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Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives. Catalysts 2023. [DOI: 10.3390/catal13010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.
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2
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Recent Advances in Synthesis and Degradation of Lignin and Lignin Nanoparticles and Their Emerging Applications in Nanotechnology. MATERIALS 2022; 15:ma15030953. [PMID: 35160893 PMCID: PMC8838035 DOI: 10.3390/ma15030953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/16/2023]
Abstract
Lignin is an important commercially produced polymeric material. It is used extensively in both industrial and agricultural activities. Recently, it has drawn much attention from the scientific community. It is abundantly present in nature and has significant application in the production of biodegradable materials. Its wide usage includes drug delivery, polymers and several forms of emerging lignin nanoparticles. The synthesis of lignin nanoparticles is carried out in a controlled manner. The traditional manufacturing techniques are costly and often toxic and hazardous to the environment. This review article highlights simple, safe, climate-friendly and ecological approaches to the synthesis of lignin nanoparticles. The changeable, complex structure and recalcitrant nature of lignin makes it challenging to degrade. Researchers have discovered a small number of microorganisms that have developed enzymatic and non-enzymatic metabolic pathways to use lignin as a carbon source. These microbes show promising potential for the biodegradation of lignin. The degradation pathways of these microbes are also described, which makes the study of biological synthesis much easier. However, surface modification of lignin nanoparticles is something that is yet to be explored. This review elucidates the recent advances in the biodegradation of lignin in the ecological system. It includes the current approaches, methods for modification, new applications and research for the synthesis of lignin and lignin nanoparticles. Additionally, the intricacy of lignin’s structure, along with its chemical nature, is well-described. This article will help increase the understanding of the utilization of lignin as an economical and alternative-resource material. It will also aid in the minimization of solid waste arising from lignin.
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3
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Bioprospecting for Biomolecules from Different Fungal Communities: An Introduction. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Kaewlaoyoong A, Cheng CY, Lin C, Chen JR, Huang WY, Sriprom P. White rot fungus Pleurotus pulmonarius enhanced bioremediation of highly PCDD/F-contaminated field soil via solid state fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139670. [PMID: 32534283 DOI: 10.1016/j.scitotenv.2020.139670] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
This study was performed to evaluate the use of white rot fungus, Pleurotus pulmonarius, to treat polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) in contaminated soil using solid state fermentation (SSF). The soil was collected from a long-closed pentachlorophenol plant in southern Taiwan. The non-sterilized soil with a total PCDD/F concentration of 14,000 ± 2400 ng I-TEQ kg-1 was mixed directly with the solid fungal inocula at dry w/w ratio of 1:1.4 (ratio-adjusted test) and incubated at 26 ± 2 °C in a controlled environment. The highest PCDD/F decomposition was observed during the mycelium colonization. Pearson correlation coefficient (r) studied during this period (35 days) indicated that laccase had no significant correlation (r = -0.53), while manganese peroxidase had a strong positive correlation (r = 0.88) with PCDD/F decomposition efficiency. After 72 days, the more toxic congeners, tetra- and penta-CDD/Fs were removed to non-detectable levels. Meanwhile, the removal efficiencies of hexa-, hepta-, and octa-CDD/Fs were >80%, >97%, and >90%, respectively. The simultaneous degradation of low and high chlorinated DD/Fs suggested that overall removal was nonspecific. The overall PCDD/F removal was 96%, and the residual concentration (276 ng I-TEQ kg-1) was below the regulatory control limit (1000 ng I-TEQ kg-1). In conclusion, this study shows that P. pulmonarius via SSF can successfully remediate the PCDD/F-contaminated field soil. Furthermore, this SSF technique overcame the well-known intractability of PCDD/F biodegradation in non-sterilized soil, making it promising for actual field application.
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Affiliation(s)
- Acharee Kaewlaoyoong
- Department of Safety, Health, and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 82445, Taiwan
| | - Chih-Yu Cheng
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Chitsan Lin
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan.
| | - Jenq-Renn Chen
- Department of Safety, Health, and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 82445, Taiwan
| | - Wen-Yen Huang
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Pongsert Sriprom
- Program of Food Process Engineering, Faculty of Agro-Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
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5
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Isotopic and compositional evidence for carbon and nitrogen dynamics during wood decomposition by saprotrophic fungi. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Liew YX, Chan YJ, Manickam S, Chong MF, Chong S, Tiong TJ, Lim JW, Pan GT. Enzymatic pretreatment to enhance anaerobic bioconversion of high strength wastewater to biogas: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136373. [PMID: 31954239 DOI: 10.1016/j.scitotenv.2019.136373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Oil and grease, carbohydrate, protein, and lignin are the main constituents of high strength wastewaters such as dairy wastewater, cheese whey wastewater, distillery wastewater, pulp and paper mill wastewater, and slaughterhouse wastewaters. These constituents have contributed to various operational problems faced by the high-rate anaerobic bioreactor (HRAB). During the hydrolysis stage of anaerobic digestion (AD), these constituents can be hydrolyzed. Since hydrolysis is known to be the rate-limiting step of AD, the overall AD can be enhanced by improving the hydrolysis stage. This can be done by introducing pretreatment that targets the degradation of these constituents. This review mainly focuses on the biological pretreatment on various high-strength wastewaters by using different types of enzymes namely lipase, amylase, protease, and ligninolytic enzymes which are responsible for catalyzing the degradation of oil and grease, carbohydrate, protein, and lignin respectively. This review provides a summary of enzymatic systems involved in enhancing the hydrolysis stage and consequently improve biogas production. The results show that the use of enzymes improves the biogas production in the range of 7 to 76%. Though these improvements are highly dependent on the operating conditions of pretreatment and the types of substrates. Therefore, the critical parameters that would affect the effectiveness of pretreatment are also discussed. This review paper will serve as a useful piece of information to those industries that face difficulties in treating their high-strength wastewaters for the appropriate process, equipment selection, and design of an anaerobic enzymatic system. However, more intensive studies on the optimum operating conditions of pretreatment in a larger-scale and synergistic effects between enzymes are necessary to make the enzymatic pretreatment economically feasible.
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Affiliation(s)
- Yuh Xiu Liew
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia
| | - Yi Jing Chan
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Sivakumar Manickam
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Mei Fong Chong
- 28, Jalan Pulau Tioman U10/94, Taman Greenhill, Shah Alam 40170, Selangor Darul Ehsan, Malaysia
| | - Siewhui Chong
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Timm Joyce Tiong
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Broga Road, Semenyih 43500, Selangor Darul Ehsan, Malaysia.
| | - Jun Wei Lim
- Department of Fundamental and Applied Sciences, Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Guan-Ting Pan
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No. 1, Section 3, Zhongxiao E Rd, Da'an District, 106 Taipei City, Taiwan, ROC.
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7
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van Erven G, Wang J, Sun P, de Waard P, van der Putten J, Frissen GE, Gosselink RJA, Zinovyev G, Potthast A, van Berkel WJH, Kabel MA. Structural Motifs of Wheat Straw Lignin Differ in Susceptibility to Degradation by the White-Rot Fungus Ceriporiopsis subvermispora. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2019; 7:20032-20042. [PMID: 31867146 PMCID: PMC6921689 DOI: 10.1021/acssuschemeng.9b05780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/29/2019] [Indexed: 05/11/2023]
Abstract
The white-rot fungus Ceriporiopsis subvermispora delignifies plant biomass extensively and selectively and, therefore, has great biotechnological potential. We previously demonstrated that after 7 weeks of fungal growth on wheat straw 70% w/w of lignin was removed and established the underlying degradation mechanisms via selectively extracted diagnostic substructures. In this work, we fractionated the residual (more intact) lignin and comprehensively characterized the obtained isolates to determine the susceptibility of wheat straw lignin's structural motifs to fungal degradation. Using 13C IS pyrolysis gas chromatography-mass spectrometry (py-GC-MS), heteronuclear single quantum coherence (HSQC) and 31P NMR spectroscopy, and size-exclusion chromatography (SEC) analyses, it was shown that β-O-4' ethers and the more condensed phenylcoumarans and resinols were equally susceptible to fungal breakdown. Interestingly, for β-O-4' ether substructures, marked cleavage preferences could be observed: β-O-4'-syringyl substructures were degraded more frequently than their β-O-4'-guaiacyl and β-O-4'-tricin analogues. Furthermore, diastereochemistry (threo > erythro) and γ-acylation (γ-OH > γ-acyl) influenced cleavage susceptibility. These results indicate that electron density of the 4'-O-coupled ring and local steric hindrance are important determinants of oxidative β-O-4' ether degradation. Our findings provide novel insight into the delignification mechanisms of C. subvermispora and contribute to improving the valorization of lignocellulosic biomass.
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Affiliation(s)
- Gijs van Erven
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Jianli Wang
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Peicheng Sun
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Pieter de Waard
- MAGNEFY
(MAGNEtic Resonance Research FacilitY), Wageningen University & Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Jacinta van der Putten
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Guus E. Frissen
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Richard J. A. Gosselink
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Grigory Zinovyev
- Department
of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences, Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria
| | - Antje Potthast
- Department
of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences, Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria
| | - Willem J. H. van Berkel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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8
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Gaikwad A, Meshram A. Effect of particle size and mixing on the laccase-mediated pretreatment of lignocellulosic biomass for enhanced saccharification of cellulose. CHEM ENG COMMUN 2019. [DOI: 10.1080/00986445.2019.1680364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ashwin Gaikwad
- Visvesvaraya National Institute of Technology, Nagpur, India
| | - Anjali Meshram
- Visvesvaraya National Institute of Technology, Nagpur, India
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9
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Li X, Zheng Y. Biotransformation of lignin: Mechanisms, applications and future work. Biotechnol Prog 2019; 36:e2922. [PMID: 31587530 DOI: 10.1002/btpr.2922] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023]
Abstract
As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.
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Affiliation(s)
- Xiang Li
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
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10
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Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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11
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Development of an RP-UHPLC-PDA method for quantification of free gossypol in cottonseed cake and fungal-treated cottonseed cake. PLoS One 2018; 13:e0196164. [PMID: 29791447 PMCID: PMC5965856 DOI: 10.1371/journal.pone.0196164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 04/06/2018] [Indexed: 11/27/2022] Open
Abstract
Cottonseed cake biomass, which is a residue of oil extraction, is potentially appropriate for use as animal feed, given the high mineral, fibre and protein content. The presence of free gossypol, however, a toxic pigment in the glands of the cotton plant, limits use of this biomass for monogastric livestock. A promising method to detoxify cottonseed cake relies on fermentation by fungi, which can eliminate up to 100% of gossypol. In order to quantify trace levels of free gossypol in different cotton materials, including cottonseed cake treated with macrofungi, a simple and rapid chromatographic detection method was developed and validated. Under optimized conditions, extraction was performed using 70% acetone. The extract was then analysed by Ultra High-Performance Liquid Chromatography (UHPLC), with gradient elution on a C18 reverse phase column KINETEX® (100 x 2.10 mm, 2.6 μm). Methanol-0.1% TFA aqueous solution was employed as mobile phase and PDA detection conducted at 254 nm. The optimized method was validated by analysis of specificity, linearity and range, limit of detection, limit of quantification, precision and accuracy. Detection and quantification limits were observed at 0.2 and 0.5 μg/mL, respectively. With good reproducibility, with precision (RSD)<10% and recovery greater than 94%, the developed assay was appropriate for quantification of low quantities of free gossypol. The validated method was successfully applied to determine trace levels of free gossypol cottonseed treated with a macrofungus.
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12
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Kannaiyan R, Mahinpey N, Kostenko V, Martinuzzi RJ. Enhanced Delignification of Wheat Straw by the Combined Effect of Hydrothermal and Fungal Treatments. CHEM ENG COMMUN 2017. [DOI: 10.1080/00986445.2017.1322961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ranjani Kannaiyan
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Canada
| | - Nader Mahinpey
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Canada
| | - Victoria Kostenko
- Calgary Center for Innovative Technology, University of Calgary, Calgary, Canada
| | - Robert J. Martinuzzi
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada
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13
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Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR. The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses. Environ Microbiol 2017; 19:1237-1250. [PMID: 28028889 DOI: 10.1111/1462-2920.13652] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 12/27/2022]
Abstract
The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.
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Affiliation(s)
- Johanna Rytioja
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marcos Di Falco
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Outi-Maaria Sietiö
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ronald P de Vries
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Miia R Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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14
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Daâssi D, Zouari-Mechichi H, Belbahri L, Barriuso J, Martínez MJ, Nasri M, Mechichi T. Phylogenetic and metabolic diversity of Tunisian forest wood-degrading fungi: a wealth of novelties and opportunities for biotechnology. 3 Biotech 2016; 6:46. [PMID: 28330115 PMCID: PMC4742418 DOI: 10.1007/s13205-015-0356-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 12/24/2015] [Indexed: 12/07/2022] Open
Abstract
In this study, 51 fungal strains were isolated from decaying wood samples collected from forests located in the Northwest of Tunisia in the vicinity of Bousalem, Ain Draham and Kef. Phylogenetic analysis based on the sequences of the internal transcribed spacers of the ribosomal DNA showed a high diversity among the 51 fungal isolates collection. Representatives of 25 genera and 29 species were identified, most of which were members of one of the following phyla (Ascomycota, Basidiomycota and Zygomycota). In addition to the phylogenetic diversity, a high diversity of secreted enzyme profiles was also detected among the fungal isolates. All fungal strains produced at least one of the following enzymes: laccase, cellulase, protease and/or lipase.
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Affiliation(s)
- Dalel Daâssi
- Laboratory of Enzyme Engineering and Microbiology, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Route de Soukra Km 4,5, BP 1173, 3038, Sfax, Tunisia.
- Department of Biology, Faculty of Sciences and Arts, Khulais, University of Jeddah, Jeddah, Saudi Arabia.
| | - Héla Zouari-Mechichi
- Laboratory of Enzyme Engineering and Microbiology, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Route de Soukra Km 4,5, BP 1173, 3038, Sfax, Tunisia
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, Rue Emile Argand 11, 2009, Neuchâtel, Switzerland
- NextBiotech, Agareb, Tunisia
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Moncef Nasri
- Laboratory of Enzyme Engineering and Microbiology, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Route de Soukra Km 4,5, BP 1173, 3038, Sfax, Tunisia
| | - Tahar Mechichi
- Laboratory of Enzyme Engineering and Microbiology, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Route de Soukra Km 4,5, BP 1173, 3038, Sfax, Tunisia.
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15
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16
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Potential of White-Rot Fungi to Treat Xenobiotic-Containing Wastewater. FUNGAL APPLICATIONS IN SUSTAINABLE ENVIRONMENTAL BIOTECHNOLOGY 2016. [DOI: 10.1007/978-3-319-42852-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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Rytioja J, Hildén K, Mäkinen S, Vehmaanperä J, Hatakka A, Mäkelä MR. Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens. PLoS One 2015; 10:e0145166. [PMID: 26660105 PMCID: PMC4682842 DOI: 10.1371/journal.pone.0145166] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 01/11/2023] Open
Abstract
White rot fungus Dichomitus squalens is an efficient lignocellulose degrading basidiomycete and a promising source for new plant cell wall polysaccharides depolymerizing enzymes. In this work, we focused on cellobiohydrolases (CBHs) of D. squalens. The native CBHI fraction of the fungus, consisting three isoenzymes, was purified and it maintained the activity for 60 min at 50°C, and was stable in acidic pH. Due to the lack of enzyme activity assay for detecting only CBHII activity, CBHII of D. squalens was produced recombinantly in an industrially important ascomycete host, Trichoderma reesei. CBH enzymes of D. squalens showed potential in hydrolysis of complex lignocellulose substrates sugar beet pulp and wheat bran, and microcrystalline cellulose, Avicel. Recombinant CBHII (rCel6A) of D. squalens hydrolysed all the studied plant biomasses. Compared to individual activities, synergistic effect between rCel6A and native CBHI fraction of D. squalens was significant in the hydrolysis of Avicel. Furthermore, the addition of laccase to the mixture of CBHI fraction and rCel6A significantly enhanced the amount of released reducing sugars from sugar beet pulp. Especially, synergy between individual enzymes is a crucial factor in the tailor-made enzyme mixtures needed for hydrolysis of different plant biomass feedstocks. Our data supports the importance of oxidoreductases in improved enzyme cocktails for lignocellulose saccharification.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | | | | | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail:
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18
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Vidal-Diez de Ulzurrun G, Baetens JM, Van den Bulcke J, Lopez-Molina C, De Windt I, De Baets B. Automated image-based analysis of spatio-temporal fungal dynamics. Fungal Genet Biol 2015; 84:12-25. [PMID: 26365383 DOI: 10.1016/j.fgb.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
Due to their ability to grow in complex environments, fungi play an important role in most ecosystems and have for that reason been the subject of numerous studies. Some of the main obstacles to the study of fungal growth are the heterogeneity of growth environments and the limited scope of laboratory experiments. Given the increasing availability of image capturing techniques, a new approach lies in image analysis. Most previous image analysis studies involve manual labelling of the fungal network, tracking of individual hyphae, or invasive techniques that do not allow for tracking the evolution of the entire fungal network. In response, this work presents a highly versatile tool combining image analysis and graph theory to monitor fungal growth through time and space for different fungal species and image resolutions. In addition, a new experimental set-up is presented that allows for a functional description of fungal growth dynamics and a quantitative mutual comparison of different growth behaviors. The presented method is completely automated and facilitates the extraction of the most studied fungal growth features such as the total length of the mycelium, the area of the mycelium and the fractal dimension. The compactness of the fungal network can also be monitored over time by computing measures such as the number of tips, the node degree and the number of nodes. Finally, the average growth angle and the internodal length can be extracted to study the morphology of the fungi. In summary, the introduced method offers an updated and broader alternative to classical and narrowly focused approaches, thus opening new avenues of investigation in the field of mycology.
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Affiliation(s)
- G Vidal-Diez de Ulzurrun
- KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - J M Baetens
- KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - J Van den Bulcke
- Laboratory of Wood Technology, Department of Forest and Water Management, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - C Lopez-Molina
- Dpto. Automática y Computación, Universidad Publica de Navarra, 31006 Pamplona, Spain; KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - I De Windt
- Laboratory of Wood Technology, Department of Forest and Water Management, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - B De Baets
- KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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19
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Bianco L, Perrotta G. Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis. Int J Mol Sci 2015; 16:5803-29. [PMID: 25775160 PMCID: PMC4394507 DOI: 10.3390/ijms16035803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/17/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022] Open
Abstract
Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.
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Affiliation(s)
- Linda Bianco
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
| | - Gaetano Perrotta
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
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20
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21
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Development of electronic nose and near infrared spectroscopy analysis techniques to monitor the critical time in SSF process of feed protein. SENSORS 2014; 14:19441-56. [PMID: 25330048 PMCID: PMC4239914 DOI: 10.3390/s141019441] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/25/2014] [Accepted: 09/29/2014] [Indexed: 11/29/2022]
Abstract
In order to assure the consistency of the final product quality, a fast and effective process monitoring is a growing need in solid state fermentation (SSF) industry. This work investigated the potential of non-invasive techniques combined with the chemometrics method, to monitor time-related changes that occur during SSF process of feed protein. Four fermentation trials conducted were monitored by an electronic nose device and a near infrared spectroscopy (NIRS) spectrometer. Firstly, principal component analysis (PCA) and independent component analysis (ICA) were respectively applied to the feature extraction and information fusion. Then, the BP_AdaBoost algorithm was used to develop the fused model for monitoring of the critical time in SSF process of feed protein. Experimental results showed that the identified results of the fusion model are much better than those of the single technique model both in the training and validation sets, and the complexity of the fusion model was also less than that of the single technique model. The overall results demonstrate that it has a high potential in online monitoring of the critical moment in SSF process by use of integrating electronic nose and NIRS techniques, and data fusion from multi-technique could significantly improve the monitoring performance of SSF process.
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23
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Lv Y, Chen Y, Sun S, Hu Y. Interaction among multiple microorganisms and effects of nitrogen and carbon supplementations on lignin degradation. BIORESOURCE TECHNOLOGY 2014; 155:144-151. [PMID: 24445191 DOI: 10.1016/j.biortech.2013.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
The mutual interactions among the consortium constructed by four indigenous bacteria and five inter-kingdom fusants and the effects of nitrogen and carbon supplementations on lignin degradation and laccase activity were investigated. Analyzed by Plackett-Burman and central composite design, the microbial consortium were optimized, Bacillus sp. (B) and PE-9 and Pseudomonas putida (Pp) and PE-9 had significant interactions on lignin degradation based on a 5% level of significance. The nitrogen and carbon supplementations played an important role in lignin degradation and laccase production. The ultimate lignin degradation efficiency of 96.0% and laccase activity of 268U/L were obtained with 0.5g/L of ammonium chloride and 2g/L of sucrose. Results suggested that a stable and effective microbial consortium in alkalescent conditions was successfully achieved through the introduction of fusants, which was significant for its industrial application.
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Affiliation(s)
- Yuancai Lv
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640, China.
| | - Yuancai Chen
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640, China; Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
| | - Shiying Sun
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640, China
| | - Yongyou Hu
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640, China; Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
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24
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Mäkelä MR, Sietiö OM, de Vries RP, Timonen S, Hildén K. Oxalate-metabolising genes of the white-rot fungus Dichomitus squalens are differentially induced on wood and at high proton concentration. PLoS One 2014; 9:e87959. [PMID: 24505339 PMCID: PMC3914892 DOI: 10.1371/journal.pone.0087959] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/03/2014] [Indexed: 11/23/2022] Open
Abstract
Oxalic acid is a prevalent fungal metabolite with versatile roles in growth and nutrition, including degradation of plant biomass. However, the toxicity of oxalic acid makes regulation of its intra- and extracellular concentration crucial. To increase the knowledge of fungal oxalate metabolism, a transcriptional level study on oxalate-catabolising genes was performed with an effective lignin-degrading white-rot fungus Dichomitus squalens, which has demonstrated particular abilities in production and degradation of oxalic acid. The expression of oxalic-acid decomposing oxalate decarboxylase (ODC) and formic-acid decomposing formate dehydrogenase (FDH) encoding genes was followed during the growth of D. squalens on its natural spruce wood substrate. The effect of high proton concentration on the regulation of the oxalate-catabolising genes was determined after addition of organic acid (oxalic acid) and inorganic acid (hydrochloric acid) to the liquid cultures of D. squalens. In order to evaluate the co-expression of oxalate-catabolising and manganese peroxidase (MnP) encoding genes, the expression of one MnP encoding gene, mnp1, of D. squalens was also surveyed in the solid state and liquid cultures. Sequential action of ODC and FDH encoding genes was detected in the studied cultivations. The odc1, fdh2 and fdh3 genes of D. squalens showed constitutive expression, whereas ODC2 and FHD1 most likely are the main responsible enzymes for detoxification of high concentrations of oxalic and formic acids. The results also confirmed the central role of ODC1 when D. squalens grows on coniferous wood. Phylogenetic analysis revealed that fungal ODCs have evolved from at least two gene copies whereas FDHs have a single ancestral gene. As a conclusion, the multiplicity of oxalate-catabolising genes and their differential regulation on wood and in acid-amended cultures of D. squalens point to divergent physiological roles for the corresponding enzymes.
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Affiliation(s)
- Miia R. Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Outi-Maaria Sietiö
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | | | - Sari Timonen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
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25
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Rytioja J, Hildén K, Hatakka A, Mäkelä MR. Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose. Fungal Genet Biol 2014; 72:91-98. [PMID: 24394946 DOI: 10.1016/j.fgb.2013.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
Abstract
The recent discovery of oxidative cellulose degradation enhancing enzymes has considerably changed the traditional concept of hydrolytic cellulose degradation. The relative expression levels of ten cellulose-acting enzyme encoding genes of the white-rot fungus Dichomitus squalens were studied on solid-state spruce wood and in microcrystalline Avicel cellulose cultures. From the cellobiohydrolase encoding genes, cel7c was detected at the highest level and showed constitutive expression whereas variable transcript levels were detected for cel7a, cel7b and cel6 in the course of four-week spruce cultivation. The cellulolytic enzyme activities detected in the liquid cultures were consistent with the transcript levels. Interestingly, the selected lytic polysaccharide monooxygenase (LPMO) encoding genes were expressed in both cultures, but showed different transcription patterns on wood compared to those in submerged microcrystalline cellulose cultures. On spruce wood, higher transcript levels were detected for the lpmos carrying cellulose binding module (CBM) than for the lpmos without CBMs. In both cultures, the expression levels of the lpmo genes were generally higher than the levels of cellobiose dehydrogenase (CDH) encoding genes. Based on the results of this work, the oxidative cellulose cleaving enzymes of D. squalens have essential role in cellulose degrading machinery of the fungus.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland.
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26
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Identification of a potential fungal species by 18S rDNA for ligninases production. World J Microbiol Biotechnol 2013; 29:2437-40. [DOI: 10.1007/s11274-013-1398-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/03/2013] [Indexed: 11/26/2022]
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27
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Knežević A, Milovanović I, Stajić M, Lončar N, Brčeski I, Vukojević J, Cilerdžić J. Lignin degradation by selected fungal species. BIORESOURCE TECHNOLOGY 2013; 138:117-23. [PMID: 23612169 DOI: 10.1016/j.biortech.2013.03.182] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 05/23/2023]
Abstract
As biological decomposition of plant biomass represents a popular alternative environmental-friendly and economically justified process, screening of ligninolytic enzyme systems of various fungal species is a topical study area. The goal of the study was to obtain clear insight into the dynamics of laccase, Mn-dependent peroxidase, and Mn-independent peroxidase activity and levels of wheat straw lignin degradation in seven wood-rotting fungi. The best laccase producers were Pleurotus ostreatus and Pleurotus eryngii. Lenzites betulinus and Fomitopsis pinicola were the best Mn-dependent peroxidase producers, and P. ostreatus the weakest one. The peak of Mn-independent peroxidase was noted in Dichomytus squalens, and the minimum value in P. ostreatus. The profiles of the three enzymes, obtained by isoelectric focusing, were variable depending on the species and cultivation period. D. squalens was the best lignin degrader (34.1% of total lignin amount), and P. ostreatus and P. eryngii the weakest ones (7.1% and 14.5%, respectively).
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Affiliation(s)
- Aleksandar Knežević
- University of Belgrade, Faculty of Biology, Takovska 43, 11000 Belgrade, Serbia.
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28
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Wang C, Zhang L, Xu H. The effects of N+ ion implantation mutagenesis on the laccase production of Ceriporiopsis subvermispora. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-012-0125-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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Fackler K, Schwanninger M. How spectroscopy and microspectroscopy of degraded wood contribute to understand fungal wood decay. Appl Microbiol Biotechnol 2012; 96:587-99. [PMID: 22983562 PMCID: PMC3466433 DOI: 10.1007/s00253-012-4369-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 12/01/2022]
Abstract
Nuclear magnetic resonance, mid and near infrared, and ultra violet (UV) spectra of wood contain information on its chemistry and composition. When solid wood samples are analysed, information on the molecular structure of the lignocellulose complex of wood e.g. crystallinity of polysaccharides and the orientation of the polymers in wood cell walls can also be gained. UV and infrared spectroscopy allow also for spatially resolved spectroscopy, and state-of-the-art mapping and imaging systems have been able to provide local information on wood chemistry and structure at the level of wood cells (with IR) or cell wall layers (with UV). During the last decades, these methods have also proven useful to follow alterations of the composition, chemistry and physics of the substrate wood after fungi had grown on it as well as changes of the interactions between the wood polymers within the lignocellulose complex caused by decay fungi. This review provides an overview on how molecular spectroscopic methods could contribute to understand these degradation processes and were able to characterise and localise fungal wood decay in its various stages starting from the incipient and early ones even if the major share of research focussed on advanced decay. Practical issues such as requirements in terms of sample preparation and sample form and present examples of optimised data analysis will also be addressed to be able to detect and characterise the generally highly variable microbial degradation processes within their highly variable substrate wood.
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Affiliation(s)
- Karin Fackler
- Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
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30
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Rapid determination of pH in solid-state fermentation of wheat straw by FT-NIR spectroscopy and efficient wavelengths selection. Anal Bioanal Chem 2012; 404:603-11. [PMID: 22688664 DOI: 10.1007/s00216-012-6128-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/09/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
Abstract
In the work discussed in this paper we investigated the feasibility of determination of the pH of a fermented substrate in solid-state fermentation (SSF) of wheat straw. Fourier-transform near-infrared (FT-NIR) spectroscopy was combined with an appropriate multivariate method of analysis. A genetic algorithm and synergy interval partial least-squares (GA-siPLS) were used to select the efficient spectral subintervals and wavelengths by k-fold cross-validation during development of the model. The performance of the final model was evaluated by use of the root mean square error of cross-validation (RMSECV) and correlation coefficient (R (c)) for the calibration set, and verified by use of the root mean square error of prediction (RMSEP) and correlation coefficient (R (p)) for the validation set. The experimental results showed that the optimum GA-siPLS model was achieved by use of seven PLS factors, when four spectral subintervals were selected by siPLS and then 45 wavelength variables were chosen by use of the GA. The predicted precision of the best model obtained was: RMSECV = 0.0583, R (c) = 0.9878, RMSEP = 0.0779, and R (p) = 0.9779. Finally, the superior performance of the GA-siPLS model was demonstrated by comparison with four other PLS models. The overall results indicated that FT-NIR spectroscopy can be successfully used for measurement of pH in solid-state fermentation, and use of the GA-siPLS algorithm is the best means of calibration of the model.
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31
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Mode of coniferous wood decay by the white rot fungus Phanerochaete carnosa as elucidated by FTIR and ToF-SIMS. Appl Microbiol Biotechnol 2012; 94:1303-11. [DOI: 10.1007/s00253-011-3830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 12/03/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
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32
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Tachibana S. Decomposition of lignin and holocellulose on Acacia mangium leaves and twigs by six fungal isolates from nature. Pak J Biol Sci 2010; 13:604-610. [PMID: 21061911 DOI: 10.3923/pjbs.2010.604.610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This research was conducted in the aim of preventing wild fire through reducing potential energy source to become in situ fertilizer. To prevent forest fires by reducing wood waste using lignocellulose-degrading fungi, six fungal isolates were tested for lignin and cellulose-degrading activity with Acacia mangium leaves and twigs over a period of 1 to 3 months. The fungi degraded 8.9-27.1% of the lignin and 14-31% of the holocellulose. The degradation rate varied depending on the fungal species. An increase in incubation time tended to decrease the amounts of holocellulose and lignin. However, the hot water soluble tended to increase following a longer incubation period. From the results obtained here, more time was needed to degrade lignin rather than other components in the sample.
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33
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Lundell TK, Mäkelä MR, Hildén K. Lignin-modifying enzymes in filamentous basidiomycetes--ecological, functional and phylogenetic review. J Basic Microbiol 2010; 50:5-20. [PMID: 20175122 DOI: 10.1002/jobm.200900338] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Filamentous fungi owe powerful abilities for decomposition of the extensive plant material, lignocellulose, and thereby are indispensable for the Earth's carbon cycle, generation of soil humic matter and formation of soil fine structure. The filamentous wood-decaying fungi belong to the phyla Basidiomycota and Ascomycota, and are unique organisms specified to degradation of the xylem cell wall components (cellulose, hemicelluloses, lignins and extractives). The basidiomycetous wood-decaying fungi form brackets, caps or resupinaceous (corticioid) fruiting bodies when growing on wood for dissemination of their sexual basidiospores. In particular, the ability to decompose the aromatic lignin polymers in wood is mostly restricted to the white rot basidiomycetes. The white-rot decay of wood is possible due to secretion of organic acids, secondary metabolites, and oxidoreductive metalloenzymes, heme peroxidases and laccases, encoded by divergent gene families in these fungi. The brown rot basidiomycetes obviously depend more on a non-enzymatic strategy for decomposition of wood cellulose and modification of lignin. This review gives a current ecological, genomic, and protein functional and phylogenetic perspective of the wood and lignocellulose-decaying basidiomycetous fungi.
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Affiliation(s)
- Taina K Lundell
- Fungal Biotechnology Group, Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, University of Helsinki, Finland.
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34
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Mäkelä MR, Hildén K, Hatakka A, Lundell TK. Oxalate decarboxylase of the white-rot fungus Dichomitus squalens demonstrates a novel enzyme primary structure and non-induced expression on wood and in liquid cultures. Microbiology (Reading) 2009; 155:2726-2738. [DOI: 10.1099/mic.0.028860-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Oxalate decarboxylase (ODC) catalyses the conversion of oxalic acid to formic acid and CO2 in bacteria and fungi. In wood-decaying fungi the enzyme has been linked to the regulation of intra- and extracellular quantities of oxalic acid, which is one of the key components in biological decomposition of wood. ODC enzymes are biotechnologically interesting for their potential in diagnostics, agriculture and environmental applications, e.g. removal of oxalic acid from industrial wastewaters. We identified a novel ODC in mycelial extracts of two wild-type isolates of Dichomitus squalens, and cloned the corresponding Ds-odc gene. The primary structure of the Ds-ODC protein contains two conserved Mn-binding cupin motifs, but at the N-terminus, a unique, approximately 60 aa alanine-serine-rich region is found. Real-time quantitative RT-PCR analysis confirmed gene expression when the fungus was cultivated on wood and in liquid medium. However, addition of oxalic acid in liquid cultures caused no increase in transcript amounts, thereby indicating a constitutive rather than inducible expression of Ds-odc. The detected stimulation of ODC activity by oxalic acid is more likely due to enzyme activation than to transcriptional upregulation of the Ds-odc gene. Our results support involvement of ODC in primary rather than secondary metabolism in fungi.
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Affiliation(s)
- Miia R. Mäkelä
- Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, PO Box 56, FIN-00014 University of Helsinki, Finland
| | - Kristiina Hildén
- Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, PO Box 56, FIN-00014 University of Helsinki, Finland
| | - Annele Hatakka
- Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, PO Box 56, FIN-00014 University of Helsinki, Finland
| | - Taina K. Lundell
- Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, PO Box 56, FIN-00014 University of Helsinki, Finland
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Abstract
In an effort to prevent forest fires after the clear cutting of plantation forests, fungi capable of degrading lignocelluloses were isolated to make a fertilizer from the logging waste. Seventy five fungal species were isolated from fruiting bodies and mycelia in plantation forests of South and North Sumatera, Indonesia. Sixty three of the fungi were identified based on the appearance and morphological characteristics of their fruiting bodies and mycelia, as Pycnoporus sanguineus, Dacryopinax spathularia, Schizophyllum commune, Polyporus sp. and Trametes sp. Twenty fungi were categorized as white-rot fungi and 12 as brown-rot fungi. Moreover, isolates 371, 368, 265, 346, 345 and 338 were selected using indicators and tested for the ability to degrade lignin and holo-cellulose in mangium wood meal over 1 to 4 weeks. Results showed that the 6 fungi could degrade lignin and holo-cellulose in wood meal. An increase in incubation time tended to decrease the amounts of lignin and holo-cellulose. Isolate 371 was found to be best at degrading lignin and holo-cellulose in mangium wood meal.
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Effects of dirhamnolipid and SDS on enzyme production from Phanerochaete chrysosporium in submerged fermentation. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mounanga TK, Gérardin P, Poaty B, Perrin D, Gérardin C. Synthesis and properties of antioxidant amphiphilic ascorbate salts. Colloids Surf A Physicochem Eng Asp 2008. [DOI: 10.1016/j.colsurfa.2007.12.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Modugno F, Ribechini E, Calderisi M, Giachi G, Colombini M. Analysis of lignin from archaeological waterlogged wood by direct exposure mass spectrometry (DE-MS) and PCA evaluation of mass spectral data. Microchem J 2008. [DOI: 10.1016/j.microc.2007.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Evaluation of the selectivity of white rot isolates using near infrared spectroscopic techniques. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Levin L, Villalba L, Da Re V, Forchiassin F, Papinutti L. Comparative studies of loblolly pine biodegradation and enzyme production by Argentinean white rot fungi focused on biopulping processes. Process Biochem 2007. [DOI: 10.1016/j.procbio.2007.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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