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Jia M, Zhu S, Xue MY, Chen H, Xu J, Song M, Tang Y, Liu X, Tao Y, Zhang T, Liu JX, Wang Y, Sun HZ. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat Microbiol 2024:10.1038/s41564-024-01723-9. [PMID: 38866938 DOI: 10.1038/s41564-024-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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Affiliation(s)
- Minghui Jia
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jinghong Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaohan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Company, Shanghai, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China.
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Kumar V, Kumar P, Maity SK, Agrawal D, Narisetty V, Jacob S, Kumar G, Bhatia SK, Kumar D, Vivekanand V. Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:72. [PMID: 38811976 PMCID: PMC11137917 DOI: 10.1186/s13068-024-02508-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/20/2024] [Indexed: 05/31/2024]
Abstract
Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.
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Affiliation(s)
- Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
- Department of Bioscience and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
| | - Pankaj Kumar
- Department of Chemical Engineering, School of Studies of Engineering and Technology, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, 495009, India
| | - Sunil K Maity
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, Telangana, 502284, India.
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, Uttarakhand, 248005, India
| | - Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, 173229, India
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology Jaipur, Jaipur, Rajasthan, 302017, India
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Narisetty V, Okibe MC, Amulya K, Jokodola EO, Coulon F, Tyagi VK, Lens PNL, Parameswaran B, Kumar V. Technological advancements in valorization of second generation (2G) feedstocks for bio-based succinic acid production. BIORESOURCE TECHNOLOGY 2022; 360:127513. [PMID: 35772717 DOI: 10.1016/j.biortech.2022.127513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Succinic acid (SA) is used as a commodity chemical and as a precursor in chemical industry to produce other derivatives such as 1,4-butaneidol, tetrahydrofuran, fumaric acid, and bio-polyesters. The production of bio-based SA from renewable feedstocks has always been in the limelight owing to the advantages of renewability, abundance and reducing climate change by CO2 capture. Considering this, the current review focuses on various 2G feedstocks such as lignocellulosic biomass, crude glycerol, and food waste for cost-effective SA production. It also highlights the importance of producing SA via separate enzymatic hydrolysis and fermentation, simultaneous saccharification and fermentation, and consolidated bioprocessing. Furthermore, recent advances in genetic engineering, and downstream SA processing are thoroughly discussed. It also elaborates on the techno-economic analysis and life cycle assessment (LCA) studies carried out to understand the economics and environmental effects of bio-based SA synthesis.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | | | - K Amulya
- National University of Ireland Galway, University Road, H91TK33 Galway, Ireland
| | | | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Vinay Kumar Tyagi
- Environmental Hydrology Division, National Institute of Hydrology (NIH), Roorkee 247667, Uttarakhand, India
| | - Piet N L Lens
- National University of Ireland Galway, University Road, H91TK33 Galway, Ireland
| | - Binod Parameswaran
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695019, India
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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Modeling the Succinic Acid Bioprocess: A Review. FERMENTATION 2022. [DOI: 10.3390/fermentation8080368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Succinic acid has attracted much interest as a key platform chemical that can be obtained in high titers from biomass through sustainable fermentation processes, thus boosting the bioeconomy as a critical production strategy for the future. After several years of development of the production of succinic acid, many studies on lab or pilot scale production have been reported. The relevant experimental data reveal underlying physical and chemical dynamic phenomena. To take advantage of this vast, but disperse, kinetic information, a number of mathematical kinetic models of the unstructured non-segregated type have been proposed in the first place. These relatively simple models feature critical aspects of interest for the design, control, optimization and operation of this key bioprocess. This review includes a detailed description of the phenomena involved in the bioprocesses and how they reflect on the most important and recent models based on macroscopic and metabolic chemical kinetics, and in some cases even coupling mass transport.
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Assessment of vine shoots and surplus grape must for succinic acid bioproduction. Appl Microbiol Biotechnol 2022; 106:4977-4994. [PMID: 35821430 DOI: 10.1007/s00253-022-12063-1] [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: 01/04/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/02/2022]
Abstract
Vine shoots and surplus grape must were assessed as feedstocks for succinic acid production with Actinobacillus succinogenes and Basfia succiniproducens. After acidic and enzymatic hydrolysis, vine shoots released 35-40 g/L total sugars. Both bacterial species produced 18-21 g/L succinic acid from this hydrolysate in 120 h. Regarding grape must fermentation, A. succinogenes clearly outperformed B. succiniproducens. Yeast extract (a source of organic nitrogen and vitamins) was the only additional nutrient needed by A. succinogenes to grow on grape must. Under mathematically optimized conditions (145.7 g/L initial sugars and 24.9 g/L yeast extract), A. succinogenes generated 88.9 ± 1.4 g/L succinic acid in 96 h, reaching a succinic acid yield of 0.66 ± 0.01 g/g and a sugar consumption of 96.64 ± 0.30%. Substrate inhibition was not observed in grape musts with 125-150 g/L initial sugars, provided that an adequate amount of yeast extract was available for bacteria. Alternative nitrogen sources to yeast extract (red wine lees, white wine lees, urea, NH4Cl, and choline chloride) were not suitable for A. succinogenes in grape must. KEY POINTS: • Vine shoots and surplus grape must were assessed for succinic acid bioproduction. • Succinic acid bioproduction was 21 g/L with vine shoots and 89 g/L with grape must. • Fermentation was efficient at high sugar loads if organic N supply was adequate.
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D’ambrosio S, Alfano A, Cimini D. Production of Succinic Acid From Basfia succiniciproducens. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.785691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Basfia succiniciproducens is a facultative anaerobic capnophilic bacterium, isolated from rumen, that naturally produces high amounts of succinic acid by fixing CO2 and using fumarate as final electron acceptor. This metabolic feature makes it one of the ideal candidates for developing biotechnological industrial routes that could eventually replace the polluting and environment unfriendly petrochemical ones that are still main sources for the production of this value-added compound. In fact, due to the large number of applications of succinic acid that range from the more traditional ones as food additive or pharmaceutical intermediate to the most recent as building block for biopolymers and bioplastic, increasing demand and market size growth are expected in the next years. In line with a “green revolution” needed to preserve our environment, the great challenge is the establishment of commercially viable production processes that exploit renewable materials and in particular preferably non-food lignocellulosic biomasses and waste products. In this review, we describe the currently available literature concerning B. succiniciproducens since the strain was first isolated, focusing on the different renewable materials and fermentation strategies used to improve succinic acid production titers to date. Moreover, an insight into the metabolic engineering approaches and the key physiological characteristics of B. succiniciproducens deduced from the different studies are presented.
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Influence of the Initial Sugar Concentration and Supplementation with Yeast Extract on Succinic Acid Fermentation in a Lactose-Based Medium. FERMENTATION 2021. [DOI: 10.3390/fermentation7040221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to investigate the production of succinic acid from lactose concentrate, a by-product of cheese-making, using Actinobacillus succinogenes and Basfia succiniciproducens. Although the ability of these strains to metabolize different sugars is already known, their application in the conversion of lactose bears high potential for optimization. With regard to B. succiniciproducens, this approach is completely novel. In particular, the effect of the medium’s sugar concentration as well as the ability of its supplementation with yeast extract to prevent a lack of essential nutrient proteins and vitamins was examined. Lactose-based media containing sugar concentrations of between 20 and 65 g L−1 and 5 g L−1 of yeast extract were fermented, with both strains showing comparable performances. The best results in terms of succinic acid yield and acid concentration—0.57 g g−1 initial sugar and 23 g L−1—were achieved at an initial sugar concentration of 43 g L−1. The necessity of yeast extract was demonstrated using the sugar-optimized medium without supplementation. As a result, the yield and concentration of succinic acid dropped to 0.34 g g−1 and 13 g L−1 and the sugar consumption decreased from more than 99 to less than 55%. Therefore, the supplementation amount of 5 g L−1 of yeast extract can be regarded as well-balanced.
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D'ambrosio S, Ventrone M, Alfano A, Schiraldi C, Cimini D. Microbioreactor (micro-Matrix) potential in aerobic and anaerobic conditions with different industrially relevant microbial strains. Biotechnol Prog 2021; 37:e3184. [PMID: 34180150 PMCID: PMC8596446 DOI: 10.1002/btpr.3184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/13/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022]
Abstract
Microscale fermentation systems are important high throughput tools in clone selection, and bioprocess set up and optimization, since they provide several parallel experiments in controlled conditions of pH, temperature, agitation, and gas flow rate. In this work we evaluated the performance of biotechnologically relevant strains with different respiratory requirements in the micro‐Matrix microbioreactor. In particular Escherichia coli K4 requires well aerated fermentation conditions to improve its native production of chondroitin‐like capsular polysaccharide, a biomedically attractive polymer. Results from batch and fed‐batch experiments demonstrated high reproducibility with those obtained on 2 L reactors, although highlighting a pronounced volume loss for longer‐term experiments. Basfia succiniciproducens and Actinobacillus succinogenes need CO2 addition for the production of succinic acid, a building block with several industrial applications. Different CO2 supply modes were tested for the two strains in 24 h batch experiments and results well compared with those obtained on lab‐scale bioreactors. Overall, it was demonstrated that the micro‐Matrix is a useful scale‐down tool that is suitable for growing metabolically different strains in simple batch process, however, a series of issues should still be addressed in order to fully exploit its potential.
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Affiliation(s)
- Sergio D'ambrosio
- Department of Experimental Medicine, Section of Biotechnology, Medical Hystology and Molecular Biology, University of Campania L. Vanvitelli, Naples, Italy
| | - Michela Ventrone
- Department of Experimental Medicine, Section of Biotechnology, Medical Hystology and Molecular Biology, University of Campania L. Vanvitelli, Naples, Italy
| | - Alberto Alfano
- Department of Experimental Medicine, Section of Biotechnology, Medical Hystology and Molecular Biology, University of Campania L. Vanvitelli, Naples, Italy
| | - Chiara Schiraldi
- Department of Experimental Medicine, Section of Biotechnology, Medical Hystology and Molecular Biology, University of Campania L. Vanvitelli, Naples, Italy
| | - Donatella Cimini
- Department of Experimental Medicine, Section of Biotechnology, Medical Hystology and Molecular Biology, University of Campania L. Vanvitelli, Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania L. Vanvitelli, Caserta, Italy
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Chen J, Yang S, Alam MA, Wang Z, Zhang J, Huang S, Zhuang W, Xu C, Xu J. Novel biorefining method for succinic acid processed from sugarcane bagasse. BIORESOURCE TECHNOLOGY 2021; 324:124615. [PMID: 33454167 DOI: 10.1016/j.biortech.2020.124615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 05/22/2023]
Abstract
Sugarcane bagasse (SCB) was pretreated with hot water (HLW), ethanol (ETH), and sodium hydroxide (SH). The obtained residuals were hydrolyzed and applied as carbon sources for succinic acid (SA) fermentation, the residue digestibility and SA conversion rate of alkali-pretreated residual were superior to others. Considering the characteristics of alkali pretreatment, enzymatic hydrolysis and succinic acid fermentation, a novel in-situ semi-simultaneous saccharification and co-fermentation (SSSCF) procedure for SA production from SCB was developed. The yield, productivity, and conversion rates of SA from SCB raw material (DRM) processed by SSSCF were 41 g/L, 300 mg/L/h, and 320 mg/g dry, respectively. For every kilogram of SA production, the developed coupling method reduced the SH and water usages, energy consumption, and effluent emission by 0.14 kg, 233.5 L 14,000 kJ and 7 L, respectively, and enhanced the SA productivity by 1.7 times compared with the non-coupling procedure.
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Affiliation(s)
- Jianjun Chen
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Shuai Yang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhongming Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Jun Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Chao Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
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10
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Chestnut Shells as Waste Material for Succinic Acid Production from Actinobacillus succinogenes 130Z. FERMENTATION 2020. [DOI: 10.3390/fermentation6040105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Currently, the full exploitation of waste materials for the production of value-added compounds is one of the potential solutions to lower costs and increase the sustainability of industrial processes. In this respect, the aim of this work was to evaluate the potential of chestnut shells (CSH) as substrate for the growth of Actinobacillus succinogenes 130Z, a natural producer of succinic acid that is a precursor of several bulk chemicals with diverse applications, such as bioplastics production. Hydrolysis of ammonia pretreated CSH in citrate buffer with the Cellic CTec2 enzyme mix was optimized and strain performance was studied in bottle experiments. Data showed co-consumption of citrate, glucose and xylose, which resulted in a change of the relative ratio of produced acids, providing an insight into the metabolism of A. succinogenes that was never described to date. Furthermore, high C:N ratios seems to have a favorable impact on succinic acid production by decreasing byproduct formation. Finally, yield and volumetric production rate of succinic acid were studied in controlled 2 L bioreactors demonstrating the potential use of CSH as renewable raw material.
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Ventrone M, Schiraldi C, Squillaci G, Morana A, Cimini D. Chestnut Shells as Waste Material for Succinic Acid Production from Actinobacillus succinogenes 130Z. FERMENTATION 2020. [DOI: 10.339/fermentation604010510.3390/fermentation6040105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Currently, the full exploitation of waste materials for the production of value-added compounds is one of the potential solutions to lower costs and increase the sustainability of industrial processes. In this respect, the aim of this work was to evaluate the potential of chestnut shells (CSH) as substrate for the growth of Actinobacillus succinogenes 130Z, a natural producer of succinic acid that is a precursor of several bulk chemicals with diverse applications, such as bioplastics production. Hydrolysis of ammonia pretreated CSH in citrate buffer with the Cellic CTec2 enzyme mix was optimized and strain performance was studied in bottle experiments. Data showed co-consumption of citrate, glucose and xylose, which resulted in a change of the relative ratio of produced acids, providing an insight into the metabolism of A. succinogenes that was never described to date. Furthermore, high C:N ratios seems to have a favorable impact on succinic acid production by decreasing byproduct formation. Finally, yield and volumetric production rate of succinic acid were studied in controlled 2 L bioreactors demonstrating the potential use of CSH as renewable raw material.
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12
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Gérardy R, Debecker DP, Estager J, Luis P, Monbaliu JCM. Continuous Flow Upgrading of Selected C 2-C 6 Platform Chemicals Derived from Biomass. Chem Rev 2020; 120:7219-7347. [PMID: 32667196 DOI: 10.1021/acs.chemrev.9b00846] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ever increasing industrial production of commodity and specialty chemicals inexorably depletes the finite primary fossil resources available on Earth. The forecast of population growth over the next 3 decades is a very strong incentive for the identification of alternative primary resources other than petro-based ones. In contrast with fossil resources, renewable biomass is a virtually inexhaustible reservoir of chemical building blocks. Shifting the current industrial paradigm from almost exclusively petro-based resources to alternative bio-based raw materials requires more than vibrant political messages; it requires a profound revision of the concepts and technologies on which industrial chemical processes rely. Only a small fraction of molecules extracted from biomass bears significant chemical and commercial potentials to be considered as ubiquitous chemical platforms upon which a new, bio-based industry can thrive. Owing to its inherent assets in terms of unique process experience, scalability, and reduced environmental footprint, flow chemistry arguably has a major role to play in this context. This review covers a selection of C2 to C6 bio-based chemical platforms with existing commercial markets including polyols (ethylene glycol, 1,2-propanediol, 1,3-propanediol, glycerol, 1,4-butanediol, xylitol, and sorbitol), furanoids (furfural and 5-hydroxymethylfurfural) and carboxylic acids (lactic acid, succinic acid, fumaric acid, malic acid, itaconic acid, and levulinic acid). The aim of this review is to illustrate the various aspects of upgrading bio-based platform molecules toward commodity or specialty chemicals using new process concepts that fall under the umbrella of continuous flow technology and that could change the future perspectives of biorefineries.
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Affiliation(s)
- Romaric Gérardy
- Center for Integrated Technology and Organic Synthesis, MolSys Research Unit, University of Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Damien P Debecker
- Institute of Condensed Matter and Nanosciences (IMCN), Université catholique de Louvain (UCLouvain), B-1348 Louvain-la-Neuve, Belgium.,Research & Innovation Centre for Process Engineering (ReCIPE), Université catholique de Louvain (UCLouvain), B-1348 Louvain-la-Neuve, Belgium
| | - Julien Estager
- Certech, Rue Jules Bordet 45, Zone Industrielle C, B-7180 Seneffe, Belgium
| | - Patricia Luis
- Research & Innovation Centre for Process Engineering (ReCIPE), Université catholique de Louvain (UCLouvain), B-1348 Louvain-la-Neuve, Belgium.,Materials & Process Engineering (iMMC-IMAP), UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Jean-Christophe M Monbaliu
- Center for Integrated Technology and Organic Synthesis, MolSys Research Unit, University of Liège, B-4000 Sart Tilman, Liège, Belgium
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Szczerba H, Dudziak K, Krawczyk M, Targoński Z. A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. Int J Mol Sci 2020; 21:ijms21144835. [PMID: 32650546 PMCID: PMC7402333 DOI: 10.3390/ijms21144835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022] Open
Abstract
Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.
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Affiliation(s)
- Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
- Correspondence: ; Tel.: +48-81-462-3402
| | - Karolina Dudziak
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland;
| | | | - Zdzisław Targoński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
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Szczerba H, Komoń-Janczara E, Dudziak K, Waśko A, Targoński Z. A novel biocatalyst, Enterobacter aerogenes LU2, for efficient production of succinic acid using whey permeate as a cost-effective carbon source. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:96. [PMID: 32514308 PMCID: PMC7257193 DOI: 10.1186/s13068-020-01739-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Succinic acid (SA), a valuable chemical compound with a broad range of industrial uses, has become a subject of global interest in recent years. The bio-based production of SA by highly efficient microbial producers from renewable feedstock is significantly important, regarding the current trend of sustainable development. RESULTS In this study, a novel bacterial strain, LU2, was isolated from cow rumen and recognized as an efficient producer of SA from lactose. Proteomic and genetic identifications as well as phylogenetic analysis were performed, and strain LU2 was classified as an Enterobacter aerogenes species. The optimal conditions for SA production were 100 g/L lactose, 10 g/L yeast extract, and 20% inoculum at pH 7.0 and 34 °C. Under these conditions, approximately 51.35 g/L SA with a yield of 53% was produced when batch fermentation was conducted in a 3-L stirred bioreactor. When lactose was replaced with whey permeate, the highest SA concentration of 57.7 g/L was achieved with a yield and total productivity of 62% and 0.34 g/(L*h), respectively. The highest productivity of 0.67 g/(L*h) was observed from 48 to 72 h of batch fermentation, when E. aerogenes LU2 produced 16.23 g/L SA. CONCLUSIONS This study shows that the newly isolated strain E. aerogenes LU2 has great potential as a new biocatalyst for producing SA from whey permeate.
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Affiliation(s)
- Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland
| | - Karolina Dudziak
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, 1 Chodźki Street, 20-093 Lublin, Poland
| | - Adam Waśko
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland
| | - Zdzisław Targoński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland
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