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Cowan DA, Albers SV, Antranikian G, Atomi H, Averhoff B, Basen M, Driessen AJM, Jebbar M, Kelman Z, Kerou M, Littlechild J, Müller V, Schönheit P, Siebers B, Vorgias K. Extremophiles in a changing world. Extremophiles 2024; 28:26. [PMID: 38683238 PMCID: PMC11058618 DOI: 10.1007/s00792-024-01341-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - S V Albers
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - G Antranikian
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073, Hamburg, Germany
| | - H Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - B Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - M Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - A J M Driessen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Jebbar
- Univ. Brest, CNRS, Ifremer, Laboratoire de Biologie Et d'Écologie Des Écosystèmes Marins Profonds (BEEP), IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Z Kelman
- Institute for Bioscience and Biotechnology Research and the National Institute of Standards and Technology, Rockville, MD, USA
| | - M Kerou
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - J Littlechild
- Henry Wellcome Building for Biocatalysis, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - V Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - P Schönheit
- Institute of General Microbiology, Christian Albrechts University, Kiel, Germany
| | - B Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, 45117, Essen, Germany
| | - K Vorgias
- Biology Department and RI-Bio3, National and Kapodistrian University of Athens, Athens, Greece
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Tunca B, Kutlar FE, Kas A, Yilmazel YD. Enhanced biohydrogen production from high loads of unpretreated cattle manure by cellulolytic bacterium Caldicellulosiruptor bescii at 75 °C. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 171:401-410. [PMID: 37776811 DOI: 10.1016/j.wasman.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic bacterium capable of fermenting crystalline cellulose identified to date, and it also has a superior ability to degrade plant biomass without any pretreatment. This study is the first to assess the potential of utilizing unpretreated cattle manure (UCM) as a feedstock for hydrogen (H2) production by C. bescii at a concentration range between 2.5-50 g volatile solids (VS)/L. At 50 g VS/L UCM concentrations, H2 production ceased due to inhibition of C. bescii. To alleviate the impacts of inhibition, two strategies were adopted: (i) reduction of H2 build-up in the reactor headspace via gas sparging and (ii) adaptation of C. bescii to UCM via adaptive laboratory evolution (ALE). The former increased H2 yield by 47% compared to the control reactors, where no sparging was applied. The latter increased H2 yield by 142% compared to the control reactors inoculated by the wild type C. bescii. The UCM-adapted C. bescii demonstrated a remarkable H2 yield of 161.3 ± 1.6 mL H2/g VSadded at 15 g VS/L. This yield represents a twofold increase compared to the maximum H2 yield reported in the literature amongst fermentation studies utilizing manure as feed. At 15 g VS/L, around 73% of UCM was solubilized, and the carbon balance indicated that most of the effluent carbon was in the sugar- and acid-form. The remarkable ability of C. bescii to produce H2 from UCM under non-sterile conditions presents a significant potential for sustainable biohydrogen production from renewable feedstocks.
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Affiliation(s)
- Berivan Tunca
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
| | - Feride Ece Kutlar
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
| | - Aykut Kas
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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Bing RG, Carey MJ, Laemthong T, Willard DJ, Crosby JR, Sulis DB, Wang JP, Adams MWW, Kelly RM. Fermentative conversion of unpretreated plant biomass: A thermophilic threshold for indigenous microbial growth. BIORESOURCE TECHNOLOGY 2023; 367:128275. [PMID: 36347479 PMCID: PMC10561188 DOI: 10.1016/j.biortech.2022.128275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Naturally occurring, microbial contaminants were found in plant biomasses from common bioenergy crops and agricultural wastes. Unexpectedly, indigenous thermophilic microbes were abundant, raising the question of whether they impact thermophilic consolidated bioprocessing fermentations that convert biomass directly into useful bioproducts. Candidate microbial platforms for biomass conversion, Acetivibrio thermocellus (basionym Clostridium thermocellum; Topt 60 °C) and Caldicellulosiruptor bescii (Topt 78 °C), each degraded a wide variety of plant biomasses, but only A. thermocellus was significantly affected by the presence of indigenous microbial populations harbored by the biomass. Indigenous microbial growth was eliminated at ≥75 °C, conditions where C. bescii thrives, but where A. thermocellus cannot survive. Therefore, 75 °C is the thermophilic threshold to avoid sterilizing pre-treatments on the biomass that prevents native microbes from competing with engineered microbes and forming undesirable by-products. Thermophiles that naturally grow at and above 75 °C offer specific advantages as platform microorganisms for biomass conversion into fuels and chemicals.
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Affiliation(s)
- Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Morgan J Carey
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Tunyaboon Laemthong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel B Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Jack P Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States.
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Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
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Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Mishra S, Singh PK, Pattnaik R, Kumar S, Ojha SK, Srichandan H, Parhi PK, Jyothi RK, Sarangi PK. Biochemistry, Synthesis, and Applications of Bacterial Cellulose: A Review. Front Bioeng Biotechnol 2022; 10:780409. [PMID: 35372299 PMCID: PMC8964354 DOI: 10.3389/fbioe.2022.780409] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
The potential of cellulose nanocomposites in the new-generation super-performing nanomaterials is huge, primarily in medical and environment sectors, and secondarily in food, paper, and cosmetic sectors. Despite substantial illumination on the molecular aspects of cellulose synthesis, various process features, namely, cellular export of the nascent polysaccharide chain and arrangement of cellulose fibrils into a quasi-crystalline configuration, remain obscure. To unleash its full potential, current knowledge on nanocellulose dispersion and disintegration of the fibrillar network and the organic/polymer chemistry needs expansion. Bacterial cellulose biosynthesis mechanism for scaled-up production, namely, the kinetics, pathogenicity, production cost, and product quality/consistency remain poorly understood. The bottom-up bacterial cellulose synthesis approach makes it an interesting area for still wider and promising high-end applications, primarily due to the nanosynthesis mechanism involved and the purity of the cellulose. This study attempts to identify the knowledge gap and potential wider applications of bacterial cellulose and bacterial nanocellulose. This review also highlights the manufacture of bacterial cellulose through low-cost substrates, that is, mainly waste from brewing, agriculture, food, and sugar industries as well as textile, lignocellulosic biorefineries, and pulp mills.
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Affiliation(s)
- Snehasish Mishra
- BDTC, Bioenergy Lab, School of Biotechnology, KIIT Deemed University, Bhubaneswar, India
| | - Puneet Kumar Singh
- BDTC, Bioenergy Lab, School of Biotechnology, KIIT Deemed University, Bhubaneswar, India
| | - Ritesh Pattnaik
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, India
| | - Subrat Kumar
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, India
| | - Sanjay Kumar Ojha
- Professor Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
| | - Haragobinda Srichandan
- BDTC, Bioenergy Lab, School of Biotechnology, KIIT Deemed University, Bhubaneswar, India
| | | | - Rajesh Kumar Jyothi
- Convergence Research Center for Development of Mineral Resources (DMR), Korea Institute of Geosciences and Mineral Resources (KIGAM), Daejeon, Korea
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Bing RG, Straub CT, Sulis DB, Wang JP, Adams MWW, Kelly RM. Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis. BIORESOURCE TECHNOLOGY 2022; 348:126780. [PMID: 35093526 PMCID: PMC10560548 DOI: 10.1016/j.biortech.2022.126780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
A variety of chemical and biological processes have been proposed for conversion of sustainable low-cost feedstocks into industrial products. Here, a biorefinery concept is formulated, modeled, and analyzed in which a naturally (hemi)cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii, is metabolically engineered to convert the carbohydrate content of lignocellulosic biomasses (i.e., soybean hulls, transgenic poplar) into green hydrogen and acetone. Experimental validation of C. bescii fermentative performance demonstrated 82% carbohydrate solubilization of soybean hulls and 55% for transgenic poplar. A detailed technical design, including equipment specifications, provides the basis for an economic analysis that establishes metabolic engineering targets. This robust industrial process leveraging metabolically engineered C. bescii yields 206 kg acetone and 25 kg H2 per metric ton of soybean hull, or 174 kg acetone and 21 kg H2 per metric ton transgenic poplar. Beyond this specific case, the model demonstrates industrial feasibility and economic advantages of thermophilic fermentation.
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Affiliation(s)
- Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel B Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Jack P Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States.
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Kubis MR, Holwerda EK, Lynd LR. Declining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic tests. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:12. [PMID: 35418299 PMCID: PMC8817502 DOI: 10.1186/s13068-022-02110-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/15/2022] [Indexed: 12/31/2022]
Abstract
Background For economically viable 2nd generation biofuels, processing of high solid lignocellulosic substrate concentrations is a necessity. The cellulolytic thermophilic anaerobe Clostridium thermocellum is one of the most effective biocatalysts for solubilization of carbohydrate harbored in lignocellulose. This study aims to document the solubilization performance of Clostridium thermocellum at increasing solids concentrations for two lignocellulosic feedstocks, corn stover and switchgrass, and explore potential effectors of solubilization performance. Results Monocultures of Clostridium thermocellum demonstrated high levels of carbohydrate solubilization for both unpretreated corn stover and switchgrass. However, fractional carbohydrate solubilization decreases with increasing solid loadings. Fermentation of model insoluble substrate (cellulose) in the presence of high solids lignocellulosic spent broth is temporarily affected but not model soluble substrate (cellobiose) fermentations. Mid-fermentation addition of cells (C. thermocellum) or model substrates did not significantly enhance overall corn stover solubilization loaded at 80 g/L, however cultures utilized the model substrates in the presence of high concentrations of corn stover. An increase in corn stover solubilization was observed when water was added, effectively diluting the solids concentration mid-fermentation. Introduction of a hemicellulose-utilizing coculture partner, Thermoanaerobacterium thermosaccharolyticum, increased the fractional carbohydrate solubilization at both high and low solid loadings. Residual solubilized carbohydrates diminished significantly in the presence of T. thermosaccharolyticum compared to monocultures of C. thermocellum, yet a small fraction of solubilized oligosaccharides of both C5 and C6 sugars remained unutilized. Conclusion Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum-mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum, which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02110-4.
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Affiliation(s)
- Matthew R Kubis
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. .,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Byrne E, Björkmalm J, Bostick JP, Sreenivas K, Willquist K, van Niel EWJ. Characterization and adaptation of Caldicellulosiruptor strains to higher sugar concentrations, targeting enhanced hydrogen production from lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:210. [PMID: 34717729 PMCID: PMC8557575 DOI: 10.1186/s13068-021-02058-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The members of the genus Caldicellulosiruptor have the potential for future integration into a biorefinery system due to their capacity to generate hydrogen close to the theoretical limit of 4 mol H2/mol hexose, use a wide range of sugars and can grow on numerous lignocellulose hydrolysates. However, members of this genus are unable to survive in high sugar concentrations, limiting their ability to grow on more concentrated hydrolysates, thus impeding their industrial applicability. In this study five members of this genus, C. owensensis, C. kronotskyensis, C. bescii, C. acetigenus and C. kristjanssonii, were developed to tolerate higher sugar concentrations through an adaptive laboratory evolution (ALE) process. The developed mixed population C. owensensis CO80 was further studied and accompanied by the development of a kinetic model based on Monod kinetics to quantitatively compare it with the parental strain. RESULTS Mixed populations of Caldicellulosiruptor tolerant to higher glucose concentrations were obtained with C. owensensis adapted to grow up to 80 g/L glucose; other strains in particular C. kristjanssonii demonstrated a greater restriction to adaptation. The C. owensensis CO80 mixed population was further studied and demonstrated the ability to grow in glucose concentrations up to 80 g/L glucose, but with reduced volumetric hydrogen productivities ([Formula: see text]) and incomplete sugar conversion at elevated glucose concentrations. In addition, the carbon yield decreased with elevated concentrations of glucose. The ability of the mixed population C. owensensis CO80 to grow in high glucose concentrations was further described with a kinetic growth model, which revealed that the critical sugar concentration of the cells increased fourfold when cultivated at higher concentrations. When co-cultured with the adapted C. saccharolyticus G5 mixed culture at a hydraulic retention time (HRT) of 20 h, C. owensensis constituted only 0.09-1.58% of the population in suspension. CONCLUSIONS The adaptation of members of the Caldicellulosiruptor genus to higher sugar concentrations established that the ability to develop improved strains via ALE is species dependent, with C. owensensis adapted to grow on 80 g/L, whereas C. kristjanssonii could only be adapted to 30 g/L glucose. Although C. owensensis CO80 was adapted to a higher sugar concentration, this mixed population demonstrated reduced [Formula: see text] with elevated glucose concentrations. This would indicate that while ALE permits adaptation to elevated sugar concentrations, this approach does not result in improved fermentation performances at these higher sugar concentrations. Moreover, the observation that planktonic mixed culture of CO80 was outcompeted by an adapted C. saccharolyticus, when co-cultivated in continuous mode, indicates that the robustness of CO80 mixed culture should be improved for industrial application.
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Affiliation(s)
- Eoin Byrne
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Johanna Björkmalm
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- RISE, Ideon Science Park, Building Beta 2 3v Scheelevägen 17, 22370, Lund, Sweden
| | - James P Bostick
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
- Coriolis Pharma Research GmbH, Fraunhoferstrasse 18B, 82152, Planegg, Germany
| | - Krishnan Sreenivas
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Karin Willquist
- RISE, Ideon Science Park, Building Beta 2 3v Scheelevägen 17, 22370, Lund, Sweden
| | - Ed W J van Niel
- Division of Applied Microbiology, Lund University, PO Box 124, 221 00, Lund, Sweden.
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Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
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Zhang K, Zhao W, Rodionov DA, Rubinstein GM, Nguyen DN, Tanwee TNN, Crosby J, Bing RG, Kelly RM, Adams MWW, Zhang Y. Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production. mSystems 2021; 6:e0135120. [PMID: 34060912 PMCID: PMC8269263 DOI: 10.1128/msystems.01351-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 12/03/2022] Open
Abstract
Metabolic modeling was used to examine potential bottlenecks that could be encountered for metabolic engineering of the cellulolytic extreme thermophile Caldicellulosiruptor bescii to produce bio-based chemicals from plant biomass. The model utilizes subsystems-based genome annotation, targeted reconstruction of carbohydrate utilization pathways, and biochemical and physiological experimental validations. Specifically, carbohydrate transport and utilization pathways involving 160 genes and their corresponding functions were incorporated, representing the utilization of C5/C6 monosaccharides, disaccharides, and polysaccharides such as cellulose and xylan. To illustrate its utility, the model predicted that optimal production from biomass-based sugars of the model product, ethanol, was driven by ATP production, redox balancing, and proton translocation, mediated through the interplay of an ATP synthase, a membrane-bound hydrogenase, a bifurcating hydrogenase, and a bifurcating NAD- and NADP-dependent oxidoreductase. These mechanistic insights guided the design and optimization of new engineering strategies for product optimization, which were subsequently tested in the C. bescii model, showing a nearly 2-fold increase in ethanol yields. The C. bescii model provides a useful platform for investigating the potential redox controls that mediate the carbon and energy flows in metabolism and sets the stage for future design of engineering strategies aiming at optimizing the production of ethanol and other bio-based chemicals. IMPORTANCE The extremely thermophilic cellulolytic bacterium, Caldicellulosiruptor bescii, degrades plant biomass at high temperatures without any pretreatments and can serve as a strategic platform for industrial applications. The metabolic engineering of C. bescii, however, faces potential bottlenecks in bio-based chemical productions. By simulating the optimal ethanol production, a complex interplay between redox balancing and the carbon and energy flow was revealed using a C. bescii genome-scale metabolic model. New engineering strategies were designed based on an improved mechanistic understanding of the C. bescii metabolism, and the new designs were modeled under different genetic backgrounds to identify optimal strategies. The C. bescii model provided useful insights into the metabolic controls of this organism thereby opening up prospects for optimizing production of a wide range of bio-based chemicals.
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Affiliation(s)
- Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Weishu Zhao
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dmitry A. Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Diep N. Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - James Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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12
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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13
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Beri D, Herring CD, Blahova S, Poudel S, Giannone RJ, Hettich RL, Lynd LR. Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:24. [PMID: 33461608 PMCID: PMC7814735 DOI: 10.1186/s13068-020-01867-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The cellulolytic thermophile Clostridium thermocellum is an important biocatalyst due to its ability to solubilize lignocellulosic feedstocks without the need for pretreatment or exogenous enzyme addition. At low concentrations of substrate, C. thermocellum can solubilize corn fiber > 95% in 5 days, but solubilization declines markedly at substrate concentrations higher than 20 g/L. This differs for model cellulose like Avicel, on which the maximum solubilization rate increases in proportion to substrate concentration. The goal of this study was to examine fermentation at increasing corn fiber concentrations and investigate possible reasons for declining performance. RESULTS The rate of growth of C. thermocellum on corn fiber, inferred from CipA scaffoldin levels measured by LC-MS/MS, showed very little increase with increasing solids loading. To test for inhibition, we evaluated the effects of spent broth on growth and cellulase activity. The liquids remaining after corn fiber fermentation were found to be strongly inhibitory to growth on cellobiose, a substrate that does not require cellulose hydrolysis. Additionally, the hydrolytic activity of C. thermocellum cellulase was also reduced to less-than half by adding spent broth. Noting that > 15 g/L hemicellulose oligosaccharides accumulated in the spent broth of a 40 g/L corn fiber fermentation, we tested the effect of various model carbohydrates on growth on cellobiose and Avicel. Some compounds like xylooligosaccharides caused a decline in cellulolytic activity and a reduction in the maximum solubilization rate on Avicel. However, there were no relevant model compounds that could replicate the strong inhibition by spent broth on C. thermocellum growth on cellobiose. Cocultures of C. thermocellum with hemicellulose-consuming partners-Herbinix spp. strain LL1355 and Thermoanaerobacterium thermosaccharolyticum-exhibited lower levels of unfermented hemicellulose hydrolysis products, a doubling of the maximum solubilization rate, and final solubilization increased from 67 to 93%. CONCLUSIONS This study documents inhibition of C. thermocellum with increasing corn fiber concentration and demonstrates inhibition of cellulase activity by xylooligosaccharides, but further work is needed to understand why growth on cellobiose was inhibited by corn fiber fermentation broth. Our results support the importance of hemicellulose-utilizing coculture partners to augment C. thermocellum in the fermentation of lignocellulosic feedstocks at high solids loading.
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Affiliation(s)
- Dhananjay Beri
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Christopher D Herring
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA.
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
- Enchi Corporation, Lebanon, NH, 03766, USA.
| | - Sofie Blahova
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Suresh Poudel
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Enchi Corporation, Lebanon, NH, 03766, USA
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14
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol 2020; 168:572-590. [PMID: 33309672 DOI: 10.1016/j.ijbiomac.2020.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Deepak K Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; Medical Biotechnology, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide 5042, Australia.
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15
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Straub CT, Bing RG, Otten JK, Keller LM, Zeldes BM, Adams MWW, Kelly RM. Metabolically engineered Caldicellulosiruptor bescii as a platform for producing acetone and hydrogen from lignocellulose. Biotechnol Bioeng 2020; 117:3799-3808. [PMID: 32770740 DOI: 10.1002/bit.27529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/12/2020] [Accepted: 08/05/2020] [Indexed: 11/10/2022]
Abstract
The production of volatile industrial chemicals utilizing metabolically engineered extreme thermophiles offers the potential for processes with simultaneous fermentation and product separation. An excellent target chemical for such a process is acetone (Tb = 56°C), ideally produced from lignocellulosic biomass. Caldicellulosiruptor bescii (Topt 78°C), an extremely thermophilic fermentative bacterium naturally capable of deconstructing and fermenting lignocellulose, was metabolically engineered to produce acetone. When the acetone pathway construct was integrated into a parent strain containing the bifunctional alcohol dehydrogenase from Clostridium thermocellum, acetone was produced at 9.1 mM (0.53 g/L), in addition to minimal ethanol 3.3 mM (0.15 g/L), along with net acetate consumption. This demonstrates that C. bescii can be engineered with balanced pathways in which renewable carbohydrate sources are converted to useful metabolites, primarily acetone and H2 , without net production of its native fermentation products, acetate and lactate.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Lisa M Keller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
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16
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Rubinstein GM, Lipscomb GL, Williams-Rhaesa AM, Schut GJ, Kelly RM, Adams MWW. Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source. J Ind Microbiol Biotechnol 2020; 47:585-597. [PMID: 32783103 DOI: 10.1007/s10295-020-02299-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/27/2020] [Indexed: 01/13/2023]
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR-Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.
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Affiliation(s)
- Gabriel M Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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17
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Sander KB, Chung D, Klingeman DM, Giannone RJ, Rodriguez M, Whitham J, Hettich RL, Davison BH, Westpheling J, Brown SD. Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:50. [PMID: 32190115 PMCID: PMC7071700 DOI: 10.1186/s13068-020-01690-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/27/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Caldicellulosiruptor bescii, a promising biocatalyst being developed for use in consolidated bioprocessing of lignocellulosic materials to ethanol, grows poorly and has reduced conversion at elevated medium osmolarities. Increasing tolerance to elevated fermentation osmolarities is desired to enable performance necessary of a consolidated bioprocessing (CBP) biocatalyst. RESULTS Two strains of C. bescii showing growth phenotypes in elevated osmolarity conditions were identified. The first strain, ORCB001, carried a deletion of the FapR fatty acid biosynthesis and malonyl-CoA metabolism repressor and had a severe growth defect when grown in high-osmolarity conditions-introduced as the addition of either ethanol, NaCl, glycerol, or glucose to growth media. The second strain, ORCB002, displayed a growth rate over three times higher than its genetic parent when grown in high-osmolarity medium. Unexpectedly, a genetic complement ORCB002 exhibited improved growth, failing to revert the observed phenotype, and suggesting that mutations other than the deleted transcription factor (the fruR/cra gene) are responsible for the growth phenotype observed in ORCB002. Genome resequencing identified several other genomic alterations (three deleted regions, three substitution mutations, one silent mutation, and one frameshift mutation), which may be responsible for the observed increase in osmolarity tolerance in the fruR/cra-deficient strain, including a substitution mutation in dnaK, a gene previously implicated in osmoresistance in bacteria. Differential expression analysis and transcription factor binding site inference indicates that FapR negatively regulates malonyl-CoA and fatty acid biosynthesis, as it does in many other bacteria. FruR/Cra regulates neighboring fructose metabolism genes, as well as other genes in global manner. CONCLUSIONS Two systems able to effect tolerance to elevated osmolarities in C. bescii are identified. The first is fatty acid biosynthesis. The other is likely the result of one or more unintended, secondary mutations present in another transcription factor deletion strain. Though the locus/loci and mechanism(s) responsible remain unknown, candidate mutations are identified, including a mutation in the dnaK chaperone coding sequence. These results illustrate both the promise of targeted regulatory manipulation for osmotolerance (in the case of fapR) and the challenges (in the case of fruR/cra).
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Affiliation(s)
- Kyle B. Sander
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Present Address: Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA
| | - Daehwan Chung
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Genetics, University of Georgia, Athens, GA USA
- Present Address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jason Whitham
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: Becton Dickinson Diagnostics, Sparks Glencoe, MD USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Genetics, University of Georgia, Athens, GA USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Bredesen Center for Interdisciplinary Graduate Research and Education, University of Tennessee, Knoxville, TN USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Skokie, IL USA
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18
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Thermal Behavior of Green Cellulose-Filled Thermoplastic Elastomer Polymer Blends. Molecules 2020; 25:molecules25061279. [PMID: 32178229 PMCID: PMC7143982 DOI: 10.3390/molecules25061279] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/19/2022] Open
Abstract
A recently developed cellulose hybrid chemical treatment consists of two steps: solvent exchange (with ethanol or hexane) and chemical grafting of maleic anhydride (MA) on the surface of fibers. It induces a significant decrease in cellulose moisture content and causes some changes in the thermal resistance of analyzed blend samples, as well as surface properties. The thermal characteristics of ethylene-norbornene copolymer (TOPAS) blends filled with hybrid chemically modified cellulose fibers (UFC100) have been widely described on the basis of differential scanning calorimetry and thermogravimetric analysis. Higher thermal stability is observed for the materials filled with the fibers which were dried before any of the treatments carried out. Dried cellulose filled samples start to degrade at approximately 330 °C while undried UFC100 specimens begin to degrade around 320 °C. Interestingly, the most elevated thermal resistance was detected for samples filled with cellulose altered only with solvents (both ethanol and hexane). In order to support the supposed thermal resistance trends of prepared blend materials, apparent activation energies assigned to cellulose degradation (EA1) and polymer matrix decomposition (EA2) have been calculated and presented in the article. It may be evidenced that apparent activation energies assigned to the first decomposition step are higher in case of the systems filled with UFC100 dried prior to the modification process. Moreover, the results have been enriched using surface free energy analysis of the polymer blends. The surface free energy polar part (Ep) raises considering samples filled with not dried UFC100. On the other hand, when cellulose fibers are dried prior to the modification process, then the blend sample’s dispersive part of surface free energy is increased with respect to that containing unmodified fiber. As polymer blend Ep exhibits higher values reflecting enhanced material degradation potential, the cellulose fibers employment leads to more eco-friendly production and responsible waste management. This is in accordance with the rules of sustainable development.
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19
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Kahn A, Moraïs S, Chung D, Sarai NS, Hengge NN, Kahn A, Himmel ME, Bayer EA, Bomble YJ. Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis. FEBS J 2020; 287:4370-4388. [DOI: 10.1111/febs.15251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
- Faculty of Natural Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - Daehwan Chung
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Nicholas S. Sarai
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Neal N. Hengge
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Audrey Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Michael E. Himmel
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Yannick J. Bomble
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
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20
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Influence of substrate loadings on the consolidated bioprocessing of rice straw and sugarcane bagasse biomass using Ruminiclostridium thermocellum. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Straub CT, Khatibi PA, Otten JK, Adams MWW, Kelly RM. Lignocellulose solubilization and conversion by extremely thermophilic
Caldicellulosiruptor bescii
improves by maintaining metabolic activity. Biotechnol Bioeng 2019; 116:1901-1908. [DOI: 10.1002/bit.26993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/12/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Christopher T. Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | - Piyum A. Khatibi
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | - Jonathan K. Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology University of Georgia Athens Georgia
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina
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Scott IM, Rubinstein GM, Poole FL, Lipscomb GL, Schut GJ, Williams-Rhaesa AM, Stevenson DM, Amador-Noguez D, Kelly RM, Adams MWW. The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. J Biol Chem 2019; 294:9995-10005. [PMID: 31097544 DOI: 10.1074/jbc.ra118.007120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/13/2019] [Indexed: 01/22/2023] Open
Abstract
Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species.
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Affiliation(s)
- Israel M Scott
- From the Department of Biochemistry and Molecular Biology and
| | | | - Farris L Poole
- From the Department of Biochemistry and Molecular Biology and
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology and
| | - Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology and
| | | | - David M Stevenson
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Daniel Amador-Noguez
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Robert M Kelly
- the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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Kahn A, Moraïs S, Galanopoulou AP, Chung D, Sarai NS, Hengge N, Hatzinikolaou DG, Himmel ME, Bomble YJ, Bayer EA. Creation of a functional hyperthermostable designer cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:44. [PMID: 30858881 PMCID: PMC6394049 DOI: 10.1186/s13068-019-1386-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/20/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Renewable energy has become a field of high interest over the past decade, and production of biofuels from cellulosic substrates has a particularly high potential as an alternative source of energy. Industrial deconstruction of biomass, however, is an onerous, exothermic process, the cost of which could be decreased significantly by use of hyperthermophilic enzymes. An efficient way of breaking down cellulosic substrates can also be achieved by highly efficient enzymatic complexes called cellulosomes. The modular architecture of these multi-enzyme complexes results in substrate targeting and proximity-based synergy among the resident enzymes. However, cellulosomes have not been observed in hyperthermophilic bacteria. RESULTS Here, we report the design and function of a novel hyperthermostable "designer cellulosome" system, which is stable and active at 75 °C. Enzymes from Caldicellulosiruptor bescii, a highly cellulolytic hyperthermophilic anaerobic bacterium, were selected and successfully converted to the cellulosomal mode by grafting onto them divergent dockerin modules that can be inserted in a precise manner into a thermostable chimaeric scaffoldin by virtue of their matching cohesins. Three pairs of cohesins and dockerins, selected from thermophilic microbes, were examined for their stability at extreme temperatures and were determined stable at 75 °C for at least 72 h. The resultant hyperthermostable cellulosome complex exhibited the highest levels of enzymatic activity on microcrystalline cellulose at 75 °C, compared to those of previously reported designer cellulosome systems and the native cellulosome from Clostridium thermocellum. CONCLUSION The functional hyperthermophilic platform fulfills the appropriate physico-chemical properties required for exothermic processes. This system can thus be adapted for other types of thermostable enzyme systems and could serve as a basis for a variety of cellulolytic and non-cellulolytic industrial objectives at high temperatures.
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Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000 Beer-Sheva, Israel
| | - Anastasia P. Galanopoulou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Neal Hengge
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Dimitris G. Hatzinikolaou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
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24
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Conway JM, Crosby JR, McKinley BS, Seals NL, Adams MWW, Kelly RM. Parsing in vivo and in vitro contributions to microcrystalline cellulose hydrolysis by multidomain glycoside hydrolases in theCaldicellulosiruptor besciisecretome. Biotechnol Bioeng 2018; 115:2426-2440. [DOI: 10.1002/bit.26773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/21/2018] [Accepted: 06/21/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Jonathan M. Conway
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - James R. Crosby
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Bennett S. McKinley
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Nathaniel L. Seals
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthens GA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
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25
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Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:189. [PMID: 30002729 PMCID: PMC6036693 DOI: 10.1186/s13068-018-1178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/18/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. RESULTS In this study, we use computational protein design to engineer the Zymomonas mobilis PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC and PDC variants using circular dichroism. We then measure and compare enzyme endurance for wild-type PDC with the PDC variants at an elevated temperature of 60 °C (thermal endurance) using differential interference contrast imaging. CONCLUSIONS We find that increases in melting temperature (Tm) do not directly correlate with increases in thermal endurance at 60 °C. We also do not find evidence that any individual mutation or design approach is the major contributor to the most thermostable PDC variant. Rather, remarkable cooperativity among sixteen thermostabilizing mutations is key to rationally designing a PDC with significantly enhanced thermal endurance. These results suggest a generalizable iterative computational protein design approach to improve thermal stability and endurance of target enzymes.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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Williams-Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Poole Ii FL, Kelly RM, Adams MWW. Engineering redox-balanced ethanol production in the cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii. Metab Eng Commun 2018; 7:e00073. [PMID: 30009131 PMCID: PMC6041484 DOI: 10.1016/j.mec.2018.e00073] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/16/2018] [Accepted: 05/27/2018] [Indexed: 11/06/2022] Open
Abstract
Caldicellulosiruptor bescii is an extremely thermophilic cellulolytic bacterium with great potential for consolidated bioprocessing of renewable plant biomass. Since it does not natively produce ethanol, metabolic engineering is required to create strains with this capability. Previous efforts involved the heterologous expression of the gene encoding a bifunctional alcohol dehydrogenase, AdhE, which uses NADH as the electron donor to reduce acetyl-CoA to ethanol. Acetyl-CoA produced from sugar oxidation also generates reduced ferredoxin but there is no known pathway for the transfer of electrons from reduced ferredoxin to NAD in C. bescii. Herein, we engineered a strain of C. bescii using a more stable genetic background than previously reported and heterologously-expressed adhE from Clostridium thermocellum (which grows optimally (Topt) at 60 °C) with and without co-expression of the membrane-bound Rnf complex from Thermoanaerobacter sp. X514 (Topt 60 °C). Rnf is an energy-conserving, reduced ferredoxin NAD oxidoreductase encoded by six genes (rnfCDGEAB). It was produced in a catalytically active form in C. bescii that utilized the largest DNA construct to be expressed in this organism. The new genetic lineage containing AdhE resulted in increased ethanol production compared to previous reports. Ethanol production was further enhanced by the presence of Rnf, which also resulted in decreased production of pyruvate, acetoin and an uncharacterized compound as unwanted side-products. Using crystalline cellulose as the growth substrate for the Rnf-containing strain, 75 mM (3.5 g/L) ethanol was produced at 60 °C, which is 5-fold higher than that reported previously. This underlines the importance of redox balancing and paves the way for achieving even higher ethanol titers in C. bescii. New stable genetic background results in higher ethanol production. Ethanol production is enhanced further by reduced ferredoxin NAD oxidoreductase (Rnf). Rnf decreases pyruvate, acetoin and an unknown compound as unwanted side products. Maximum ethanol production is five-times higher than that achieved previously.
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Affiliation(s)
| | - Gabriel M Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Israel M Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Farris L Poole Ii
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Biomass based hydrogen production by dark fermentation — recent trends and opportunities for greener processes. Curr Opin Biotechnol 2018; 50:136-145. [DOI: 10.1016/j.copbio.2017.12.024] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 12/30/2017] [Indexed: 01/01/2023]
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28
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Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL, Kelly RM, Adams MWW, Hettich RL. The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:80. [PMID: 29588665 PMCID: PMC5865380 DOI: 10.1186/s13068-018-1076-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. RESULTS Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. CONCLUSIONS This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Mirko Basen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Present Address: Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt Am Main, Germany
| | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Farris L. Poole
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert M. Kelly
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Michael W. W. Adams
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Sun P, Zhang J, Esquivel-Elizondo S, Ma L, Wu Y. Uncovering the flocculating potential of extracellular polymeric substances produced by periphytic biofilms. BIORESOURCE TECHNOLOGY 2018; 248:56-60. [PMID: 28668493 DOI: 10.1016/j.biortech.2017.06.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to study the characteristics and flocculating properties of extracellular polymeric substances (EPS) extracted from periphytic biofilms. The periphytic EPS, with an extracted yield of 491.8mg/g, were mainly composed of hetero-polysaccharides and proteins, and the elements C1s, N1s, and O1s. Polysaccharides represented 53.28% of the periphytic EPS. Proteins constituted 20.26% of the EPS, and contributed to at least 34.65% of the total flocculating activity. The periphytic EPS showed high turbidity removal capacity (86.76±1.52%, 10min) and efficient aniline blue (AB) removal capacity (56.46±1.41%, 30min). The mechanism of AB removal by the periphytic EPS seemed to be a combined technique of "adsorption-flocculation". This study reveals the flocculating capability of periphytic EPS, and suggests that periphytic biofilms are novel sources for bioflocculants preparation.
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Affiliation(s)
- Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jianhong Zhang
- Resources & Environment Business Dept., International Engineering Consulting Corporation, Beijing 100048, China
| | - Sofia Esquivel-Elizondo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287-5701, USA
| | - Lan Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, Nanjing 210008, China.
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30
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Verbeke TJ, Garcia GM, Elkins JG. The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:233. [PMID: 29213307 PMCID: PMC5708108 DOI: 10.1186/s13068-017-0917-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/08/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Efficient deconstruction and bioconversion of solids at high mass loadings is necessary to produce industrially relevant titers of biofuels from lignocellulosic biomass. To date, only a few studies have investigated the effect of solids loadings on microorganisms of interest for consolidated bioprocessing. Here, the effects that various switchgrass loadings have on Clostridium thermocellum solubilization and bioconversion are investigated. RESULTS Clostridium thermocellum was grown for 10 days on 10, 25, or 50 g/L switchgrass or Avicel at equivalent glucan loadings. Avicel was completely consumed at all loadings, but total cellulose solubilization decreased from 63 to 37% as switchgrass loadings increased from 10 to 50 g/L. Washed, spent switchgrass could be additionally hydrolyzed and fermented in second-round fermentations suggesting that access to fermentable substrates was not the limiting factor at higher feedstock loadings. Results from fermentations on Avicel or cellobiose using culture medium supplemented with 50% spent fermentation broth demonstrated that compounds present in the supernatants from the 25 or 50 g/L switchgrass loadings were the most inhibitory to continued fermentation. CONCLUSIONS Recalcitrance alone cannot fully account for differences in solubilization and end-product formation between switchgrass and Avicel at increased substrate loadings. Experiments aimed at separating metabolic inhibition from inhibition of hydrolysis suggest that C. thermocellum's hydrolytic machinery is more vulnerable to inhibition from switchgrass-derived compounds than its fermentative metabolism.
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Affiliation(s)
- Tobin J. Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Present Address: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Gabriela M. Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
| | - James G. Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
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31
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Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii. Appl Environ Microbiol 2017. [PMID: 28625990 DOI: 10.1128/aem.00969-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates to C. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(-) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15% (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.IMPORTANCE Key to a microbial process for solubilization of plant biomass is the organism's access to the carbohydrate content of lignocellulose. Economically viable routes will characteristically minimize physical, chemical, and biological pretreatment such that microbial steps contribute to the greatest extent possible. Recently, transgenic versions of plants and trees have been developed with the intention of lowering the barrier to lignocellulose conversion, with particular focus on lignin content and composition. Here, the extremely thermophilic bacterium Caldicellulosiruptor bescii was used to solubilize natural and genetically modified switchgrass lines, with and without the aid of hydrothermal treatment. For lignocellulose conversion, it is clear that the microorganism, plant biomass substrate, and processing steps must all be considered simultaneously to achieve optimal results. Whether switchgrass lines engineered for low lignin or natural variants with desirable properties are used, conversion will depend on microbial access to crystalline cellulose in the plant cell wall.
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32
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Lusk BG, Colin A, Parameswaran P, Rittmann BE, Torres CI. Simultaneous fermentation of cellulose and current production with an enriched mixed culture of thermophilic bacteria in a microbial electrolysis cell. Microb Biotechnol 2017; 11:63-73. [PMID: 28557303 PMCID: PMC5743814 DOI: 10.1111/1751-7915.12733] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
An enriched mixed culture of thermophilic (60°C) bacteria was assembled for the purpose of using cellulose to produce current in thermophilic microbial electrolysis cells (MECs). Cellulose was fermented into sugars and acids before being consumed by anode‐respiring bacteria (ARB) for current production. Current densities (j) were sustained at 6.5 ± 0.2 A m−2 in duplicate reactors with a coulombic efficiency (CE) of 84 ± 0.3%, a coulombic recovery (CR) of 54 ± 11% and without production of CH4. Low‐scan rate cyclic voltammetry (LSCV) revealed a mid‐point potential (Eka) of −0.17 V versus SHE. Pyrosequencing analysis of the V4 hypervariable region of 16S rDNA and scanning electron microscopy present an enriched thermophilic microbial community consisting mainly of the phylum Firmicutes with the Thermoanaerobacter (46 ± 13%) and Thermincola (28 ± 14%) genera occupying the biofilm anode in high relative abundance and Tepidmicrobium (38 ± 6%) and Moorella (11 ± 8%) genera present in high relative abundance in the bulk medium. The Thermoanaerobacter (15 ± 16%) and Brevibacillus (21 ± 30%) genera were also present in the bulk medium; however, their relative abundance varied by reactor. This study indicates that thermophilic consortia can obtain high CE and CR, while sustaining high current densities from cellulose in MECs.
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Affiliation(s)
- Bradley G Lusk
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,#ScienceTheEarth, Mesa, AZ, 85201, USA
| | - Alexandra Colin
- Ecole Normale Superieure, 45, rue d'Ulm, 75230, Paris Cedex 05, France
| | - Prathap Parameswaran
- Department of Civil Engineering, Kansas State University, 2123 Fiedler Hall, Manhattan, KS, 66502, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Cesar I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
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SGNH hydrolase-type esterase domain containing Cbes-AcXE2: a novel and thermostable acetyl xylan esterase from Caldicellulosiruptor bescii. Extremophiles 2017; 21:687-697. [DOI: 10.1007/s00792-017-0934-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
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Counts JA, Zeldes BM, Lee LL, Straub CT, Adams MWW, Kelly RM. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28206708 DOI: 10.1002/wsbm.1377] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Abstract
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Laura L Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Smith PJ, Wang HT, York WS, Peña MJ, Urbanowicz BR. Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:286. [PMID: 29213325 PMCID: PMC5708106 DOI: 10.1186/s13068-017-0973-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/20/2017] [Indexed: 05/02/2023]
Abstract
Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20-35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.
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Affiliation(s)
- Peter J. Smith
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - William S. York
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Maria J. Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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Abreu AA, Tavares F, Alves MM, Pereira MA. Boosting dark fermentation with co-cultures of extreme thermophiles for biohythane production from garden waste. BIORESOURCE TECHNOLOGY 2016; 219:132-138. [PMID: 27484669 DOI: 10.1016/j.biortech.2016.07.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Proof of principle of biohythane and potential energy production from garden waste (GW) is demonstrated in this study in a two-step process coupling dark fermentation and anaerobic digestion. The synergistic effect of using co-cultures of extreme thermophiles to intensify biohydrogen dark fermentation is demonstrated using xylose, cellobiose and GW. Co-culture of Caldicellulosiruptor saccharolyticus and Thermotoga maritima showed higher hydrogen production yields from xylose (2.7±0.1molmol(-1) total sugar) and cellobiose (4.8±0.3molmol(-1) total sugar) compared to individual cultures. Co-culture of extreme thermophiles C. saccharolyticus and Caldicellulosiruptor bescii increased synergistically the hydrogen production yield from GW (98.3±6.9Lkg(-1) (VS)) compared to individual cultures and co-culture of T. maritima and C. saccharolyticus. The biochemical methane potential of the fermentation end-products was 322±10Lkg(-1) (CODt). Biohythane, a biogas enriched with 15% hydrogen could be obtained from GW, yielding a potential energy generation of 22.2MJkg(-1) (VS).
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Affiliation(s)
- Angela A Abreu
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Fábio Tavares
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Madalena Alves
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Clostridium thermocellum releases coumaric acid during degradation of untreated grasses by the action of an unknown enzyme. Appl Microbiol Biotechnol 2016; 100:2907-15. [PMID: 26762388 DOI: 10.1007/s00253-016-7294-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/20/2015] [Accepted: 12/26/2015] [Indexed: 12/17/2022]
Abstract
Clostridium thermocellum is an anaerobic thermophile with the ability to digest lignocellulosic biomass that has not been pretreated with high temperatures. Thermophilic anaerobes have previously been shown to more readily degrade grasses than wood. Part of the explanation for this may be the presence of relatively large amounts of coumaric acid in grasses, with linkages to both hemicellulose and lignin. We found that C. thermocellum and cell-free cellulase preparations both release coumaric acid from bagasse and switchgrass. Cellulase preparations from a mutant strain lacking the scaffoldin cipA still showed activity, though diminished. Deletion of all three proteins in C. thermocellum with ferulic acid esterase domains, either singly or in combination, did not eliminate the activity. Further work will be needed to identify the novel enzyme(s) responsible for the release of coumaric acid from grasses and to determine whether these enzymes are important factors of microbial biomass degradation.
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Dumitrache A, Akinosho H, Rodriguez M, Meng X, Yoo CG, Natzke J, Engle NL, Sykes RW, Tschaplinski TJ, Muchero W, Ragauskas AJ, Davison BH, Brown SD. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:31. [PMID: 26855670 PMCID: PMC4743434 DOI: 10.1186/s13068-016-0445-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/20/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Higher ratios of syringyl-to-guaiacyl (S/G) lignin components of Populus were shown to improve sugar release by enzymatic hydrolysis using commercial blends. Cellulolytic microbes are often robust biomass hydrolyzers and may offer cost advantages; however, it is unknown whether their activity can also be significantly influenced by the ratio of different monolignol types in Populus biomass. Hydrolysis and fermentation of autoclaved, but otherwise not pretreated Populus trichocarpa by Clostridium thermocellum ATCC 27405 was compared using feedstocks that had similar carbohydrate and total lignin contents but differed in S/G ratios. RESULTS Populus with an S/G ratio of 2.1 was converted more rapidly and to a greater extent compared to similar biomass that had a ratio of 1.2. For either microbes or commercial enzymes, an approximate 50 % relative difference in total solids solubilization was measured for both biomasses, which suggests that the differences and limitations in the microbial breakdown of lignocellulose may be largely from the enzymatic hydrolytic process. Surprisingly, the reduction in glucan content per gram solid in the residual microbially processed biomass was similar (17-18 %) irrespective of S/G ratio, pointing to a similar mechanism of solubilization that proceeded at different rates. Fermentation metabolome testing did not reveal the release of known biomass-derived alcohol and aldehyde inhibitors that could explain observed differences in microbial hydrolytic activity. Biomass-derived p-hydroxybenzoic acid was up to nine-fold higher in low S/G ratio biomass fermentations, but was not found to be inhibitory in subsequent test fermentations. Cellulose crystallinity and degree of polymerization did not vary between Populus lines and had minor changes after fermentation. However, lignin molecular weights and cellulose accessibility determined by Simons' staining were positively correlated to the S/G content. CONCLUSIONS Higher S/G ratios in Populus biomass lead to longer and more linear lignin chains and greater access to surface cellulosic content by microbe-bound enzymatic complexes. Substrate access limitation is suggested as a primary bottleneck in solubilization of minimally processed Populus, which has important implications for microbial deconstruction of lignocellulose biomass. Our findings will allow others to examine different Populus lines and to test if similar observations are possible for other plant species.
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Affiliation(s)
- Alexandru Dumitrache
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Hannah Akinosho
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Miguel Rodriguez
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Xianzhi Meng
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Chang Geun Yoo
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jace Natzke
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Nancy L. Engle
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Robert W. Sykes
- />National Renewable Energy Laboratory, US Department of Energy, Golden, CO 80401 USA
| | - Timothy J. Tschaplinski
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Wellington Muchero
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Arthur J. Ragauskas
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Department of Chemical and Biomolecular Engineering, Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Brian H. Davison
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
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Putro JN, Soetaredjo FE, Lin SY, Ju YH, Ismadji S. Pretreatment and conversion of lignocellulose biomass into valuable chemicals. RSC Adv 2016. [DOI: 10.1039/c6ra09851g] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Lignocellulose biomass can be utilized in many sectors of industry such as energy, chemical, and transportation. However, pretreatment is needed to break down the intricate bonding before converting it into wanted product.
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Affiliation(s)
- Jindrayani Nyoo Putro
- Department of Chemical Engineering
- National Taiwan University of Science and Technology
- Taipei 10607
- Taiwan
| | - Felycia Edi Soetaredjo
- Department of Chemical Engineering
- Widya Mandala Surabaya Catholic University
- Surabaya 60114
- Indonesia
| | - Shi-Yow Lin
- Department of Chemical Engineering
- National Taiwan University of Science and Technology
- Taipei 10607
- Taiwan
| | - Yi-Hsu Ju
- Department of Chemical Engineering
- National Taiwan University of Science and Technology
- Taipei 10607
- Taiwan
| | - Suryadi Ismadji
- Department of Chemical Engineering
- Widya Mandala Surabaya Catholic University
- Surabaya 60114
- Indonesia
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Sun P, Hui C, Bai N, Yang S, Wan L, Zhang Q, Zhao Y. Revealing the characteristics of a novel bioflocculant and its flocculation performance in Microcystis aeruginosa removal. Sci Rep 2015; 5:17465. [PMID: 26626432 PMCID: PMC4667227 DOI: 10.1038/srep17465] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/30/2015] [Indexed: 11/09/2022] Open
Abstract
In the present work, a novel bioflocculant, EPS-1, was prepared and used to flocculate the kaolin suspension and Microcystis aeruginosa. We focused on the characteristics and flocculation performance of EPS-1, especially with regard to its protein components. An important attribute of EPS-1 was its protein content, with 18 protein types identified that occupied a total content of 31.70% in the EPS-1. Moreover, the flocculating activity of these protein components was estimated to be no less than 33.93%. Additionally, polysaccharides that occupied 57.12% of the total EPS-1 content consisted of four monosaccharides: maltose, D-xylose, mannose, and D-fructose. In addition, carbonyl, amino, and hydroxyl groups were identified as the main functional groups. Three main elements, namely C1s, N1s, and O1s, were present in EPS-1 with relative atomic percentages of 62.63%, 24.91%, and 10.5%, respectively. Zeta potential analysis indicated that charge neutralization contributed to kaolin flocculation, but was not involved in M. aeruginosa flocculation. The flocculation conditions of EPS-1 were optimized, and the maximum flocculating efficiencies were 93.34% within 2 min for kaolin suspension and 87.98% within 10 min for M. aeruginosa. These results suggest that EPS-1 could be an alternative to chemical flocculants for treating wastewaters and cyanobacterium-polluted freshwater.
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Affiliation(s)
- Pengfei Sun
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Cai Hui
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Naling Bai
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Shengmao Yang
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, 310021 Hangzhou, Zhejiang, China
| | - Li Wan
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 37235-1604, Nashville, Tennessee, USA
| | - Qichun Zhang
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - YuHua Zhao
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
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A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria. Appl Environ Microbiol 2015; 81:7339-47. [PMID: 26276113 DOI: 10.1128/aem.01634-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/30/2015] [Indexed: 12/18/2022] Open
Abstract
Caldicellulosiruptor bescii grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment. C. bescii ferments both C5 and C6 sugars primarily to hydrogen gas, lactate, acetate, and CO2 and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the C. bescii genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of C. bescii has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in C. bescii was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon Pyrococcus furiosus. Furthermore, C. bescii also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in C. bescii, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
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Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization. Appl Environ Microbiol 2015; 81:7159-70. [PMID: 26253670 DOI: 10.1128/aem.01622-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/26/2015] [Indexed: 11/20/2022] Open
Abstract
Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2, and H2. Caldicellulosiruptor bescii, C. kronotskyensis, and C. saccharolyticus solubilized 38%, 36%, and 29% (by weight) of unpretreated switchgrass (Panicum virgatum) (5 g/liter), respectively, which was about half of the amount of crystalline cellulose (Avicel; 5 g/liter) that was solubilized under the same conditions. The lower yields with C. saccharolyticus, not appreciably greater than the thermal control for switchgrass, were unexpected, given that its genome encodes the same glycoside hydrolase 9 (GH9)-GH48 multidomain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing cellulose to switchgrass showed that many carbohydrate ABC transporters and multidomain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagellum biosynthesis were upregulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.
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Urbieta MS, Porati GW, Segretín AB, González-Toril E, Giaveno MA, Donati ER. Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity. Microorganisms 2015; 3:344-63. [PMID: 27682093 PMCID: PMC5023244 DOI: 10.3390/microorganisms3030344] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 01/25/2023] Open
Abstract
The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.
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Affiliation(s)
- María Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Graciana Willis Porati
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Ana Belén Segretín
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Elena González-Toril
- Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial (INTA-CSIC), Carretera de Ajalvir Km. 4, 28850, Torrejón de Ardoz, Madrid 28850, Spain.
| | - María Alejandra Giaveno
- Laboratorio de Biolixiviación, Departamentoo de Química-Facultad de Ingeniería, Universidad Nacional del Comahue, PROBIEN (CONICET-UNCo) Buenos Aires 1400 (8300) Neuquén, Argentina.
| | - Edgardo Rubén Donati
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
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Urbieta MS, Donati ER, Chan KG, Shahar S, Sin LL, Goh KM. Thermophiles in the genomic era: Biodiversity, science, and applications. Biotechnol Adv 2015; 33:633-47. [PMID: 25911946 DOI: 10.1016/j.biotechadv.2015.04.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/18/2014] [Accepted: 04/14/2015] [Indexed: 01/30/2023]
Abstract
Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.
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Affiliation(s)
- M Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Edgardo R Donati
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saleha Shahar
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Lee Li Sin
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia.
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Sun PF, Lin H, Wang G, Lu LL, Zhao YH. Preparation of a new-style composite containing a key bioflocculant produced by Pseudomonas aeruginosa ZJU1 and its flocculating effect on harmful algal blooms. JOURNAL OF HAZARDOUS MATERIALS 2015; 284:215-21. [PMID: 25463236 DOI: 10.1016/j.jhazmat.2014.11.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 05/22/2023]
Abstract
A novel composite consisting of clay, bioflocculant, and inorganic flocculant was designed, and its flocculating effect on harmful algal blooms (HABs) was studied in this study. The extracellular polymeric substances (EPS), produced with a yield of 3.58±0.11 g/L by a newly isolated Pseudomonas aeruginosa ZJU1, was indicated to be a key component in the composite. The components and functional groups of the EPS were analyzed, and it showed that polysaccharides, proteins, and nucleic acids are the main components; polar functional groups in the EPS are responsible for its flocculating activity. The novel composite was optimized by the response surface methodology and after optimization, the optical components and contents of the composite were Kaolin 2.38 g/L, CaCl2 0.28 g/L, KAl(SO4)2 0.09 g/L, and EPS 1.75 mg/L. The flocculating rates of the composite were tested, and it could rapidly reach 100±0.13% within 2 min when OD680 of Microcystis aeruginosa was 0.1; it could reach 100±0.08% within 5 min for OD680 of M. aeruginosa in HABs up to 1.0. These results suggest that the novel composite will be a highly efficient material for the treatment of HABs caused by M. aeruginosa.
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Affiliation(s)
- Peng-Fei Sun
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Hui Lin
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou 310021, PR China
| | - Guan Wang
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Li-Ling Lu
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China
| | - Yu-Hua Zhao
- College of Life Sciences, Zhejiang University, 310058 Hangzhou, Zhejiang, PR China.
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Chung D, Cha M, Snyder EN, Elkins JG, Guss AM, Westpheling J. Cellulosic ethanol production via consolidated bioprocessing at 75 °C by engineered Caldicellulosiruptor bescii. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:163. [PMID: 26442761 PMCID: PMC4595190 DOI: 10.1186/s13068-015-0346-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/21/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND The C. bescii genome does not encode an acetaldehyde/alcohol dehydrogenase or an acetaldehyde dehydrogenase and no ethanol production is detected in this strain. The recent introduction of an NADH-dependent AdhE from C. thermocellum (Fig. 1a) in an ldh mutant of this strain resulted in production of ethanol from un-pretreated switchgrass, but the thermolability of the C. thermocellum AdhE at the optimum growth temperature of C. bescii (78 °C) meant that ethanol was not produced above 65 °C.Fig. 1Proposed scheme for the pyruvate to ethanol pathway in C. thermocellum and T. pseudethanolicus 39E. a The C. thermocellum ethanol pathway. The red colored AdhE (Cthe_0423) is already expressed and tested in C. bescii [26]. b The T. pseudethanolicus 39E ethanol pathway. The green colored AdhE (Teth39_0206) and blue colored AdhB (Teth39_0218) are expressed and tested in C. bescii in this study. RESULTS The adhB and adhE genes from Thermoanaerobacter pseudethanolicus 39E, an anaerobic thermophile that produces ethanol as a major fermentation product at 70 °C, were cloned and expressed in an ldh deletion mutant of C. bescii. The engineered strains produced ethanol at 75 °C, near the ethanol boiling point. The AdhB expressing strain produced ethanol (1.4 mM on Avicel, 0.4 mM on switchgrass) as well as acetate (13.0 mM on Avicel, 15.7 mM on switchgrass). The AdhE expressing strain produced more ethanol (2.3 mM on Avicel, 1.6 mM on switchgrass) and reduced levels of acetate (12.3 mM on Avicel, 15.1 mM on switchgrass). These engineered strains produce cellulosic ethanol at the highest temperature of any microorganism to date. In addition, the addition of 40 mM MOPS to the growth medium increased the maximal growth yield of C. bescii by approximately twofold. CONCLUSIONS The utilization of thermostable enzymes will be critical to achieving high temperature CBP in bacteria such as C. bescii. The ability to produce ethanol at 75 °C, near its boiling point, raises the possibility that process optimization could allow in situ product removal of this end product to mitigate ethanol toxicity.
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Affiliation(s)
- Daehwan Chung
- />Department of Genetics, University of Georgia, Athens, GA USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Minseok Cha
- />Department of Genetics, University of Georgia, Athens, GA USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Elise N. Snyder
- />Department of Genetics, University of Georgia, Athens, GA USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - James G. Elkins
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Adam M. Guss
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Janet Westpheling
- />Department of Genetics, University of Georgia, Athens, GA USA
- />The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Chung D, Verbeke TJ, Cross KL, Westpheling J, Elkins JG. Expression of a heat-stable NADPH-dependent alcohol dehydrogenase in Caldicellulosiruptor bescii results in furan aldehyde detoxification. BIOTECHNOLOGY FOR BIOFUELS 2015. [PMID: 26203301 PMCID: PMC4511240 DOI: 10.1186/s13068-015-0287-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
BACKGROUND Compounds such as furfural and 5-hydroxymethylfurfural (5-HMF) are generated through the dehydration of xylose and glucose, respectively, during dilute-acid pretreatment of lignocellulosic biomass and are also potent microbial growth and fermentation inhibitors. The enzymatic reduction of these furan aldehydes to their corresponding, and less toxic, alcohols is an engineering approach that has been successfully implemented in both Saccharomyces cerevisiae and ethanologenic Escherichia coli, but has not yet been investigated in thermophiles relevant to biofuel production through consolidated bioprocessing (CBP). Developing CBP-relevant biocatalysts that are either naturally resistant to such inhibitors, or are amenable to engineered resistance, is therefore, an important component in making biofuels production from lignocellulosic biomass feasible. RESULTS A butanol dehydrogenase encoding gene from Thermoanaerobacter pseudethanolicus 39E (Teth39_1597), previously shown to have furfural and 5-HMF reducing capabilities, was cloned into a suicide plasmid, pDCW171 and transformed into a lactate dehydrogenase mutant of Caldicellulosiruptor bescii. Integration of the gene into the C. bescii chromosome was verified via PCR amplification and stable expression was observed up to 75°C. Heterologous expression of the NADPH-dependent BdhA enzyme conferred increased resistance of the engineered strain to both furfural and 5-HMF relative to the wild-type and parental strains. Further, when challenged with 15 mM concentrations of either furan aldehyde, the ability to eliminate furfural or 5-HMF from the culture medium was significantly improved in the engineered strain. CONCLUSIONS A genetically engineered strain of C. bescii (JWCB044) has been constructed that shows both an improved tolerance to furan aldehydes and an improved ability to eliminate furfural and 5-HMF from the culture medium. The work presented here represents the first example of engineering furan aldehyde resistance into a CBP-relevant thermophile and further validates C. bescii as being a genetically tractable microbe of importance for lignocellulosic biofuel production.
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Affiliation(s)
- Daehwan Chung
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Department of Genetics, University of Georgia, Athens, GA 30602-7223 USA
| | - Tobin J Verbeke
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Karissa L Cross
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Janet Westpheling
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Department of Genetics, University of Georgia, Athens, GA 30602-7223 USA
| | - James G Elkins
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
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A hybrid synthetic pathway for butanol production by a hyperthermophilic microbe. Metab Eng 2014; 27:101-106. [PMID: 25461832 DOI: 10.1016/j.ymben.2014.11.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/04/2014] [Accepted: 11/12/2014] [Indexed: 01/19/2023]
Abstract
Biologically produced alcohols are of great current interest for renewable solvents and liquid transportation fuels. While bioethanol is now produced on a massive scale, butanol has superior fuel characteristics and an additional value as a solvent and chemical feedstock. Butanol production has been demonstrated at ambient temperatures in metabolically-engineered mesophilic organisms, but the ability to engineer a microbe for in vivo high-temperature production of commodity chemicals has several distinct advantages. These include reduced contamination risk, facilitated removal of volatile products, and a wide temperature range to modulate and balance both the engineered pathway and the host׳s metabolism. We describe a synthetic metabolic pathway assembled from genes obtained from three different sources for conversion of acetyl-CoA to 1-butanol, and 1-butanol generation from glucose was demonstrated near 70°C in a microorganism that grows optimally near 100°C. The module could also be used in thermophiles capable of degrading plant biomass.
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Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii. Proc Natl Acad Sci U S A 2014; 111:8931-6. [PMID: 24889625 DOI: 10.1073/pnas.1402210111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ethanol is the most widely used renewable transportation biofuel in the United States, with the production of 13.3 billion gallons in 2012 [John UM (2013) Contribution of the Ethanol Industry to the Economy of the United States]. Despite considerable effort to produce fuels from lignocellulosic biomass, chemical pretreatment and the addition of saccharolytic enzymes before microbial bioconversion remain economic barriers to industrial deployment [Lynd LR, et al. (2008) Nat Biotechnol 26(2):169-172]. We began with the thermophilic, anaerobic, cellulolytic bacterium Caldicellulosiruptor bescii, which efficiently uses unpretreated biomass, and engineered it to produce ethanol. Here we report the direct conversion of switchgrass, a nonfood, renewable feedstock, to ethanol without conventional pretreatment of the biomass. This process was accomplished by deletion of lactate dehydrogenase and heterologous expression of a Clostridium thermocellum bifunctional acetaldehyde/alcohol dehydrogenase. Whereas wild-type C. bescii lacks the ability to make ethanol, 70% of the fermentation products in the engineered strain were ethanol [12.8 mM ethanol directly from 2% (wt/vol) switchgrass, a real-world substrate] with decreased production of acetate by 38% compared with wild-type. Direct conversion of biomass to ethanol represents a new paradigm for consolidated bioprocessing, offering the potential for carbon neutral, cost-effective, sustainable fuel production.
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