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Candry P, Godfrey BJ, Winkler MKH. Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates. ISME COMMUNICATIONS 2024; 4:ycae068. [PMID: 38800124 PMCID: PMC11126157 DOI: 10.1093/ismeco/ycae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/29/2024]
Abstract
Particulate carbon (C) degradation in soils is a critical process in the global C cycle governing greenhouse gas fluxes and C storage. Millimeter-scale soil aggregates impose strong controls on particulate C degradation by inducing chemical gradients of e.g. oxygen, as well as limiting microbial mobility in pore structures. To date, experimental models of soil aggregates have incorporated porosity and chemical gradients but not particulate C. Here, we demonstrate a proof-of-concept encapsulating microbial cells and particulate C substrates in hydrogel matrices as a novel experimental model for soil aggregates. Ruminiclostridium cellulolyticum was co-encapsulated with cellulose in millimeter-scale polyethyleneglycol-dimethacrylate (PEGDMA) hydrogel beads. Microbial activity was delayed in hydrogel-encapsulated conditions, with cellulose degradation and fermentation activity being observed after 13 days of incubation. Unexpectedly, hydrogel encapsulation shifted product formation of R. cellulolyticum from an ethanol-lactate-acetate mixture to an acetate-dominated product profile. Fluorescence microscopy enabled simultaneous visualization of the PEGDMA matrix, cellulose particles, and individual cells in the matrix, demonstrating growth on cellulose particles during incubation. Together, these microbe-cellulose-PEGDMA hydrogels present a novel, reproducible experimental soil surrogate to connect single cells to process outcomes at the scale of soil aggregates and ecosystems.
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Affiliation(s)
- Pieter Candry
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Seattle, WA 98195-2700, United States
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands. E-mail:
| | - Bruce J Godfrey
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Seattle, WA 98195-2700, United States
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2
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Cheng HH, Whang LM. Applying metabolic flux analysis to hydrogen fermentation using a metabolic network constructed for anaerobic mixed cultures. ENVIRONMENTAL RESEARCH 2023; 235:116636. [PMID: 37442252 DOI: 10.1016/j.envres.2023.116636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
In this study, a mixed-cultural metabolic network for anaerobic digestion that included the concept of a "universal bacterium" was constructed, and metabolic flux analysis (MFA) applying this network was conducted to evaluate the flow of electrons and materials during H2 fermentation under various conditions. The MFA results from two H2 fermenters feeding glucose with (GP) or without (GA) the addition of peptone suggest that hydraulic retention time (HRT) presents a significant impact on hydrogen production, and the reversed trends could be observed at HRTs below and above 4 h. From the MFA results of lactate/acetate-fed H2 fermenter, the highest flux of H2 production is associated with more significant acetate consumption and the following pathways toward the anaplerotic reactions cycle that produces NADH. The occurrence of acetogenesis in the H2 fermenters using various types of bioethanol-fermented residues (BEFRs) was also identified according to the MFA results. By analyzing the MFA results of all 49 sets of data from H2 fermenters via Pearson's correlation, it was revealed that the flux of H2 production positively correlates to the reduction of ferredoxin with pyruvate oxidation, acetate formation, and acetate emission when lactate was produced in the system. On the contrary, negative relationships were found between the flux of H2 production and these three fluxes. The extended application of MFA provides additional information, including the fluxes between intracellular metabolites, and the information has the potential to be used in decision-making systems during the future operation of anaerobic processes by connecting operational parameters.
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Affiliation(s)
- Hai-Hsuan Cheng
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan
| | - Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan; Sustainable Environment Research Laboratory (SERL), National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan.
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3
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The Roles of Nicotinamide Adenine Dinucleotide Phosphate Reoxidation and Ammonium Assimilation in the Secretion of Amino Acids as Byproducts of Clostridium thermocellum. Appl Environ Microbiol 2023; 89:e0175322. [PMID: 36625594 PMCID: PMC9888227 DOI: 10.1128/aem.01753-22] [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] [Indexed: 01/11/2023] Open
Abstract
Clostridium thermocellum is a cellulolytic thermophile that is considered for the consolidated bioprocessing of lignocellulose to ethanol. Improvements in ethanol yield are required for industrial implementation, but the incompletely understood causes of amino acid secretion impede progress. In this study, amino acid secretion was investigated via gene deletions in ammonium-regulated, nicotinamide adenine dinucleotide phosphate (NADPH)-supplying and NADPH-consuming pathways as well as via physiological characterization in cellobiose-limited or ammonium-limited chemostats. First, the contribution of the NADPH-supplying malate shunt was studied with strains using either the NADPH-yielding malate shunt (Δppdk) or a redox-independent conversion of PEP to pyruvate (Δppdk ΔmalE::Peno-pyk). In the latter, branched-chain amino acids, especially valine, were significantly reduced, whereas the ethanol yield increased from 46 to 60%, suggesting that the secretion of these amino acids balances the NADPH surplus from the malate shunt. The unchanged amino acid secretion in Δppdk falsified a previous hypothesis on an ammonium-regulated PEP-to-pyruvate flux redistribution. The possible involvement of another NADPH-supplier, namely, NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (nfnAB), was also excluded. Finally, the deletion of glutamate synthase (gogat) in ammonium assimilation resulted in the upregulation of NADPH-linked glutamate dehydrogenase activity and decreased amino acid yields. Since gogat in C. thermocellum is putatively annotated as ferredoxin-linked, a claim which is supported by the product redistribution observed in this study, this deletion likely replaced ferredoxin with NADPH in ammonium assimilation. Overall, these findings indicate that a need to reoxidize NADPH is driving the observed amino acid secretion, likely at the expense of the NADH needed for ethanol formation. This suggests that metabolic engineering strategies that simplify the redox metabolism and ammonium assimilation can contribute to increased ethanol yields. IMPORTANCE Improving the ethanol yield of C. thermocellum is important for the industrial implementation of this microorganism in consolidated bioprocessing. A central role of NADPH in driving amino acid byproduct formation was demonstrated by eliminating the NADPH-supplying malate shunt and separately by changing the cofactor specificity in ammonium assimilation. With amino acid secretion diverting carbon and electrons away from ethanol, these insights are important for further metabolic engineering to reach industrial requirements on ethanol yield. This study also provides chemostat data that are relevant for training genome-scale metabolic models and for improving the validity of their predictions, especially considering the reduced degree-of-freedom in the redox metabolism of the strains generated here. In addition, this study advances the fundamental understanding on the mechanisms underlying amino acid secretion in cellulolytic Clostridia as well as on the regulation and cofactor specificity in ammonium assimilation. Together, these efforts aid in the development of C. thermocellum for the sustainable consolidated bioprocessing of lignocellulose to ethanol with minimal pretreatment.
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Experimental investigation and mathematical modelling of batch and semi-continuous anaerobic digestion of cellulose at high concentrations and long residence times. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
AbstractIn the context of the anaerobic digestion of slowly biodegradable substrates for energy and chemicals production, this study investigated the anaerobic digestion of cellulose without any chemical pre-treatments using open (undefined) mixed microbial cultures. The anaerobic conversion of cellulose was investigated in extended-length (run length in the range 518–734 days) batch and semi-continuous runs (residence time 20–80 days), at high cellulose concentration (20–40 g L−1), at temperatures of 25 and 35 °C. The maximum cellulose removal was 77% in batch (after 412 days) and 60% (at 80 days residence time) in semi-continuous experiments. In semi-continuous experiments, cellulose removal increased as the residence time increased however the cellulose removal rate showed a maximum (0.17 g L−1 day−1) at residence time 40–60 days. Both cellulose removal and removal rate decreased when cellulose concentration in the feed was increased from 20 to 40 g L−1. Liquid-phase products (ethanol and short chain organic acids) were only observed under transient conditions but not at the steady state of semi-continuous runs. Most of the observed results were well described by a mathematical model which included cellulose hydrolysis and growth on the produced glucose. The model provided insight into the physical phenomena behind the observed results.
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Doloman A, Mahajan A, Pererva Y, Flann NS, Miller CD. A Model for Bioaugmented Anaerobic Granulation. Front Microbiol 2020; 11:566826. [PMID: 33117315 PMCID: PMC7575707 DOI: 10.3389/fmicb.2020.566826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Anaerobic granular sludge comprises of highly organized microorganisms with a sophisticated metabolic network. Such aggregates can withstand storage, temperature fluctuations and changes in the substrate supplied for anaerobic digestion. However, substrate change leads to long adaptation of granular consortia, creating lags in the reactor operations. To speed up adaptation and increase digestion efficiency, bioaugmentation with a robust consortium can be performed. The computational study described here aims to elucidate the mechanisms of bioaugmenting anaerobic granules, utilizing the current body of knowledge on metabolic and biochemical interactions between bacteria in such aggregates. Using a cDynoMiCs simulation environment, an agent-based model was developed to describe bioaugmentation for adaptation of cellobiose-degrading granular consortium to a lipid-rich feed. Lipolytic bacteria were successfully incorporated in silico to the stable granular consortia after 40 days of simulation. The ratio of cellobiose and the lipid-derivative, oleate, in the feed played key role to ensure augmentation. At 0.5 g/L of both cellobiose and oleate in the feed, a homogeneous stable augmented consortium was formed and converted the given amount of substrate to 10.9 mg/L of methane as a final product of anaerobic digestion. The demonstrated model can be used as a planning tool for anaerobic digestion facilities considering transition of the inoculum to a new type of feed.
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Affiliation(s)
- Anna Doloman
- Department of Biological Engineering, Utah State University, Logan, UT, United States
| | - Amitesh Mahajan
- Department of Computer Science, Utah State University, Logan, UT, United States
| | - Yehor Pererva
- Department of Biological Engineering, Utah State University, Logan, UT, United States
| | - Nicholas S Flann
- Department of Computer Science, Utah State University, Logan, UT, United States
| | - Charles D Miller
- Department of Biological Engineering, Utah State University, Logan, UT, United States
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Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries. BIORESOURCE TECHNOLOGY 2017; 239:496-506. [PMID: 28535986 DOI: 10.1016/j.biortech.2017.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 05/28/2023]
Abstract
Complete hydrolysis of cellulose has been a key characteristic of biomass technology because of the limitation of industrial production hosts to use cellodextrin, the partial hydrolysis product of cellulose. Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin of the enzymatic hydrolysis (via endoglucanase and exoglucanase) of cellulose. Conversion of cellobiose to glucose is executed by β-glucosidase. The complete extracellular hydrolysis of celluloses has several critical barriers in biomass technology. An alternative bioengineering strategy to make the bioprocessing less challenging is to engineer microbes with the abilities to hydrolyze and assimilate the cellulosic-hydrolysate cellodextrin. Microorganisms engineered to metabolize cellobiose rather than the monomeric glucose can provide several advantages for lignocellulose-based biorefineries. This review describes the recent advances and challenges in engineering efficient intracellular cellobiose metabolism in industrial hosts. This review also describes the limitations of and future prospectives in engineering intracellular cellobiose metabolism.
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Affiliation(s)
- Vinuselvi Parisutham
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sathesh-Prabu Chandran
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, KogleAllé, DK2970 Hørsholm, Denmark; Synthetic Biology Engineering Research Center (Synberc), Berkeley, CA 94720, USA
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7
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Lü F, Chai L, Shao L, He P. Precise pretreatment of lignocellulose: relating substrate modification with subsequent hydrolysis and fermentation to products and by-products. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:88. [PMID: 28400859 PMCID: PMC5387280 DOI: 10.1186/s13068-017-0775-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/05/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pretreatment is a crucial step for valorization of lignocellulosic biomass into valuable products such as H2, ethanol, acids, and methane. As pretreatment can change several decisive factors concurrently, it is difficult to predict its effectiveness. Furthermore, the effectiveness of pretreatments is usually assessed by enzymatic digestibility or merely according to the yield of the target fermentation products. The present study proposed the concept of "precise pretreatment," distinguished the major decisive factors of lignocellulosic materials by precise pretreatment, and evaluated the complete profile of all fermentation products and by-products. In brief, hemicellulose and lignin were selectively removed from dewaxed rice straw, and the cellulose was further modified to alter the crystalline allomorphs. The subsequent fermentation performance of the selectively pretreated lignocellulose was assessed using the cellulolytic, ethanologenic, and hydrogenetic Clostridium thermocellum through a holistic characterization of the liquid, solid, and gaseous products and residues. RESULTS The transformation of crystalline cellulose forms from I to II and from Iα to Iβ improved the production of H2 and ethanol by 65 and 29%, respectively. At the same time, the hydrolysis efficiency was merely improved by 10%, revealing that the crystalline forms not only influenced the accessibility of cellulose but also affected the metabolic preferences and flux of the system. The fermentation efficiency was independent of the specific surface area and degree of polymerization. Furthermore, the pretreatments resulted in 43-45% of the carbon in the liquid hydrolysates unexplainable by forming ethanol and acetate products. A tandem pretreatment with peracetic acid and alkali improved ethanol production by 45.5%, but also increased the production of non-ethanolic low-value by-products by 136%, resulting in a huge burden on wastewater treatment requirements. CONCLUSION Cellulose allomorphs significantly affected fermentation metabolic pathway, except for hydrolysis efficiency. Furthermore, with the increasing effectiveness of the pretreatment for ethanol production, more non-ethanolic low-value by-products or contaminants were produced, intensifying environmental burden. Therefore, the effectiveness of the pretreatment should not only be determined on the basis of energy auditing and inhibitors generated, but should also be assessed in terms of the environmental benefits of the whole integrated system from a holistic view.
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Affiliation(s)
- Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092 China
| | - Lina Chai
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092 China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092 China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092 China
- Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban–Rural Development (MOHURD) of China, Shanghai, 200092 China
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8
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Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, Amador-Noguez D, Brown SD, Guss AM. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum. Metab Eng 2017; 41:182-191. [PMID: 28400329 DOI: 10.1016/j.ymben.2017.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/27/2017] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
Abstract
Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.
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Affiliation(s)
- Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Margaret Sladek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Evert K Holwerda
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Thayer School of Engineering at Dartmouth College, Hanover, NH, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
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9
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Singh G, Chandoha-Lee C, Zhang W, Renneckar S, Vikesland PJ, Pruden A. Biodegradation of nanocrystalline cellulose by two environmentally-relevant consortia. WATER RESEARCH 2016; 104:137-146. [PMID: 27522024 DOI: 10.1016/j.watres.2016.07.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Nanocellulose is growing in popularity due to its versatile properties and applications. However, there is a void of knowledge regarding the environmental fate of nanocellulose and the response of environmental microbial communities that are historically adapted to non-nano cellulose forms. Given its distinction in terms of size and chemical and physical properties, nanocellulose could potentially resist biodegradation and/or pose a xenobiotic influence on microbial communities during wastewater treatment or in receiving environments. In this study, biodegradation of H2SO4 hydrolyzed nanocrystalline cellulose (HNC) was compared with that of microcrystalline cellulose using two distinct anaerobic cellulose-degrading microbial consortia initially sourced from anaerobic digester (AD) and wetland (W) inocula. Equivalent cellulose masses were dosed and monitored with time by measurement of liberated glucose. HNC biodegraded at slightly faster rate than microcrystalline cellulose (1st order decay constants: 0.62 ± 0.08 wk-1 for HNC versus 0.39 ± 0.05 wk-1 for microcrystalline cellulose for the AD consortium; 0.69 ± 0.04 wk-1for HNCversus 0.58 ± 0.05 wk-1 for microcrystalline cellulose for the W consortium). 16S rRNA (total bacteria) and cel48 (glycoside hydrolase gene family 48, indicative of cellulose-degrading potential) genes were observed to be more enriched in the HNC condition for both consortia. According to Illumina amplicon sequencing of 16S rRNA genes, the composition of the consortia underwent distinct shifts in concert with HNC versus microcrystalline cellulose degradation. This study demonstrates that the biodegradation of cellulose is not inhibited in the nano-size range, particularly in the crystalline form, though the microbes and pathways involved likely differ.
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Affiliation(s)
- Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Wei Zhang
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, VA 24060, USA; Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Scott Renneckar
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
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Bansal R, Helmus RA, Stanley BA, Zhu J, Liermann LJ, Brantley SL, Tien M. Survival During Long-Term Starvation: Global Proteomics Analysis of Geobacter sulfurreducens under Prolonged Electron-Acceptor Limitation. J Proteome Res 2013; 12:4316-26. [DOI: 10.1021/pr400266m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Reema Bansal
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Ruth A. Helmus
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Bruce A. Stanley
- Section
of Research Resources, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, United States
| | - Junjia Zhu
- Department
of Public Health Sciences, The Pennsylvania University State College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, United States
| | - Laura J. Liermann
- Earth
and Environmental Systems Institute, The Pennsylvania State University, 2217 Earth-Engineering Sciences Building, University Park, Pennsylvania 16802, United States
| | - Susan L. Brantley
- Earth
and Environmental Systems Institute, The Pennsylvania State University, 2217 Earth-Engineering Sciences Building, University Park, Pennsylvania 16802, United States
| | - Ming Tien
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania 16802, United States
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11
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van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, Engle NL, van den Berg RA, Argyros AD, Caiazza NC, Guss AM, Lynd LR. Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways. J Ind Microbiol Biotechnol 2013; 40:725-34. [PMID: 23645383 DOI: 10.1007/s10295-013-1275-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Δldh) and/or acetate (Δpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Δldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Δhpt Δspo0A). The Δpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75 % more ethanol. A Δldh Δpta double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Δpta. Free amino acids were secreted by all examined strains, with both Δpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Δldh Δpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Δpta and 16-fold in the Δldh Δpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP⁺ through increased production of amino acids.
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12
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You C, Chen H, Myung S, Sathitsuksanoh N, Ma H, Zhang XZ, Li J, Zhang YHP. Enzymatic transformation of nonfood biomass to starch. Proc Natl Acad Sci U S A 2013; 110:7182-7. [PMID: 23589840 PMCID: PMC3645547 DOI: 10.1073/pnas.1302420110] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The global demand for food could double in another 40 y owing to growth in the population and food consumption per capita. To meet the world's future food and sustainability needs for biofuels and renewable materials, the production of starch-rich cereals and cellulose-rich bioenergy plants must grow substantially while minimizing agriculture's environmental footprint and conserving biodiversity. Here we demonstrate one-pot enzymatic conversion of pretreated biomass to starch through a nonnatural synthetic enzymatic pathway composed of endoglucanase, cellobiohydrolyase, cellobiose phosphorylase, and alpha-glucan phosphorylase originating from bacterial, fungal, and plant sources. A special polypeptide cap in potato alpha-glucan phosphorylase was essential to push a partially hydrolyzed intermediate of cellulose forward to the synthesis of amylose. Up to 30% of the anhydroglucose units in cellulose were converted to starch; the remaining cellulose was hydrolyzed to glucose suitable for ethanol production by yeast in the same bioreactor. Next-generation biorefineries based on simultaneous enzymatic biotransformation and microbial fermentation could address the food, biofuels, and environment trilemma.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department
| | - Hongge Chen
- Biological Systems Engineering Department
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Suwan Myung
- Biological Systems Engineering Department
- Institute for Critical Technology and Applied Science, and
| | - Noppadon Sathitsuksanoh
- Biological Systems Engineering Department
- Institute for Critical Technology and Applied Science, and
| | - Hui Ma
- Gate Fuels, Inc., Blacksburg, VA 24060
| | - Xiao-Zhou Zhang
- Biological Systems Engineering Department
- Gate Fuels, Inc., Blacksburg, VA 24060
| | - Jianyong Li
- Biochemistry Department, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Y.-H. Percival Zhang
- Biological Systems Engineering Department
- Institute for Critical Technology and Applied Science, and
- Gate Fuels, Inc., Blacksburg, VA 24060
- BioEnergy Science Center, Department of Energy, Oak Ridge, TN 37831; and
- Cell Free Bioinnovations, Inc., Blacksburg, VA 24060
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Continuous cellulosic bioethanol fermentation by cyclic fed-batch cocultivation. Appl Environ Microbiol 2012; 79:1580-9. [PMID: 23275517 DOI: 10.1128/aem.02617-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cocultivation of cellulolytic and saccharolytic microbial populations is a promising strategy to improve bioethanol production from the fermentation of recalcitrant cellulosic materials. Earlier studies have demonstrated the effectiveness of cocultivation in enhancing ethanolic fermentation of cellulose in batch fermentation. To further enhance process efficiency, a semicontinuous cyclic fed-batch fermentor configuration was evaluated for its potential in enhancing the efficiency of cellulose fermentation using cocultivation. Cocultures of cellulolytic Clostridium thermocellum LQRI and saccharolytic Thermoanaerobacter pseudethanolicus strain X514 were tested in the semicontinuous fermentor as a model system. Initial cellulose concentration and pH were identified as the key process parameters controlling cellulose fermentation performance in the fixed-volume cyclic fed-batch coculture system. At an initial cellulose concentration of 40 g liter(-1), the concentration of ethanol produced with pH control was 4.5-fold higher than that without pH control. It was also found that efficient cellulosic bioethanol production by cocultivation was sustained in the semicontinuous configuration, with bioethanol production reaching 474 mM in 96 h with an initial cellulose concentration of 80 g liter(-1) and pH controlled at 6.5 to 6.8. These results suggested the advantages of the cyclic fed-batch process for cellulosic bioethanol fermentation by the cocultures.
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Tsavkelova EA, Netrusov AI. Biogas production from cellulose-containing substrates: A review. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812050134] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Salimi F, Zhuang K, Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J 2010; 5:726-38. [PMID: 20665645 DOI: 10.1002/biot.201000159] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An alternative consolidated bioprocessing approach is the use of a co-culture containing cellulolytic and solventogenic clostridia. It has been demonstrated that the rate of cellulose utilization in the co-culture of Clostridium acetobutylicum and Clostridium cellulolyticum is improved compared to the mono-culture of C. cellulolyticum, suggesting the presence of syntrophy between these two species. However, the metabolic interactions in the co-culture are not well understood. To understand the metabolic interactions in the co-culture, we developed a genome-scale metabolic model of C. cellulolyticum comprising of 431 genes, 621 reactions, and 603 metabolites. The C. cellulolyticum model can successfully predict the chemostat growth and byproduct secretion with cellulose as the substrate. However, a growth arrest phenomenon, which occurs in batch cultures of C. cellulolyticum at cellulose concentrations higher than 6.7 g/L, cannot be predicted by dynamic flux balance analysis due to the lack of understanding of the underlying mechanism. These genome-scale metabolic models of the pure cultures have also been integrated using a community modeling framework to develop a dynamic model of metabolic interactions in the co-culture. Co-culture simulations suggest that cellobiose inhibition cannot be the main factor that is responsible for improved cellulose utilization relative to mono-culture of C. cellulolyticum.
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Affiliation(s)
- Fahimeh Salimi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada
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Miller LD, Mosher JJ, Venkateswaran A, Yang ZK, Palumbo AV, Phelps TJ, Podar M, Schadt CW, Keller M. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiol 2010; 10:149. [PMID: 20497531 PMCID: PMC2906461 DOI: 10.1186/1471-2180-10-149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 05/24/2010] [Indexed: 01/03/2023] Open
Abstract
Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.
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Affiliation(s)
- Lance D Miller
- Biosciences and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Liang Y, Feng Z, Yesuf J, Blackburn JW. Optimization of Growth Medium and Enzyme Assay Conditions for Crude Cellulases Produced by a Novel Thermophilic and Cellulolytic Bacterium, Anoxybacillus sp. 527. Appl Biochem Biotechnol 2009; 160:1841-52. [DOI: 10.1007/s12010-009-8677-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 05/18/2009] [Indexed: 11/29/2022]
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18
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Magnusson L, Cicek N, Sparling R, Levin D. Continuous hydrogen production during fermentation of α-cellulose by the thermophillic bacteriumClostridium thermocellum. Biotechnol Bioeng 2009; 102:759-66. [DOI: 10.1002/bit.22092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Song H, Clarke WP. Cellulose hydrolysis by a methanogenic culture enriched from landfill waste in a semi-continuous reactor. BIORESOURCE TECHNOLOGY 2009; 100:1268-1273. [PMID: 18929482 DOI: 10.1016/j.biortech.2008.08.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 08/03/2008] [Accepted: 08/05/2008] [Indexed: 05/26/2023]
Abstract
This study investigates the hydrolysis of cellulose by a mixed culture enriched from landfill waste in a continuous reactor operated under prolonged residence times to accommodate methanogenic conditions. Chemostat studies of hydrolysis under balance methanogenic conditions are rarely reported, despite the importance of hydrolysis under these conditions in waste management and renewable energy industries. Continuous digestion was studied in a 1.25l digester, fed with a 1% (w/v) slurry of 50mum cellulose in sterilized leachate drawn from a 220l digester operated on a feedstock of mixed municipal solid waste. Unsterilized leachate was used as the inoculum. Stable and rapid hydrolytic conditions were established at residence time of 2.5, 3.5 and 5d with a 1st order hydrolysis rate 0.45+/-0.07d(-1) and high methane yields ranging from 57% to 62% of solubilised cellulose on a COD basis. Biomass yields were between 32% and 35% of solubilised cellulose on a COD basis, over three times that observed with fermentative cultures. This is attributed to the diversity of the microbial population which fully converted solubilised COD to methane, as evident by VFA yields of less than 8% on a COD basis.
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Affiliation(s)
- Hyohak Song
- School of Engineering, The University of Queensland, Brisbane, St Lucia, QLD, Australia
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20
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Chou CJ, Jenney FE, Adams MW, Kelly RM. Hydrogenesis in hyperthermophilic microorganisms: Implications for biofuels. Metab Eng 2008; 10:394-404. [DOI: 10.1016/j.ymben.2008.06.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 06/20/2008] [Indexed: 11/25/2022]
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21
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Chou CJ, Shockley KR, Conners SB, Lewis DL, Comfort DA, Adams MWW, Kelly RM. Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 2007; 73:6842-53. [PMID: 17827328 PMCID: PMC2074980 DOI: 10.1128/aem.00597-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycoside linkage (cellobiose versus maltose) dramatically influenced bioenergetics to different extents and by different mechanisms in the hyperthermophilic archaeon Pyrococcus furiosus when it was grown in continuous culture at a dilution rate of 0.45 h(-1) at 90 degrees C. In the absence of S(0), cellobiose-grown cells generated twice as much protein and had 50%-higher specific H(2) generation rates than maltose-grown cultures. Addition of S(0) to maltose-grown cultures boosted cell protein production fourfold and shifted gas production completely from H(2) to H(2)S. In contrast, the presence of S(0) in cellobiose-grown cells caused only a 1.3-fold increase in protein production and an incomplete shift from H(2) to H(2)S production, with 2.5 times more H(2) than H(2)S formed. Transcriptional response analysis revealed that many genes and operons known to be involved in alpha- or beta-glucan uptake and processing were up-regulated in an S(0)-independent manner. Most differentially transcribed open reading frames (ORFs) responding to S(0) in cellobiose-grown cells also responded to S(0) in maltose-grown cells; these ORFs included ORFs encoding a membrane-bound oxidoreductase complex (MBX) and two hypothetical proteins (PF2025 and PF2026). However, additional genes (242 genes; 108 genes were up-regulated and 134 genes were down-regulated) were differentially transcribed when S(0) was present in the medium of maltose-grown cells, indicating that there were different cellular responses to the two sugars. These results indicate that carbohydrate characteristics (e.g., glycoside linkage) have a major impact on S(0) metabolism and hydrogen production in P. furiosus. Furthermore, such issues need to be considered in designing and implementing metabolic strategies for production of biofuel by fermentative anaerobes.
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Affiliation(s)
- Chung-Jung Chou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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22
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Abstract
Carbon metabolism in anaerobic cellulolytic bacteria has been investigated essentially in Clostridium thermocellum, Clostridium cellulolyticum, Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus. While cellulose depolymerization into soluble sugars by various cellulases is undoubtedly the first step in bacterial metabolisation of cellulose, it is not the only one to consider. Among anaerobic cellulolytic bacteria, C. cellulolyticum has been investigated metabolically the most in the past few years. Summarizing metabolic flux analyses in continuous culture using either cellobiose (a soluble cellodextrin resulting from cellulose hydrolysis) or cellulose (an insoluble biopolymer), this review aims to stress the importance of the insoluble nature of a carbon source on bacterial metabolism. Furthermore, some general and specific traits of anaerobic cellulolytic bacteria trends, namely, the importance and benefits of (i) cellodextrins with degree of polymerization higher than 2, (ii) intracellular phosphorolytic cleavage, (iii) glycogen cycling on cell bioenergetics, and (iv) carbon overflows in regulation of carbon metabolism, as well as detrimental effects of (i) soluble sugars and (ii) acidic environment on bacterial growth. Future directions for improving bacterial cellulose degradation are discussed.
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Affiliation(s)
- Mickaël Desvaux
- INRA (Institut National de la Recherche Agronomique), Centre de Clermont-Ferrand, UR454 Unité de Microbiologie, Site de Theix, Saint-Genès Champanelle, F-63122 France.
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Islam R, Cicek N, Sparling R, Levin D. Effect of substrate loading on hydrogen production during anaerobic fermentation by Clostridium thermocellum 27405. Appl Microbiol Biotechnol 2006; 72:576-83. [PMID: 16685495 DOI: 10.1007/s00253-006-0316-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 12/28/2005] [Accepted: 01/01/2006] [Indexed: 11/27/2022]
Abstract
We have investigated hydrogen (H2) production by the cellulose-degrading anaerobic bacterium, Clostridium thermocellum. In the following experiments, batch-fermentations were carried out with cellobiose at three different substrate concentrations to observe the effects of carbon-limited or carbon-excess conditions on the carbon flow, H2-production, and synthesis of other fermentation end products, such as ethanol and organic acids. Rates of cell growth were unaffected by different substrate concentrations. H2, carbon dioxide (CO2), acetate, and ethanol were the main products of fermentation. Other significant end products detected were formate and lactate. In cultures where cell growth was severely limited due to low initial substrate concentrations, hydrogen yields of 1 mol H2/mol of glucose were obtained. In the cultures where growth ceased due to carbon depletion, lactate and formate represented a small fraction of the total end products produced, which consisted mainly of H2, CO2, acetate, and ethanol throughout growth. In cultures with high initial substrate concentrations, cellobiose consumption was incomplete and cell growth was limited by factors other than carbon availability. H2-production continued even in stationary phase and H2/CO2 ratios were consistently greater than 1 with a maximum of 1.2 at the stationary phase. A maximum specific H2 production rate of 14.6 mmol g dry cell(-1) h(-1) was observed. As cells entered stationary phase, extracellular pyruvate production was observed in high substrate concentration cultures and lactate became a major end product.
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Affiliation(s)
- Rumana Islam
- Deptartment of Biosystems Engineering, University of Manitoba, Winnipeg, R3T 5V6 MB, Canada.
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Collet C, Girbal L, Péringer P, Schwitzguébel JP, Soucaille P. Metabolism of lactose by Clostridium thermolacticum growing in continuous culture. Arch Microbiol 2006; 185:331-9. [PMID: 16508746 DOI: 10.1007/s00203-006-0098-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 01/18/2006] [Accepted: 02/07/2006] [Indexed: 11/24/2022]
Abstract
The objective of the present study was to characterize the metabolism of Clostridium thermolacticum, a thermophilic anaerobic bacterium, growing continuously on lactose (10 g l(-1)) and to determine the enzymes involved in the pathways leading to the formation of the fermentation products. Biomass and metabolites concentration were measured at steady-state for different dilution rates, from 0.013 to 0.19 h(-1). Acetate, ethanol, hydrogen and carbon dioxide were produced at all dilution rates, whereas lactate was detected only for dilution rates below 0.06 h(-1). The presence of several key enzymes involved in lactose metabolism, including beta-galactosidase, glyceraldehyde-3-phosphate dehydrogenase, pyruvate:ferredoxin oxidoreductase, acetate kinase, ethanol dehydrogenase and lactate dehydrogenase, was demonstrated. Finally, the intracellular level of NADH, NAD+, ATP and ADP was also measured for different dilution rates. The production of ethanol and lactate appeared to be linked with the re-oxidation of NADH produced during glycolysis, whereas hydrogen produced should come from reduced ferredoxin generated during pyruvate decarboxylation. To produce more hydrogen or more acetate from lactose, it thus appears that an efficient H2 removal system should be used, based on a physical (membrane) or a biological approach, respectively, by cultivating C. thermolacticum with efficient H2 scavenging and acetate producing microorganisms.
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Affiliation(s)
- Christophe Collet
- Laboratory for Environmental Biotechnology (LBE), Swiss Federal Institute of Technology Lausanne (EPFL), Station 6, 1015, Lausanne, Switzerland
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26
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Song H, Clarke WP, Blackall LL. Concurrent microscopic observations and activity measurements of cellulose hydrolyzing and methanogenic populations during the batch anaerobic digestion of crystalline cellulose. Biotechnol Bioeng 2005; 91:369-78. [PMID: 15991234 DOI: 10.1002/bit.20517] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study compares process data with microscopic observations from an anaerobic digestion of organic particles. As the first part of the study, this article presents detailed observations of microbial biofilm architecture and structure in a 1.25-L batch digester where all particles are of an equal age. Microcrystalline cellulose was used as the sole carbon and energy source. The digestions were inoculated with either leachate from a 220-L anaerobic municipal solid waste digester or strained rumen contents from a fistulated cow. The hydrolysis rate, when normalized by the amount of cellulose remaining in the reactor, was found to reach a constant value 1 day after inoculation with rumen fluid, and 3 days after inoculating with digester leachate. A constant value of a mass specific hydrolysis rate is argued to represent full colonization of the cellulose surface and first-order kinetics only apply after this point. Additionally, the first-order hydrolysis rate constant, once surfaces were saturated with biofilm, was found to be two times higher with a rumen inoculum, compared to a digester leachate inoculum. Images generated by fluorescence in situ hybridization (FISH) probing and confocal laser scanning microscopy show that the microbial communities involved in the anaerobic biodegradation process exist entirely within the biofilm. For the reactor conditions used in these experiments, the predominant methanogens exist in ball-shaped colonies within the biofilm.
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Affiliation(s)
- Hyohak Song
- School of Engineering, The University of Queensland, St. Lucia QLD4072, Australia
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28
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Zhang YHP, Lynd LR. Regulation of cellulase synthesis in batch and continuous cultures of Clostridium thermocellum. J Bacteriol 2005; 187:99-106. [PMID: 15601693 PMCID: PMC538832 DOI: 10.1128/jb.187.1.99-106.2005] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Accepted: 09/19/2004] [Indexed: 11/20/2022] Open
Abstract
Regulation of cell-specific cellulase synthesis (expressed in milligrams of cellulase per gram [dry weight] of cells) by Clostridium thermocellum was investigated using an enzyme-linked immunosorbent assay protocol based on antibody raised against a peptide sequence from the scaffoldin protein of the cellulosome (Zhang and Lynd, Anal. Chem. 75:219-227, 2003). The cellulase synthesis in Avicel-grown batch cultures was ninefold greater than that in cellobiose-grown batch cultures. In substrate-limited continuous cultures, however, the cellulase synthesis with Avicel-grown cultures was 1.3- to 2.4-fold greater than that in cellobiose-grown cultures, depending on the dilution rate. The differences between the cellulase yields observed during carbon-limited growth on cellulose and the cellulase yields observed during carbon-limited growth on cellobiose at the same dilution rate suggest that hydrolysis products other than cellobiose affect cellulase synthesis during growth on cellulose and/or that the presence of insoluble cellulose triggers an increase in cellulase synthesis. Continuous cellobiose-grown cultures maintained either at high dilution rates or with a high feed substrate concentration exhibited decreased cellulase synthesis; there was a large (sevenfold) decrease between 0 and 0.2 g of cellobiose per liter, and there was a much more gradual further decrease for cellobiose concentrations >0.2 g/liter. Several factors suggest that cellulase synthesis in C. thermocellum is regulated by catabolite repression. These factors include: (i) substantially higher cellulase yields observed during batch growth on Avicel than during batch growth on cellobiose, (ii) a strong negative correlation between the cellobiose concentration and the cellulase yield in continuous cultures with varied dilution rates at a constant feed substrate concentration and also with varied feed substrate concentrations at a constant dilution rate, and (iii) the presence of sequences corresponding to key elements of catabolite repression systems in the C. thermocellum genome.
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Desvaux M. Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia. FEMS Microbiol Rev 2004; 29:741-64. [PMID: 16102601 DOI: 10.1016/j.femsre.2004.11.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 04/27/2004] [Accepted: 11/01/2004] [Indexed: 11/22/2022] Open
Abstract
Clostridium cellulolyticum ATCC 35319 is a non-ruminal mesophilic cellulolytic bacterium originally isolated from decayed grass. As with most truly cellulolytic clostridia, C. cellulolyticum possesses an extracellular multi-enzymatic complex, the cellulosome. The catalytic components of the cellulosome release soluble cello-oligosaccharides from cellulose providing the primary carbon substrates to support bacterial growth. As most cellulolytic bacteria, C. cellulolyticum was initially characterised by limited carbon consumption and subsequent limited growth in comparison to other saccharolytic clostridia. The first metabolic studies performed in batch cultures suggested nutrient(s) limitation and/or by-product(s) inhibition as the reasons for this limited growth. In most recent investigations using chemostat cultures, metabolic flux analysis suggests a self-intoxication of bacterial metabolism resulting from an inefficiently regulated carbon flow. The investigation of C. cellulolyticum physiology with cellobiose, as a model of soluble cellodextrin, and with pure cellulose, as a carbon source more closely related to lignocellulosic compounds, strengthen the idea of a bacterium particularly well adapted, and even restricted, to a cellulolytic lifestyle. The metabolic flux analysis from continuous cultures revealed that (i) in comparison to cellobiose, the cellulose hydrolysis by the cellulosome introduces an extra regulation of entering carbon flow resulting in globally lower metabolic fluxes on cellulose than on cellobiose, (ii) the glucose 1-phosphate/glucose 6-phosphate branch point controls the carbon flow directed towards glycolysis and dissipates carbon excess towards the formation of cellodextrins, glycogen and exopolysaccharides, (iii) the pyruvate/acetyl-CoA metabolic node is essential to the regulation of electronic and energetic fluxes. This in-depth analysis of C. cellulolyticum metabolism has permitted the first attempt to engineer metabolically a cellulolytic microorganism.
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Affiliation(s)
- Mickaël Desvaux
- Institute for Biomedical Research, The University of Birmingham - The Medical School, Edgbaston, UK.
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Zhang YHP, Lynd LR. Kinetics and relative importance of phosphorolytic and hydrolytic cleavage of cellodextrins and cellobiose in cell extracts of Clostridium thermocellum. Appl Environ Microbiol 2004; 70:1563-9. [PMID: 15006779 PMCID: PMC368386 DOI: 10.1128/aem.70.3.1563-1569.2004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rates of phosphorolytic cleavage of beta-glucan substrates were determined for cell extracts from Clostridium thermocellum ATCC 27405 and were compared to rates of hydrolytic cleavage. Reactions with cellopentaose and cellobiose were evaluated for both cellulose (Avicel)- and cellobiose-grown cultures, with more limited data also obtained for cellotetraose. To measure the reaction rate in the chain-shortening direction at elevated temperatures, an assay protocol was developed featuring discrete sampling at 60 degrees C followed by subsequent analysis of reaction products (glucose and glucose-1-phosphate) at 35 degrees C. Calculated rates of phosphorolytic cleavage for cell extract from Avicel-grown cells exceeded rates of hydrolytic cleavage by > or = 20-fold for both cellobiose and cellopentaose over a 10-fold range of beta-glucan concentrations (0.5 to 5 mM) and for cellotetraose at a single concentration (2 mM). Rates of phosphorolytic cleavage of beta-glucosidic bonds measured in cell extracts were similar to rates observed in growing cultures. Comparisons of V(max) values indicated that cellobiose- and cellodextrin-phosphorylating activities are synthesized during growth on both cellobiose and Avicel but are subject to some degree of metabolic control. The apparent K(m) for phosphorolytic cleavage was lower for cellopentaose (mean value for Avicel- and cellobiose-grown cells, 0.61 mM) than for cellobiose (mean value, 3.3 mM).
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Regulation of the cellulosomal CelS (cel48A) gene of Clostridium thermocellum is growth rate dependent. J Bacteriol 2003. [PMID: 12730163 DOI: 10.1128/jb.185.10.3042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Clostridium thermocellum produces an extracellular multienzyme complex, termed cellulosome, that allows efficient solubilization of crystalline cellulose. One of the major enzymes in this complex is the CelS (Cel48A) exoglucanase. The regulation of CelS at the protein and transcriptional levels was studied using batch and continuous cultures. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analyses indicated that the amount of CelS in the supernatant fluids of cellobiose-grown cultures is lower than that of cellulose-grown cultures. The transcriptional level of celS mRNA was determined quantitatively by RNase protection assays with batch and continuous cultures under carbon and nitrogen limitation. The amount of celS mRNA transcripts per cell was about 180 for cells grown under carbon limitation at growth rates of 0.04 to 0.21 h(-1) and 80 and 30 transcripts per cell for batch cultures at growth rates of 0.23 and 0.35 h(-1), respectively. Under nitrogen limitation, the corresponding levels were 110, 40, and 30 transcripts/cell for growth rates of 0.07, 0.11, and 0.14 h(-1), respectively. Two major transcriptional start sites were detected at positions -140 and -145 bp, upstream of the translational start site of the celS gene. The potential promoters exhibited homology to known sigma factors (i.e., sigma(A) and sigma(B)) of Bacillus subtilis. The relative activity of the two promoters remained constant under the conditions studied and was in agreement with the results of the RNase protection assay, in which the observed transcriptional activity was inversely proportional to the growth rate.
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Dror TW, Morag E, Rolider A, Bayer EA, Lamed R, Shoham Y. Regulation of the cellulosomal CelS (cel48A) gene of Clostridium thermocellum is growth rate dependent. J Bacteriol 2003; 185:3042-8. [PMID: 12730163 PMCID: PMC154088 DOI: 10.1128/jb.185.10.3042-3048.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium thermocellum produces an extracellular multienzyme complex, termed cellulosome, that allows efficient solubilization of crystalline cellulose. One of the major enzymes in this complex is the CelS (Cel48A) exoglucanase. The regulation of CelS at the protein and transcriptional levels was studied using batch and continuous cultures. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analyses indicated that the amount of CelS in the supernatant fluids of cellobiose-grown cultures is lower than that of cellulose-grown cultures. The transcriptional level of celS mRNA was determined quantitatively by RNase protection assays with batch and continuous cultures under carbon and nitrogen limitation. The amount of celS mRNA transcripts per cell was about 180 for cells grown under carbon limitation at growth rates of 0.04 to 0.21 h(-1) and 80 and 30 transcripts per cell for batch cultures at growth rates of 0.23 and 0.35 h(-1), respectively. Under nitrogen limitation, the corresponding levels were 110, 40, and 30 transcripts/cell for growth rates of 0.07, 0.11, and 0.14 h(-1), respectively. Two major transcriptional start sites were detected at positions -140 and -145 bp, upstream of the translational start site of the celS gene. The potential promoters exhibited homology to known sigma factors (i.e., sigma(A) and sigma(B)) of Bacillus subtilis. The relative activity of the two promoters remained constant under the conditions studied and was in agreement with the results of the RNase protection assay, in which the observed transcriptional activity was inversely proportional to the growth rate.
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Affiliation(s)
- Tali W Dror
- Department of Food Engineering and Biotechnology, Technion-Israel Institute of Technology, Haifa, Israel
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Ward OP, Singh A. Bioethanol technology: developments and perspectives. ADVANCES IN APPLIED MICROBIOLOGY 2003; 51:53-80. [PMID: 12236060 DOI: 10.1016/s0065-2164(02)51001-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Owen P Ward
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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34
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Abstract
The extension of (13)C-nuclear magnetic resonance (NMR) techniques to study cellular metabolism over recent years has provided valuable data supporting the occurrence, diversity and extent of carbon cycling in the carbohydrate metabolism of micro-organisms. The occurrence of such cycles, resulting from the simultaneous operation of different and sometimes opposite individual steps, is inherently related to the network organisation of cellular metabolism. These cycles are tentatively classified here as 'reversibility', 'metabolic' and 'substrate' cycles on the basis of their balance in carbon and cofactors. Current hypotheses concerning the physiological relevance of carbohydrate cycles are discussed in light of the (13)C-NMR data. They most likely represent system-level mechanisms for coherent and timely partitioning of carbon resources to fit with the various biosynthetic, energetic or redox needs of cells and/or additional strategies in the adaptive capacity of micro-organisms to face variation in environmental conditions.
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Affiliation(s)
- Jean-Charles Portais
- Laboratoire de Génie Cellulaire, UMR CNRS 6022, Faculté des Sciences, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France.
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35
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002. [PMID: 12209002 DOI: 10.1128/mmbr.66.3.506] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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36
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002; 66:506-77, table of contents. [PMID: 12209002 PMCID: PMC120791 DOI: 10.1128/mmbr.66.3.506-577.2002] [Citation(s) in RCA: 2307] [Impact Index Per Article: 104.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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37
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Lynd LR, Zhang Y. Quantitative determination of cellulase concentration as distinct from cell concentration in studies of microbial cellulose utilization: analytical framework and methodological approach. Biotechnol Bioeng 2002; 77:467-75. [PMID: 11787020 DOI: 10.1002/bit.10142] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In analyzing microbial cellulose utilization, it would be useful to independently measure the mass concentration of cells and cellulase enzymes. Such measurements would allow investigation of the allocation of cellular resources between synthesis of cells and cellulase, in vivo cell- and cellulase-specific cellulose hydrolysis rates, and bioenergetics. Methodological protocols are not established for independent determination of cell and cellulase concentrations for the common case in which a substantial fraction of cellulase is attached to the cell surface. Alternative analytical approaches by which to develop such protocols are examined from the perspective of error minimization. For cell concentration measurement, acceptable accuracy is expected when the concentrations of a cell-specific component (e.g., DNA) is determined or when total protein is determined in conjunction with a measurement specific to cellulase. For cellulase concentration measurement, acceptable accuracy is expected when a measurement specific to cellulase such as ELISA is used. Several analytical approaches are rejected based on large expected errors.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, USA.
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38
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Guedon E, Desvaux M, Petitdemange H. Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering. Appl Environ Microbiol 2002; 68:53-8. [PMID: 11772608 PMCID: PMC126586 DOI: 10.1128/aem.68.1.53-58.2002] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2001] [Accepted: 10/02/2001] [Indexed: 11/20/2022] Open
Abstract
Cellulolytic clostridia have evolved to catabolize lignocellulosic materials at a seasonal biorhythm, so their biotechnological exploitation requires genetic improvements. As high carbon flux leads to pyruvate accumulation, which is responsible for the cessation of growth of Clostridium cellulolyticum, this accumulation is decreased by heterologous expression of pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis. In comparison with that of the wild strain, growth of the recombinant strain at the same specific rate but for 145 h instead of 80 h led to a 150% increase in cellulose consumption and a 180% increase in cell dry weight. The fermentation pattern was shifted significantly: lactate production decreased by 48%, whereas the concentrations of acetate and ethanol increased by 93 and 53%, respectively. This study demonstrates that the fermentation of cellulose, the most abundant and renewable polymer on earth, can be greatly improved by using genetically engineered C. cellulolyticum.
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Affiliation(s)
- Emmanuel Guedon
- Laboratoire de Biochimie des Bactéries Gram Positif, Faculté des Sciences, Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy Cedex, France
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39
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Guedon E, Desvaux M, Petitdemange H. Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering. Appl Environ Microbiol 2002; 68:53-58. [PMID: 11772608 DOI: 10.1128/aem.68.1.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Cellulolytic clostridia have evolved to catabolize lignocellulosic materials at a seasonal biorhythm, so their biotechnological exploitation requires genetic improvements. As high carbon flux leads to pyruvate accumulation, which is responsible for the cessation of growth of Clostridium cellulolyticum, this accumulation is decreased by heterologous expression of pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis. In comparison with that of the wild strain, growth of the recombinant strain at the same specific rate but for 145 h instead of 80 h led to a 150% increase in cellulose consumption and a 180% increase in cell dry weight. The fermentation pattern was shifted significantly: lactate production decreased by 48%, whereas the concentrations of acetate and ethanol increased by 93 and 53%, respectively. This study demonstrates that the fermentation of cellulose, the most abundant and renewable polymer on earth, can be greatly improved by using genetically engineered C. cellulolyticum.
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Affiliation(s)
- Emmanuel Guedon
- Laboratoire de Biochimie des Bactéries Gram Positif, Faculté des Sciences, Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy Cedex, France
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40
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Desvaux M, Guedon E, Petitdemange H. Kinetics and metabolism of cellulose degradation at high substrate concentrations in steady-state continuous cultures of Clostridium cellulolyticum on a chemically defined medium. Appl Environ Microbiol 2001; 67:3837-45. [PMID: 11525975 PMCID: PMC93099 DOI: 10.1128/aem.67.9.3837-3845.2001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrolysis and fermentation of insoluble cellulose were investigated using continuous cultures of Clostridium cellulolyticum with increasing amounts of carbon substrate. At a dilution rate (D) of 0.048 h(-1), biomass formation increased proportionately to the cellulose concentration provided by the feed reservoir, but at and above 7.6 g of cellulose x liter(-1) the cell density at steady state leveled off. The percentage of cellulose degradation declined from 32.3 to 8.3 with 1.9 and 27.0 g of cellulose x liter(-1), respectively, while cellodextrin accumulation rose and represented up to 4.0% of the original carbon consumed. The shift from cellulose-limited to cellulose-sufficient conditions was accompanied by an increase of both the acetate/ethanol ratio and lactate biosynthesis. A kinetics study of C. cellulolyticum metabolism in cellulose saturation was performed by varying D with 18.1 g of cellulose x liter(-1). Compared to cellulose limitation (M. Desvaux, E. Guedon, and H. Petitdemange, J. Bacteriol. 183:119-130, 2001), in cellulose-sufficient continuous culture (i) the ATP/ADP, NADH/NAD+, and q(NADH produced)/q(NADH used) ratios were higher and were related to a more active catabolism, (ii) the acetate/ethanol ratio increased while the lactate production decreased as D rose, and (iii) the maximum growth yield (Y(max)X/S) (40.6 g of biomass per mol of hexose equivalent) and the maximum energetic yield (Y(max)ATP) (19.4 g of biomass per mol of ATP) were lowered. C. cellulolyticum was then able to regulate and optimize carbon metabolism under cellulose-saturated conditions. However, the facts that some catabolized hexose and hence ATP were no longer associated with biomass production with a cellulose excess and that concomitantly lactate production and pyruvate leakage rose suggest the accumulation of an intracellular inhibitory compound(s), which could further explain the establishment of steady-state continuous cultures under conditions of excesses of all nutrients. The following differences were found between growth on cellulose in this study and growth under cellobiose-sufficient conditions (E. Guedon, S. Payot, M. Desvaux, and H. Petitdemange, Biotechnol. Bioeng. 67:327-335, 2000): (i) while with cellobiose, a carbon flow into the cell of as high as 5.14 mmol of hexose equivalent g of cells(-1) x h(-1) could be reached, the maximum entering carbon flow obtained here on cellulose was 2.91 mmol of hexose equivalent g of cells(-1) x h(-1); (ii) while the NADH/NAD+ ratio could reach 1.51 on cellobiose, it was always lower than 1 on cellulose; and (iii) while a high proportion of cellobiose was directed towards exopolysaccharide, extracellular protein, and free amino acid excretions, these overflows were more limited under cellulose-excess conditions. Such differences were related to the carbon consumption rate, which was higher on cellobiose than on cellulose.
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Affiliation(s)
- M Desvaux
- Laboratoire de Biochimie des Bactéries Gram +, Domaine Scientifique Victor Grignard, Université Henri Poincaré, Faculté des Sciences, 54506 Vandouvre-lès-Nancy Cédex, France
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Desvaux M, Petitdemange H. Flux analysis of the metabolism of Clostridium cellulolyticum grown in cellulose-fed continuous culture on a chemically defined medium under ammonium-limited conditions. Appl Environ Microbiol 2001; 67:3846-51. [PMID: 11525976 PMCID: PMC93100 DOI: 10.1128/aem.67.9.3846-3851.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2001] [Accepted: 05/31/2001] [Indexed: 11/20/2022] Open
Abstract
An investigation of cellulose degradation by the nonruminal, cellulolytic, mesophilic bacterium Clostridium cellulolyticum was performed in cellulose-fed chemostat cultures with ammonium as the growth-limiting nutrient. At any dilution rate (D), acetate was always the main product of the catabolism, with a yield of product from substrate ranging between 37.7 and 51.5 g per mol of hexose equivalent fermented and an acetate/ethanol ratio always higher than 1. As D rose, the acetyl coenzyme A was rerouted in favor of ethanol pathways, and ethanol production could represent up to 17.7% of the carbon consumed. Lactate was significantly produced, but with increasing D, the specific lactate production rate declined, as did the specific rate of production of extracellular pyruvate. The proportion of the original carbon directed towards phosphoglucomutase remained constant, and the carbon surplus was balanced mainly by exopolysaccharide and glycogen biosyntheses at high D values, while cellodextrin excretion occurred mainly at lower ones. With increasing D, the specific rate of carbon flowing down catabolites increased as well, but when expressed as a percentage of carbon it declined, while the percentage of carbon directed through biosynthesis pathways was enhanced. The maximum growth and energetic yields were lower than those obtained in cellulose-limited chemostats and were related to an uncoupling between catabolism and anabolism leading to an excess of energy. Compared to growth on cellobiose in ammonium-limited chemostats (E. Guedon, M. Desvaux, and H. Petitdemange, J. Bacteriol. 182:2010-2017, 2000), (i) a specific consumption rate of carbon of as high as 26.72 mmol of hexose equivalent g of cells(-1) x h(-1) could not be reached and (ii) the proportions of carbon directed towards cellodextrin, glycogen, and exopolysaccharide pathways were not as high as first determined on cellobiose. While the use of cellobiose allows highlighting of metabolic limitation and regulation of C. cellulolyticum under ammonium-limited conditions, some of these events should then rather be interpreted as distortions of the metabolism. Growth of cellulolytic bacteria on easily available carbon and nitrogen sources represents conditions far different from those of the natural lignocellulosic compounds.
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Affiliation(s)
- M Desvaux
- Laboratoire de Biochimie des Bactéries Gram +, Domaine Scientifique Victor Grignard, Université Henri Poincaré, Faculté des Sciences, 54506 Vandouvre-lès-Nancy Cédex, France
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Abstract
Owing to technical improvements in the processes used to produce ethanol from biomass, construction of at least two waste-to-ethanol production plants in the United States is expected to start this year. Although there are a number of robust fermentation microorganisms available, initial pretreatment of the biomass and costly cellulase enzymes remain critical targets for process and cost improvements. A highly efficient, very low-acid pretreatment process is approaching pilot testing, while research on cellulases for ethanol production is expanding at both enzyme and organism level.
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Affiliation(s)
- J R Mielenz
- White Cliff Biosystems Co, 107 Lake Meadow Drive, Johnson City, Tennessee 37615, USA.
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Desvaux M, Guedon E, Petitdemange H. Metabolic flux in cellulose batch and cellulose-fed continuous cultures of Clostridium cellulolyticum in response to acidic environment. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1461-1471. [PMID: 11390677 DOI: 10.1099/00221287-147-6-1461] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Clostridium cellulolyticum, a nonruminal cellulolytic mesophilic bacterium, was grown in batch and continuous cultures on cellulose using a chemically defined medium. In batch culture with unregulated pH, less cellulose degradation and higher accumulation of soluble glucides were obtained compared to a culture with the pH controlled at 7.2. The gain in cellulose degradation achieved with pH control was offset by catabolite production rather than soluble sugar accumulation. The pH-controlled condition improved biomass, ethanol and acetate production, whereas maximum lactate and extracellular pyruvate concentrations were lower than in the non-pH-controlled condition. In a cellulose-fed chemostat at constant dilution rate and pH values ranging from 7.4 to 6.2, maximum cell density was obtained at pH 7.0. Environmental acidification chiefly influenced biomass formation, since at pH 6.4 the dry weight of cells was more than fourfold lower compared to that at pH 7.0, whereas the specific rate of cellulose assimilation decreased only from 11.74 to 10.13 milliequivalents of carbon (g cells)(-1) h(-1). The molar growth yield and the energetic growth yield did not decline as pH was lowered, and an abrupt transition to washout was observed. Decreasing the pH induced a shift from an acetate-ethanol fermentation to a lactate-ethanol fermentation. The acetate/ethanol ratio decreased as the pH declined, reaching close to 1 at pH 6.4. Whatever the pH conditions, lactate dehydrogenase was always greatly in excess. As pH decreased, both the biosynthesis and the catabolic efficiency of the pyruvate-ferredoxin oxidoreductase declined, as indicated by the ratio of the specific enzyme activity to the specific metabolic rate, which fell from 9.8 to 1.8. Thus a change of only 1 pH unit induced considerable metabolic change and ended by washout at around pH 6.2. C. cellulolyticum appeared to be similar to rumen cellulolytic bacteria in its sensitivity to acidic conditions. Apparently, the cellulolytic anaerobes studied thus far do not thrive when the pH drops below 6.0, suggesting that they evolved in environments where acid tolerance was not required for successful competition with other microbes.
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Affiliation(s)
- Mickaël Desvaux
- Laboratoire de Biochimie des Bactéries Gram +, Domaine Scientifique Victor Grignard, Université Henri Poincaré, Faculté des Sciences, BP 239, 54506 Vandœuvre-lès-Nancy Cédex, France1
| | - Emmanuel Guedon
- Laboratoire de Biochimie des Bactéries Gram +, Domaine Scientifique Victor Grignard, Université Henri Poincaré, Faculté des Sciences, BP 239, 54506 Vandœuvre-lès-Nancy Cédex, France1
| | - Henri Petitdemange
- Laboratoire de Biochimie des Bactéries Gram +, Domaine Scientifique Victor Grignard, Université Henri Poincaré, Faculté des Sciences, BP 239, 54506 Vandœuvre-lès-Nancy Cédex, France1
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