group, Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, US
| | - Alexander V Ulanov
- Carver Metabolomics Core, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois, US
| | - Michael R La Frano
- Carver Metabolomics Core, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois, US
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois, US.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois, US.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, US.
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4
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Liu X, Li L, Zhao G, Xiong P. Optimization strategies for CO 2 biological fixation. Biotechnol Adv 2024; 73:108364. [PMID: 38642673 DOI: 10.1016/j.biotechadv.2024.108364] [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: 09/18/2023] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
Global sustainable development faces a significant challenge in effectively utilizing CO2. Meanwhile, CO2 biological fixation offers a promising solution. CO2 has the highest oxidation state (+4 valence state), whereas typical multi‑carbon chemicals have lower valence states. The Gibbs free energy (ΔG) changes of CO2 reductive reactions are generally positive and this renders it necessary to input different forms of energy. Although biological carbon fixation processes are friendly to operate, the thermodynamic obstacles must be overcome. To make this reaction occur favorably and efficiently, diverse strategies to enhance CO2 biological fixation efficiency have been proposed by numerous researchers. This article reviews recent advances in optimizing CO2 biological fixation and intends to provide new insights into achieving efficient biological utilization of CO2. It first outlines the thermodynamic characteristics of diverse carbon fixation reactions and proposes optimization directions for CO2 biological fixation. A comprehensive overview of the catalytic mechanisms, optimization strategies, and challenges encountered by common carbon-fixing enzymes is then provided. Subsequently, potential routes for improving the efficiency of biological carbon fixation are discussed, including the ATP supply, reducing power supply, energy supply, reactor design, and carbon enrichment system modules. In addition, effective artificial carbon fixation pathways were summarized and analyzed. Finally, prospects are made for the research direction of continuously improving the efficiency of biological carbon fixation.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
| | - Linqing Li
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China.
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
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5
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Zhang N, Chen K, Wang X, Ji W, Yang Z, Wang X, Li J. Response Mechanism of cbbM Carbon Sequestration Microbial Community Characteristics in Different Wetland Types in Qinghai Lake. BIOLOGY 2024; 13:333. [PMID: 38785815 PMCID: PMC11117618 DOI: 10.3390/biology13050333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Carbon-sequestering microorganisms play an important role in the carbon cycle of wetland ecosystems. However, the response mechanism of carbon-sequestering microbial communities to wetland type changes and their relationship with soil carbon remain unclear. To explore these differences and identify the main influencing factors, this study selected marsh wetlands, river wetlands and lakeside wetlands around Qinghai Lake as research subjects. High-throughput sequencing was employed to analyze the functional gene cbbM of carbon-sequestering microorganisms. The results revealed that the alpha diversity of cbbM carbon-sequestering microorganisms mirrored the trend in total carbon content, with the highest diversity observed in marsh wetlands and the lowest in lakeside wetlands. The dominant bacterial phylum was Proteobacteria, with prevalent genera including Thiothrix, Acidithiobacillus, and Thiodictyon. Acidithiobacillus served as a biomarker in lakeside wetlands, while two other genera were indicative of marsh wetlands. The hierarchical partitioning analysis indicated that the diversity of cbbM carbon-fixing microorganisms was primarily influenced by the total nitrogen content, while the community structure was significantly affected by the soil total carbon content. Moreover, an increased soil temperature and humidity were found to favor the carbon fixation processes of Thiomicrospira, Thiomonas, Polaromonas, and Acidithiobacillus. In summary, changes in wetland types seriously affected the characteristics of cbbM carbon sequestration in microbial communities, and a warm and humid climate may be conducive to wetland carbon sequestration.
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Affiliation(s)
- Ni Zhang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Kelong Chen
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Xinye Wang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Wei Ji
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Ziwei Yang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Xia Wang
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining 810008, China; (N.Z.); (X.W.); (W.J.); (Z.Y.); (X.W.)
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), Qinghai Normal University, Xining 810008, China
- National Positioning Observation and Research Station of Qinghai Lake Wetland Ecosystem in Qinghai, National Forestry and Grassland Administration, Haibei 812300, China
| | - Junmin Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China;
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6
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Kabasakal BV, Cotton CAR, Murray JW. Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction. Biochimie 2024; 219:12-20. [PMID: 37952891 DOI: 10.1016/j.biochi.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Malonyl-Coenzyme A Reductase (MCR) in Chloroflexus aurantiacus, a characteristic enzyme of the 3-hydroxypropionate (3-HP) cycle, catalyses the reduction of malonyl-CoA to 3-HP. MCR is a bi-functional enzyme; in the first step, malonyl-CoA is reduced to the free intermediate malonate semialdehyde by the C-terminal region of MCR, and this is further reduced to 3-HP by the N-terminal region of MCR. Here we present the crystal structures of both N-terminal and C-terminal regions of the MCR from C. aurantiacus. A catalytic mechanism is suggested by ligand and substrate bound structures, and structural and kinetic studies of MCR variants. Both MCR structures reveal one catalytic, and one non-catalytic SDR (short chain dehydrogenase/reductase) domain. C-terminal MCR has a lid domain which undergoes a conformational change and controls the reaction. In the proposed mechanism of the C-terminal MCR, the conversion of malonyl-CoA to malonate semialdehyde is based on the reduction of malonyl-CoA by NADPH, followed by the decomposition of the hemithioacetal to produce malonate semialdehyde and coenzyme A. Conserved arginines, Arg734 and Arg773 are proposed to play key roles in the mechanism and conserved Ser719, and Tyr737 are other essential residues forming an oxyanion hole for the substrate intermediates.
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Affiliation(s)
- Burak V Kabasakal
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Turkish Accelerator and Radiation Laboratory, Gölbaşı, 06830, Ankara, Turkiye
| | - Charles A R Cotton
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Cambrium GmbH, Max-Urich-Strasse 3, 13355, Berlin, Germany
| | - James W Murray
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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Li J, Xie N, Feng C, Wang C, Huang R, Tao Q, Tang X, Wu Y, Luo Y, Li Q, Li B. Pore size and organic carbon of biochar limit the carbon sequestration potential of Bacillus cereus SR. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 274:116229. [PMID: 38508101 DOI: 10.1016/j.ecoenv.2024.116229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Carbon-fixing functional strain-loaded biochar may have significant potential in carbon sequestration given the global warming situation. The carbon-fixing functional strain Bacillus cereus SR was loaded onto rice straw biochar pyrolyzed at different temperatures with the anticipation of clarifying the carbon sequestration performance of this strain on biochar and the interaction effects with biochar. During the culture period, the content of dissolved organic carbon (DOC), easily oxidizable organic carbon, and microbial biomass carbon in biochar changed. This finding indicated that B. cereus SR utilized organic carbon for survival and enhanced carbon sequestration on biochar to increase organic carbon, manifested by changes in CO2 emissions and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) enzyme activity. Linear regression analysis showed that the strain was likely to consume DOC on 300 °C biochar, although the Rubisco enzyme activity was higher. In contrast, the strain had a higher carbon sequestration potential on 500 °C biochar. Correlation analysis showed that Rubisco enzyme activity was controlled by the physical structure of the biochar. Our results highlight the differences in the survival mode and carbon sequestration potential of B. cereus SR on biochar pyrolyzed at different temperatures.
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Affiliation(s)
- Jie Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Ningyi Xie
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changchun Feng
- China National Tobacco Corporation Sichuan, Chengdu 610041, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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8
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Sheppard TJ, Specht DA, Barstow B. Efficiency estimates for electromicrobial production of branched-chain hydrocarbons. iScience 2024; 27:108773. [PMID: 38283329 PMCID: PMC10821168 DOI: 10.1016/j.isci.2023.108773] [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: 11/08/2023] [Revised: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
In electromicrobial production (EMP), electricity is used as microbial energy to produce complex molecules starting from simple compounds like CO2. The aviation industry requires sustainable fuel alternatives that can meet demands for high-altitude performance and modern emissions standards. EMP of jet fuel components provides a unique opportunity to generate fuel blends compatible with modern engines producing net-neutral emissions. Branched-chain hydrocarbons modulate the boiling and freezing points of liquid fuels at high altitudes. In this study, we analyze the pathways necessary to generate branched-chain hydrocarbons in vivo utilizing extracellular electron uptake (EEU) and H2-oxidation for electron delivery, the Calvin cycle for CO2-fixation and the aldehyde deformolating oxygenase decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies to be 40.0 - 4.4 + 0.6 % and 39.8 - 4.5 + 0.7 % . For a model blend containing straight-chain, branched-chain, and terpenoid components, increasing the fraction of branched-chain alkanes from zero to 47% only lowers the electrical energy conversion efficiency from 40.1 - 4.5 + 0.7 % to 39.5 - 4.6 + 0.7 % .
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Affiliation(s)
- Timothy J. Sheppard
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - David A. Specht
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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9
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Li X, Liu H, Lin Z, Richardson JJ, Xie W, Chen F, Lin W, Caruso F, Zhou J, Liu B. Cytoprotective Metal-Phenolic Network Sporulation to Modulate Microalgal Mobility and Division. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308026. [PMID: 38014599 PMCID: PMC10797472 DOI: 10.1002/advs.202308026] [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: 10/24/2023] [Indexed: 11/29/2023]
Abstract
Synthetic cell exoskeletons created from abiotic materials have attracted interest in materials science and biotechnology, as they can regulate cell behavior and create new functionalities. Here, a facile strategy is reported to mimic microalgal sporulation with on-demand germination and locomotion via responsive metal-phenolic networks (MPNs). Specifically, MPNs with tunable thickness and composition are deposited on the surface of microalgae cells via one-step coordination, without any loss of cell viability or intrinsic cell photosynthetic properties. The MPN coating keeps the cells in a dormant state, but can be disassembled on-demand in response to environmental pH or chemical stimulus, thereby reviving the microalgae within 1 min. Moreover, the artificial sporulation of microalgae resulted in resistance to environmental stresses (e.g., metal ions and antibiotics) akin to the function of natural sporulation. This strategy can regulate the life cycle of complex cells, providing a synthetic strategy for designing hybrid microorganisms.
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Affiliation(s)
- Xiaojie Li
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Hai Liu
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Zhixing Lin
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Joseph J. Richardson
- Department of Chemical and Environmental EngineeringRMIT UniversityMelbourneVictoria3000Australia
| | - Weiying Xie
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Wei Lin
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Frank Caruso
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Jiajing Zhou
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Bin Liu
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
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10
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Sheppard TJ, Specht DA, Barstow B. Upper limit efficiency estimates for electromicrobial production of drop-in jet fuels. Bioelectrochemistry 2023; 154:108506. [PMID: 37473694 DOI: 10.1016/j.bioelechem.2023.108506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/22/2023]
Abstract
Microbes which participate in extracellular electron uptake (EEU) or H2 oxidation have the ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be valuable to efficiently synthesize drop-in jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-fuel conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency is 37.8-4.3+1.8% when using EEU for electron delivery and 40.1-4.6+0.7% when using H2 oxidation. The production efficiency can be raised to 44.2-3.7+0.5% when using the Formolase formate-assimilation pathway, and to 49.2-2.1+0.3% with the Wood-Ljungdahl pathway. This efficiency can be further raised by swapping the well-known Aldehyde Deformolating Oxygenase (ADO) termination pathway with the recently discovered Fatty Acid Photodecarboxylase (FAP) pathway. If these systems were supplied with electricity from a maximally-efficient silicon solar photovoltaic, even the least efficient pathway exceeds the maximum solar-to-fuel efficiency of all known forms of photosynthesis.
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Affiliation(s)
- Timothy J Sheppard
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - David A Specht
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
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11
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [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: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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12
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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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Orsi E, Nikel PI, Nielsen LK, Donati S. Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy. Nat Commun 2023; 14:6673. [PMID: 37865689 PMCID: PMC10590403 DOI: 10.1038/s41467-023-42166-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g. CO2, formate, methanol, etc.) are converted by microbial cell factories into value-added goods (i.e. food, feed, and chemicals). To render C1-based biomanufacturing cost-competitive, we must adapt microbial metabolism to perform chemical conversions at high rates and yields. To this end, the biotechnology community has undertaken two (seemingly opposing) paths: optimizing natural C1-trophic microorganisms versus engineering synthetic C1-assimilation de novo in model microorganisms. Here, we pose how these approaches can instead create synergies for strengthening the competitiveness of C1-based biomanufacturing as a whole.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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14
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Tang R, Yuan X, Yang J. Problems and corresponding strategies for converting CO 2 into value-added products in Cupriavidus necator H16 cell factories. Biotechnol Adv 2023; 67:108183. [PMID: 37286176 DOI: 10.1016/j.biotechadv.2023.108183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.
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Affiliation(s)
- Ruohao Tang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Xianzheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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15
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Li Y, Shi X, Tan W, Ling Q, Pei F, Luo S, Qin P, Yuan H, Huang L, Yu F. Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132033. [PMID: 37453352 DOI: 10.1016/j.jhazmat.2023.132033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/24/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Xinwei Shi
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Weilan Tan
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Qiujie Ling
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Fengmei Pei
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Shiyu Luo
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Peiqing Qin
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Huijian Yuan
- Hunan Suining Huayuange National Wetland Park, Suining, China
| | - Liuan Huang
- Hunan Suining Huayuange National Wetland Park, Suining, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China.
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16
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Li Y, Wang C, Chang H, Zhang Y, Liu S, He W. Metagenomics reveals the effect of long-term fertilization on carbon cycle in the maize rhizosphere. Front Microbiol 2023; 14:1170214. [PMID: 37275135 PMCID: PMC10235612 DOI: 10.3389/fmicb.2023.1170214] [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: 02/20/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
Long-term fertilization can result in the changes in carbon (C) cycle in the maize rhizosphere soil. However, there have been few reports on the impacts of microbial regulatory mechanisms on the C cycle in soil. In the study, we analyzed the response of functional genes that regulate the C fixation, decomposition and methane (CH4) metabolism in maize rhizosphere soil to different fertilization treatments using metagenomics analysis. As the dominant C fixation pathway in maize rhizosphere soil, the abundance of the functional genes regulating the reductive citrate cycle (rTCA cycle) including korA, korB, and IHD1 was higher under the chemical nitrogen (N) fertilizer treatments [nitrogen fertilizer (N), compound chemical fertilization (NPK), the combination of compound chemical fertilizer with maize straw (NPKS)] than maize straw return treatments [maize straw return (S), the combination of phosphorus and potassium fertilizer with maize straw (PKS)]. The NPK treatment decreased the abundance of functional genes involved in 3-hydroxypropionate bicycle (3-HP cycle; porA, porB, and porD), which was one of the major C fixation pathways in soil aside from dicarboxylate-hydroxybutyrate (DC/4-HB cycle) and Calvin cycle. The abundance of functional genes related to C degradation was higher in S, PKS and NPKS treatments than N and NPK treatments, and chemical N fertilizer application had a significant effect on C degradation. The dominant Methanaogenesis pathway in maize rhizosphere soil, used acetate as a substrate, and was significantly promoted under chemical N fertilizer application. The functional genes that were related to CH4 oxidation (i.e., pmoA and pmoB) were reduced under N and NPK treatments. Moreover, soil chemical properties had a significant impact on the functional genes related to C fixation and degradation, with SOC (r2 = 0.79) and NO3--N (r2 = 0.63) being the main regulators. These results implied that N fertilization rather than maize straw return had a greater influence on the C cycle in maize rhizosphere soil.
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Affiliation(s)
- Yanan Li
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Jilin Agricultural University, Changchun, China
| | - Chengyu Wang
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Jilin Agricultural University, Changchun, China
| | - Hongyan Chang
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Jilin Agricultural University, Changchun, China
| | - Yumang Zhang
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Jilin Agricultural University, Changchun, China
| | - Shuxia Liu
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Jilin Agricultural University, Changchun, China
| | - Wentian He
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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17
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Baleeiro FCF, Varchmin L, Kleinsteuber S, Sträuber H, Neumann A. Formate-induced CO tolerance and methanogenesis inhibition in fermentation of syngas and plant biomass for carboxylate production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:26. [PMID: 36805806 PMCID: PMC9936662 DOI: 10.1186/s13068-023-02271-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/29/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Production of monocarboxylates using microbial communities is highly dependent on local and degradable biomass feedstocks. Syngas or different mixtures of H2, CO, and CO2 can be sourced from biomass gasification, excess renewable electricity, industrial off-gases, and carbon capture plants and co-fed to a fermenter to alleviate dependence on local biomass. To understand the effects of adding these gases during anaerobic fermentation of plant biomass, a series of batch experiments was carried out with different syngas compositions and corn silage (pH 6.0, 32 °C). RESULTS Co-fermentation of syngas with corn silage increased the overall carboxylate yield per gram of volatile solids (VS) by up to 29% (0.47 ± 0.07 g gVS-1; in comparison to 0.37 ± 0.02 g gVS-1 with a N2/CO2 headspace), despite slowing down biomass degradation. Ethylene and CO exerted a synergistic effect in preventing methanogenesis, leading to net carbon fixation. Less than 12% of the electrons were misrouted to CH4 when either 15 kPa CO or 5 kPa CO + 1.5 kPa ethylene was used. CO increased the selectivity to acetate and propionate, which accounted for 85% (electron equivalents) of all products at 49 kPa CO, by favoring lactic acid bacteria and actinobacteria over n-butyrate and n-caproate producers. Inhibition of n-butyrate and n-caproate production by CO happened even when an inoculum preacclimatized to syngas and lactate was used. Intriguingly, the effect of CO on n-butyrate and n-caproate production was reversed when formate was present in the broth. CONCLUSIONS The concept of co-fermenting syngas and plant biomass shows promise in three aspects: by making anaerobic fermentation a carbon-fixing process, by increasing the yields of short-chain carboxylates (propionate and acetate), and by minimizing electron losses to CH4. Moreover, a model was proposed for how formate can alleviate CO inhibition in certain acidogenic bacteria. Testing the fermentation of syngas and plant biomass in a continuous process could potentially improve selectivity to n-butyrate and n-caproate by enriching chain-elongating bacteria adapted to CO and complex biomass.
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Affiliation(s)
- Flávio C F Baleeiro
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Lukas Varchmin
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany.
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Recent Advances In Microbe-Photocatalyst Hybrid Systems for Production of Bulk Chemicals: A Review. Appl Biochem Biotechnol 2023; 195:1574-1588. [PMID: 36346559 DOI: 10.1007/s12010-022-04169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Solar-driven biocatalysis technologies can combine inorganic photocatalytic materials with biological catalysts to convert CO2, light, and water into chemicals, offering the promise of high energy efficiency and a broader product scope than that of natural photosynthesis. Solar energy is the most abundant renewable energy source on earth, but it cannot be directly utilized by current industrial microorganisms. Therefore, the establishment of a solar-driven bio-catalysis platform, a bridge between solar energy and heterotrophic microorganisms, can dramatically increase carbon flux in biomanufacturing systems and consequently may revolutionize the biorefinery. This review first discusses the main applications of microbe-photocatalyst hybrid (MPH) systems in biorefinery processes. Then, various strategies to improve the electron transfer by microorganisms at the inorganic photocatalytic material interface are discussed, especially biohybrid systems based on autotrophic or heterotrophic bacteria and photocatalytic materials. Finally, we discuss the current challenges and offer potential solutions for the development of MPH systems.
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Lv X, Yu W, Zhang C, Ning P, Li J, Liu Y, Du G, Liu L. C1-based biomanufacturing: Advances, challenges and perspectives. BIORESOURCE TECHNOLOGY 2023; 367:128259. [PMID: 36347475 DOI: 10.1016/j.biortech.2022.128259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Baima Future Foods Research Institute, Nanjing 211225, China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chenyang Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Peng Ning
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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20
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Ergün BG, Laçın K, Çaloğlu B, Binay B. Second generation Pichia pastoris strain and bioprocess designs. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:150. [PMID: 36581872 PMCID: PMC9798597 DOI: 10.1186/s13068-022-02234-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/04/2022] [Indexed: 12/30/2022]
Abstract
Yeast was the first microorganism used by mankind for biotransformation processes that laid the foundations of industrial biotechnology. In the last decade, Pichia pastoris has become the leading eukaryotic host organism for bioproduct generation. Most of the P. pastoris bioprocess operations has been relying on toxic methanol and glucose feed. In the actual bioeconomy era, for sustainable value-added bioproduct generation, non-conventional yeast P. pastoris bioprocess operations should be extended to low-cost and renewable substrates for large volume bio-based commodity productions. In this review, we evaluated the potential of P. pastoris for the establishment of circular bioeconomy due to its potential to generate industrially relevant bioproducts from renewable sources and waste streams in a cost-effective and environmentally friendly manner. Furthermore, we discussed challenges with the second generation P. pastoris platforms and propose novel insights for future perspectives. In this regard, potential of low cost substrate candidates, i.e., lignocellulosic biomass components, cereal by-products, sugar industry by-products molasses and sugarcane bagasse, high fructose syrup by-products, biodiesel industry by-product crude glycerol, kitchen waste and other agri-food industry by products were evaluated for P. pastoris cell growth promoting effects and recombinant protein production. Further metabolic pathway engineering of P. pastoris to construct renewable and low cost substrate utilization pathways was discussed. Although, second generation P. pastoris bioprocess operations for valorisation of wastes and by-products still in its infancy, rapidly emerging synthetic biology tools and metabolic engineering of P. pastoris will pave the way for more sustainable environment and bioeconomy. From environmental point of view, second generation bioprocess development is also important for waste recycling otherwise disposal of carbon-rich effluents creates environmental concerns. P. pastoris high tolerance to toxic contaminants found in lignocellulosic biomass hydrolysate and industrial waste effluent crude glycerol provides the yeast with advantages to extend its applications toward second generation P. pastoris strain design and bioprocess engineering, in the years to come.
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Affiliation(s)
- Burcu Gündüz Ergün
- grid.18376.3b0000 0001 0723 2427National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey ,Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey
| | - Kübra Laçın
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Buse Çaloğlu
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Barış Binay
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey ,grid.448834.70000 0004 0595 7127BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400 Gebze Kocaeli, Turkey
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Srivastava RK, Sarangi PK, Vivekanand V, Pareek N, Shaik KB, Subudhi S. Microbial fuel cells for waste nutrients minimization: Recent process technologies and inputs of electrochemical active microbial system. Microbiol Res 2022; 265:127216. [DOI: 10.1016/j.micres.2022.127216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
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22
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Bankefa OE, Claassens NJ. Hybrid chem-bio production from electricity and CO2 via two-carbon mediators. Chem 2022. [DOI: 10.1016/j.chempr.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Guan X, Erşan S, Hu X, Atallah TL, Xie Y, Lu S, Cao B, Sun J, Wu K, Huang Y, Duan X, Caram JR, Yu Y, Park JO, Liu C. Maximizing light-driven CO 2 and N 2 fixation efficiency in quantum dot-bacteria hybrids. Nat Catal 2022; 5:1019-1029. [PMID: 36844635 PMCID: PMC9956923 DOI: 10.1038/s41929-022-00867-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022]
Abstract
Integrating light-harvesting materials with microbial biochemistry is a viable approach to produce chemicals with high efficiency from the air, water, and sunlight. Yet it remains unclear whether all absorbed photons in the materials can be transferred through the material-biology interface for solar-to-chemical production and whether the presence of materials beneficially affect the microbial metabolism. Here we report a microbe-semiconductor hybrid by interfacing CO2/N2-fixing bacterium Xanthobacter autotrophicus with CdTe quantum dots for light-driven CO2 and N2 fixation with internal quantum efficiencies of 47.2 ± 7.3% and 7.1 ± 1.1%, respectively, reaching the biochemical limits of 46.1% and 6.9% imposed by the stoichiometry in biochemical pathways. Photophysical studies suggest fast charge-transfer kinetics at the microbe-semiconductor interfaces, while proteomics and metabolomics indicate a material-induced regulation of microbial metabolism favoring higher quantum efficiencies compared to the biological counterparts alone.
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Affiliation(s)
- Xun Guan
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Sevcan Erşan
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Xiangchen Hu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Timothy L. Atallah
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, Denison University, Granville, Ohio 43023, United States
| | - Yongchao Xie
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shengtao Lu
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Bocheng Cao
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jingwen Sun
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Ke Wu
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yu Huang
- Department of Materials Science and Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Xiangfeng Duan
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Justin R. Caram
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yi Yu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junyoung O. Park
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California 90095, United States
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24
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Fang Y, Liu X, Liu Z, Han L, Ai J, Zhao G, Terasaki O, Cui C, Yang J, Liu C, Zhou Z, Chen L, Che S. Synthesis of amino acids by electrocatalytic reduction of CO2 on chiral Cu surfaces. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Meng X, Liu L, Chen X. Bacterial photosynthesis: state-of-the-art in light-driven carbon fixation in engineered bacteria. Curr Opin Microbiol 2022; 69:102174. [DOI: 10.1016/j.mib.2022.102174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022]
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26
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Yilmaz S, Nyerges A, van der Oost J, Church GM, Claassens NJ. Towards next-generation cell factories by rational genome-scale engineering. Nat Catal 2022. [DOI: 10.1038/s41929-022-00836-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Zhu X, Lei C, Qi J, Zhen G, Lu X, Xu S, Zhang J, Liu H, Zhang X, Wu Z. The role of microbiome in carbon sequestration and environment security during wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155793. [PMID: 35550899 DOI: 10.1016/j.scitotenv.2022.155793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Wastewater treatment is an essential aspect of the earth's sustainable future. However, different wastewater treatment methods are responsible for carbon discharge into the environment, raising environmental risks. Hence, such wastewater treatment methods are required that can minimize carbon release without compromising the treatment quality. Microbiome-based carbon sequestration is a potential method for achieving this goal. Limited studies have been carried out to investigate how microbes can capture and utilize CO2. This review summarizes the approaches including microbial electrolytic carbon capture, microbial electrosynthesis, microbial fuel cell, microalgae cultivation, and constructed wetlands that employ microbes to capture and utilize CO2. Electroactive Bacteria (EAB) convert carbon dioxide to carbonates and bicarbonates in subsequent steps after organic matter decomposition. Similarly, microbial electrosynthesis (MES) not only helps capture carbon but also produces secondary products (production of polyhydroxyalkanoates by Gram-negative rod Aeromonas hydrophila bacteria) of commercial importance during wastewater treatment. In addition to this, microbial carbon capture cells (MCCs) have been now utilized for energy generation and carbon sequestration at the same time during wastewater treatment. Moreover, microalgae cultivation has also been found to capture CO2 at a rapid pace while releasing O2 as a consequence of photosynthesis. Hence, microbe-based wastewater treatment has quite a potential due to two-fold benefits like carbon sequestration and by-product formation.
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Affiliation(s)
- Xuefeng Zhu
- School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, PR China.
| | - Cheng Lei
- School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Jing Qi
- School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xueqin Lu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Suyun Xu
- School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Jie Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China.
| | - Hongbo Liu
- School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, PR China.
| | - Xuedong Zhang
- Department of Environmental Engineering, Faculty of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, PR China
| | - Zhichao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
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28
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Janasch M, Crang N, Asplund-Samuelsson J, Sporre E, Bruch M, Gynnå A, Jahn M, Hudson EP. Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator. Metab Eng 2022; 73:256-269. [PMID: 35987434 DOI: 10.1016/j.ymben.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/10/2022] [Accepted: 08/06/2022] [Indexed: 11/30/2022]
Abstract
The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields from formate for different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were then verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified additional reactions associated with low and high PHB yield. Proteomics analysis of the engineered strains confirmed an increased abundance of aconitase and cofactor balancing. The findings of this study aid in understanding metabolic adaptation. Furthermore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria.
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Affiliation(s)
- Markus Janasch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Nick Crang
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Emil Sporre
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Manuel Bruch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Arvid Gynnå
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Michael Jahn
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Elton P Hudson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
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29
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García Martínez JB, Pearce JM, Throup J, Cates J, Lackner M, Denkenberger DC. Methane Single Cell Protein: Potential to Secure a Global Protein Supply Against Catastrophic Food Shocks. Front Bioeng Biotechnol 2022; 10:906704. [PMID: 35957636 PMCID: PMC9358032 DOI: 10.3389/fbioe.2022.906704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/07/2022] [Indexed: 01/18/2023] Open
Abstract
Global catastrophes such as a supervolcanic eruption, asteroid impact, or nuclear winter could cause global agricultural collapse due to reduced sunlight reaching the Earth's surface. The human civilization's food production system is unprepared to respond to such events, but methane single cell protein (SCP) could be a key part of the solution. Current preparedness centers around food stockpiling, an excessively expensive solution given that an abrupt sunlight reduction scenario (ASRS) could hamper conventional agriculture for 5-10 years. Instead, it is more cost-effective to consider resilient food production techniques requiring little to no sunlight. This study analyses the potential of SCP produced from methane (natural gas and biogas) as a resilient food source for global catastrophic food shocks from ASRS. The following are quantified: global production potential of methane SCP, capital costs, material and energy requirements, ramp-up rates, and retail prices. In addition, potential bottlenecks for fast deployment are considered. While providing a more valuable, protein-rich product than its alternatives, the production capacity could be slower to ramp up. Based on 24/7 construction of facilities, 7%-11% of the global protein requirements could be fulfilled at the end of the first year. Despite significant remaining uncertainties, methane SCP shows significant potential to prevent global protein starvation during an ASRS at an affordable price-US$3-5/kg dry.
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Affiliation(s)
| | - Joshua M. Pearce
- Department of Electrical and Computer Engineering, Western University, London, ON, Canada
| | - James Throup
- Alliance to Feed the Earth in Disasters (ALLFED), Fairbanks, AK, United States
| | - Jacob Cates
- Alliance to Feed the Earth in Disasters (ALLFED), Fairbanks, AK, United States
| | - Maximilian Lackner
- FH Technikum Wien, Wien, Austria
- Circe Biotechnologie GmbH, Wien, Austria
| | - David C. Denkenberger
- Alliance to Feed the Earth in Disasters (ALLFED), Fairbanks, AK, United States
- University of Alaska Fairbanks (Mechanical Engineering and Alaska Center for Energy and Power), Fairbanks, AK, United States
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30
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Srisawat P, Higuchi-Takeuchi M, Numata K. Microbial autotrophic biorefineries: Perspectives for biopolymer production. Polym J 2022. [DOI: 10.1038/s41428-022-00675-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractThe use of autotrophic microorganisms to fabricate biochemical products has attracted much attention in both academia and industry. Unlike heterotrophic microorganisms that require carbohydrates and amino acids for growth, autotrophic microorganisms have evolved to utilize either light (photoautotrophs) or chemical compounds (chemolithotrophs) to fix carbon dioxide (CO2) and drive metabolic processes. Several biotechnological approaches, including synthetic biology and metabolic engineering, have been proposed to harness autotrophic microorganisms as a sustainable/green production platform for commercially essential products such as biofuels, commodity chemicals, and biopolymers. Here, we review the recent advances in natural autotrophic microorganisms (photoautotrophic and chemoautotrophic), focusing on the biopolymer production. We present current state-of-the-art technologies to engineer autotrophic microbial cell factories for efficient biopolymer production.
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31
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Wang Q, Kalathil S, Pornrungroj C, Sahm CD, Reisner E. Bacteria–photocatalyst sheet for sustainable carbon dioxide utilization. Nat Catal 2022. [DOI: 10.1038/s41929-022-00817-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Marecos S, Brigham R, Dressel A, Gaul L, Li L, Satish K, Tjokorda I, Zheng J, Schmitz AM, Barstow B. Practical and Thermodynamic Constraints on Electromicrobially-Accelerated CO2 Mineralization. iScience 2022; 25:104769. [PMID: 35992063 PMCID: PMC9385556 DOI: 10.1016/j.isci.2022.104769] [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: 01/27/2022] [Revised: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 10/30/2022] Open
Abstract
By the end of the century, tens of gigatonnes of CO2 will need to be removed from the atmosphere every year to maintain global temperatures. Natural weathering of ultramafic rocks and subsequent mineralization reactions can convert CO2 into ultra-stable carbonates. Although this will draw down all excess CO2, it will take thousands of years. CO2 mineralization could be accelerated by weathering ultramafic rocks with biodegradable lixiviants. We show that if these lixiviants come from cellulosic biomass, this demand could monopolize the world’s biomass supply. We demonstrate that electromicrobial production technologies (EMP) that combine renewable electricity and microbial metabolism could produce lixiviants for as little as $200 to $400 per tonne at solar electricity prices achievable within the decade. We demonstrate that EMP could make enough lixiviants to sequester a tonne of CO2 for less than $100. This work highlights the potential of this approach and the need for extensive R&D. Bio-production of acids to sequester 20 GtCO2 yr−1 could monopolize global agriculture Electromicrobial production could produce acids for as little as $200 to $400 per tonne Electromicrobial production could make acids to sequester 1 tonne CO2 for under $100
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33
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Cestellos-Blanco S, Chan RR, Shen YX, Kim JM, Tacken TA, Ledbetter R, Yu S, Seefeldt LC, Yang P. Photosynthetic biohybrid coculture for tandem and tunable CO 2 and N 2 fixation. Proc Natl Acad Sci U S A 2022; 119:e2122364119. [PMID: 35727971 PMCID: PMC9245687 DOI: 10.1073/pnas.2122364119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms powered by electrochemical reducing equivalents assimilate CO2, H2O, and N2 building blocks. However, products from autotrophic whole-cell biocatalysts are limited. Furthermore, biocatalysts tasked with N2 reduction are constrained by simultaneous energy-intensive autotrophy. To overcome these challenges, we designed a biohybrid coculture for tandem and tunable CO2 and N2 fixation to value-added products, allowing the different species to distribute bioconversion steps and reduce the individual metabolic burden. This consortium involves acetogen Sporomusa ovata, which reduces CO2 to acetate, and diazotrophic Rhodopseudomonas palustris, which uses the acetate both to fuel N2 fixation and for the generation of a biopolyester. We demonstrate that the coculture platform provides a robust ecosystem for continuous CO2 and N2 fixation, and its outputs are directed by substrate gas composition. Moreover, we show the ability to support the coculture on a high-surface area silicon nanowire cathodic platform. The biohybrid coculture achieved peak faradaic efficiencies of 100, 19.1, and 6.3% for acetate, nitrogen in biomass, and ammonia, respectively, while maintaining product tunability. Finally, we established full solar to chemical conversion driven by a photovoltaic device, resulting in solar to chemical efficiencies of 1.78, 0.51, and 0.08% for acetate, nitrogenous biomass, and ammonia, correspondingly. Ultimately, our work demonstrates the ability to employ and electrochemically manipulate bacterial communities on demand to expand the suite of CO2 and N2 bioelectrosynthesis products.
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Affiliation(s)
- Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
| | - Rachel R. Chan
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Yue-xiao Shen
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ji Min Kim
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
| | - Tom A. Tacken
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Rhesa Ledbetter
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Sunmoon Yu
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Lance C. Seefeldt
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Peidong Yang
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
- Center for the Utilization of Biological Engineering in Space, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Kavli Energy Nanosciences Institute, Berkeley, CA 94720
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34
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Photocatalytic Material-Microorganism Hybrid System and Its Application—A Review. MICROMACHINES 2022; 13:mi13060861. [PMID: 35744475 PMCID: PMC9230708 DOI: 10.3390/mi13060861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/21/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023]
Abstract
The photocatalytic material-microorganism hybrid system is an interdisciplinary research field. It has the potential to synthesize various biocompounds by using solar energy, which brings new hope for sustainable green energy development. Many valuable reviews have been published in this field. However, few reviews have comprehensively summarized the combination methods of various photocatalytic materials and microorganisms. In this critical review, we classified the biohybrid designs of photocatalytic materials and microorganisms, and we summarized the advantages and disadvantages of various photocatalytic material/microorganism combination systems. Moreover, we introduced their possible applications, future challenges, and an outlook for future developments.
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35
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Azemtsop Matanfack G, Taubert M, Reilly-Schott V, Küsel K, Rösch P, Popp J. Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D 2O Labeling. Anal Chem 2022; 94:7759-7766. [PMID: 35608509 DOI: 10.1021/acs.analchem.1c04097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO2) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D2O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D2O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Vincent Reilly-Schott
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
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36
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Zhang C, Ottenheim C, Weingarten M, Ji L. Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients. Front Bioeng Biotechnol 2022; 10:874612. [PMID: 35480982 PMCID: PMC9035589 DOI: 10.3389/fbioe.2022.874612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO2, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Congqiang Zhang, ,
| | - Christoph Ottenheim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Melanie Weingarten
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - LiangHui Ji
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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38
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González JM, Martí-Arbona R, Chen JCH, Unkefer CJ. The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding. Acta Crystallogr F Struct Biol Commun 2022; 78:177-184. [PMID: 35400670 PMCID: PMC8996150 DOI: 10.1107/s2053230x22003612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
A structure-function characterization of Synechococcus elongatus enolase (SeEN) is presented, representing the first structural report on a cyanobacterial enolase. X-ray crystal structures of SeEN in its apoenzyme form and in complex with phosphoenolpyruvate are reported at 2.05 and 2.30 Å resolution, respectively. SeEN displays the typical fold of enolases, with a conformationally flexible loop that closes the active site upon substrate binding, assisted by two metal ions that stabilize the negatively charged groups. The enzyme exhibits a catalytic efficiency of 1.2 × 105 M-1 s-1 for the dehydration of 2-phospho-D-glycerate, which is comparable to the kinetic parameters of related enzymes. These results expand the understanding of the biophysical features of these enzymes, broadening the toolbox for metabolic engineering applications.
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Affiliation(s)
- Javier M. González
- Instituto de Bionanotecnología del NOA (INBIONATEC–CONICET), Universidad Nacional de Santiago del Estero (UNSE), RN9, Km1125, G4206XCP Santiago del Estero, Argentina
| | | | - Julian C.-H. Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Clifford J. Unkefer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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39
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Turning waste gases into valuables. Synth Syst Biotechnol 2022; 7:847-848. [PMID: 35572765 PMCID: PMC9079231 DOI: 10.1016/j.synbio.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Liu YF, Yang L, Liu ZL, Chen J, Fang B, Zhou L, Liu JF, Yang SZ, Gu JD, Mu BZ. Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales. Environ Microbiol 2022; 24:3063-3080. [PMID: 35254697 DOI: 10.1111/1462-2920.15965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, P.R. China
| | - Liu Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Bo Fang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
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41
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Papanikolaou G, Centi G, Perathoner S, Lanzafame P. Catalysis for e-Chemistry: Need and Gaps for a Future De-Fossilized Chemical Production, with Focus on the Role of Complex (Direct) Syntheses by Electrocatalysis. ACS Catal 2022; 12:2861-2876. [PMID: 35280435 PMCID: PMC8902748 DOI: 10.1021/acscatal.2c00099] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/29/2022] [Indexed: 12/29/2022]
Abstract
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The prospects, needs
and limits in current approaches in catalysis
to accelerate the transition to e-chemistry, where
this term indicates a fossil fuel-free chemical production, are discussed.
It is suggested that e-chemistry is a necessary element
of the transformation to meet the targets of net zero emissions by
year 2050 and that this conversion from the current petrochemistry
is feasible. However, the acceleration of the development of catalytic
technologies based on the use of renewable energy sources (indicated
as reactive catalysis) is necessary, evidencing that these are part
of a system of changes and thus should be assessed from this perspective.
However, it is perceived that the current studies in the area are
not properly addressing the needs to develop the catalytic technologies
required for e-chemistry, presenting a series of
relevant aspects and directions in which research should be focused
to develop the framework system transformation necessary to implement e-chemistry.
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Affiliation(s)
- Georgia Papanikolaou
- University of Messina, Dept. ChiBioFarAm, ERIC aisbl and CASPE/INSTM, V. le F. Stagno d’ Alcontres 31, 98166 Messina, Italy
| | - Gabriele Centi
- University of Messina, Dept. ChiBioFarAm, ERIC aisbl and CASPE/INSTM, V. le F. Stagno d’ Alcontres 31, 98166 Messina, Italy
| | - Siglinda Perathoner
- University of Messina, Dept. ChiBioFarAm, ERIC aisbl and CASPE/INSTM, V. le F. Stagno d’ Alcontres 31, 98166 Messina, Italy
| | - Paola Lanzafame
- University of Messina, Dept. ChiBioFarAm, ERIC aisbl and CASPE/INSTM, V. le F. Stagno d’ Alcontres 31, 98166 Messina, Italy
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42
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Wise L, Marecos S, Randolph K, Hassan M, Nshimyumukiza E, Strouse J, Salimijazi F, Barstow B. Thermodynamic Constraints on Electromicrobial Protein Production. Front Bioeng Biotechnol 2022; 10:820384. [PMID: 35265598 PMCID: PMC8899463 DOI: 10.3389/fbioe.2022.820384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/14/2022] [Indexed: 02/03/2023] Open
Abstract
Global consumption of protein is projected to double by the middle of the 21st century. However, protein production is one of the most energy intensive and environmentally damaging parts of the food supply system today. Electromicrobial production technologies that combine renewable electricity and CO2-fixing microbial metabolism could dramatically increase the energy efficiency of commodity chemical production. Here we present a molecular-scale model that sets an upper limit on the performance of any organism performing electromicrobial protein production. We show that engineered microbes that fix CO2 and N2 using reducing equivalents produced by H2-oxidation or extracellular electron uptake could produce amino acids with energy inputs as low as 64 MJ kg-1, approximately one order of magnitude higher than any previous estimate of the efficiency of electromicrobial protein production. This work provides a roadmap for development of engineered microbes that could significantly expand access to proteins produced with a low environmental footprint.
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Affiliation(s)
- Lucas Wise
- >
Department of Food Sciences, Cornell University, Ithaca, NY, United States
| | - Sabrina Marecos
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Katie Randolph
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Mohamed Hassan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Eric Nshimyumukiza
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Jacob Strouse
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
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43
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Hanko EKR, Sherlock G, Minton NP, Malys N. Biosensor-informed engineering of Cupriavidus necator H16 for autotrophic D-mannitol production. Metab Eng 2022; 72:24-34. [PMID: 35149227 DOI: 10.1016/j.ymben.2022.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/26/2023]
Abstract
Cupriavidus necator H16 is one of the most researched carbon dioxide (CO2)-fixing bacteria. It can store carbon in form of the polymer polyhydroxybutyrate and generate energy by aerobic hydrogen oxidation under lithoautotrophic conditions, making C. necator an ideal chassis for the biological production of value-added compounds from waste gases. Despite its immense potential, however, the experimental evidence of C. necator utilisation for autotrophic biosynthesis of chemicals is limited. Here, we genetically engineered C. necator for the high-level de novo biosynthesis of the industrially relevant sugar alcohol mannitol directly from Calvin-Benson-Bassham (CBB) cycle intermediates. To identify optimal mannitol production conditions in C. necator, a mannitol-responsive biosensor was applied for screening of mono- and bifunctional mannitol 1-phosphate dehydrogenases (MtlDs) and mannitol 1-phosphate phosphatases (M1Ps). We found that MtlD/M1P from brown alga Ectocarpus siliculosus performed overall the best under heterotrophic growth conditions and was selected to be chromosomally integrated. Consequently, autotrophic fermentation of recombinant C. necator yielded up to 3.9 g/L mannitol, representing a substantial improvement over mannitol biosynthesis using recombinant cyanobacteria. Importantly, we demonstrate that at the onset of stationary growth phase nearly 100% of carbon can be directed from the CBB cycle into mannitol through the glyceraldehyde 3-phosphate and fructose 6-phosphate intermediates. This study highlights for the first time the potential of C. necator to generate sugar alcohols from CO2 utilising precursors derived from the CBB cycle.
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Affiliation(s)
- Erik K R Hanko
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom; Present address: Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Gillian Sherlock
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Naglis Malys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
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44
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Improved polyhydroxybutyrate production by Cupriavidus necator and the photocatalyst graphitic carbon nitride from fructose under low light intensity. Int J Biol Macromol 2022; 203:526-534. [PMID: 35120931 DOI: 10.1016/j.ijbiomac.2022.01.179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/21/2022]
Abstract
The photocatalyst graphitic carbon nitride (g-C3N4) is known to photostimulate the production of the bioplastic polyhydroxybutyrate (PHB) by Cupriavidus necator. In previous studies, the combination of C. necator and g-C3N4 increased PHB yield from either an organic or inorganic carbon substrate under a light intensity of 4200 lx. Here, different parameters including light intensity, pH, temperature, nitrogen and carbon concentrations, aeration, and inoculum size were explored to maximize PHB production by hybrid photosynthesis from fructose and visible light. A g-C3N4/C. necator culture grown with a lower light intensity of 2100 lx, an inoculum size of 128.30 × 106 CFU ml-1, and constant aeration produced 7.16 g l-1 d-1 PHB with a product yield from fructose of 60.94%. Furthermore, the ratio of incident photons harvested by g-C3N4 converted into NADPH+H+ by C. necator for PHB production was improved to 19.74% after the process optimization. In comparison, the PHB production rate of a non-optimized g-C3N4/C. necator system exposed to 4200 lx was only 2.94 g l-1 d-1 with a product yield from fructose of 33.29%. These results demonstrate that hybrid photosynthesis productivity can be significantly augmented by decreasing light intensity and adjusting other parameters, which is promising for future bioproduction applications.
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45
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Rin Kim S, Kim SJ, Kim SK, Seo SO, Park S, Shin J, Kim JS, Park BR, Jin YS, Chang PS, Park YC. Yeast metabolic engineering for carbon dioxide fixation and its application. BIORESOURCE TECHNOLOGY 2022; 346:126349. [PMID: 34800639 DOI: 10.1016/j.biortech.2021.126349] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
As numerous industrial bioprocesses rely on yeast fermentation, developing CO2-fixing yeast strains can be an attractive option toward sustainable industrial processes and carbon neutrality. Recent studies have shown that the expression of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) in yeasts, such as Saccharomyces cerevisiae and Kluyveromyces marxianus, enables mixotrophic CO2 fixation and production of biofuels. Also, the expression of a synthetic Calvin-Benson-Bassham (CBB) cycle including RuBisCO in Pichia pastoris enables autotrophic growth on CO2. This review highlights recent advances in metabolic engineering strategies to enable CO2 fixation in yeasts. Also, we discuss the potentials of other natural and synthetic metabolic pathways independent of RuBisCO for developing CO2-fixing yeast strains capable of producing value-added biochemicals.
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Affiliation(s)
- Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Nutrition, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Sujeong Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jamin Shin
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bo-Ram Park
- Department of Agro-food Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pahn-Shick Chang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Republic of Korea.
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46
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Yamada S, Takamatsu Y, Ikeda S, Kouzuma A, Watanabe K. Towards Application of Electro-Fermentation for the Production of Value-Added Chemicals From Biomass Feedstocks. Front Chem 2022; 9:805597. [PMID: 35127650 PMCID: PMC8807546 DOI: 10.3389/fchem.2021.805597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/03/2022] Open
Abstract
According to recent social demands for sustainable developments, the value of biomass as feedstocks for chemical industry is increasing. With the aid of metabolic engineering and genome editing, microbial fermentation has been developed for producing value-added chemicals from biomass feedstocks, while further improvements are desired for producing more diverse chemicals and increasing the production efficiency. The major intrinsic limitation in conventional fermentation technologies is associated with the need for balancing the net redox equivalents between substrates and products, resulting in limited repertories of fermentation products. One solution for this limitation would be “electro-fermentation (EF)” that utilizes bioelectrochemical systems for modifying the intracellular redox state of electrochemically active bacteria, thereby overcoming the redox constraint of fermentation. Recent studies have attempted the production of chemicals based on the concept of EF, while its utility has not been sufficiently demonstrated in terms of low production efficiencies. Here we discuss EF in terms of its concept, current status and future directions, which help us develop its practical applications to sustainable chemical industries.
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47
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Talekar S, Jo BH, Dordick JS, Kim J. Carbonic anhydrase for CO 2 capture, conversion and utilization. Curr Opin Biotechnol 2022; 74:230-240. [PMID: 34992045 DOI: 10.1016/j.copbio.2021.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/07/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
Carbonic anhydrase (CA) enzymes, catalyzing the CO2 hydration at a high turnover number, can be employed in expediting CO2 capture, conversion and utilization to aid in carbon neutrality. Despite extensive research over the last decade, there remain challenges in CA-related technologies due to poor stability and suboptimal use of CAs. Herein, we discuss recent advances in CA stabilization by protein engineering and enzyme immobilization, and shed light on state-of-the-art of in vitro and in vivo CA-mediated CO2 conversion for improved production of value-added chemicals using CO2 as a feedstock.
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Affiliation(s)
- Sachin Talekar
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Byung Hoon Jo
- Division of Life Science and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy 12180, NY, USA.
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
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48
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Engineering the Reductive Glycine Pathway: A Promising Synthetic Metabolism Approach for C1-Assimilation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:299-350. [DOI: 10.1007/10_2021_181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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49
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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50
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Abel AJ, Hilzinger JM, Arkin AP, Clark DS. Systems-informed genome mining for electroautotrophic microbial production. Bioelectrochemistry 2022; 145:108054. [DOI: 10.1016/j.bioelechem.2022.108054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
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