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Xu Z, Lei P, Zhai R, Wen Z, Jin M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:32. [PMID: 30815030 PMCID: PMC6376720 DOI: 10.1186/s13068-019-1376-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
Lignin is the most abundant aromatic substrate on Earth and its valorization technologies are still under developed. Depolymerization and fragmentation are the predominant preparatory strategies for valorization of lignin to chemicals and fuels. However, due to the structural heterogeneity of lignin, depolymerization and fragmentation typically result in diverse product species, which require extensive separation and purification procedures to obtain target products. For lignin valorization, bacterial-based systems have attracted increasing attention because of their diverse metabolisms, which can be used to funnel multiple lignin-based compounds into specific target products. Here, recent advances in lignin valorization using bacteria are critically reviewed, including lignin-degrading bacteria that are able to degrade lignin and use lignin-associated aromatics, various associated metabolic pathways, and application of bacterial cultures for lignin valorization. This review will provide insight into the recent breakthroughs and future trends of lignin valorization based on bacterial systems.
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Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Peng Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, 211111 China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
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102
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Besser K, Malyon GP, Eborall WS, Paro da Cunha G, Filgueiras JG, Dowle A, Cruz Garcia L, Page SJ, Dupree R, Kern M, Gomez LD, Li Y, Elias L, Sabbadin F, Mohamad SE, Pesante G, Steele-King C, Ribeiro de Azevedo E, Polikarpov I, Dupree P, Cragg SM, Bruce NC, McQueen-Mason SJ. Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans. Nat Commun 2018; 9:5125. [PMID: 30510200 PMCID: PMC6277391 DOI: 10.1038/s41467-018-07575-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining.
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Affiliation(s)
- Katrin Besser
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Graham P Malyon
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - William S Eborall
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Giovanni Paro da Cunha
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Jefferson G Filgueiras
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Lourdes Cruz Garcia
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Samuel J Page
- Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Marcelo Kern
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Luisa Elias
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Shaza E Mohamad
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.,Malaysia Japan International Institute of Technology, University of Technology, Malaysia, 54100, Kuala Lumpur, Malaysia
| | - Giovanna Pesante
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Clare Steele-King
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | | | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, United Kingdom
| | - Simon M Cragg
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
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103
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Xu R, Zhang K, Liu P, Han H, Zhao S, Kakade A, Khan A, Du D, Li X. Lignin depolymerization and utilization by bacteria. BIORESOURCE TECHNOLOGY 2018; 269:557-566. [PMID: 30219494 DOI: 10.1016/j.biortech.2018.08.118] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 05/21/2023]
Abstract
Lignin compound wastes are generated as a result of agricultural and industrial practices. Microorganism-mediated bio-catalytic processes can depolymerize and utilize lignin eco-friendly. Although fungi have been studied since several decades for their ability to depolymerize lignin, strict growth conditions of fungus limit it's industrial application. Compared with fungi, bacteria can tolerate wider pH, temperature, oxygen ranges and are easy to manipulate. Several studies have focused on bacteria involved in the process of lignin depolymerization and utilization. Pseudomonas have been used for paper mill wastewater treatment while Rhodococcus are widely reported to accumulate lipid. In this review, the recent studies on bacterial utilization in paper wastewater treatment, lignin conversion to biofuels, bioplastic, biofertilizers and other value-added chemicals are summarized. As bacteria possess remarkable advantages in industrial production, they may play a promising role in the future commercial lignin utilization.
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Affiliation(s)
- Rong Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Kai Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Pu Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Huawen Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Shuai Zhao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Apurva Kakade
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Daolin Du
- Institute for Energy Research, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China.
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104
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Guo H, Wang XD, Lee DJ. Proteomic researches for lignocellulose-degrading enzymes: A mini-review. BIORESOURCE TECHNOLOGY 2018; 265:532-541. [PMID: 29884341 DOI: 10.1016/j.biortech.2018.05.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 05/14/2023]
Abstract
Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Xiao-Dong Wang
- Research Center of Engineering Thermophysics, North China Electric Power University, Beijing 102206, China; School of Energy Power and Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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105
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Hogancamp TN, Mabanglo MF, Raushel FM. Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry 2018; 57:5841-5850. [PMID: 30207699 DOI: 10.1021/acs.biochem.8b00713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LigJ from the soil bacterium Sphingobium sp. SYK-6 catalyzes the reversible hydration of (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) in the degradation of lignin in the protocatechuate 4,5-cleavage pathway. LigJ is a member of the amidohydrolase superfamily and an enzyme in cog2159. The three-dimensional crystal structure of wild-type LigJ was determined in the presence [Protein Data Bank (PDB) entry 6DXQ ] and absence of the product CHA (PDB entry 6DWV ). The protein folds as a distorted (β/α)8-barrel, and a single zinc ion is bound in the active site at the C-terminal end of the central β-barrel. The product CHA is ligated to the zinc ion in the active site via the displacement of a single water molecule from the coordination shell of the metal center in LigJ. The product-bound structure reveals that the enzyme catalyzes the hydration of KCH with the formation of a chiral center at C4 with S stereochemistry. The E284Q mutant was unable to catalyze the hydration of KCH to CHA, and the structure of this mutant was determined in the presence of the substrate KCH (PDB entry 6DXS ). On the basis of the structure of LigJ in the presence of KCH and CHA, it is proposed that the side chain carboxylate of Glu-284 functions as a general base in the abstraction of a proton from a bound water molecule for nucleophilic attack at C4 of the substrate. The reaction is facilitated by the delocalization of the negative charge to the metal center via the carbonyl group at C2 of the substrate. C3 of the substrate is subsequently protonated by Glu-284 functioning as a general acid. The overall reaction occurs by the syn addition of water to the double bond between C4 and C3 of the substrate KCH. The kinetic constants for the hydration of KCH to CHA by LigJ at pH 8.0 are 25 s-1 ( kcat) and 2.6 × 106 M-1 s-1 ( kcat/ Km).
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Affiliation(s)
- Tessily N Hogancamp
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mark F Mabanglo
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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106
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Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR. Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). BIOTECHNOLOGY FOR BIOFUELS 2018; 11:266. [PMID: 30275906 PMCID: PMC6158898 DOI: 10.1186/s13068-018-1261-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/19/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Producing valuable fuels and chemicals from lignin is a key factor for making lignocellulosic biomass economically feasible; however, significant roadblocks exist due to our lack of detailed understanding of how lignin is enzymatically depolymerized and of the range of possible lignin fragments that can be produced. Development of suitable enzymatic assays for characterization of putative lignin active enzymes is an important step towards improving our understanding of the catalytic activities of relevant enzymes. Previously, we have successfully built an assay platform based on glycan substrates containing a charged perfluorinated tag and nanostructure-initiator mass spectrometry to study carbohydrate active enzymes, especially various glycosyl hydrolyses. Here, we extend this approach to develop a reliable and rapid assay to study lignin-modifying enzymes. RESULTS Two β-aryl ether bond containing model lignin dimer substrates, designed to be suitable for studying the activities of lignin-modifying enzymes (LMEs) by nanostructure-initiator mass spectrometry (NIMS), were successful synthesized. Small-angle neutron scattering experiments showed that these substrates form micelles in solution. Two LMEs, laccase from the polypore mushroom Trametes versicolor, and manganese peroxidase (MnP) from white rot fungus Nematoloma frowardii, were tested for catalytic activity against the two model substrates. We show that the reaction of laccase and MnP with phenolic substrate yields products that arise from the cleavage of the carbon-carbon single bond between the α-carbon and the adjacent aryl carbon, consistent with the mechanism for producing phenoxy radical as reaction intermediates. Reactions of the nonphenolic substrate with laccase, on the other hand, adopt a different pathway by producing an α-oxidation product; as well as the cleavage of the β-aryl ether bond. No cleavage of the carbon-carbon bond between the α-carbon and the aryl carbon was observed. To facilitate understanding of reaction kinetics, the reaction time course for laccase activity on the phenolic substrate (I) was generated by the simultaneous measurement of all products at different time points of the reaction. Withdrawal of only a small sample aliquot (0.2 μL at each time point) ensured minimum perturbation of the reaction. The time course can help us to understand the enzyme kinetics. CONCLUSIONS A new assay procedure has been developed for studying lignin-modifying enzymes by nanostructure-initiator mass spectrometry. Enzyme assays of a laccase and a MnP on phenolic and nonphenolic β-aryl ether substrates revealed different primary reaction pathways due to the availability of the phenoxy radical intermediates. Our assay provides a wealth of information on bond cleavage events not available using conventional colorimetric assays and can easily be carried out in microliter volumes and the quantitative analysis of product formation and kinetics is rapidly achieved by NIMS. This is the first time that NIMS technology was applied to study the activities of lignin-modifying enzymes. Unlike other previous works, our use of amphiphilic guaiacylglycerol β-O-4 substrate (I) enables the formation of micelles. This approach helps avoid the re-polymerization of the resulting monomeric product. As a result, our assay can clearly demonstrate the degradation pathways of phenolic guaiacylglycerol β-O-4 type of molecules with laccase and MnP.
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Affiliation(s)
- Kai Deng
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Jijiao Zeng
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
- Sichuan University of Science & Engineering, Zigong, 643000 Sichuan China
| | - Gang Cheng
- Beijing University of Chemical Technology, Beijing, 100080 China
| | - Jian Gao
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Anup K. Singh
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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107
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Unraveling the cellulolytic and hemicellulolytic potential of two novel Streptomyces strains. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1374-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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108
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Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:240. [PMID: 30202435 PMCID: PMC6123935 DOI: 10.1186/s13068-018-1240-7] [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: 05/24/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the degradation rate of native or technical lignin is low, and depolymerization is needed to obtain reasonable conversion rates. In the current study, base-catalyzed depolymerization-using NaOH (5 wt%)-of softwood Kraft lignin was conducted in a continuous-flow reactor system at temperatures in the range 190-240 °C and residence times of 1 or 2 min. The ability of growth of nine bacterial strains belonging to the genera Pseudomonas and Rhodococcus was tested using the alkaline-treated lignin as a sole carbon source. RESULTS Pseudomonas fluorescens and Rhodococcus opacus showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized lignin (DL) at a concentration of 1 g/L. Size exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low and high molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | | | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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109
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Goacher RE, Braham EJ, Michienzi CL, Flick RM, Yakunin AF, Master ER. Direct analysis by time-of-flight secondary ion mass spectrometry reveals action of bacterial laccase-mediator systems on both hardwood and softwood samples. PHYSIOLOGIA PLANTARUM 2018; 164:5-16. [PMID: 29286544 DOI: 10.1111/ppl.12688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
The modification and degradation of lignin play a vital role in carbon cycling as well as production of biofuels and bioproducts. The possibility of using bacterial laccases for the oxidation of lignin offers a route to utilize existing industrial protein expression techniques. However, bacterial laccases are most frequently studied on small model compounds that do not capture the complexity of lignocellulosic materials. This work studied the action of laccases from Bacillus subtilis and Salmonella typhimurium (EC 1.10.3.2) on ground wood samples from yellow birch (Betula alleghaniensis) and red spruce (Picea rubens). The ability of bacterial laccases to modify wood can be facilitated by small molecule mediators. Herein, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), gallic acid and sinapic acid mediators were tested. Direct analysis of the wood samples was achieved by time-of-flight secondary ion mass spectrometry (ToF-SIMS), a surface sensitive mass spectrometry technique that has characteristic peaks for H, G and S lignin. The action of the bacterial laccases on both wood samples was demonstrated and revealed a strong mediator influence. The ABTS mediator led to delignification, evident in an overall increase of polysaccharide peaks in the residual solid, along with equal loss of G and S-lignin peaks. The gallic acid mediator demonstrated minimal laccase activity. Meanwhile, the sinapic acid mediator altered the S/G peak ratio consistent with mediator attaching to the wood solids. The current investigation demonstrates the action of bacterial laccase-mediator systems directly on woody materials, and the potential of using ToF-SIMS to uncover the fundamental and applied role of bacterial enzymes in lignocellulose conversion.
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Affiliation(s)
- Robyn E Goacher
- Department of Biochemistry, Chemistry and Physics, Niagara University, 5795 Lewiston Road, Lewiston, NY, 14109, USA
| | - Erick J Braham
- Department of Biochemistry, Chemistry and Physics, Niagara University, 5795 Lewiston Road, Lewiston, NY, 14109, USA
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, TX, 77843, USA
| | - Courtney L Michienzi
- Department of Biochemistry, Chemistry and Physics, Niagara University, 5795 Lewiston Road, Lewiston, NY, 14109, USA
| | - Robert M Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Kemistintie 1, Espoo, Finland
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Probst M, Gómez-Brandón M, Bardelli T, Egli M, Insam H, Ascher-Jenull J. Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories. Environ Microbiol 2018; 20:3657-3670. [DOI: 10.1111/1462-2920.14359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/26/2018] [Accepted: 07/08/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Maraike Probst
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Departamento de Ecología y Biología Animal; Universidad de Vigo; Vigo Spain
| | - Tommaso Bardelli
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
| | - Markus Egli
- Department of Geography; University of Zürich; Zürich Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - Judith Ascher-Jenull
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
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111
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Alternatives for Chemical and Biochemical Lignin Valorization: Hot Topics from a Bibliometric Analysis of the Research Published During the 2000–2016 Period. Processes (Basel) 2018. [DOI: 10.3390/pr6080098] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A complete bibliometric analysis of the Scopus database was performed to identify the research trends related to lignin valorization from 2000 to 2016. The results from this analysis revealed an exponentially increasing number of publications and a high relevance of interdisciplinary collaboration. The simultaneous valorization of the three main components of lignocellulosic biomass (cellulose, hemicellulose, and lignin) has been revealed as a key aspect and optimal pretreatment is required for the subsequent lignin valorization. Research covers the determination of the lignin structure, isolation, and characterization; depolymerization by thermal and thermochemical methods; chemical, biochemical and biological conversion of depolymerized lignin; and lignin applications. Most methods for lignin depolymerization are focused on the selective cleavage of the β-O-4 linkage. Although many depolymerization methods have been developed, depolymerization with sodium hydroxide is the dominant process at industrial scale. Oxidative conversion of lignin is the most used method for the chemical lignin upgrading. Lignin uses can be classified according to its structure into lignin-derived aromatic compounds, lignin-derived carbon materials and lignin-derived polymeric materials. There are many advances in all approaches, but lignin-derived polymeric materials appear as a promising option.
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Biological Pretreatment Strategies for Second-Generation Lignocellulosic Resources to Enhance Biogas Production. ENERGIES 2018; 11:1797. [PMID: 30881604 PMCID: PMC6420082 DOI: 10.3390/en11071797] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With regard to social and environmental sustainability, second-generation biofuel and biogas production from lignocellulosic material provides considerable potential, since lignocellulose represents an inexhaustible, ubiquitous natural resource, and is therefore one important step towards independence from fossil fuel combustion. However, the highly heterogeneous structure and recalcitrant nature of lignocellulose restricts its commercial utilization in biogas plants. Improvements therefore rely on effective pretreatment methods to overcome structural impediments, thus facilitating the accessibility and digestibility of (ligno)cellulosic substrates during anaerobic digestion. While chemical and physical pretreatment strategies exhibit inherent drawbacks including the formation of inhibitory products, biological pretreatment is increasingly being advocated as an environmentally friendly process with low energy input, low disposal costs, and milder operating conditions. Nevertheless, the promising potential of biological pretreatment techniques is not yet fully exploited. Hence, we intended to provide a detailed insight into currently applied pretreatment techniques, with a special focus on biological ones for downstream processing of lignocellulosic biomass in anaerobic digestion.
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113
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Kumar M, Verma S, Gazara RK, Kumar M, Pandey A, Verma PK, Thakur IS. Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:154. [PMID: 29991962 PMCID: PMC5987411 DOI: 10.1186/s13068-018-1148-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/17/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. RESULTS Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA. CONCLUSIONS The unusual aerobic '-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.
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Affiliation(s)
- Madan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Manish Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, 31 MG Marg, Lucknow, 226 001 India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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114
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Bhatnagar JM, Peay KG, Treseder KK. Litter chemistry influences decomposition through activity of specific microbial functional guilds. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1303] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Kabir G. Peay
- Department of Biology Stanford University Stanford California 94305 USA
| | - Kathleen K. Treseder
- Department of Ecology and Evolutionary Biology University of California, Irvine Irvine California 92697 USA
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115
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Zhuo S, Yan X, Liu D, Si M, Zhang K, Liu M, Peng B, Shi Y. Use of bacteria for improving the lignocellulose biorefinery process: importance of pre-erosion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:146. [PMID: 29796087 PMCID: PMC5964970 DOI: 10.1186/s13068-018-1146-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/11/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Biological pretreatment is an important alternative strategy for biorefining lignocellulose and has attracted increasing attention in recent years. However, current designs for this pretreatment mainly focus on using various white rot fungi, overlooking the bacteria. To the best of our knowledge, for the first time, we evaluated the potential contribution of bacteria to lignocellulose pretreatment, with and without a physicochemical process, based on the bacterial strain Pandoraea sp. B-6 (hereafter B-6) that was isolated from erosive bamboo slips. Moreover, the mechanism of the improvement of reducing sugar yield by bacteria was elucidated via analyses of the physicochemical changes of corn stover (CS) before and after pretreatment. RESULTS The digestibility of CS pretreated with B-6 was equivalent to that of untreated CS. The recalcitrant CS surface provided fewer mediators for contact with the extracellular enzymes of B-6. A pre-erosion strategy using a tetrahydrofuran-water co-solvent system was shown to destroy the recalcitrant CS surface. The optimal condition for pre-erosion showed a 6.5-fold increase in enzymatic digestibility compared with untreated CS. The pre-erosion of CS can expose more phenolic compounds that were chelated to oxidized Mn3+ and also provided mediators for combination with laccase, which was attributable to B-6 pretreatment. B-6 pretreatment following pre-erosion exhibited a sugar yield that was 91.2 mg/g greater than that of pre-erosion alone and 7.5-fold higher than that of untreated CS. This pre-erosion application was able to destroy the recalcitrant CS surface, thus leading to a rough and porous architecture that better facilitated the diffusion and transport of lignin derivatives. This enhanced the ability of laccase and manganese peroxidase secreted by B-6 to improve the efficiency of this biological pretreatment. CONCLUSION Bacteria were not found useful alone as a biological pretreatment, but they significantly improved enzymatic digestion after lignocellulose breakdown via other physicochemical methods. Nonetheless, phenyl or phenoxy radicals were used by laccase and manganese peroxidase in B-6 for lignin attack or lignin depolymerization. These particular mediators released from the recalcitrance network of lignocellulose openings are important for the efficacy of this bacterial pretreatment. Our findings thus offer a novel perspective on the effective design of biological pretreatment methods for lignocellulose.
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Affiliation(s)
- Shengnan Zhuo
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
| | - Xu Yan
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083 China
| | - Dan Liu
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
| | - Mengying Si
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
| | - Kejing Zhang
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
| | - Mingren Liu
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
| | - Bing Peng
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083 China
| | - Yan Shi
- School of Metallurgy and Environment, Central South University, Changsha, 410083 China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083 China
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116
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Woo HL, Hazen TC. Enrichment of Bacteria From Eastern Mediterranean Sea Involved in Lignin Degradation via the Phenylacetyl-CoA Pathway. Front Microbiol 2018; 9:922. [PMID: 29867833 PMCID: PMC5954211 DOI: 10.3389/fmicb.2018.00922] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/20/2018] [Indexed: 02/01/2023] Open
Abstract
The degradation of allochthonous terrestrial organic matter, such as recalcitrant lignin and hemicellulose from plants, occurs in the ocean. We hypothesize that bacteria instead of white-rot fungi, the model organisms of aerobic lignin degradation within terrestrial environments, are responsible for lignin degradation in the ocean due to the ocean's oligotrophy and hypersalinity. Warm oxic seawater from the Eastern Mediterranean Sea was enriched on lignin in laboratory microcosms. Lignin mineralization rates by the lignin-adapted consortia improved after two sequential incubations. Shotgun metagenomic sequencing detected a higher abundance of aromatic compound degradation genes in response to lignin, particularly phenylacetyl-CoA, which may be an effective strategy for marine microbes in fluctuating oxygen concentrations. 16S rRNA gene amplicon sequencing detected a higher abundance of Gammaproteobacteria and Alphaproteobacteria bacteria such as taxonomic families Idiomarinaceae, Alcanivoraceae, and Alteromonadaceae in response to lignin. Meanwhile, fungal Ascomycetes and Basidiomycetes remained at very low abundance. Our findings demonstrate the significant potential of bacteria and microbes utilizing the phenylacetyl-CoA pathway to contribute to lignin degradation in the Eastern Mediterranean where environmental conditions are unfavorable for fungi. Exploring the diversity of bacterial lignin degraders may provide important enzymes for lignin conversion in industry. Enzymes may be key in breaking down high molecular weight lignin and enabling industry to use it as a low-cost and sustainable feedstock for biofuels or other higher-value products.
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Affiliation(s)
- Hannah L Woo
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Science, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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117
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Ufarté L, Potocki-Veronese G, Cecchini D, Tauzin AS, Rizzo A, Morgavi DP, Cathala B, Moreau C, Cleret M, Robe P, Klopp C, Laville E. Highly Promiscuous Oxidases Discovered in the Bovine Rumen Microbiome. Front Microbiol 2018; 9:861. [PMID: 29780372 PMCID: PMC5945886 DOI: 10.3389/fmicb.2018.00861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 04/13/2018] [Indexed: 11/17/2022] Open
Abstract
The bovine rumen hosts a diverse microbiota, which is highly specialized in the degradation of lignocellulose. Ruminal bacteria, in particular, are well equipped to deconstruct plant cell wall polysaccharides. Nevertheless, their potential role in the breakdown of the lignin network has never been investigated. In this study, we used functional metagenomics to identify bacterial redox enzymes acting on polyaromatic compounds. A new methodology was developed to explore the potential of uncultured microbes to degrade lignin derivatives, namely kraft lignin and lignosulfonate. From a fosmid library covering 0.7 Gb of metagenomic DNA, three hit clones were identified, producing enzymes able to oxidize a wide variety of polyaromatic compounds without the need for the addition of copper, manganese, or mediators. These promiscuous redox enzymes could thus be of potential interest both in plant biomass refining and dye remediation. The enzymes were derived from uncultured Clostridia, and belong to complex gene clusters involving proteins of different functional types, including hemicellulases, which likely work in synergy to produce substrate degradation.
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Affiliation(s)
- Lisa Ufarté
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Gabrielle Potocki-Veronese
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Davide Cecchini
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Alexandra S Tauzin
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Angeline Rizzo
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | | | - Bernard Cathala
- UR1268 Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Céline Moreau
- UR1268 Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Megane Cleret
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | | | - Christophe Klopp
- Plateforme Bio-informatique Toulouse Genopole, UBIA INRA, BP 52627, Castanet-Tolosan, France
| | - Elisabeth Laville
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
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118
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Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives. Appl Microbiol Biotechnol 2018; 102:5391-5401. [PMID: 29728724 DOI: 10.1007/s00253-018-9040-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 01/05/2023]
Abstract
Lignin is the major aromatic biopolymer in nature, and it is considered a valuable feedstock for the future supply of aromatics. Hence, its valorisation in biorefineries is of high importance, and various chemical and enzymatic approaches for lignin depolymerisation have been reported. Among the enzymes known to act on lignin, β-etherases offer the possibility for a selective cleavage of the β-O-4 aryl ether bonds present in lignin. These enzymes, together with glutathione lyases, catalyse a reductive, glutathione-dependent ether bond cleavage displaying high stereospecificity. β-Etherases and glutathione lyases both belong to the superfamily of glutathione transferases, and several structures have been solved recently. Additionally, different approaches for their application in lignin valorisation have been reported in the last years. This review gives an overview on the current knowledge on β-etherases and glutathione lyases, their biochemical and structural features, and critically discusses their potential for application in biorefineries.
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119
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Hogancamp TN, Raushel FM. Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6. Biochemistry 2018; 57:2837-2845. [DOI: 10.1021/acs.biochem.8b00295] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tessily N. Hogancamp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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120
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Granja-Travez RS, Wilkinson RC, Persinoti GF, Squina FM, Fülöp V, Bugg TDH. Structural and functional characterisation of multi-copper oxidase CueO from lignin-degrading bacterium Ochrobactrum sp. reveal its activity towards lignin model compounds and lignosulfonate. FEBS J 2018; 285:1684-1700. [PMID: 29575798 DOI: 10.1111/febs.14437] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/23/2018] [Accepted: 03/09/2018] [Indexed: 01/09/2023]
Abstract
The identification of enzymes responsible for oxidation of lignin in lignin-degrading bacteria is of interest for biotechnological valorization of lignin to renewable chemical products. The genome sequences of two lignin-degrading bacteria, Ochrobactrum sp., and Paenibacillus sp., contain no B-type DyP peroxidases implicated in lignin degradation in other bacteria, but contain putative multicopper oxidase genes. Multi-copper oxidase CueO from Ochrobactrum sp. was expressed and reconstituted as a recombinant laccase-like enzyme, and kinetically characterized. Ochrobactrum CueO shows activity for oxidation of β-aryl ether and biphenyl lignin dimer model compounds, generating oxidized dimeric products, and shows activity for oxidation of Ca-lignosulfonate, generating vanillic acid as a low molecular weight product. The crystal structure of Ochrobactrum CueO (OcCueO) has been determined at 1.1 Å resolution (PDB: 6EVG), showing a four-coordinate mononuclear type I copper center with ligands His495, His434 and Cys490 with Met500 as an axial ligand, similar to that of Escherichia coli CueO and bacterial azurin proteins, whereas fungal laccase enzymes contain a three-coordinate type I copper metal center. A trinuclear type 2/3 copper cluster was modeled into the active site, showing similar structure to E. coli CueO and fungal laccases, and three solvent channels leading to the active site. Site-directed mutagenesis was carried out on amino acid residues found in the solvent channels, indicating the importance for residues Asp102, Gly103, Arg221, Arg223, and Asp462 for catalytic activity. The work identifies a new bacterial multicopper enzyme with activity for lignin oxidation, and implicates a role for bacterial laccase-like multicopper oxidases in some lignin-degrading bacteria. DATABASE Structural data are available in the PDB under the accession number 6EVG.
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Affiliation(s)
| | | | - Gabriela Felix Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Brazil
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry, UK
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121
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Wu W, Liu F, Singh S. Toward engineering E. coli with an autoregulatory system for lignin valorization. Proc Natl Acad Sci U S A 2018; 115:2970-2975. [PMID: 29500185 PMCID: PMC5866589 DOI: 10.1073/pnas.1720129115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics' toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. This study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization.
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Affiliation(s)
- Weihua Wu
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550
| | - Fang Liu
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550
| | - Seema Singh
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550;
- Joint BioEnergy Institute, Emeryville, CA 94608
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108
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Ravi K, García-Hidalgo J, Nöbel M, Gorwa-Grauslund MF, Lidén G. Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea. AMB Express 2018; 8:32. [PMID: 29500726 PMCID: PMC5834416 DOI: 10.1186/s13568-018-0563-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
Bacterial strains were isolated from the sediments of the Baltic Sea using ferulic acid, guaiacol or a lignin-rich softwood waste stream as substrate. In total nine isolates were obtained, five on ferulic acid, two on guaiacol and two on a lignin-rich softwood stream as a carbon source. Three of the isolates were found to be Pseudomonas sp. based on 16S rRNA sequencing. Among them, isolate 9.1, which showed the fastest growth in defined M9 medium, was tentatively identified as a Pseudomonas deceptionensis strain based on the gyrB sequencing. The growth of isolate 9.1 was further examined on six selected lignin model compounds (ferulate, p-coumarate, benzoate, syringate, vanillin and guaiacol) from different upper funneling aromatic pathways and was found able to grow on four out of these six compounds. No growth was detected on syringate and guaiacol. The highest specific growth and uptake rates were observed for benzoate (0.3 h-1 and 4.2 mmol g CDW-1 h-1) whereas the lowest were for the compounds from the coniferyl branch. Interestingly, several pathway intermediates were excreted during batch growth. Vanillyl alcohol was found to be excreted during growth on vanillin. Several other intermediates like cis,cis-muconate, catechol, vanillate and 4-hydroxybenzoate from the known bacterial catabolic pathways were excreted during growth on the model compounds.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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Ho JCH, Pawar SV, Hallam SJ, Yadav VG. An Improved Whole-Cell Biosensor for the Discovery of Lignin-Transforming Enzymes in Functional Metagenomic Screens. ACS Synth Biol 2018; 7:392-398. [PMID: 29182267 DOI: 10.1021/acssynbio.7b00412] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery and utilization of biocatalysts that selectively valorize lignocellulose is critical to the profitability of next-generation biorefineries. Here, we report the development of a refactored, whole-cell, GFP-based biosensor for high-throughput identification of biocatalysts that transform lignin into specialty chemicals from environmental DNA of uncultivable archaea and bacteria. The biosensor comprises the transcriptional regulator and promoter of the emrRAB operon of E. coli, and the configuration of the biosensor was tuned with the aid of mathematical model. The biosensor sensitively and selectively detects vanillin and syringaldehyde, and responds linearly over a wide detection range. We employed the biosensor to screen 42 520 fosmid clones comprising environmental DNA isolated from two coal beds and successfully identified 147 clones that transform hardwood kraft lignin to vanillin and syringaldehyde.
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Affiliation(s)
- Joe C. H. Ho
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sandip V. Pawar
- Department of Chemical & Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Steven J. Hallam
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Vikramaditya G. Yadav
- Department of Chemical & Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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Raveendran S, Parameswaran B, Ummalyma SB, Abraham A, Mathew AK, Madhavan A, Rebello S, Pandey A. Applications of Microbial Enzymes in Food Industry. Food Technol Biotechnol 2018; 56:16-30. [PMID: 29795993 DOI: 10.17113/ftb.56.01.18.5491] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.
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Affiliation(s)
- Sindhu Raveendran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Binod Parameswaran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Sabeela Beevi Ummalyma
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India.,Institute of Bioresources and Sustainable Development, 795001 Imphal, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | | | - Sharrel Rebello
- Communicable Disease Research Laboratory, St. Joseph's College, 680121 Irinjalakuda, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 226001 Lucknow, India
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125
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Svensson T, Montelius M, Andersson M, Lindberg C, Reyier H, Rietz K, Danielsson Å, Bastviken D. Influence of Multiple Environmental Factors on Organic Matter Chlorination in Podsol Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:14114-14123. [PMID: 29172517 DOI: 10.1021/acs.est.7b03196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Natural chlorination of organic matter is common in soils. The abundance of chlorinated organic compounds frequently exceeds chloride in surface soils, and the ability to chlorinate soil organic matter (SOM) appears widespread among microorganisms. Yet, the environmental control of chlorination is unclear. Laboratory incubations with 36Cl as a Cl tracer were performed to test how combinations of environmental factors, including levels of soil moisture, nitrate, chloride, and labile organic carbon, influenced chlorination of SOM from a boreal forest. Total chlorination was hampered by addition of nitrate or by nitrate in combination with water but enhanced by addition of chloride or most additions including labile organic matter (glucose and maltose). The greatest chlorination was observed after 15 days when nitrate and water were added together with labile organic matter. The effect that labile organic matter strongly stimulated the chlorination rates was confirmed by a second independent experiment showing higher stimulation at increased availability of labile organic matter. Our results highlight cause-effect links between chlorination and the studied environmental variables in podsol soil-with consistent stimulation by labile organic matter that did overrule the negative effects of nitrate.
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Affiliation(s)
- Teresia Svensson
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Malin Montelius
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Malin Andersson
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Cecilia Lindberg
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Henrik Reyier
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Karolina Rietz
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - Åsa Danielsson
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
| | - David Bastviken
- Department of Thematic Studies, Environmental Change, Linköping University , SE-581 83 Linköping, Sweden
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126
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McGee CF. Microbial ecology of the Agaricus bisporus mushroom cropping process. Appl Microbiol Biotechnol 2017; 102:1075-1083. [PMID: 29222576 DOI: 10.1007/s00253-017-8683-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
Agaricus bisporus is the most widely cultivated mushroom species in the world. Cultivation is commenced by inoculating beds of semi-pasteurised composted organic substrate with a pure spawn of A. bisporus. The A. bisporus mycelium subsequently colonises the composted substrate by degrading the organic material to release nutrients. A layer of peat, often called "casing soil", is laid upon the surface of the composted substrate to induce the development of the mushroom crop and maintain compost environmental conditions. Extensive research has been conducted investigating the biochemistry and genetics of A. bisporus throughout the cultivation process; however, little is currently known about the wider microbial ecology that co-inhabits the composted substrate and casing layers. The compost and casing microbial communities are known to play important roles in the mushroom production process. Microbial species present in the compost and casing are known for (1) being an important source of nitrogen for the A. bisporus mycelium, (2) releasing sugar residues through the degradation of the wheat straw in the composted substrate, (3) playing a critical role in inducing development of the A. bisporus fruiting bodies and (4) acting as pathogens by parasitising the mushroom mycelium/crop. Despite a long history of research into the mushroom cropping process, an extensive review of the microbial communities present in the compost and casing has not as of yet been undertaken. The aim of this review is to provide a comprehensive summary of the literature investigating the compost and casing microbial communities throughout cultivation of the A. bisporus mushroom crop.
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Affiliation(s)
- Conor F McGee
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland.
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127
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Lignin Biodegradation in Pulp-and-Paper Mill Wastewater by Selected White Rot Fungi. WATER 2017. [DOI: 10.3390/w9120935] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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128
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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129
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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130
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Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
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131
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Trevathan-Tackett SM, Seymour JR, Nielsen DA, Macreadie PI, Jeffries TC, Sanderman J, Baldock J, Howes JM, Steven ADL, Ralph PJ. Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions. FEMS Microbiol Ecol 2017; 93:3071444. [PMID: 28334391 DOI: 10.1093/femsec/fix033] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/12/2017] [Indexed: 11/14/2022] Open
Abstract
Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.
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Affiliation(s)
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Daniel A Nielsen
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Peter I Macreadie
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia.,School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC 3125, Australia
| | - Thomas C Jeffries
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia.,Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW 2750, Australia
| | - Jonathan Sanderman
- CSIRO Agriculture and Food, Glen Osmond, SA 5064, Australia.,Woods Hole Research Center, Falmouth, MA 02540, USA
| | - Jeff Baldock
- CSIRO Agriculture and Food, Glen Osmond, SA 5064, Australia
| | - Johanna M Howes
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | | | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
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132
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Yang CX, Wang T, Gao LN, Yin HJ, Lü X. Isolation, identification and characterization of lignin-degrading bacteria from Qinling, China. J Appl Microbiol 2017; 123:1447-1460. [PMID: 28801977 DOI: 10.1111/jam.13562] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 07/19/2017] [Accepted: 08/01/2017] [Indexed: 11/30/2022]
Abstract
AIMS Lignin is an aromatic heteropolymer forming a physical barrier and it is a big challenge in biomass utilization. This paper first investigated lignin-degradation bacteria from rotten wood in Qinling Mountain. METHODS AND RESULTS Nineteen potential strains were selected and ligninolytic enzyme activities were determined over 84 h. Strains that had higher enzyme activities were selected. Further, the biodegradation of wheat straw lignin and alkali lignin was evaluated indicating that Burkholderia sp. H1 had the highest capability. It was confirmed by gel permeation chromatography and field emission scanning electron microscope that alkali lignin was depolymerized into small fragments. The degraded products were analysed using gas chromatography-mass spectrometry. The total ion chromatograph of products treated for 7 days showed the formation of aromatic compounds, an important intermediate from lignin degradation. Interestingly, they disappeared in 15 days while the aldehyde and ester compounds increased. CONCLUSIONS The results suggest that the lignin-degrading bacteria are abundant in rotten wood and strain H1 has high potential to break down lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The diversity of lignin-degrading bacteria in Qinling Mountain is revealed. The study of Burkholderia sp. H1 expands the range of bacteria for lignin degradation and provides novel bacteria for application to lignocellulosic biomass.
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Affiliation(s)
- C-X Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - T Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - L-N Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - H-J Yin
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - X Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
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133
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Orellana R, Chaput G, Markillie LM, Mitchell H, Gaffrey M, Orr G, DeAngelis KM. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. PLoS One 2017; 12:e0186440. [PMID: 29049419 PMCID: PMC5648182 DOI: 10.1371/journal.pone.0186440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.
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Affiliation(s)
- Roberto Orellana
- Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Gina Chaput
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
| | - Lye Meng Markillie
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Hugh Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matt Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kristen M. DeAngelis
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
- * E-mail:
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134
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Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal 2017; 7:6352-6364. [PMID: 29308295 PMCID: PMC5751952 DOI: 10.1021/acscatal.7b01861] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
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Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Gaochao Huang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - David A. Meekins
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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135
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Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals. Sci Rep 2017; 7:8420. [PMID: 28827602 PMCID: PMC5566326 DOI: 10.1038/s41598-017-07895-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/06/2017] [Indexed: 11/26/2022] Open
Abstract
Naturally, many aerobic organisms degrade lignin-derived aromatics through conserved intermediates including protocatechuate and catechol. Employing this microbial approach offers a potential solution for valorizing lignin into valuable chemicals for a potential lignocellulosic biorefinery and enabling bioeconomy. In this study, two hybrid biochemical routes combining lignin chemical depolymerization, plant metabolic engineering, and synthetic pathway reconstruction were demonstrated for valorizing lignin into value-added products. In the biochemical route 1, alkali lignin was chemically depolymerized into vanillin and syringate as major products, which were further bio-converted into cis, cis-muconic acid (ccMA) and pyrogallol, respectively, using engineered Escherichia coli strains. In the second biochemical route, the shikimate pathway of Tobacco plant was engineered to accumulate protocatechuate (PCA) as a soluble intermediate compound. The PCA extracted from the engineered Tobacco was further converted into ccMA using the engineered E. coli strain. This study reports a direct process for converting lignin into ccMA and pyrogallol as value-added chemicals, and more importantly demonstrates benign methods for valorization of polymeric lignin that is inherently heterogeneous and recalcitrant. Our approach also validates the promising combination of plant engineering with microbial chassis development for the production of value added and speciality chemicals.
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136
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137
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Derrien M, Lee YK, Park JE, Li P, Chen M, Lee SH, Lee SH, Lee JB, Hur J. Spectroscopic and molecular characterization of humic substances (HS) from soils and sediments in a watershed: comparative study of HS chemical fractions and the origins. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16933-16945. [PMID: 28577143 DOI: 10.1007/s11356-017-9225-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/08/2017] [Indexed: 05/26/2023]
Abstract
Optical properties and molecular composition of humic substances (HS) can provide valuable information on the sources and the history of the associated biogeochemical processes. In this study, many well-known spectral and molecular characteristics were examined in eight different HS samples, which were extracted from soils and sediments located in a forested watershed, via two advanced tools including fluorescence excitation emission matrix-parallel factor analysis (EEM-PARAFAC) and high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Two humic-like (C1 and C2) and one protein-like (C3) components were identified from EEM-PARAFAC. Irrespective of the origins, humic acid (HA) fractions were distinguished from fulvic acid (FA) fractions by the HS characteristics of specific UV absorbance (SUVA), the number of formulas, maximum fluorescence intensities of C1 and C2, condensed aromatics, tannins, and CHON, CHOS, and CHONS classes. In contrast, only five HS indices, including C3 intensity, H%, modified aromatic index (AImod), the percentages of carbohydrates, and unsaturated hydrocarbons, were found to be significant factors in discriminating between the two HS origins (i.e., soils and sediments). The ordination of the Bray-Curtis dissimilarity matrix further confirmed that the HS chemical fraction (i.e., HA or FA) was the more important factor to determine the measured HS characteristics than the HS origin. Our results provided an in-depth insight into the chemical and structural heterogeneity of bulk HS, which could be even beyond the differences observed along the two HS origins. This study also delivers a cautious message that the two operationally defined HS chemical fractions should be carefully considered in tracking the origins of different HS samples.
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Affiliation(s)
- Morgane Derrien
- Department of Environment and Energy, Sejong University, Seoul, 05006, South Korea
| | - Yun Kyung Lee
- Department of Environment and Energy, Sejong University, Seoul, 05006, South Korea
| | - Jae-Eun Park
- Research Group for Mass Spectrometry, Korea Basic Science Institute, Ochang, Chungbuk, 28119, South Korea
| | - Penghui Li
- Department of Environment and Energy, Sejong University, Seoul, 05006, South Korea
| | - Meilian Chen
- Department of Environment and Energy, Sejong University, Seoul, 05006, South Korea
| | - Sang Hee Lee
- Environmental measurement analysis center, National Institute of Environmental Research (NIER), Incheon, 22689, South Korea
| | - Soo Hyung Lee
- Water environmental engineering research division, National Institute of Environmental Research (NIER), Incheon, 22689, South Korea
| | - Jun-Bae Lee
- Geum River water environmental research center, National Institute of Environmental Research (NIER), Okcheon, Chungchung, 29029, South Korea
| | - Jin Hur
- Department of Environment and Energy, Sejong University, Seoul, 05006, South Korea.
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138
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Gong G, Kim S, Lee SM, Woo HM, Park TH, Um Y. Complete genome sequence of Bacillus sp. 275, producing extracellular cellulolytic, xylanolytic and ligninolytic enzymes. J Biotechnol 2017; 254:59-62. [DOI: 10.1016/j.jbiotec.2017.05.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 11/26/2022]
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139
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de Boer W. Upscaling of fungal-bacterial interactions: from the lab to the field. Curr Opin Microbiol 2017; 37:35-41. [PMID: 28437664 DOI: 10.1016/j.mib.2017.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
Abstract
Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Soil Quality, Wageningen University, Wageningen, The Netherlands.
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140
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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141
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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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142
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Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
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Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
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143
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A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde. Sci Rep 2017; 7:44422. [PMID: 28294121 PMCID: PMC5353671 DOI: 10.1038/srep44422] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/07/2017] [Indexed: 01/18/2023] Open
Abstract
Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed similar kcat/Km values for syringaldehyde (2100 s−1·mM−1) and vanillin (1700 s−1·mM−1), whereas LigV substantially preferred vanillin (8800 s−1·mM−1) over syringaldehyde (1.4 s−1·mM−1). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster.
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144
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Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol 2017; 122:940-952. [PMID: 28092137 DOI: 10.1111/jam.13401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.
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Affiliation(s)
- C A Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M Prabhakaran
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - K D Ramachandriya
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, Stillwater, OK, USA
| | - P Canaan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - B Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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145
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Enhanced delignification of steam-pretreated poplar by a bacterial laccase. Sci Rep 2017; 7:42121. [PMID: 28169340 PMCID: PMC5294454 DOI: 10.1038/srep42121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022] Open
Abstract
The recalcitrance of woody biomass, particularly its lignin component, hinders its sustainable transformation to fuels and biomaterials. Although the recent discovery of several bacterial ligninases promises the development of novel biocatalysts, these enzymes have largely been characterized using model substrates: direct evidence for their action on biomass is lacking. Herein, we report the delignification of woody biomass by a small laccase (sLac) from Amycolatopsis sp. 75iv3. Incubation of steam-pretreated poplar (SPP) with sLac enhanced the release of acid-precipitable polymeric lignin (APPL) by ~6-fold, and reduced the amount of acid-soluble lignin by ~15%. NMR spectrometry revealed that the APPL was significantly syringyl-enriched relative to the original material (~16:1 vs. ~3:1), and that sLac preferentially oxidized syringyl units and altered interunit linkage distributions. sLac's substrate preference among monoaryls was also consistent with this observation. In addition, sLac treatment reduced the molar mass of the APPL by over 50%, as determined by gel-permeation chromatography coupled with multi-angle light scattering. Finally, sLac acted synergistically with a commercial cellulase cocktail to increase glucose production from SPP ~8%. Overall, this study establishes the lignolytic activity of sLac on woody biomass and highlights the biocatalytic potential of bacterial enzymes.
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146
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Pornsuwan S, Maenpuen S, Kamutira P, Watthaisong P, Thotsaporn K, Tongsook C, Juttulapa M, Nijvipakul S, Chaiyen P. 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover. PLoS One 2017; 12:e0171135. [PMID: 28158217 PMCID: PMC5291488 DOI: 10.1371/journal.pone.0171135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/15/2017] [Indexed: 11/18/2022] Open
Abstract
3,4-dihydroxyphenylacetate (DHPA) dioxygenase (DHPAO) from Pseudomonas aeruginosa (PaDHPAO) was overexpressed in Escherichia coli and purified to homogeneity. As the enzyme lost activity over time, a protocol to reactivate and conserve PaDHPAO activity has been developed. Addition of Fe(II), DTT and ascorbic acid or ROS scavenging enzymes (catalase or superoxide dismutase) was required to preserve enzyme stability. Metal content and activity analyses indicated that PaDHPAO uses Fe(II) as a metal cofactor. NMR analysis of the reaction product indicated that PaDHPAO catalyzes the 2,3-extradiol ring-cleavage of DHPA to form 5-carboxymethyl-2-hydroxymuconate semialdehyde (CHMS) which has a molar absorptivity of 32.23 mM-1cm-1 at 380 nm and pH 7.5. Steady-state kinetics under air-saturated conditions at 25°C and pH 7.5 showed a Km for DHPA of 58 ± 8 μM and a kcat of 64 s-1, indicating that the turnover of PaDHPAO is relatively fast compared to other DHPAOs. The pH-rate profile of the PaDHPAO reaction shows a bell-shaped plot that exhibits a maximum activity at pH 7.5 with two pKa values of 6.5 ± 0.1 and 8.9 ± 0.1. Study of the effect of temperature on PaDHPAO activity indicated that the enzyme activity increases as temperature increases up to 55°C. The Arrhenius plot of ln(k’cat) versus the reciprocal of the absolute temperature shows two correlations with a transition temperature at 35°C. Two activation energy values (Ea) above and below the transition temperature were calculated as 42 and 14 kJ/mol, respectively. The data imply that the rate determining steps of the PaDHPAO reaction at temperatures above and below 35°C may be different. Sequence similarity network analysis indicated that PaDHPAO belongs to the enzyme clusters that are largely unexplored. As PaDHPAO has a high turnover number compared to most of the enzymes previously reported, understanding its biochemical and biophysical properties should be useful for future applications in biotechnology.
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Affiliation(s)
- Soraya Pornsuwan
- Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Philaiwarong Kamutira
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pratchaya Watthaisong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kittisak Thotsaporn
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Chanakan Tongsook
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Maneerat Juttulapa
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarayut Nijvipakul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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147
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Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification. GENOME ANNOUNCEMENTS 2017; 5:5/5/e01562-16. [PMID: 28153904 PMCID: PMC5289690 DOI: 10.1128/genomea.01562-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pseudonocardia autotrophica strain DSM 43083 is a filamentous actinobacterium and was described to degrade or modify lignin. Here, we present its draft genome sequence, with a size of 5.8 Mb, to unravel the gene set coding for promising monooxygenases, dioxygenases, and DyP-type peroxidases associated with aromatic metabolism and lignin modification.
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148
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Lei Y, Hannoufa A, Yu P. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage. Int J Mol Sci 2017; 18:E298. [PMID: 28146083 PMCID: PMC5343834 DOI: 10.3390/ijms18020298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/25/2022] Open
Abstract
Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO) in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding.
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Affiliation(s)
- Yaogeng Lei
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada.
| | - Peiqiang Yu
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
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149
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Casciello C, Tonin F, Berini F, Fasoli E, Marinelli F, Pollegioni L, Rosini E. A valuable peroxidase activity from the novel species Nonomuraea gerenzanensis growing on alkali lignin. ACTA ACUST UNITED AC 2017; 13:49-57. [PMID: 28352563 PMCID: PMC5361131 DOI: 10.1016/j.btre.2016.12.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/07/2016] [Accepted: 12/21/2016] [Indexed: 11/22/2022]
Abstract
Actinomycetes represent an attractive source of ligninolytic enzymes. 43 actinomycetes were screened for laccase and peroxidase activities. The novel species N. gerenzanensis produces a valuable bacterial peroxidase activity. The dye-decolorizing activity paves the way for an industrial use of this peroxidase.
Degradation of lignin constitutes a key step in processing biomass to become useful monomers but it remains challenging. Compared to fungi, bacteria are much less characterized with respect to their lignin metabolism, although it is reported that many soil bacteria, especially actinomycetes, attack and solubilize lignin. In this work, we screened 43 filamentous actinomycetes by assaying their activity on chemically different substrates including a soluble and semi-degraded lignin derivative (known as alkali lignin or Kraft lignin), and we discovered a novel and valuable peroxidase activity produced by the recently classified actinomycete Nonomuraea gerenzanensis. Compared to known fungal manganese and versatile peroxidases, the stability of N. gerenzanensis peroxidase activity at alkaline pHs and its thermostability are significantly higher. From a kinetic point of view, N. gerenzanensis peroxidase activity shows a Km for H2O2 similar to that of Phanerochaete chrysosporium and Bjerkandera enzymes and a lower affinity for Mn2+, whereas it differs from the six Pleurotus ostreatus manganese peroxidase isoenzymes described in the literature. Additionally, N. gerenzanensis peroxidase shows a remarkable dye-decolorizing activity that expands its substrate range and paves the way for an industrial use of this enzyme. These results confirm that by exploring new bacterial diversity, we may be able to discover and exploit alternative biological tools putatively involved in lignin modification and degradation.
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Key Words
- 2,4-DCP, 2,4-dichlorophenol
- 2,6-DMP, 2,6-dimethoxyphenol
- ABTS, 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid)
- Alkali lignin
- DyP, dye decolorizing peroxidase
- Filamentous actinomycetes
- Kraft lignin
- LiP, lignin peroxidase
- MAM, mannitol agar medium
- MM-L, minimal salt medium plus lignin
- MnP, manganese peroxidase
- Nonomuraea gerenzanensis
- Peroxidases
- RB5, reactive black 5
- RBBR, remazol brilliant blue R
- VP, versatile peroxidase
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Affiliation(s)
- Carmine Casciello
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Fabio Tonin
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico of Milano, via Mancinelli 7, 20131, Milano, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
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150
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Rais D, Zibek S. Biotechnological and Biochemical Utilization of Lignin. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:469-518. [PMID: 28540404 DOI: 10.1007/10_2017_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.
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Affiliation(s)
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
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