1
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Zhang C, Traitrongsat P, Zeng AP. Electrochemically mediated bioconversion and integrated purification greatly enhanced co-production of 1,3-propanediol and organic acids from glycerol in an industrial bioprocess. Bioprocess Biosyst Eng 2023; 46:565-575. [PMID: 36648555 DOI: 10.1007/s00449-022-02841-6] [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: 10/09/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023]
Abstract
In this study, we show how electrochemically mediated bioconversion can greatly increase the co-production of 1,3-propanediol and organic acids from glycerol in an industrial bioprocess using a Clostridum pasteurianum mutant. Remarkably, an enhanced butyrate formation was observed due to a weakened butanol pathway of the mutant. This allowed the strain to have a higher ATP generation for an enhanced growth, higher glycerol consumption and PDO production. The PDO titer reached as high as 120.67 g/L at a cathodic current of -400 mA, which is 33% higher than that without electricity, with a concurrent increase of butyric acid by 80%. To fully recover the increased PDO and organic acids, a novel downstream process combining thin film evaporation of PDO and esterification of organic acids with ethanol was developed. This enables the efficient co-production of PDO, ethyl acetate and ethyl butyrate with a high overall carbon use of 87%.
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Affiliation(s)
- Chijian Zhang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany.,Hua An Tang Biotech Group Co., Ltd, Guangzhou, China
| | - Pawin Traitrongsat
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - An-Ping Zeng
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, China. .,Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany.
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2
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Atasoy M, Cetecioglu Z. The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115700. [PMID: 35982552 DOI: 10.1016/j.jenvman.2022.115700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Volatile fatty acids, intermediate products of anaerobic digestion, are one of the most promising biobased products. In this study, the effects of acidic (pH 5), neutral (without pH adjustment) and alkali (pH 10) pH on production efficiency and composition of volatile fatty acids (VFAs) and bacterial community profile were analyzed. The anaerobic sequencing batch reactors were fed cheese production wastewater as substrate and inoculated by anaerobic granular seed sludge. The results showed that acidic pH improved VFA production yield (0.92 at pH 5; 0.42 at pH 10 and 0.21 gCOD/gVS at neutral pH). Furthermore, propionic acid was dominant under both pH 10 (64 ± 20%) and neutral pH (72 ± 8%), whereas, acetic acid (23 ± 20%4), propionic acid (22 ± 3%), butyric acid (21 ± 4%) and valeric acid (15 ± 8%) were almost equally distributed under pH 5. Adaptation of bacterial community to different pH conditions might steer the acid profile: Bacteroidetes (50.07 ± 2%) under pH 10, Proteobacteria (40.74 ± 7%) under neutral pH and Firmicutes (47.64 ± 9%) under pH 5 were the most dominant phylum, respectively. Results indicated pH plays a significant role in VFA production, acid composition, and bacterial community structure. However, in order to gain a concrete understanding effects of pH, characterization of intracellular and extracellular metabolites with dynamics of the microbial community is required.
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Affiliation(s)
- Merve Atasoy
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden; UNLOCK, Wageningen University and Research, 6708 PB, the Netherlands.
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden; Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, 11421, Stockholm, Sweden
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3
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Zhang C, Sharma S, Ma C, Zeng AP. Strain evolution and novel downstream processing with integrated catalysis enable highly efficient co-production of 1,3-Propanediol and organic acid esters from crude glycerol. Biotechnol Bioeng 2022; 119:1450-1466. [PMID: 35234295 DOI: 10.1002/bit.28070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/05/2022] [Accepted: 02/20/2022] [Indexed: 11/09/2022]
Abstract
Bioconversion of natural microorganisms generally results in a mixture of various compounds. Downstream processing (DSP) which only targets a single product often lacks economic competitiveness due to incomplete use of raw material and high cost of waste treatment for by-products. Here, we show with the efficient microbial conversion of crude glycerol by an artificially evolved strain and how a catalytic conversion strategy can improve the total products yield and process economy of the DSP. Specifically, Clostridium pasteurianum was first adapted to increased concentration of crude glycerol in a novel automatic laboratory evolution system. At m3 scale bioreactor the strain achieved a simultaneous production of 1,3-propanediol (PDO), acetic and butyric acids at 81.21, 18.72 and 11.09 g/L within only 19 h, respectively, representing the most efficient fermentation of crude glycerol to targeted products. A heterogeneous catalytic step was developed and integrated into the DSP process to obtain high-value methyl esters from acetic and butyric acids at high yields. The co-production of the esters also greatly simplified the recovery of PDO. For example, a cosmetic grade PDO (96% PDO) was easily obtained by a simple single-stage distillation process (with an overall yield more than 77%). This integrated approach provides an industrially attractive route for the simultaneous production of three appealing products from the crude glycerol fermentation broth, which greatly improve the process economy and ecology. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chijian Zhang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany.,Hua An Tang Biotech Group Co., Ltd, Guangzhou, China
| | - Shubhang Sharma
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Chengwei Ma
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
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4
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He Y, Lens PNL, Veiga MC, Kennes C. Effect of Endogenous and Exogenous Butyric Acid on Butanol Production From CO by Enriched Clostridia. Front Bioeng Biotechnol 2022; 10:828316. [PMID: 35252136 PMCID: PMC8888879 DOI: 10.3389/fbioe.2022.828316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Butanol is a potential renewable fuel. To increase the selectivity for butanol during CO fermentation, exogenous acetic acid and ethanol, exogenous butyric acid or endogenous butyric acid from glucose fermentation have been investigated using CO as reducing power, with a highly enriched Clostridium sludge. Addition of 3.2 g/L exogenous butyric acid led to the highest 1.9 g/L butanol concentration with a conversion efficiency of 67%. With exogenous acetate and ethanol supply, the butanol concentration reached 1.6 g/L at the end of the incubation. However, the presence of acetic acid and ethanol favoured butanol production to 2.6 g/L from exogenous butyric acid by the enriched sludge. Finally, exogenous 14 g/L butyric acid yielded the highest butanol production of 3.4 g/L, which was also among the highest butanol concentration from CO/syngas fermentation reported so far. CO addition triggered butanol production from endogenous butyric acid (produced from glucose, Glucose + N2) with as high as 58.6% conversion efficiency and 62.1% butanol yield. However, no efficient butanol production was found from glucose and CO co-fermentation (Glucose + CO), although a similar amount of endogenous butyric acid was produced compared to Glucose + N2. The Clostridium genus occupied a relative abundance as high as 82% from the initial inoculum, while the Clostridia and Bacilli classes were both enriched and dominated in Glucose + N2 and Glucose + CO incubations. This study shows that the supply of butyric acid is a possible strategy for enhancing butanol production by CO fed anaerobic sludge, either via exogenous butyric acid, or via endogenous production by sugar fermentation.
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Affiliation(s)
- Yaxue He
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), A Coruña, Spain
- National University of Ireland Galway, Galway, Ireland
| | | | - María C. Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), A Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), A Coruña, Spain
- *Correspondence: Christian Kennes,
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5
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Hong Y, Nguyen T, Arbter P, Utesch T, Zeng A. Phenotype analysis of cultivation processes via unsupervised machine learning: Demonstration for Clostridium pasteurianum. Eng Life Sci 2022; 22:85-99. [PMID: 35140556 PMCID: PMC8811730 DOI: 10.1002/elsc.202100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/02/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
A novel approach of phenotype analysis of fermentation-based bioprocesses based on unsupervised learning (clustering) is presented. As a prior identification of phenotypes and conditional interrelations is desired to control fermentation performance, an automated learning method to output reference phenotypes (defined as vector of biomass-specific rates) was developed and the necessary computing process and parameters were assessed. For its demonstration, time series data of 90 Clostridium pasteurianum cultivations were used which feature a broad spectrum of solventogenic and acidogenic phenotypes, while 14 clusters of phenotypic manifestations were identified. The analysis of reference phenotypes showed distinct differences, where potential conditionalities were exemplary isolated. Further, cluster-based balancing of carbon and ATP or the use of reference phenotypes as indicator for bioprocess monitoring were demonstrated to highlight the perks of this approach. Overall, such analysis depends strongly on the quality of the data and experimental validations will be required before conclusions. However, the automated, streamlined and abstracted approach diminishes the need of individual evaluation of all noisy dataset and showed promising results, which could be transferred to strains with comparably wide-ranging phenotypic manifestations or as indicators for repeated bioprocesses with clearly defined target.
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Affiliation(s)
- Yaeseong Hong
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyTUHHHamburgGermany
| | - Tom Nguyen
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyTUHHHamburgGermany
| | - Philipp Arbter
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyTUHHHamburgGermany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyTUHHHamburgGermany
| | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyTUHHHamburgGermany
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6
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Valorization of waste frying oil to lipopeptide biosurfactant by indigenous Bacillus licheniformis through co-utilization in mixed substrate fermentation. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2021. [DOI: 10.1007/s43153-021-00170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Yuan H, Wang X, Lin TY, Kim J, Liu WT. Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Sci Rep 2021; 11:15140. [PMID: 34302023 PMCID: PMC8302695 DOI: 10.1038/s41598-021-94628-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.
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Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
| | - Xuehao Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
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8
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Arbter P, Sabra W, Utesch T, Hong Y, Zeng A. Metabolomic and kinetic investigations on the electricity-aided production of butanol by Clostridium pasteurianum strains. Eng Life Sci 2021; 21:181-195. [PMID: 33716617 PMCID: PMC7923553 DOI: 10.1002/elsc.202000035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/18/2020] [Accepted: 11/11/2020] [Indexed: 12/03/2022] Open
Abstract
In this contribution, we studied the effect of electro-fermentation on the butanol production of Clostridium pasteurianum strains by a targeted metabolomics approach. Two strains were examined: an electrocompetent wild type strain (R525) and a mutant strain (dhaB mutant) lacking formation of 1,3-propanediol (PDO). The dhaB-negative strain was able to grow on glycerol without formation of PDO, but displayed a high initial intracellular NADH/NAD ratio which was lowered subsequently by upregulation of the butanol production pathway. Both strains showed a 3-5 fold increase of the intracellular NADH/NAD ratio when exposed to cathodic current in a bioelectrochemical system (BES). This drove an activation of the butanol pathway and resulted in a higher molar butanol to PDO ratio for the R525 strain. Nonetheless, macroscopic electron balances suggest that no significant amount of electrons derived from the BES was harvested by the cells. Overall, this work points out that electro-fermentation can be used to trigger metabolic pathways and improve product formation, even when the used microbe cannot be considered electroactive. Accordingly, further studies are required to unveil the underlying (regulatory) mechanisms.
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Affiliation(s)
- Philipp Arbter
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Yaeseong Hong
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
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9
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Jiang Y, Wu R, Lu J, Dong W, Zhou J, Zhang W, Xin F, Jiang M. Quantitative proteomic analysis to reveal expression differences for butanol production from glycerol and glucose by Clostridium sp. strain CT7. Microb Cell Fact 2021; 20:12. [PMID: 33422075 PMCID: PMC7797090 DOI: 10.1186/s12934-021-01508-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/02/2021] [Indexed: 11/16/2022] Open
Abstract
Clostridium sp. strain CT7 is a new emerging microbial cell factory with high butanol production ratio owing to its non-traditional butanol fermentation mode with uncoupled acetone and 1,3-propanediol formation. Significant changes of metabolic products profile were shown in glycerol- and glucose-fed strain CT7, especially higher butanol and lower volatile fatty acids (VFAs) production occurred from glycerol-fed one. However, the mechanism of this interesting phenomenon was still unclear. To better elaborate the bacterial response towards glycerol and glucose, the quantitative proteomic analysis through iTRAQ strategy was performed to reveal the regulated proteomic expression levels under different substrates. Proteomics data showed that proteomic expression levels related with carbon metabolism and solvent generation under glycerol media were highly increased. In addition, the up-regulation of hydrogenases, ferredoxins and electron-transferring proteins may attribute to the internal redox balance, while the earlier triggered sporulation response in glycerol-fed media may be associated with the higher butanol production. This study will pave the way for metabolic engineering of other industrial microorganisms to obtain efficient butanol production from glycerol.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China
| | - Jiasheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 211800, Nanjing, P.R. China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 211800, Nanjing, P.R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 211800, Nanjing, P.R. China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, 211800, Nanjing, P. R. China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 211800, Nanjing, P.R. China.
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10
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Increased Selectivity for Butanol in Clostridium Pasteurianum Fermentations via Butyric Acid Addition or Dual Feedstock Strategy. FERMENTATION 2020. [DOI: 10.3390/fermentation6030067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Volatility of the petroleum market has renewed research into butanol as an alternate fuel. In order to increase the selectivity for butanol during glycerol fermentation with Clostridium pasteurianum, butyric acid can be added to the medium. In this manuscript, different methods of extracellular butyric acid addition are explored, as well as self-generation of butyric acid fermented from sugars in a co-substrate strategy. Molasses was used as an inexpensive sugar substrate, and the optimal molasses to glycerol ratio was found to allow the butyric acid to be taken back up into the cells and increase the productivity of butanol from all carbon sources. When butyric acid is added directly into the media, there was no significant difference between chemically pure butyric acid, or butyric acid rich supernatant from a separate fermentation. When low concentrations of butyric acid (1 or 2 g/L) are added to the initial media, an inhibitory effect is observed, with no influence on the butanol selectivity. However, when added later to the fermentation, over 1 g/L butyric acid is taken into the cells and increased the relative carbon yield from 0.449 to 0.519 mols carbon in product/mols carbon in substrate. An optimized dual substrate fermentation strategy in a pH-controlled reactor resulted in the relative carbon yield rising from 0.439 when grown on solely glycerol, to 0.480 mols C product/mols C substrate with the dual substrate strategy. An additional benefit is the utilization of a novel source of sugars to produce butanol from C. pasteurianum. The addition of butyric acid, regardless of how it is generated, under the proper conditions can allow for increased selectivity for butanol from all substrates.
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11
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Munch G, Schulte A, Mann M, Dinger R, Regestein L, Rehmann L, Büchs J. Online measurement of CO2 and total gas production in parallel anaerobic shake flask cultivations. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Sarchami T, Rehmann L. Increased Butanol Yields through Cosubstrate Fermentation of Jerusalem Artichoke Tubers and Crude Glycerol by Clostridium pasteurianum DSM 525. ACS OMEGA 2019; 4:15521-15529. [PMID: 31572853 PMCID: PMC6761685 DOI: 10.1021/acsomega.9b00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Clostridium pasteurianum DSM 525 can produce butanol, 1,3-propanediol, and ethanol from glycerol. The product distribution can be tilted toward butanol when adding butyric acid. The strain predominantly produces acetic and butyric acids when grown on saccharides. Hence, butyrate formed from saccharide conversion can be used to stimulate butanol production from glycerol under cosubstrate cultivation. The optimal cosubstrate ratio was determined, and under optimal conditions, a butanol yield and a productivity of 0.27 ± 0.01 gbutanol g-1 (glycerol + sugar) -1 and 0.74 ± 0.02 g L-1 h-1 were obtained. On the basis of these results, batch fermentation in a 5 L bioreactor was performed using Jerusalem artichoke hydrolysate (carbohydrate source) and crude glycerol (residue from biodiesel production) at the previously determined optimal condition. A butanol yield and a productivity of 0.28 ± 0.007 gbutanol g(glycerol+sugar) -1 and 0.55 ± 0.008 g L-1 h-1 were achieved after 27 h fermentation, indicating the suitability of those low-cost carbon sources as cosubstrates for butanol production via C. pasteurianum.
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13
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Cañadas IC, Groothuis D, Zygouropoulou M, Rodrigues R, Minton NP. RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium. ACS Synth Biol 2019; 8:1379-1390. [PMID: 31181894 DOI: 10.1021/acssynbio.9b00075] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Members of the genus Clostridium represent a diverse assemblage of species exhibiting both medical and industrial importance. Deriving both a greater understanding of their biology, while at the same time enhancing their exploitable properties, requires effective genome editing tools. Here, we demonstrate the first implementation in the genus of theophylline-dependent, synthetic riboswitches exhibiting a full set of dynamic ranges, also suitable for applications where tight control of gene expression is required. Their utility was highlighted by generating a novel riboswitch-based editing tool-RiboCas-that overcomes the main obstacles associated with CRISPR/Cas9 systems, including low transformation efficiencies and excessive Cas9 toxicity. The universal nature of the tool was established by obtaining chromosomal modifications in C. pasteurianum, C. difficile, and C. sporogenes, as well as by carrying out the first reported example of CRISPR-targeted gene disruption in C. botulinum. The high efficiency (100% mutant generation) and ease of application of RiboCas make it suitable for use in a diverse range of microorganisms.
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Affiliation(s)
- Inés C. Cañadas
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Daphne Groothuis
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Maria Zygouropoulou
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Raquel Rodrigues
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2RD, U.K
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14
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Utesch T, Sabra W, Prescher C, Baur J, Arbter P, Zeng A. Enhanced electron transfer of different mediators for strictly opposite shifting of metabolism inClostridium pasteurianumgrown on glycerol in a new electrochemical bioreactor. Biotechnol Bioeng 2019; 116:1627-1643. [DOI: 10.1002/bit.26963] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Tyll Utesch
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Christin Prescher
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Julian Baur
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Philipp Arbter
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Chaoyang District Beijing China
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15
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Schmitz R, Sabra W, Arbter P, Hong Y, Utesch T, Zeng AP. Improved electrocompetence and metabolic engineering of Clostridium pasteurianum reveals a new regulation pattern of glycerol fermentation. Eng Life Sci 2018; 19:412-422. [PMID: 32625019 DOI: 10.1002/elsc.201800118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/06/2018] [Accepted: 11/16/2018] [Indexed: 12/11/2022] Open
Abstract
Clostridium pasteurianum produces industrially valuable chemicals such as n-butanol and 1,3-propanediol from fermentations of glycerol and glucose. Metabolic engineering for increased yields of selective compounds is not well established in this microorganism. In order to study carbon fluxes and to selectively increase butanol yields, we integrated the latest advances in genome editing to obtain an electrocompetent Clostridium pasteurianum strain for further engineering. Deletion of the glycerol dehydratase large subunit (dhaB) using an adapted S. pyogenes Type II CRISPR/Cas9 nickase system resulted in a 1,3-propanediol-deficient mutant producing butanol as the main product. Surprisingly, the mutant was able to grow on glycerol as the sole carbon source. In spite of reduced growth, butanol yields were highly increased. Metabolic flux analysis revealed an important role of the newly identified electron bifurcation pathway for crotonyl-CoA to butyryl-CoA conversion in the regulation of redox balance. Compared to the parental strain, the electron bifurcation pathway flux of the dhaB mutant increased from 8 to 46% of the overall flux from crotonyl-CoA to butyryl-CoA and butanol, indicating a new, 1,3-propanediol-independent pattern of glycerol fermentation in Clostridium pasteurianum.
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Affiliation(s)
- Rebekka Schmitz
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Philipp Arbter
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Yaeseong Hong
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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Utesch T, Zeng AP. A novel All-in-One electrolysis electrode and bioreactor enable better study of electrochemical effects and electricity-aided bioprocesses. Eng Life Sci 2018; 18:600-610. [PMID: 32624940 DOI: 10.1002/elsc.201700198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/21/2018] [Accepted: 04/19/2018] [Indexed: 11/11/2022] Open
Abstract
An autoclavable All-in-One electrolysis electrode in a rod shape assembly is developed as a new tool for bioelectrochemical systems and electricity-aided bioprocesses. It can replace the classic two-chamber bioelectrochemical system for electrolysis reactions, be inserted into conventional bioreactors and is easily adaptable as electrocatalytic surface or generator of super-fine bubbles (H2 and O2) for bioconversion processes. Whereas the bioreactor itself functions as the working electrode chamber, a well-integrated inner counter electrode chamber enables water electrolysis without the normally encountered undesired ion-transfer effect. The efficiencies of the electrode are characterized and its advantages and usefulness compared to the classic H-Cell bioelectrochemical system (BES) are demonstrated with glycerol fermentations by Clostridium pasteurianum DSM 525.
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Affiliation(s)
- Tyll Utesch
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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17
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Kaushal M, Chary KVN, Ahlawat S, Palabhanvi B, Goswami G, Das D. Understanding regulation in substrate dependent modulation of growth and production of alcohols in Clostridium sporogenes NCIM 2918 through metabolic network reconstruction and flux balance analysis. BIORESOURCE TECHNOLOGY 2018; 249:767-776. [PMID: 29136931 DOI: 10.1016/j.biortech.2017.10.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
Flux Balance Analysis was performed for Clostridium sporogenes NCIM 2918 grown on sole glucose and glycerol or glucose-glycerol combinations at varied concentrations. During acidogenesis, glucose and glucose-glycerol combinations favored improved growth and butyric acid production. Glycerol fermentation was however marked by reduced growth and predominant ethanol synthesis. Further, with increase of glycerol fraction in glucose-glycerol blend, flux towards ethanol synthesis linearly increased with simultaneous decrease in butanol flux. Elevated ATP demand due to improved growth was satisfied by upregulated carbon flux towards butyric acid synthesis during both glucose and dual substrate fermentations. Possible repression of pyruvate carboxylase by glycerol resulting in downturn of carbon uptake flux towards TCA cycle through anaplerotic reaction may be responsible for reduced growth in glycerol fermentation. Ammonium acetate mediated induction of acetic acid utilization, during acidogenesis, led to excess acetyl-CoA generation and its subsequent metabolism to lesser reduced products, butyric acid or ethanol.
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Affiliation(s)
- Mehak Kaushal
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - K Venkata Narayana Chary
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Saumya Ahlawat
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Basavaraj Palabhanvi
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Gargi Goswami
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Debasish Das
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, Assam 781039, India; DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology, Guwahati, Assam 781039, India.
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Campbell K, Xia J, Nielsen J. The Impact of Systems Biology on Bioprocessing. Trends Biotechnol 2017; 35:1156-1168. [DOI: 10.1016/j.tibtech.2017.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022]
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Sabra W, Bommareddy RR, Maheshwari G, Papanikolaou S, Zeng AP. Substrates and oxygen dependent citric acid production by Yarrowia lipolytica: insights through transcriptome and fluxome analyses. Microb Cell Fact 2017; 16:78. [PMID: 28482902 PMCID: PMC5421321 DOI: 10.1186/s12934-017-0690-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/23/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Unlike the well-studied backer yeast where catabolite repression represents a burden for mixed substrate fermentation, Yarrowia lipolytica, an oleaginous yeast, is recognized for its potential to produce single cell oils and citric acid from different feedstocks. These versatilities of Y. lipolytica with regards to substrate utilization make it an attractive host for biorefinery application. However, to develop a commercial process for the production of citric acid by Y. lipolytica, it is necessary to better understand the primary metabolism and its regulation, especially for growth on mixed substrate. RESULTS Controlling the dissolved oxygen concentration (pO2) in Y. lipolytica cultures enhanced citric acid production significantly in cultures grown on glucose in mono- or dual substrate fermentations, whereas with glycerol as mono-substrate no significant effect of pO2 was found on citrate production. Growth on mixed substrate with glucose and glycerol revealed a relative preference of glycerol utilization by Y. lipolytica. Under optimized conditions with pO2 control, the citric acid titer on glucose in mono- or in dual substrate cultures was 55 and 50 g/L (with productivity of 0.6 g/L*h in both cultures), respectively, compared to a maximum of 18 g/L (0.2 g/L*h) with glycerol in monosubstrate culture. Additionally, in dual substrate fermentation, glycerol limitation was found to trigger citrate consumption despite the presence of enough glucose in pO2-limited culture. The metabolic behavior of this yeast on different substrates was investigated at transcriptomic and 13C-based fluxomics levels. CONCLUSION Upregulation of most of the genes of the pentose phosphate pathway was found in cultures with highest citrate production with glucose in mono- or in dual substrate fermentation with pO2 control. The activation of the glyoxylate cycle in the oxygen limited cultures and the imbalance caused by glycerol limitation might be the reason for the re-consumption of citrate in dual substrate fermentations. This study provides interesting targets for metabolic engineering of this industrial yeast.
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Affiliation(s)
- Wael Sabra
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, 21071 Hamburg, Germany
| | - Rajesh Reddy Bommareddy
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, 21071 Hamburg, Germany
- Synthetic Biology Research Centre, University of Nottingham, Nottingham, NG7 2RD UK
| | - Garima Maheshwari
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, 21071 Hamburg, Germany
| | - Seraphim Papanikolaou
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, 21071 Hamburg, Germany
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Groeger C, Wang W, Sabra W, Utesch T, Zeng AP. Metabolic and proteomic analyses of product selectivity and redox regulation in Clostridium pasteurianum grown on glycerol under varied iron availability. Microb Cell Fact 2017; 16:64. [PMID: 28424096 PMCID: PMC5395762 DOI: 10.1186/s12934-017-0678-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/09/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Clostridium pasteurianum as an emerging new microbial cell factory can produce both n-butanol (BuOH) and 1,3-propanediol (1,3-PDO), and the pattern of product formation changes significantly with the composition of the culture medium. Among others iron content in the medium was shown to strongly affect the products selectivity. However, the mechanism behind this metabolic regulation is still unclear. For a better understanding of such metabolic regulation and for process optimization, we carried out fermentation experiments under either iron excess or iron limitation conditions, and performed metabolic, stoichiometric and proteomic analyses. RESULTS 1,3-PDO is most effectively produced under iron limited condition (Fe-), whereas 1,3-PDO and BuOH were both produced under iron rich condition (Fe+). With increased iron availability the BuOH/1,3-PDO ratio increased significantly from 0.27 mol/mol (at Fe-) to 1.4 mol/mol (at Fe+). Additionally, hydrogen production was enhanced significantly under Fe+ condition. Proteomic analysis revealed differentiated expression of many proteins including several ones of the central carbon metabolic pathway. Among others, pyruvate: ferredoxin oxidoreductase, hydrogenases, and several electron transfer flavoproteins was found to be strongly up-regulated under Fe+ condition, pointing to their strong involvement in the regeneration of the oxidized form of ferredoxin, and consequently their influences on the product selectivity in C. pasteurianum. Of particular significance is the finding that H2 formation in C. pasteurianum is coupled to the ferredoxin-dependent butyryl-CoA dehydrogenase catalyzed reaction, which significantly affects the redox balance and thus the product selectivity. CONCLUSIONS The metabolic, stoichiometric and proteomic results clearly show the key roles of hydrogenases and ferredoxins dependent reactions in determining the internal redox balance and hence product selectivity. Not only the NADH pool but also the regulation of the ferredoxin pool could explain such product variation under different iron conditions.
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Affiliation(s)
- Christin Groeger
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr.15, 21073 Hamburg, Germany
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr.15, 21073 Hamburg, Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr.15, 21073 Hamburg, Germany
| | - Tyll Utesch
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr.15, 21073 Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr.15, 21073 Hamburg, Germany
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21
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Groeger C, Sabra W, Zeng AP. Simultaneous production of 1,3-propanediol andn-butanol byClostridium pasteurianum: In situ gas stripping and cellular metabolism. Eng Life Sci 2016. [DOI: 10.1002/elsc.201600058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Christin Groeger
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
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