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Xu Y, Deng MY, Li SJ, Yuan YC, Sun HY, Wang Q, Chen RP, Yu L. Enhancing biohydrogen production from xylose through natural FeS 2 ore: Mechanistic insights. BIORESOURCE TECHNOLOGY 2024; 399:130632. [PMID: 38552859 DOI: 10.1016/j.biortech.2024.130632] [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: 01/13/2024] [Revised: 02/13/2024] [Accepted: 03/24/2024] [Indexed: 04/01/2024]
Abstract
In this study, we investigated the advantages of utilizing natural FeS2 ore in the context of dark fermentative hydrogen production within a fermentation system employing heat-treated anaerobic granular sludge with xylose as the carbon source. The results demonstrated a significant improvement in both hydrogen production and the maximum rate, with increases of 2.58 and 4.2 times, respectively. Moreover, the presence of FeS2 ore led to a reduction in lag time by more than 2-3 h. The enhanced biohydrogen production performance was attributed to factors such as the intracellular NADH/NAD+ ratio, redox-active components of extracellular polymeric substances, secreted flavins, as well as the presence of hydrogenase and nitrogenase. Furthermore, the FeS2 ore served as a direct electron donor and acceptor during biohydrogen production. This study shed light on the underlying mechanisms contributing to the improved performance of biohydrogen production from xylose during dark fermentation through the supplementation of natural FeS2 ore.
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Affiliation(s)
- Yun Xu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Miao-Yu Deng
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Si-Jia Li
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yi-Cheng Yuan
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hao-Yu Sun
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Quan Wang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Rong-Ping Chen
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Yu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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2
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Xu F, Zhang W, Wang Y, Tian X, Chu J. Enhancing and monitoring spore production in Clostridium butyricum using pH-based regulation strategy and a robust soft sensor based on back-propagation neural networks. Biotechnol Bioeng 2024; 121:551-565. [PMID: 37921467 DOI: 10.1002/bit.28597] [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: 05/17/2023] [Revised: 09/11/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Clostridium butyricum is a probiotic that forms anaerobic spores and plays a crucial role in regulating gut microbiota. However, the total viable cell count and spore yield of C. butyricum in industrial production are comparatively low. To this end, we investigated the metabolic characteristics of the strain and proposed three distinct pH regulation strategies for enhancing spore production. In addition, precise measurement of fermentation parameters such as substrate concentration, total viable cell count, and spore concentration is crucial for successful industrial probiotics production. Nevertheless, online measurement of these intricate parameters in the fermentation of C. butyricum poses a considerable challenge owing to the complex, nonlinear, multivariate, and strongly coupled characteristics of the production process. Therefore, we analyzed the capacitance and conductivity acquired from a viable cell sensor as the core parameters for the fermentation process. Subsequently, a robust soft sensor was developed using a seven-input back-propagation neural network model with input variables of fermentation time, capacitance, conductivity, pH, initial total sugar concentration, ammonium ion concentration, and calcium ion concentration. The model enables the online monitoring of total viable biomass count, substrate concentrations, and spore yield, and can be extended to similar fermentation processes with pH changes as a characteristic feature.
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Affiliation(s)
- Feng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- School of Biotechnology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Wenxiao Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- School of Biotechnology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- School of Biotechnology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- School of Biotechnology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
- School of Biotechnology, East China University of Science and Technology, Shanghai, People's Republic of China
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Iqbal K, Saxena A, Pande P, Tiwari A, Chandra Joshi N, Varma A, Mishra A. Microalgae-bacterial granular consortium: Striding towards sustainable production of biohydrogen coupled with wastewater treatment. BIORESOURCE TECHNOLOGY 2022; 354:127203. [PMID: 35462016 DOI: 10.1016/j.biortech.2022.127203] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Anthropogenic activities have drastically affected the environment, leading to increased waste accumulation in atmospheric bodies, including water. Wastewater treatment is an energy-consuming process and typically requires thousands of kilowatt hours of energy. This enormous energy demand can be fulfilled by utilizing the microbial electrolysis route to breakdown organic pollutants in wastewater which produces clean water and biohydrogen as a by-product of the reaction. Microalgae are the promising microorganism for the biohydrogen production, and it has been investigated that the interaction between microalgae and bacteria can be used to boost the yield of biohydrogen. Consortium of algae and bacteria resulting around 50-60% more biohydrogen production compared to the biohydrogen production of algae and bacteria separately. This review summarises the recent development in different microalgae-bacteria granular consortium systems successfully employed for biohydrogen generation. We also discuss the limitations in biohydrogen production and factors affecting its production from wastewater.
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Affiliation(s)
- Khushboo Iqbal
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Abhishek Saxena
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Priyanshi Pande
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India
| | - Arti Mishra
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201301, India.
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Morra S. Fantastic [FeFe]-Hydrogenases and Where to Find Them. Front Microbiol 2022; 13:853626. [PMID: 35308355 PMCID: PMC8924675 DOI: 10.3389/fmicb.2022.853626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.
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Affiliation(s)
- Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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5
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Arizzi M, Morra S, Gilardi G, Pugliese M, Gullino ML, Valetti F. Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:182. [PMID: 34530890 PMCID: PMC8444407 DOI: 10.1186/s13068-021-02028-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 08/28/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Bio-hydrogen production via dark fermentation of low-value waste is a potent and simple mean of recovering energy, maximising the harvesting of reducing equivalents to produce the cleanest fuel amongst renewables. Following several position papers from companies and public bodies, the hydrogen economy is regaining interest, especially in combination with circular economy and the environmental benefits of short local supply chains, aiming at zero net emission of greenhouse gases (GHG). The biomasses attracting the largest interest are agricultural and urban green wastes (pruning of trees, collected leaves, grass clippings from public parks and boulevards), which are usually employed in compost production, with some concerns over the GHG emission during the process. Here, an alternative application of green wastes, low-value compost and intermediate products (partially composted but unsuitable for completing the process) is studied, pointing at the autochthonous microbial consortium as an already selected source of implementation for biomass degradation and hydrogen production. The biocatalysts investigated as mainly relevant for hydrogen production were the [FeFe]-hydrogenases expressed in Clostridia, given their very high turnover rates. RESULTS Bio-hydrogen accumulation was related to the modulation of gene expression of multiple [FeFe]-hydrogenases from two strains (Clostridium beijerinckii AM2 and Clostridium tyrobutyricum AM6) isolated from the same waste. Reverse Transcriptase quantitative PCR (RT-qPCR) was applied over a period of 288 h and the RT-qPCR results showed that C. beijerinckii AM2 prevailed over C. tyrobutyricum AM6 and a high expression modulation of the 6 different [FeFe]-hydrogenase genes of C. beijerinckii in the first 23 h was observed, sustaining cumulative hydrogen production of 0.6 to 1.2 ml H2/g VS (volatile solids). These results are promising in terms of hydrogen yields, given that no pre-treatment was applied, and suggested a complex cellular regulation, linking the performance of dark fermentation with key functional genes involved in bio-H2 production in presence of the autochthonous consortium, with different roles, time, and mode of expression of the involved hydrogenases. CONCLUSIONS An applicative outcome of the hydrogenases genes quantitative expression analysis can be foreseen in optimising (on the basis of the acquired functional data) hydrogen production from a nutrient-poor green waste and/or low added value compost, in a perspective of circular bioeconomy.
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Affiliation(s)
- M Arizzi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Acea Engineering Laboratories Research Innovation SpA, Roma, Italy
| | - S Morra
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - G Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - M Pugliese
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - M L Gullino
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - F Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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Palacios PA, Francis WR, Rotaru AE. A Win-Loss Interaction on Fe 0 Between Methanogens and Acetogens From a Climate Lake. Front Microbiol 2021; 12:638282. [PMID: 34054747 PMCID: PMC8158942 DOI: 10.3389/fmicb.2021.638282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/29/2021] [Indexed: 12/23/2022] Open
Abstract
Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe0-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe0, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win-loss) interaction on Fe0 between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe0. Since abiotic H2 failed to explain the high metabolic rates on Fe0, we examined whether cell exudates (spent media filtrate) promoted the H2-evolving reaction on Fe0 above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H2 than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H2 evolution from Fe0 and found candidate H2-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H2-evolving reaction on Fe0, explaining the significant H2 evolved by spent media exposed to Fe0. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H2-consuming neighbors-Methanobacterium-fare five times better in their presence. The particular enzymes and constituents promoting H2 evolution from Fe0 remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.
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Affiliation(s)
| | | | - Amelia-Elena Rotaru
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
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7
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Li Z, Gu J, Ding J, Ren N, Xing D. Molecular mechanism of ethanol-H 2 co-production fermentation in anaerobic acidogenesis: Challenges and perspectives. Biotechnol Adv 2020; 46:107679. [PMID: 33316366 DOI: 10.1016/j.biotechadv.2020.107679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Ethanol-type fermentation (ETF) is one of three fermentation types during the acidogenesis of the anaerobic biological treatment. Ethanoligenens, a representative genus of ETF, displays acidophilic, autoaggregative, and ethanol-H2 co-producing characteristics and facilitates subsequent methanogenesis. Here, the latest advances in the molecular mechanisms of the metabolic regulation of ethanol-H2 co-producing bacteria based on multi-omics studies were comprehensively reviewed. Comparative genomics demonstrated a low genetic similarity between Ethanoligenens and other hydrogen-producing genera. FeFe‑hydrogenases (FeFe-H2ases) and pyruvate ferredoxin oxidoreductase (PFOR) played critical roles in the ethanol-H2 co-metabolic pathway of Ethanoligenens. Global transcriptome analysis revealed that highly expressed [FeFe]-H2ases and ferredoxins drove hydrogen production by Ethanoligenens at low pH conditions (4.0-4.5). Quantitative proteomic analysis also proved that this genus resists acetic acid-induced intracellular acidification through the up-regulated expression of pyrimidine metabolism related proteins. The autoaggregation of Ethanoligenen facilitated its granulation with acetate-oxidizing bacteria in co-culture systems and mitigated a fast pH drop, providing a new approach for solving a pH imbalance and improving hydrogen production. In-depth studies of the regulatory mechanism underlying ethanol-H2 co-production metabolism and the syntrophic interactions of ethanol-H2 co-producing Ethanoligenens with other microorganisms will provide insights into the improvement of bioenergy recovery in anaerobic biotechnology. The coupling of ETF with other biotechnologies, which based on the regulation of electron flow direction, syntrophic interaction, and metabolic flux, can be potential strategies to enhance the cascade recovery of energy and resources.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jiayu Gu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Li Z, Wang J, Feng K, Li Y, Ding J, Liu B, Ren N, Xing D. Rapid recruitment of hydrogen-producing biofilms for hydrogen production in a moving bed biofilm reactor by a sequential immobilization and deoxygenization approach. BIORESOURCE TECHNOLOGY 2020; 317:123979. [PMID: 32799080 DOI: 10.1016/j.biortech.2020.123979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
To reduce start-up time and enhance hydrogen production efficiency, a sequential immobilization and deoxygenization (SIDO) strategy for hydrogen production was investigated in continuous-flow moving bed biofilm reactors (MBBRs). The pre-immobilization process accelerated the initial enrichment of hydrogen-producing bacteria (HPB) and promoted the biofilm formation, which contribute to higher hydrogen production efficiency in SIDO-MBBRs compared to a non-immobilized reactor. A similar deoxygenization effect was achieved by inoculation with Pseudomonas aeruginosa compared with N2 sparging, and the P. aeruginosa pre-immobilized MBBR (Pse-MBBR) showed a higher H2 yield in the initial stage of operation. Microbial community analysis found a higher abundance of putative HPB in the range of 82.82-96.56%, with the predominant populations in the SIDO-MBBR assigned to genera Clostridium and Enterobacter. The results suggest that the SIDO-MBBR is an effective approach for rapid recruitment of HPB and start-up of fermentative hydrogen production.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kun Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yitian Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Zhou JJ, Shen JT, Wang XL, Sun YQ, Xiu ZL. Metabolism, morphology and transcriptome analysis of oscillatory behavior of Clostridium butyricum during long-term continuous fermentation for 1,3-propanediol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:191. [PMID: 33292405 PMCID: PMC7690194 DOI: 10.1186/s13068-020-01831-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/16/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Oscillation is a special cell behavior in microorganisms during continuous fermentation, which poses threats to the output stability for industrial productions of biofuels and biochemicals. In previous study, a spontaneous oscillatory behavior was observed in Clostridium butyricum-intensive microbial consortium in continuous fermentation for 1,3-propanediol (1,3-PDO) production from glycerol, which led to the discovery of oscillation in species C. butyricum. RESULTS Spontaneous oscillations by C. butyricum tended to occur under glycerol-limited conditions at low dilution rates. At a glycerol feed concentration of 88 g/L and a dilution rate of 0.048 h-1, the oscillatory behavior of C. butyricum was observed after continuous operation for 146 h and was sustained for over 450 h with an average oscillation period of 51 h. During oscillations, microbial glycerol metabolism exhibited dramatic periodic changes, in which productions of lactate, formate and hydrogen significantly lagged behind that of other products including biomass, 1,3-PDO and butyrate. Analysis of extracellular oxidation-reduction potential and intracellular ratio of NAD+/NADH indicated that microbial cells experienced distinct redox changes during oscillations, from oxidized to reduced state with decreasing of growth rate. Meanwhile, C. butyricum S3 exhibited periodic morphological changes during oscillations, with aggregates, elongated shape, spores or cell debris at the trough of biomass production. Transcriptome analysis indicated that expression levels of multiple genes were up-regulated when microbial cells were undergoing stress, including that for pyruvate metabolism, conversion of acetyl-CoA to acetaldehyde as well as stress response. CONCLUSION This study for the first time systematically investigated the oscillatory behavior of C. butyricum in aspect of occurrence condition, metabolism, morphology and transcriptome. Based on the experimental results, two hypotheses were put forward to explain the oscillatory behavior: disorder of pyruvate metabolism, and excessive accumulation of acetaldehyde.
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Affiliation(s)
- Jin-Jie Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, People's Republic of China
| | - Jun-Tao Shen
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, People's Republic of China
| | - Xiao-Li Wang
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, People's Republic of China
| | - Ya-Qin Sun
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, People's Republic of China
| | - Zhi-Long Xiu
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, People's Republic of China.
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10
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Zou W, Ye G, Zhang K, Yang H, Yang J. Analysis of the core genome and pangenome of Clostridium butyricum. Genome 2020; 64:51-61. [PMID: 33105087 DOI: 10.1139/gen-2020-0072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Clostridium butyricum is an anaerobic bacterium that inhabits broad niches. Clostridium butyricum is known for its production of butyrate, 1,3-propanediol, and hydrogen. This study aimed to present a comparative pangenome analysis of 24 strains isolated from different niches. We sequenced and annotated the genome of C. butyricum 3-3 isolated from the Chinese baijiu ecosystem. The pangenome of C. butyricum was open. The core genome, accessory genome, and strain-specific genes comprised 1011, 4543, and 1473 genes, respectively. In the core genome, Carbohydrate metabolism was the largest category, and genes in the biosynthetic pathway of butyrate and glycerol metabolism were conserved (in the core or soft-core genome). Furthermore, the 1,3-propanediol operon existed in 20 strains. In the accessory genome, numerous mobile genetic elements belonging to the Replication, recombination, and repair (L) category were identified. In addition, genome islands were identified in all 24 strains, ranging from 2 (strain KNU-L09) to 53 (strain SU1), and phage sequences were found in 17 of the 24 strains. This study provides an important genomic framework that could pave the way for the exploration of C. butyricum and future studies on the genetic diversification of C. butyricum.
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Affiliation(s)
- Wei Zou
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China.,Research Laboratory of Baijiu Resource Microorganisms and Big data, Sichuan University of Science & Engineering, 188 University town, Lingang District, Yibin, Sichuan 644005, China
| | - Guangbin Ye
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
| | - Kaizheng Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jiangang Yang
- College of Bioengineering, Sichuan University of Science & Engineering, 188, University town, Lingang District, Yibin, Sichuan 644005, China
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11
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Li Z, Liu B, Cui H, Ding J, Li H, Xie G, Ren N, Xing D. The complete genome sequence of Ethanoligenens harbinense reveals the metabolic pathway of acetate-ethanol fermentation: A novel understanding of the principles of anaerobic biotechnology. ENVIRONMENT INTERNATIONAL 2019; 131:105053. [PMID: 31357089 DOI: 10.1016/j.envint.2019.105053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 05/05/2023]
Abstract
Ethanol-type fermentation is one of three main fermentation types in the acidogenesis of anaerobic treatment systems. Non-spore-forming Ethanoligenens is as a typical genus capable of ethanol-type fermentation in mixed culture (i.e. acetate-ethanol fermentation). This genus can produce ethanol, acetate, CO2, and H2 using carbohydrates, and has application potential in anaerobic bioprocesses. Here, the complete genome sequences and methylome of Ethanoligenens harbinense strains with different autoaggregative and coaggregative abilities were obtained using the PacBio single-molecule real-time sequencing platform. The genome size of E. harbinense strains was about 2.97-3.10 Mb with 55.5% G+C content. 3020-3153 genes were annotated, most of which were methylated at specific sites or motifs. The methylation types included 6mA, 4mC, and unknown types. Comparative genomic analysis demonstrated low levels of genetic similarity between E. harbinense and other well-known hydrogen-producing bacteria (i.e., Clostridium and Thermoanaerobacter) in phylogenesis. Hydrogen production of E. harbinense was catalyzed by genes that encode [FeFe]‑hydrogenases and that were synthesized by three maturases of [FeFe]-H2ase. The metabolic mechanism of H2-ethanol co-production fermentation, catalyzed by pyruvate ferredoxin oxidoreductase was proposed. This study provides genetic and evolutionary information of a model genus for the further investigation of the metabolic pathway and regulatory network of ethanol-type fermentation and anaerobic bioprocesses for waste or wastewater treatment.
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Affiliation(s)
- Zhen Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bingfeng Liu
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han Cui
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Huahua Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guojun Xie
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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12
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Park JH, Kim DH, Kim HS, Wells GF, Park HD. Granular activated carbon supplementation alters the metabolic flux of Clostridium butyricum for enhanced biohydrogen production. BIORESOURCE TECHNOLOGY 2019; 281:318-325. [PMID: 30826518 DOI: 10.1016/j.biortech.2019.02.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
In this work, the effects of granular activated carbon (GAC) supplementation on hydrogen fermentation were investigated in Clostridium butyricum. Maximum hydrogen production rate and ultimate hydrogen volume increased up to 1.7 and 1.9 fold, respectively, with 1 g/L GAC supplementation. Indicators of stable hydrogen production, such as acetate and butyrate formation increased with increasing GAC concentration. To identify the factors for hydrogen production enhancement, transcriptome analysis was conducted. Functional genes related to hydrogen production increased by GAC supplementation (1.75 fold for pfor and 1.48 fold for oxct). On the other hand, functional genes related to hydrogen consumption decreased (1.78 fold for ldh, 0.67 fold for adh, 1.64 fold for hbd, 2.4 fold for crt, and 0.71 fold for buk). Considered together, these results suggested that GAC supplementation increased biohydrogen production by changing the metabolic flux associated with hydrogen production and consumption pathways.
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Affiliation(s)
- Jeong-Hoon Park
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, United States; School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 20841, South Korea
| | - Do-Hyung Kim
- Intelligent Sustainable R&D Group, Korea Institute of Industrial Technology (KITECH), Chonan-si, Chungnam 31056, South Korea
| | - Han-Shin Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 20841, South Korea
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, United States
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 20841, South Korea; KU-KIST Green School, Graduate School of Energy and Environment, Korea University, Seoul 02841, South Korea.
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13
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The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnol Adv 2018; 36:2165-2186. [DOI: 10.1016/j.biotechadv.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 02/02/2023]
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14
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Sheng T, Zhao L, Gao L, Liu W, Wu G, Wu J, Wang A. Enhanced biohydrogen production from nutrient-free anaerobic fermentation medium with edible fungal pretreated rice straw. RSC Adv 2018; 8:22924-22930. [PMID: 35540149 PMCID: PMC9081587 DOI: 10.1039/c8ra03361g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/18/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022] Open
Abstract
An edible fungal pretreatment of rice straw was proposed for enhanced hydrogen production while reducing the chemical cost for traditional biological hydrogen production from lignocellulose. In this research, rice straw was pretreated by edible fungus Gymnopus contrarius J2 at room temperature under static conditions for 15 d at first. The highest hydrogen yield of 5.71 mmol g-1-pretreated rice straw was obtained, 74% higher than the counterpart without pretreatment. Chemical composition analysis demonstrated that lignin removal was up to 22.4% with a little cellulose and hemicellulose loss of 13.3% and 17.1%, respectively, which is in favor of hydrogen production. Additionally, microscopic structure observation combined with FT-IR and XRD analysis illustrated the structural disruption of pretreated rice straw, and the crystalline index of rice straw can be decreased by 46.2% after pretreatment, which might account for the hydrogen production enhancement. The results also indicated that the hydrogen yield from pretreated rice straw was not affected without the addition of yeast extract and vitamins to the culture medium, which is substantial evidence that edible fungal pretreated rice straw could provide prerequisite nutrients for hydrogen-producing bacteria. Overall, edible fungal pretreatment has great potential under the mild conditions for high hydrogen yields and thus leads to a new direction to realize a highly efficient and economically competitive biological hydrogen production process from lignocellulosic biomass.
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Affiliation(s)
- Tao Sheng
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology Harbin 150090 China +86 451 86282110
- College of Environmental and Chemical Engineering, Heilongjiang Institute of Science and Technology Harbin China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology Harbin 150090 China +86 451 86282110
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland Brisbane Queensland 4072 Australia
| | - Lingfang Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing China
| | - Wenzong Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing China
| | - Guofeng Wu
- College of Life Sciences, Heilongjiang University Harbin China
| | - Jieting Wu
- School of Environmental Science, Liaoning University Shenyang China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology Harbin 150090 China +86 451 86282110
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing China
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15
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Sekoai PT, Daramola MO. Effect of metal ions on dark fermentative biohydrogen production using suspended and immobilized cells of mixed bacteria. CHEM ENG COMMUN 2018. [DOI: 10.1080/00986445.2018.1428958] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Patrick T. Sekoai
- Sustainable Energy and Environment Research Unit, Faculty of Engineering and the Built Environment, School of Chemical and Metallurgical Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael O. Daramola
- Sustainable Energy and Environment Research Unit, Faculty of Engineering and the Built Environment, School of Chemical and Metallurgical Engineering, University of the Witwatersrand, Johannesburg, South Africa
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16
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Baba R, Morita M, Asakawa S, Watanabe T. Transcription of [FeFe]-Hydrogenase Genes during H 2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil. Microbes Environ 2017; 32:125-132. [PMID: 28502969 PMCID: PMC5478535 DOI: 10.1264/jsme2.me16171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H2 production was differently regulated among the paralogs in H2 producers isolated from paddy field soil.
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Affiliation(s)
- Ryuko Baba
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Mayumi Morita
- Laboratory of Soil Biology and Chemistry, School of Agricultural Sciences, Nagoya University
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Takeshi Watanabe
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
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17
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Wu YR, Mao A, Sun C, Shanmugam S, Li J, Zhong M, Hu Z. Catalytic hydrolysis of starch for biohydrogen production by using a newly identified amylase from a marine bacterium Catenovulum sp. X3. Int J Biol Macromol 2017. [PMID: 28647525 DOI: 10.1016/j.ijbiomac.2017.06.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An identified cold-adaptive, organic solvents-tolerant alkaline α-amylase (HP664) from Catenovulum sp. strain X3 was heterologously expressed and characterized in E. coli, and it was further applied to starch saccharification for biohydrogen production. The recombinant HP664 belongs to a member of glycoside hydrolase family 13 (GH13), with a molecular weight of 69.6kDa without signal peptides, and also shares a relatively low similarity (49%) to other reported amylases. Biochemical characterization demonstrated that the maximal enzymatic activity of HP664 was observed at 35°C and pH 9.0. Most metal ions inhibited its activity; however, low polar organic solvents (e.g., benzene and n-hexane) could enhance the activity by 35-50%. Additionally, HP664 also exhibited the catalytic capability on various polysaccharides, including potato starch, amylopectin, dextrin and agar. In order to increase the bioavailability of starch for H2 production, HP664 was utilized to elevate fermentable oligosaccharide level, and the results revealed that the maximal hydrolytic percentage of starch was up to 44% with 12h of hydrolysis using 5.63U of HP664. Biohydrogen fermentation of the starch hydrolysate by Clostridium sp. strain G1 yielded 297.7mL of H2 after 84h of fermentation, which is 3.73-fold higher than the control without enzymatic treatment of HP664.
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Affiliation(s)
- Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Aihua Mao
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Chongran Sun
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | | | - Jin Li
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Mingqi Zhong
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063 China.
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18
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Serrano-Bermúdez LM, González Barrios AF, Maranas CD, Montoya D. Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol. BMC SYSTEMS BIOLOGY 2017; 11:58. [PMID: 28571567 PMCID: PMC5455137 DOI: 10.1186/s12918-017-0434-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled. RESULTS We reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example, Clostridium maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions, Clostridium grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than iCbu641 perturbations for improving PDO yields. CONCLUSIONS The agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing Clostridium strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.
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Affiliation(s)
- Luis Miguel Serrano-Bermúdez
- Bioprocesses and Bioprospecting Group, Universidad Nacional de Colombia. Ciudad Universitaria, Carrera 30 No. 45-03, Bogotá, D.C Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Carrera 1 N.° 18A – 12, Bogotá, Colombia
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802 USA
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Universidad Nacional de Colombia. Ciudad Universitaria, Carrera 30 No. 45-03, Bogotá, D.C Colombia
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Sekoai PT, Awosusi AA, Yoro KO, Singo M, Oloye O, Ayeni AO, Bodunrin M, Daramola MO. Microbial cell immobilization in biohydrogen production: a short overview. Crit Rev Biotechnol 2017; 38:157-171. [PMID: 28391705 DOI: 10.1080/07388551.2017.1312274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The high dependence on fossil fuels has escalated the challenges of greenhouse gas emissions and energy security. Biohydrogen is projected as a future alternative energy as a result of its non-polluting characteristics, high energy content (122 kJ/g), and economic feasibility. However, its industrial production has been hampered by several constraints such as low process yields and the formation of biohydrogen-competing reactions. This necessitates the search for other novel strategies to overcome this problem. Cell immobilization technology has been in existence for many decades and is widely used in various processes such as wastewater treatment, food technology, and pharmaceutical industry. In recent years, this technology has caught the attention of many researchers within the biohydrogen production field owing to its merits such as enhanced process yields, reduced microbial contamination, and improved homogeneity. In addition, the use of immobilization in biohydrogen production prevents washout of microbes, stabilizes the pH of the medium, and extends microbial activity during continuous processes. In this short review, an insight into the potential of cell immobilization is presented. A few immobilization techniques such as entrapment, adsorption, encapsulation, and synthetic polymers are discussed. In addition, the effects of process conditions on the performance of immobilized microbial cells during biohydrogen production are discussed. Finally, the review concludes with suggestions on improvement of cell immobilization technologies in biohydrogen production.
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Affiliation(s)
- Patrick Thabang Sekoai
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
| | - Ayotunde A Awosusi
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
| | - Kelvin Odafe Yoro
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
| | - Muofhe Singo
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
| | - Olawale Oloye
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
| | - Augustine Omoniyi Ayeni
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa.,b Department of Chemical Engineering, College of Engineering , Covenant University , Ota , Ogun State , Nigeria
| | - Michael Bodunrin
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa.,c Department of Metallurgical and Materials Engineering , Federal university of Technology , Akure , Ondo State , Nigeria
| | - Michael Olawale Daramola
- a School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment , University of the Witwatersrand , Johannesburg , South Africa
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20
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Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT. Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria. Microbes Environ 2016; 31:288-92. [PMID: 27431485 PMCID: PMC5017805 DOI: 10.1264/jsme2.me16057] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The syntrophic degradation of branched-chain fatty acids (BCFAs) such as 2-methylbutyrate and isobutyrate is an essential step in the production of methane from proteins/amino acids in anaerobic ecosystems. While a few syntrophic BCFA-degrading bacteria have been isolated, their metabolic pathways in BCFA and short-chain fatty acid (SCFA) degradation as well as energy conservation systems remain unclear. In an attempt to identify these pathways, we herein performed comparative genomics of three syntrophic bacteria: 2-methylbutyrate-degrading “Syntrophomonas wolfei subsp. methylbutyratica” strain JCM 14075T (=4J5T), isobutyrate-degrading Syntrophothermus lipocalidus strain TGB-C1T, and non-BCFA-metabolizing S. wolfei subsp. wolfei strain GöttingenT. We demonstrated that 4J5 and TGB-C1 both encode multiple genes/gene clusters involved in β-oxidation, as observed in the Göttingen genome, which has multiple copies of genes associated with butyrate degradation. The 4J5 genome possesses phylogenetically distinct β-oxidation genes, which may be involved in 2-methylbutyrate degradation. In addition, these Syntrophomonadaceae strains harbor various hydrogen/formate generation systems (i.e., electron-bifurcating hydrogenase, formate dehydrogenase, and membrane-bound hydrogenase) and energy-conserving electron transport systems, including electron transfer flavoprotein (ETF)-linked acyl-CoA dehydrogenase, ETF-linked iron-sulfur binding reductase, ETF dehydrogenase (FixABCX), and flavin oxidoreductase-heterodisulfide reductase (Flox-Hdr). Unexpectedly, the TGB-C1 genome encodes a nitrogenase complex, which may function as an alternative H2 generation mechanism. These results suggest that the BCFA-degrading syntrophic strains 4J5 and TGB-C1 possess specific β-oxidation-related enzymes for BCFA oxidation as well as appropriate energy conservation systems to perform thermodynamically unfavorable syntrophic metabolism.
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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21
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Complete genome sequence of Clostridium butyricum JKY6D1 isolated from the pit mud of a Chinese flavor liquor-making factory. J Biotechnol 2016; 220:23-4. [DOI: 10.1016/j.jbiotec.2016.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/08/2016] [Indexed: 11/23/2022]
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