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Sun C, Wang Z, Yu X, Zhang H, Cao J, Fang J, Wang J, Zhang L. The Phylogeny and Metabolic Potentials of an Aromatics-Degrading Marivivens Bacterium Isolated from Intertidal Seawater in East China Sea. Microorganisms 2024; 12:1308. [PMID: 39065077 PMCID: PMC11278965 DOI: 10.3390/microorganisms12071308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Lignocellulosic materials, made up of cellulose, hemicellulose, and lignin, constitute some of the most prevalent types of biopolymers in marine ecosystems. The degree to which marine microorganisms participate in the breakdown of lignin and their impact on the cycling of carbon in the oceans is not well understood. Strain LCG002, a novel Marivivens species isolated from Lu Chao Harbor's intertidal seawater, is distinguished by its ability to metabolize lignin and various aromatic compounds, including benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate and phenylacetate. It also demonstrates a broad range of carbon source utilization, including carbohydrates, amino acids and carboxylates. Furthermore, it can oxidize inorganic gases, such as hydrogen and carbon monoxide, providing alternative energy sources in diverse marine environments. Its diversity of nitrogen metabolism is supported by nitrate/nitrite, urea, ammonium, putrescine transporters, as well as assimilatory nitrate reductase. For sulfur assimilation, it employs various pathways to utilize organic and inorganic substrates, including the SOX system and DSMP utilization. Overall, LCG002's metabolic versatility and genetic profile contribute to its ecological significance in marine environments, particularly in the degradation of lignocellulosic material and aromatic monomers.
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Affiliation(s)
- Chengwen Sun
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Zekai Wang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Xi Yu
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Hongcai Zhang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Junwei Cao
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Jiasong Fang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jiahua Wang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
| | - Li Zhang
- Shanghai Engineering Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (C.S.); (Z.W.); (X.Y.); (H.Z.); (J.C.); (J.F.)
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Chen X, Liang X, Shi N, He L, Ma Y, Zhu D, Ni Z, Chen H. New wheat straw fermentation feed: recombinant Schizosaccharomyces pombe efficient degradation of lignocellulose and increase feed protein. Prep Biochem Biotechnol 2024:1-9. [PMID: 38824495 DOI: 10.1080/10826068.2024.2353637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
Wheat straw contains a high amount of lignin, hindering the action of cellulase and hemicellulase enzymes, leading to difficulties in nutrient absorption by animals from straw feed. However, currently, the biological treatment of straw relies primarily on fungal degradation and cannot be directly utilized for the preparation of livestock feed. This study focuses on enzymatic co-fermentation of wheat straw to produce high-protein, low-cellulose biological feed, integrating lignin degradation with feed manufacturing, thereby simplifying the feed production process. After the optimization using Box-Behnken Design for the feed formulation, with a glucose oxidase addition of 2.46%, laccase addition of 3.4%, and malonic acid addition of 0.6%, the wheat straw feed prepared in this experiment exhibited a true protein content of 9.35%. This represented a fourfold increase compared to the non-fermented state, and the lignocellulose degradation rate of wheat straw reached 45.42%. These results not only highlight the substantial enhancement in protein content but also underscore the significant advancement in lignocellulose breakdown. This formulation significantly enhanced the palatability and nutritional value of the straw feed, contributing to the industrial development of straw feed.
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Affiliation(s)
- Xihua Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoyu Liang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Na Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lu He
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yi Ma
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Daochen Zhu
- School of Environmental Safety, Jiangsu University, Zhenjiang, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Nizzy AM, Kannan S, Kanmani S. Utilization of plant-derived wastes as the potential biohydrogen source: a sustainable strategy for waste management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:34839-34858. [PMID: 38744759 DOI: 10.1007/s11356-024-33610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
The sustainable economy has shown a renewed interest in acquiring access to the resources required to promote innovative practices that favor recycling and the reuse of existing, unconsidered things over newly produced ones. The production of biohydrogen through dark anaerobic fermentation of organic wastes is one of the intriguing possibilities for replacing fossil-based fuels through the circular economy. At present, plant-derived waste from the agro-based industry is the main global concern. When these wastes are improperly disposed of in landfills, they become the habitat for several pathogens. Additionally, it contaminates surface water as a result of runoff, and the leachate that is created from the waste enters groundwater and degrades its quality. However, cellulose and hemicellulose-rich plant wastes from agriculture fields and agro-based industries have been employed as the most efficient feedstock since carbohydrates are the primary substrate for the synthesis of biohydrogen. To produce biohydrogen from plant-derived wastes on a large scale, it is necessary to explore comprehensive knowledge of lab-scale parameters and pretreatment strategies. This paper summarizes the problems associated with the improper management of plant-derived wastes and discusses the recent developments in dark fermentation and substrate pretreatment techniques with the goal of gaining significant insight into the biohydrogen production process. It also highlights the utilization of anaerobic digestate, which is left over after biohydrogen gas as feedstock for the development of value-added products such as volatile fatty acids (VFA), biochar, and biofertilizer.
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Affiliation(s)
| | - Suruli Kannan
- Department of Environmental Studies, School of Energy Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Sellappa Kanmani
- Centre for Environmental Studies, Anna University, Chennai, Tamil Nadu, 625021, India
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4
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Adnane I, Taoumi H, Elouahabi K, Lahrech K, Oulmekki A. Valorization of crop residues and animal wastes: Anaerobic co-digestion technology. Heliyon 2024; 10:e26440. [PMID: 38439870 PMCID: PMC10909651 DOI: 10.1016/j.heliyon.2024.e26440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
To switch the over-reliance on fossil-based resources, curb environmental quality deterioration, and promote the use of renewable fuels, much attention has recently been directed toward the implementation of sustainable and environmentally benign 'waste-to-energy' technology exploiting a clean, inexhaustible, carbon-neutral, and renewable energy source, namely agricultural biomass. From this perspective, anaerobic co-digestion (AcoD) technology emerges as a potent and plausible approach to attain sustainable energy development, foster environmental sustainability, and, most importantly, circumvent the key challenges associated with mono-digestion. This review article provides a comprehensive overview of AcoD as a biochemical valorization pathway of crop residues and livestock manure for biogas production. Furthermore, this manuscript aims to assess the different biotic and abiotic parameters affecting co-digestion efficiency and present recent advancements in pretreatment technologies designed to enhance feedstock biodegradability and conversion rate. It can be concluded that the substantial quantities of crop residues and animal waste generated annually from agricultural practices represent valuable bioenergy resources that can contribute to meeting global targets for affordable renewable energy. Nevertheless, extensive and multidisciplinary research is needed to evolve the industrial-scale implementation of AcoD technology of livestock waste and crop residues, particularly when a pretreatment phase is included, and bridge the gap between small-scale studies and real-world applications.
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Affiliation(s)
- Imane Adnane
- Sidi Mohamed Ben Abdellah University (USMBA), IPI Laboratory, ENS, Fez, Morocco
| | - Hamza Taoumi
- Sidi Mohamed Ben Abdellah University (USMBA), IPI Laboratory, ENS, Fez, Morocco
| | - Karim Elouahabi
- Sidi Mohamed Ben Abdellah University (USMBA), IPI Laboratory, ENS, Fez, Morocco
| | - Khadija Lahrech
- Sidi Mohamed Ben Abdellah University (USMBA), ENSA, Fez, Morocco
| | - Abdellah Oulmekki
- Laboratory of Processes, Materials and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Islam MT, Al Mamun MA, Halim AFMF, Peila R, Sanchez Ramirez DO. Current trends in textile wastewater treatment-bibliometric review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:19166-19184. [PMID: 38383927 PMCID: PMC10927897 DOI: 10.1007/s11356-024-32454-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
A bibliometric study using 1992 to 2021 database of the Science Citation Index Expanded was carried out to identify which are the current trends in textile wastewater treatment research. The study aimed to analyze the performance of scholarly scientific communications in terms of yearly publications/citations, total citations, scientific journals, and their categories in the Web of Sciences, top institutions/countries and research trends. The annual publication of scientific articles fluctuated in the first ten years, with a steady decrease for the last twenty years. An analysis of the most common terms used in the authors' keywords, publications' titles, and KeyWords Plus was carried out to predict future trends and current research priorities. Adsorbent nanomaterials would be the future of wastewater treatment for decoloration of the residual dyes in the wastewater. Membranes and electrolysis are important to demineralize textile effluent for reusing wastewater. Modern filtration techniques such as ultrafiltration and nanofiltration are advanced membrane filtration applications.
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Affiliation(s)
- Mohammad Tajul Islam
- Department of Textile Engineering, Ahsanullah University of Science and Technology, Dhaka, Bangladesh
| | - Md Abdullah Al Mamun
- Department of Corporate Leadership and Marketing, Szechenyi Istvan University, Gyor, Hungary
| | | | - Roberta Peila
- CNR-STIIMA (National Research Council of Italy-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing), Biella, Italy
| | - Diego Omar Sanchez Ramirez
- CNR-STIIMA (National Research Council of Italy-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing), Biella, Italy.
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6
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Liu Y, Li Y, Wu H, Xu S, Zhang B, Li S, Du R, Jiang M, Chen Z, Lv Y, Wang ZG. Robust Oxidase-Mimetic Supramolecular Nanocatalyst for Lignin Biodegradation. NANO LETTERS 2024; 24:2520-2528. [PMID: 38359360 DOI: 10.1021/acs.nanolett.3c04505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Enzymatic catalysis presents an eco-friendly, energy-efficient method for lignin degradation. However, challenges arise due to the inherent incompatibility between enzymes and native lignin. In this work, we introduce a supramolecular catalyst composed of fluorenyl-modified amino acids and Cu2+, designed based on the aromatic stacking of the fluorenyl group, which can operate in ionic liquid environments suitable for the dissolution of native lignin. Amino acids and halide anions of ionic liquids shape the copper site's coordination sphere, showcasing remarkable catechol oxidase-mimetic activity. The catalyst exhibits thermophilic property, and maintains oxidative activity up to 75 °C, which allows the catalyzed degradation of the as-dissolved native lignin with high efficiency even without assistance of the electron mediator. In contrast, at this condition, the native copper-dependent oxidase completely lost its activity. This catalyst with superior stability and activity offer promise for sustainable lignin valorization through biocatalytic routes compatible with ionic liquid pretreatment, addressing limitations in native enzymes for industrially relevant conditions.
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Affiliation(s)
- Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yan Li
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Baoli Zhang
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shan Li
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ruikai Du
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Minquan Jiang
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ziman Chen
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yongqin Lv
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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7
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Xu X, Lin X, Ma W, Huo M, Tian X, Wang H, Huang L. Biodegradation strategies of veterinary medicines in the environment: Enzymatic degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169598. [PMID: 38157911 DOI: 10.1016/j.scitotenv.2023.169598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
One Health closely integrates healthy farming, human medicine, and environmental ecology. Due to the ecotoxicity and risk of transmission of drug resistance, veterinary medicines (VMs) are regarded as emerging environmental pollutants. To reduce or mitigate the environmental risk of VMs, developing friendly, safe, and effective removal technologies is an important means of environmental remediation for VMs. Many previous studies have proved that biodegradation has significant advantages in removing VMs, and biodegradation based on enzyme catalysis presents higher operability and specificity. This review focused on biodegradation strategies of environmental pollutants and reviewed the enzymatic degradation of VMs including antimicrobial drugs, insecticides, and disinfectants. We reviewed the sources and catalytic mechanisms of peroxidase, laccase, and organophosphorus hydrolases, and summarized the latest research status of immobilization methods and bioengineering techniques in improving the performance of degrading enzymes. The mechanism of enzymatic degradation for VMs was elucidated in the current research. Suggestions and prospects for researching and developing enzymatic degradation of VMs were also put forward. This review will offer new ideas for the biodegradation of VMs and have a guide significance for the risk mitigation and detoxification of VMs in the environment.
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Affiliation(s)
- Xiangyue Xu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China
| | - Xvdong Lin
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China
| | - Wenjin Ma
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China
| | - Meixia Huo
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China
| | - Xiaoyuan Tian
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China
| | - Hanyu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China; National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan 430070, China; National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
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8
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Fukuda Y, Lintuluoto M, Kurihara K, Hasegawa K, Inoue T, Tamada T. Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography. Biochemistry 2024; 63:339-347. [PMID: 38232298 DOI: 10.1021/acs.biochem.3c00517] [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: 01/19/2024]
Abstract
Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.
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Affiliation(s)
- Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Osaka, Japan
| | - Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai 319-1106, Ibaraki, Japan
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Hyogo, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita 565-0871, Osaka, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Chiba, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba 263-8552, Chiba, Japan
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9
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Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
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Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
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10
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Kumagawa E, Katsumata M, Nishimura H, Watanabe T, Ishii S, Ohta Y. The etherase system of Novosphingobium sp. MBES04 functions as a sensor of lignin fragments through phenylpropanone production to induce specific transcriptional responses. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13210. [PMID: 37950419 PMCID: PMC10866074 DOI: 10.1111/1758-2229.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023]
Abstract
The MBES04 strain of Novosphingobium accumulates phenylpropanone monomers as end-products of the etherase system, which specifically and reductively cleaves the β-O-4 ether bond (a major bond in lignin molecules). However, it does not utilise phenylpropanone monomers as an energy source. Here, we studied the response to the lignin-related perturbation to clarify the physiological significance of its etherase system. Transcriptome analysis revealed two gene clusters, each consisting of four tandemly linked genes, specifically induced by a lignin preparation extracted from hardwood (Eucalyptus globulus) and a β-O-4-type lignin model biaryl compound, but not by vanillin. The most strongly induced gene was a 2,4'-dihydroxyacetophenone dioxygenase-like protein, which leads to energy production through oxidative degradation. The other cluster was related to multidrug resistance. The former cluster was transcriptionally regulated by a common promoter, where a phenylpropanone monomer acted as one of the effectors responsible for gene induction. These results indicate that the physiological significance of the etherase system of the strain lies in its function as a sensor for lignin fragments. This may be a survival strategy to detect nutrients and gain tolerance to recalcitrant toxic compounds, while the strain preferentially utilises easily degradable aromatic compounds with lower energy demands for catabolism.
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Affiliation(s)
- Eri Kumagawa
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
| | - Madoka Katsumata
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
| | - Hiroshi Nishimura
- Research Institute for Sustainable HumanosphereKyoto UniversityUjiKyotoJapan
| | - Takashi Watanabe
- Research Institute for Sustainable HumanosphereKyoto UniversityUjiKyotoJapan
| | - Shun'ichi Ishii
- Institute for Extra‐cutting‐edge Science and Technology Avant‐garde Research (X‐star)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawaJapan
| | - Yukari Ohta
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
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11
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Kumar V, Pallavi P, Sen SK, Raut S. Harnessing the potential of white rot fungi and ligninolytic enzymes for efficient textile dye degradation: A comprehensive review. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10959. [PMID: 38204323 DOI: 10.1002/wer.10959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/27/2023] [Accepted: 11/17/2023] [Indexed: 01/12/2024]
Abstract
The contamination of wastewater with textile dyes has emerged as a pressing environmental concern due to its persistent nature and harmful effects on ecosystems. Conventional dye treatment methods have proven inadequate in effectively breaking down complex dye molecules. However, a promising alternative for textile dye degradation lies in the utilization of white rot fungi, renowned for their remarkable lignin-degrading capabilities. This review provides a comprehensive analysis of the potential of white rot fungi in degrading textile dyes, with a particular focus on their ligninolytic enzymes, specifically examining the roles of lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase in the degradation of lignin and their applications in textile dye degradation. The primary objective of this paper is to elucidate the enzymatic mechanisms involved in dye degradation, with a spotlight on recent research advancements in this field. Additionally, the review explores factors influencing enzyme production, including culture conditions and genetic engineering approaches. The challenges associated with implementing white rot fungi and their ligninolytic enzymes in textile dye degradation processes are also thoroughly examined. Textile dye contamination poses a significant environmental threat due to its resistance to conventional treatment methods. White rot fungi, known for their ligninolytic capabilities, offer an innovative approach to address this issue. The review delves into the intricate mechanisms through which white rot fungi and their enzymes, including LiP, MnP, and laccase, break down complex dye molecules. These enzymes play a pivotal role in lignin degradation, a process that can be adapted for textile dye removal. The review also emphasizes recent developments in this field, shedding light on the latest findings and innovations. It discusses how culture conditions and genetic engineering techniques can influence the production of these crucial enzymes, potentially enhancing their efficiency in textile dye degradation. This highlights the potential for tailored enzyme production to address specific dye contaminants effectively. The paper also confronts the challenges associated with integrating white rot fungi and their ligninolytic enzymes into practical textile dye degradation processes. These challenges encompass issues like scalability, cost-effectiveness, and regulatory hurdles. By acknowledging these obstacles, the review aims to pave the way for practical and sustainable applications of white rot fungi in wastewater treatment. In conclusion, this comprehensive review offers valuable insights into how white rot fungi and their ligninolytic enzymes can provide a sustainable solution to the urgent problem of textile dye-contaminated wastewater. It underscores the enzymatic mechanisms at play, recent research breakthroughs, and the potential of genetic engineering to optimize enzyme production. By addressing the challenges of implementation, this review contributes to the ongoing efforts to mitigate the environmental impact of textile dye pollution. PRACTITIONER POINTS: Ligninolytic enzymes from white rot fungi, like LiP, MnP, and laccase, are crucial for degrading textile dyes. Different dyes and enzymatic mechanisms is vital for effective wastewater treatment. Combine white rot fungi-based strategies with mediator systems, co-culturing, or sequential treatment approaches to enhance overall degradation efficiency. Emphasize the broader environmental impact of textile dye pollution and position white rot fungi as a promising avenue for contributing to mitigation efforts. This aligns with the overarching goal of sustainable wastewater treatment practices and environmental conservation. Consider scalability, cost-effectiveness, and regulatory compliance to pave the way for sustainable applications that can effectively mitigate the environmental impact of textile dye pollution.
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Affiliation(s)
- Vikas Kumar
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Preeti Pallavi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
| | | | - Sangeeta Raut
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
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12
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Khan SI, Sahinkaya M, Colak DN, Zada NS, Uzuner U, Belduz AO, Çanakçi S, Khan AZ, Khan S, Badshah M, Shah AA. Production and characterization of novel thermostable CotA-laccase from Bacillus altitudinis SL7 and its application for lignin degradation. Enzyme Microb Technol 2024; 172:110329. [PMID: 37804741 DOI: 10.1016/j.enzmictec.2023.110329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
Laccases are multi-copper oxidases and found in ligninolytic bacteria catalyzing the oxidation of both phenolic and non-phenolic compounds, however its application in lignin degradation suffers due to low oxidation rate, which have intensified the search for new laccases. In the present study, spore coat A protein (CotA) encoding gene having laccase like activity from Bacillus altitudinis SL7 (CotA-SL7) was cloned and expressed in Escherichia coli. The purified CotA-SL7 was active at wide range of temperature and pH with optimum activity at 55 °C and pH 5.0. The kinetic parameters of CotA-SL7 was determined with Km, Vmax, and kcat values 0.4 mM, 2777 μmol/min/mg, and 5194 s-1, respectively. Molecular docking revealed the presence of Pro, Phe, Asp, Asn, His, and Ile residues at the active site taking part in the oxidation of ABTS. The purified CotA-SL7 reduced lignin contents by 31 % and changes in lignin structure were analyzed through fourier transformed infrared spectroscopy (FTIR), scanning electron microsscopy (SEM) and gas chromatography mass-spectrometry (GC-MS). The appearance of low molecular size compounds clearly indicates the cleavage of lignin polymer and opening of the benzene ring by purified CotA-SL7. Thus, high catalytic efficiency of CotA-SL7 makes it a suitable bio-catalyst for remediation of lignin contaminated wastewater from pulp and paper industries with clear insights into lignin degradation at molecular level.
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Affiliation(s)
- Sanam Islam Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Miray Sahinkaya
- Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Dilsat Nigar Colak
- Giresun University, Dereli Vocational School, Department of Forestry, Giresun, Turkey
| | - Numan Saleh Zada
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Ugur Uzuner
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, Trabzon 61080, Turkey
| | - Ali Osman Belduz
- Department of Biology, Karadeniz Technical University, Trabzon, Turkey.
| | - Sabriye Çanakçi
- Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Alam Zeb Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Malik Badshah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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13
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Tanis MH, Wallberg O, Galbe M, Al-Rudainy B. Lignin Extraction by Using Two-Step Fractionation: A Review. Molecules 2023; 29:98. [PMID: 38202680 PMCID: PMC10779531 DOI: 10.3390/molecules29010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Lignocellulosic biomass represents the most abundant renewable carbon source on earth and is already used for energy and biofuel production. The pivotal step in the conversion process involving lignocellulosic biomass is pretreatment, which aims to disrupt the lignocellulose matrix. For effective pretreatment, a comprehensive understanding of the intricate structure of lignocellulose and its compositional properties during component disintegration and subsequent conversion is essential. The presence of lignin-carbohydrate complexes and covalent interactions between them within the lignocellulosic matrix confers a distinctively labile nature to hemicellulose. Meanwhile, the recalcitrant characteristics of lignin pose challenges in the fractionation process, particularly during delignification. Delignification is a critical step that directly impacts the purity of lignin and facilitates the breakdown of bonds involving lignin and lignin-carbohydrate complexes surrounding cellulose. This article discusses a two-step fractionation approach for efficient lignin extraction, providing viable paths for lignin-based valorization described in the literature. This approach allows for the creation of individual process streams for each component, tailored to extract their corresponding compounds.
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Affiliation(s)
| | | | | | - Basel Al-Rudainy
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (M.H.T.); (O.W.); (M.G.)
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14
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Silva MC, de Castro AA, Lopes KL, Ferreira IFL, Bretz RR, Ramalho TC. Combining computational tools and experimental studies towards endocrine disruptors mitigation: A review of biocatalytic and adsorptive processes. CHEMOSPHERE 2023; 344:140302. [PMID: 37788749 DOI: 10.1016/j.chemosphere.2023.140302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
The endocrine disruptors (EDCs) are an important group of emerging contaminants, and their mitigation has been a huge challenge due to their chemistry complexity and variety of these compounds. The traditional treatments are inefficient to completely remove EDCs, and adsorptive processes are the major alternative investigated on their removal. Also, the use of EDCs degrading enzymes has been encouraged due to ecofriendly approach of biocatalytic processes. This paper highlights the occurrence, classification, and toxicity of EDCs with special focus in the use of enzyme-based and adsorptive technologies in the elimination of EDCs from ambiental matrices. Numerous prior reviews have focused on the discussions toward these technologies. However, the literature lacks theoretical discussions about important aspects of these methods such as the mechanisms of EDCs adsorption on the adsorbent surface or the interactions between degrading enzymes - EDCs. In this sense, theoretical calculations combined to experimental studies may help in the development of more efficient technologies to EDCs mitigation. In this review, we point out how computational tools such as molecular docking and molecular dynamics have to contribute to the design of new adsorbents and efficient catalytic processes towards endocrine disruptors mitigation.
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Affiliation(s)
- Maria Cristina Silva
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil.
| | | | - Karla Lara Lopes
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Igor F Lara Ferreira
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Raphael Resende Bretz
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
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15
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Lu H, Xue M, Nie X, Luo H, Tan Z, Yang X, Shi H, Li X, Wang T. Glycoside hydrolases in the biodegradation of lignocellulosic biomass. 3 Biotech 2023; 13:402. [PMID: 37982085 PMCID: PMC10654287 DOI: 10.1007/s13205-023-03819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 11/21/2023] Open
Abstract
Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03819-1.
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Affiliation(s)
- Honglin Lu
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Maoyuan Xue
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xinling Nie
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Hongzheng Luo
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Zhongbiao Tan
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xiao Yang
- Department of Poultry Science, The University of Georgia, Athens, GA 30602 USA
| | - Hao Shi
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Tao Wang
- Department of Microbiology, The University of Georgia, Athens, GA 30602 USA
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16
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Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
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Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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17
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Yong KJ, Wu TY. Recent advances in the application of alcohols in extracting lignin with preserved β-O-4 content from lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2023; 384:129238. [PMID: 37245662 DOI: 10.1016/j.biortech.2023.129238] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Utilizing lignocellulosic biomass wastes to produce bioproducts is essential to address the reliance on depleting fossil fuels. However, lignin is often treated as a low-value-added component in lignocellulosic wastes. Valorization of lignin into value-added products is crucial to improve the economic competitiveness of lignocellulosic biorefinery. Monomers obtained from lignin depolymerization could be upgraded into fuel-related products. However, lignins obtained from conventional methods are low in β-O-4 content and, therefore, unsuitable for monomer production. Recent literature has demonstrated that lignins extracted with alcohol-based solvents exhibit preserved structures with high β-O-4 content. This review discusses the recent advances in utilizing alcohols to extract β-O-4-rich lignin, where discussion based on different alcohol groups is considered. Emerging strategies in employing alcohols for β-O-4-rich lignin extraction, including alcohol-based deep eutectic solvent, flow-through fractionation, and microwave-assisted fractionation, are reviewed. Finally, strategies for recycling or utilizing the spent alcohol solvents are also discussed.
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Affiliation(s)
- Khai Jie Yong
- Department of Chemical Engineering, School of Engineering, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Ta Yeong Wu
- Department of Chemical Engineering, School of Engineering, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; Monash-Industry Plant Oils Research Laboratory (MIPO), School of Engineering, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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18
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Wei T, Chen H, Wu D, Gao D, Cai Y, Cao X, Xu H, Yang J, Guo P. Response surface methodology for the mixed fungal fermentation of Codonopsis pilosula straw using Trichoderma reesei and Coprinus comatus. PeerJ 2023; 11:e15757. [PMID: 37601264 PMCID: PMC10434135 DOI: 10.7717/peerj.15757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/26/2023] [Indexed: 08/22/2023] Open
Abstract
The objective of this study was to investigate the cellulose degradation rate (CDR) and lignin degradation rate (LDR) of Codonopsis pilosula straw (CPS) and the optimal fermentation parameters for mixed fungal fermentation. Single-factor tests were used to study the effects of the fungal ratio (Trichoderma reesei: Coprinus comatus), fungal inoculum, corn flour content, and fermentation time on the degradation rate of cellulose and lignin. Based on the results of this experiment, the optimal fermentation factors were identified, and the effects of various factors and their interactions on the degradation rates of cellulose and lignin were further evaluated using the response surface method. The quadratic polynomial mathematical model of degradation rates of the cellulose and lignin in CPS by mixed fungus fermentation was established using Design Expert software v8.0.6. Under the optimal parameters for fungal fermentation of CPS straw (fungal ratio 4:6, fungal inoculum 8%, corn flour content 10%, fermentation time of 15 d), the CDR and LDR reached 13.65% and 10.73%, respectively. Collectively, the mixed fungal fermentation of CPS resulted in decreased lignin and cellulose content, better retention of nutrients, and enhanced fermentation quality. The results of this study indicate that fermentation using Trichoderma reesei and Coprinus comatus is a productive method for straw degradation, providing a theoretical basis for the development of CPS as feed.
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Affiliation(s)
- Ti Wei
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Hongfu Chen
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Dengyu Wu
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
- Taizishan Ecosystem Observatory of Carbon Neutralization, Northwest Minzu University, Lanzhou, Gansu, China
| | - Dandan Gao
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Taizishan Ecosystem Observatory of Carbon Neutralization, Northwest Minzu University, Lanzhou, Gansu, China
- Institute of Livestock and Poultry Genetic Resources Conservation and Utilization of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yong Cai
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
- Taizishan Ecosystem Observatory of Carbon Neutralization, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xin Cao
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
- Institute of Livestock and Poultry Genetic Resources Conservation and Utilization of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Hongwei Xu
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Institute of Livestock and Poultry Genetic Resources Conservation and Utilization of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jutian Yang
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
- Institute of Livestock and Poultry Genetic Resources Conservation and Utilization of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
| | - Penghui Guo
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
- Ecological Industry Development Research Institute of the Upper Yellow River, Northwest Minzu University, Lanzhou, Gansu, China
- Taizishan Ecosystem Observatory of Carbon Neutralization, Northwest Minzu University, Lanzhou, Gansu, China
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19
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Wu F, Guo Z, Cui K, Dong D, Yang X, Li J, Wu Z, Li L, Dai Y, Pan T. Insights into characteristics of white rot fungus during environmental plastics adhesion and degradation mechanism of plastics. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130878. [PMID: 36731319 DOI: 10.1016/j.jhazmat.2023.130878] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Since the 1980s, plastic waste in the environment has been accumulating, and little is known about fungi biodegradation, especially in dry environments. Therefore, the research on plastic degradation technology is urgent. In this study, we demonstrated that Phanerochaete chrysosporium (P. chrysposporium), a typical species of white rot fungi, could react as a highly efficient biodegrader of polylactic acid (PLA), and 34.35 % of PLA degradation was obtained during 35-day incubation. A similar mass loss of 19.71 % could be achieved for polystyrene (PS) degradation. Here, we presented the visualization of the plastic deterioration process and their negative reciprocal on cell development, which may be caused by the challenge of using PS as a substrate. The RNA-seq analysis indicated that adaptations in energy metabolism and cellular defense were downregulated in the PS group, while lipid synthesis was upregulated in the PLA-treated group. Possible differentially expressed genes (DEG) of plastic degradation, such as hydrophobic proteins, lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac), Cytochrome P450 (CYP450), and genes involved in styrene or benzoic acid degradation pathways have been recorded, and we proposed a PS degradation pathway.
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Affiliation(s)
- Feiyan Wu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Zhi Guo
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China.
| | - Kangping Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Dazhuang Dong
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Xue Yang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Jie Li
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Zhangzhen Wu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Lele Li
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Yaodan Dai
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
| | - Tao Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei 230009, China
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20
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Shanthi Kumari BS, Kumar KD, Golla N, Krishna SBN, Geetha KS, Vyshnava SS, Reddy BR. Effect of lignocellulosic materials and chlorpyrifos pesticide on secretion of ligninolytic enzymes by the white rot fungus – Stereum ostrea. BIOREMEDIATION JOURNAL 2023; 27:147-157. [DOI: 10.1080/10889868.2022.2029823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- B. S. Shanthi Kumari
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh, India
| | - Kanderi Dileep Kumar
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh, India
| | - Narasimha Golla
- Department of Virology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Suresh Babu Naidu Krishna
- Department of Biomedical and Clinical Technology, Durban University of Technology, Durban, South Africa
| | - K. Sai Geetha
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh, India
| | | | - B. Rajasekhar Reddy
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh, India
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21
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Harrison TR, Gupta VK, Alam P, Perriman AW, Scarpa F, Thakur VK. From trash to treasure: Sourcing high-value, sustainable cellulosic materials from living bioreactor waste streams. Int J Biol Macromol 2023; 233:123511. [PMID: 36773882 DOI: 10.1016/j.ijbiomac.2023.123511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/16/2023] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
The appreciation of how conventional and fossil-based materials could be harmful to our planet is growing, especially when considering single-use and non-biodegradable plastics manufactured from fossil fuels. Accordingly, tackling climate change and plastic waste pollution entails a more responsible approach to sourcing raw materials and the adoption of less destructive end-of-life pathways. Livestock animals, in particular ruminants, process plant matter using a suite of mechanical, chemical and biological mechanisms through the act of digestion. The manure from these "living bioreactors" is ubiquitous and offers a largely untapped source of lignocellulosic biomass for the development of bio-based and biodegradable materials. In this review, we assess recent studies made into manure-based cellulose materials in terms of their material characteristics and implications for sustainability. Despite the surprisingly diverse body of research, it is apparent that progress towards the commercialisation of manure-derived cellulose materials is hindered by a lack of truly sustainable options and robust data to assess the performance against conventional materials alternatives. Nanocellulose, a natural biopolymer, has been successfully produced by living bioreactors and is presented as a candidate for future developments. Life cycle assessments from non-wood sources are however minimal, but there are some initial indications that manure-derived nanocellulose would offer environmental benefits over traditional wood-derived sources.
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Affiliation(s)
- Thomas R Harrison
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Institute for Materials and Processes, The University of Edinburgh, Edinburgh, UK
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Parvez Alam
- Institute for Materials and Processes, The University of Edinburgh, Edinburgh, UK
| | - Adam Willis Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; John Curtain School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Fabrizio Scarpa
- Bristol Composites Institute, University of Bristol, Bristol BS8 1TR, UK
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; School of Engineering, University of Petroleum & Energy Studies (UPES), Dehradun 248007, Uttarakhand, India.
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22
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Abdullah T, İlyasoğlu G, Memić A. Designing Lignin-Based Biomaterials as Carriers of Bioactive Molecules. Pharmaceutics 2023; 15:pharmaceutics15041114. [PMID: 37111600 PMCID: PMC10143462 DOI: 10.3390/pharmaceutics15041114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
There is a need to develop circular and sustainable economies by utilizing sustainable, green, and renewable resources in high-tech industrial fields especially in the pharmaceutical industry. In the last decade, many derivatives of food and agricultural waste have gained considerable attention due to their abundance, renewability, biocompatibility, environmental amiability, and remarkable biological features. Particularly, lignin, which has been used as a low-grade burning fuel in the past, recently attracted a lot of attention for biomedical applications because of its antioxidant, anti-UV, and antimicrobial properties. Moreover, lignin has abundant phenolic, aliphatic hydroxyl groups, and other chemically reactive sites, making it a desirable biomaterial for drug delivery applications. In this review, we provide an overview of designing different forms of lignin-based biomaterials, including hydrogels, cryogels, electrospun scaffolds, and three-dimensional (3D) printed structures and how they have been used for bioactive compound delivery. We highlight various design criteria and parameters that influence the properties of each type of lignin-based biomaterial and corelate them to various drug delivery applications. In addition, we provide a critical analysis, including the advantages and challenges encountered by each biomaterial fabrication strategy. Finally, we highlight the prospects and future directions associated with the application of lignin-based biomaterials in the pharmaceutical field. We expect that this review will cover the most recent and important developments in this field and serve as a steppingstone for the next generation of pharmaceutical research.
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23
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Islam S, Cullen JM. Criteria for Assessing Sustainability of Lignocellulosic Wastes: Applied to the Cellulose Nanofibril Packaging Production in the UK. Polymers (Basel) 2023; 15:polym15061336. [PMID: 36987116 PMCID: PMC10053347 DOI: 10.3390/polym15061336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
Extensive use of petrochemical plastic packaging leads to the greenhouse gas emission and contamination to soil and oceans, posing major threats to the ecosystem. The packaging needs, hence, are shifting to bioplastics with natural degradability. Lignocellulose, the biomass from forest and agriculture, can produce cellulose nanofibrils (CNF), a biodegradable material with acceptable functional properties, that can make packaging among other products. Compared to primary sources, CNF extracted from lignocellulosic wastes reduces the feedstock cost without causing an extension to agriculture and associated emissions. Most of these low value feedstocks go to alternative applications, making their use in CNF packaging competitive. To transfer the waste materials from current practices to the packaging production, it is imperative to assess their sustainability, encompassing environmental and economic impacts along with the feedstock physical and chemical properties. A combined overview of these criteria is absent in the literature. This study consolidates thirteen attributes, delineating sustainability of lignocellulosic wastes for commercial CNF packaging production. These criteria data are gathered for the UK waste streams, and transformed into a quantitative matrix, evaluating the waste feedstock sustainability for CNF packaging production. The presented approach can be adopted to decision scenarios in bioplastics packaging conversion and waste management.
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24
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Fang W, Feng S, Jiang Z, Liang W, Li P, Wang B. Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS AU 2023; 3:536-549. [PMID: 36873691 PMCID: PMC9976348 DOI: 10.1021/jacsau.2c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
pH buffer plays versatile roles in both biology and chemistry. In this study, we unravel the critical role of pH buffer in accelerating degradation of the lignin substrate in lignin peroxidase (LiP) using QM/MM MD simulations and the nonadiabatic electron transfer (ET) and proton-coupled electron transfer (PCET) theories. As a key enzyme involved in lignin degradation, LiP accomplishes the oxidation of lignin via two consecutive ET reactions and the subsequent C-C cleavage of the lignin cation radical. The first one involves ET from Trp171 to the active species of Compound I, while the second one involves ET from the lignin substrate to the Trp171 radical. Differing from the common view that pH = 3 may enhance the oxidizing power of Cpd I via protonation of the protein environment, our study shows that the intrinsic electric fields have minor effects on the first ET step. Instead, our study shows that the pH buffer of tartaric acid plays key roles during the second ET step. Our study shows that the pH buffer of tartaric acid can form a strong H-bond with Glu250, which can prevent the proton transfer from the Trp171-H•+ cation radical to Glu250, thereby stabilizing the Trp171-H•+ cation radical for the lignin oxidation. In addition, the pH buffer of tartaric acid can enhance the oxidizing power of the Trp171-H•+ cation radical via both the protonation of the proximal Asp264 and the second-sphere H-bond with Glu250. Such synergistic effects of pH buffer facilitate the thermodynamics of the second ET step and reduce the overall barrier of lignin degradation by ∼4.3 kcal/mol, which corresponds to a rate acceleration of 103-fold that agrees with experiments. These findings not only expand our understanding on pH-dependent redox reactions in both biology and chemistry but also provide valuable insights into tryptophan-mediated biological ET reactions.
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Affiliation(s)
- Wenhan Fang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Shishi Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Zhihui Jiang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Wanzhen Liang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Pengfei Li
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1068 W. Sheridan Rd., Chicago, Illinois60660, United States
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
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Characterization of Fungal Foams from Edible Mushrooms Using Different Agricultural Wastes as Substrates for Packaging Material. Polymers (Basel) 2023; 15:polym15040873. [PMID: 36850157 PMCID: PMC9966758 DOI: 10.3390/polym15040873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Agricultural wastes and leaves, which are classified as lignocellulosic biomass, have been used as substrates in the production of fungal foams due to the significant growth of the mushroom industry in recent years. Foam derived from fungi can be utilized in a variety of industrial applications, including the production of packaging materials. Here, white oyster mushrooms (Pleurotus florida) and yellow oyster mushrooms (Pleurotus citrinopileatus) were cultivated on rice husk, sawdust, sugarcane bagasse, and teak leaves. Fungal foams were produced after 30 days of incubation, which were then analyzed using scanning electron microscopy (SEM), thermal analysis (TGA), and chemical structure using Fourier-transform infrared spectroscopy. Mechanical testing examined the material's hardness, resilience, and springiness, and water absorption tests were used to determine the durability of the fungal foams. Our findings demonstrated that fungal foams made from rice husk and teak leaves in both mycelium species showed better mechanical properties, thermal stability, and minimal water absorption compared to the other substrates, and can thus have great potential as efficient packaging materials.
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26
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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27
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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28
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Sun S, Liu P, Ullah M. Efficient Azo Dye Biodecolorization System Using Lignin-Co-Cultured White-Rot Fungus. J Fungi (Basel) 2023; 9:jof9010091. [PMID: 36675912 PMCID: PMC9866751 DOI: 10.3390/jof9010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
The extensive use of azo dyes by the global textile industry induces significant environmental and human health hazards, which makes efficient remediation crucial but also challenging. Improving dye removal efficiency will benefit the development of bioremediation techniques for textile effluents. In this study, an efficient system for azo dye (Direct Red 5B, DR5B) biodecolorization is reported, which uses the white-rot fungus Ganoderma lucidum EN2 and alkali lignin. This study suggests that the decolorization of DR5B could be effectively enhanced (from 40.34% to 95.16%) within 48 h in the presence of alkali lignin. The dye adsorption test further confirmed that the alkali-lignin-enhanced decolorization of DR5B was essentially due to biodegradation rather than physical adsorption, evaluating the role of alkali lignin in the dye biodegradation system. Moreover, the gas chromatography/mass spectrometry analysis and DR5B decolorization experiments also indicated that alkali lignin carried an excellent potential for promoting dye decolorization and displayed a significant role in improving the activity of lignin-modifying enzymes. This was mainly because of the laccase-mediator system, which was established by the induced laccase activity and lignin-derived small aromatic compounds.
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Affiliation(s)
- Su Sun
- College of Urban Construction, Wuchang Shouyi University, Wuhan 430064, China
- Key Laboratory of Molecular Biophysics of MOE, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Correspondence:
| | - Pengyang Liu
- Key Laboratory of Molecular Biophysics of MOE, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Key Laboratory of Molecular Biophysics of MOE, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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29
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Bioethanol Production from Lignocellulosic Biomass-Challenges and Solutions. Molecules 2022; 27:molecules27248717. [PMID: 36557852 PMCID: PMC9785513 DOI: 10.3390/molecules27248717] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Regarding the limited resources for fossil fuels and increasing global energy demands, greenhouse gas emissions, and climate change, there is a need to find alternative energy sources that are sustainable, environmentally friendly, renewable, and economically viable. In the last several decades, interest in second-generation bioethanol production from non-food lignocellulosic biomass in the form of organic residues rapidly increased because of its abundance, renewability, and low cost. Bioethanol production fits into the strategy of a circular economy and zero waste plans, and using ethanol as an alternative fuel gives the world economy a chance to become independent of the petrochemical industry, providing energy security and environmental safety. However, the conversion of biomass into ethanol is a challenging and multi-stage process because of the variation in the biochemical composition of biomass and the recalcitrance of lignin, the aromatic component of lignocellulose. Therefore, the commercial production of cellulosic ethanol has not yet become well-received commercially, being hampered by high research and production costs, and substantial effort is needed to make it more widespread and profitable. This review summarises the state of the art in bioethanol production from lignocellulosic biomass, highlights the most challenging steps of the process, including pretreatment stages required to fragment biomass components and further enzymatic hydrolysis and fermentation, presents the most recent technological advances to overcome the challenges and high costs, and discusses future perspectives of second-generation biorefineries.
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30
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Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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31
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Gong X, Yu Y, Hao Y, Wang Q, Ma J, Jiang Y, Lv G, Li L, Qian C. Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments. Front Microbiol 2022; 13:1003157. [PMID: 36545193 PMCID: PMC9760696 DOI: 10.3389/fmicb.2022.1003157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/10/2022] Open
Abstract
Corn straw is an abundant lignocellulose resource and by-product of agricultural production. With the continuous increase in agricultural development, the output of corn straw is also increasing significantly. However, the inappropriate disposal of straw results in wasting of resources, and also causes a serious ecological crisis. Screening microorganisms with the capacity to degrade straw and understanding their mechanism of action is an efficient approach to solve such problems. For this purpose, our research group isolated three actinomycete strains with efficient lignocellulose degradation ability from soil in the cold region of China: Streptomyces sp. G1T, Streptomyces sp. G2T and Streptomyces sp. G3T. Their microbial properties and taxonomic status were assessed to improve our understanding of these strains. The three strains showed typical characteristics of the genus Streptomyces, and likely represent three different species. Genome functional annotation indicated that most of their genes were related to functions like carbohydrate transport and metabolism. In addition, a similar phenomenon also appeared in the COG and CAZyme analyses, with a large number of genes encoding carbohydrate-related hydrolases, such as cellulase, glycosidase and endoglucanase, which could effectively destroy the structure of lignocellulose in corn straw. This unambiguously demonstrated the potential of the three microorganisms to hydrolyze macromolecular polysaccharides at the molecular level. In addition, in the straw-returning test, the decomposing consortium composed of the three Streptomyces isolates (G123) effectively destroyed the recalcitrant bonds between the various components of straw, and significantly reduced the content of active components in corn straw. Furthermore, microbial diversity analysis indicated that the relative abundance of Proteobacteria, reportedly associated with soil antibiotic resistance and antibiotic degradation, was significantly improved with straw returning at both tested time points. The microbial diversity of each treatment was also dramatically changed by supplementing with G123. Taken together, G123 has important biological potential and should be further studied, which will provide new insights and strategies for appropriate treatment of corn straw.
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Affiliation(s)
- Xiujie Gong
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yang Yu
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yubo Hao
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiuju Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Juntao Ma
- Institute of Biotechnology, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yubo Jiang
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guoyi Lv
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liang Li
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chunrong Qian
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China,*Correspondence: Chunrong Qian,
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32
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Civzele A, Mezule L. Microalgae Harvesting after Tertiary Wastewater Treatment with White-Rot Fungi. J Fungi (Basel) 2022; 8:1232. [PMID: 36422053 PMCID: PMC9697617 DOI: 10.3390/jof8111232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 07/28/2023] Open
Abstract
Tertiary wastewater treatment with microalgae incorporates environmental sustainability with future technologies and high exploitation costs. Despite the apparent ecological benefits of microalgae-assisted wastewater treatment/biomass-based resource production, technological improvements are still essential to compete with other technologies. Bio-flocculation instead of mechanical harvesting has been demonstrated as an alternative cost-effective approach. So far, mostly filamentous fungi of genus Aspergillus have been used for this purpose. Within this study, we demonstrate a novel approach of using white-rot fungi, with especially high potential of algae-Irpex lacteus complex that demonstrates efficiency with various microalgae species at a broad range of temperatures (5-20 °C) and various pH levels. Harvesting of microalgae from primary and secondary wastewater resulted in 73-93% removal efficiencies within the first 24 h and up to 95% after 48 h. The apparent reuse potential of the algae-I. lacteus pellets further complements the reduced operating costs and environmental sustainability of bio-flocculation technology.
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33
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Electrochemical Valorization of Lignin: Status, Challenges, and Prospects. JOURNAL OF BIORESOURCES AND BIOPRODUCTS 2022. [DOI: 10.1016/j.jobab.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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da Costa RMF, Bosch M, Simister R, Gomez LD, Canhoto JM, Batista de Carvalho LAE. Valorisation Potential of Invasive Acacia dealbata, A. longifolia and A. melanoxylon from Land Clearings. Molecules 2022; 27:7006. [PMID: 36296599 PMCID: PMC9610895 DOI: 10.3390/molecules27207006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 08/02/2023] Open
Abstract
Acacia spp. are invasive in Southern Europe, and their high propagation rates produce excessive biomass, exacerbating wildfire risk. However, lignocellulosic biomass from Acacia spp. may be utilised for diverse biorefinery applications. In this study, attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR), high-performance anion-exchange chromatography pulsed amperometric detection (HPAEC-PAD) and lignin content determinations were used for a comparative compositional characterisation of A. dealbata, A. longifolia and A. melanoxylon. Additionally, biomass was treated with three white-rot fungi species (Ganoderma lucidum, Pleurotus ostreatus and Trametes versicolor), which preferentially degrade lignin. Our results showed that the pre-treatments do not significantly alter neutral sugar composition while reducing lignin content. Sugar release from enzymatic saccharification was enhanced, in some cases possibly due to a synergy between white-rot fungi and mild alkali pretreatments. For example, in A. dealbata stems treated with alkali and P. ostreatus, saccharification yield was 702.3 nmol mg-1, which is higher than the samples treated only with alkali (608.1 nmol mg-1), and 2.9-fold higher than the non-pretreated controls (243.9 nmol mg-1). By characterising biomass and pretreatments, generated data creates value for unused biomass resources, contributing to the implementation of sustainable biorefining systems. In due course, the generated value will lead to economic incentives for landowners to cut back invasive Acacia spp. more frequently, thus reducing excess biomass, which exacerbates wildfire risk.
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Affiliation(s)
- Ricardo M. F. da Costa
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EE, UK
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Jorge M. Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís A. E. Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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Kielb PJ, Teutloff C, Bittl R, Gray HB, Winkler JR. Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site? J Phys Chem B 2022; 126:7943-7949. [PMID: 36191240 PMCID: PMC10231039 DOI: 10.1021/acs.jpcb.2c04835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.
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Affiliation(s)
- Patrycja J. Kielb
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | | | - Robert Bittl
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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37
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Valorization of Lignin and Its Derivatives Using Yeast. Processes (Basel) 2022. [DOI: 10.3390/pr10102004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As the third most plentiful biopolymer after other lignocellulosic derivates such as cellulose and hemicellulose, lignin carries abundant potential as a substitute for petroleum-based products. However, the efficient, practical, value-added product valorization of lignin remains quite challenging. Although several studies have reviewed the valorization of lignin by microorganisms, this present review covers recent studies on the valorization of lignin by employing yeast to obtain products such as single-cell oils (SCOs), enzymes, and other chemical compounds. The use of yeasts has been found to be suitable for the biological conversion of lignin and might provide new insights for future research to develop a yeast strain for lignin to produce other valuable chemical compounds.
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38
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Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186055. [PMID: 36144795 PMCID: PMC9500909 DOI: 10.3390/molecules27186055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/27/2022]
Abstract
The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.
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Torres-García JL, Ahuactzin-Pérez M, Fernández FJ, Cortés-Espinosa DV. Bisphenol A in the environment and recent advances in biodegradation by fungi. CHEMOSPHERE 2022; 303:134940. [PMID: 35588877 DOI: 10.1016/j.chemosphere.2022.134940] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA) is a compound used in the manufacture of a wide variety of everyday materials that, when released into the environment, causes multiple detrimental effects on humans and other organisms. The reason for this review is to provide an overview of the presence, distribution, and concentration of BPA in water, soil, sediment, and air, as well as the process of release and migration, biomagnification, and exposure mechanisms that cause various toxic effects in humans. Therefore, it is important to seek efficient and economic strategies that allow its removal from the environment and prevent it from reaching humans through food chains. Likewise, the main removal techniques are analyzed, focusing on biological treatments, particularly the most recent advances in the degradation of BPA in different environmental matrices through the use of ligninolytic fungi, non-ligninolytic fungi and yeasts, as well as the possible routes of metabolic processes that allow their biotransformation or biodegradation due to their efficient extracellular enzyme systems. This review supports the importance of the application of new biotechnological tools for the degradation of BPA.
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Affiliation(s)
- J L Torres-García
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, 09340, Ciudad de México, México
| | - M Ahuactzin-Pérez
- Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, Autopista Tlaxcala-San Martín Km 10.5, 90120, San Felipe Ixtacuixtla, Tlaxcala, Mexico
| | - F J Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Vicentina, 09340, Ciudad de México, México
| | - Diana V Cortés-Espinosa
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada. Carretera Estatal San Inés Tecuexcomac-Tepetitla Km 1.5, 90700, Tepetitla de Lardizabal, Tlaxcala, Mexico.
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40
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Ali NS, Huang F, Qin W, Yang TC. Identification and Characterization of a New Serratia proteamaculans Strain That Naturally Produces Significant Amount of Extracellular Laccase. Front Microbiol 2022; 13:878360. [PMID: 35923404 PMCID: PMC9339997 DOI: 10.3389/fmicb.2022.878360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Natural biodegradation processes hold promises for the conversion of agro-industrial lignocellulosic biomaterials into biofuels and fine chemicals through lignin-degrading enzymes. The high cost and low stability of these enzymes remain a significant challenge to economic lignocellulosic biomass conversion. Wood-degrading microorganisms are a great source for novel enzyme discoveries. In this study, the decomposed wood samples were screened, and a promising γ-proteobacterial strain that naturally secreted a significant amount of laccase enzyme was isolated and identified as Serratia proteamaculans AORB19 based on its phenotypic and genotypic characteristics. The laccase activities in culture medium of strain AORB19 were confirmed both qualitatively and quantitatively. Significant cultural parameters for laccase production under submerged conditions were identified following a one-factor-at-a-time (OFAT) methodology: temperature 30°C, pH 9, yeast extract (2 g/l), Li+, Cu2+, Ca2+, and Mn2+ (0.5 mM), and acetone (5%). Under the selected conditions, a 6-fold increase (73.3 U/L) in laccase production was achieved when compared with the initial culturing conditions (12.18 U/L). Furthermore, laccase production was enhanced under alkaline and mesophilic growth conditions in the presence of metal ions and organic solvents. The results of the study suggest the promising potential of the identified strain and its enzymes in the valorization of lignocellulosic wastes. Further optimization of culturing conditions to enhance the AORB19 strain laccase secretion, identification and characterization of the purified enzyme, and heterologous expression of the specific enzyme may lead to practical industrial and environmental applications.
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Affiliation(s)
- Nadia Sufdar Ali
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
| | - Fang Huang
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
- *Correspondence: Wensheng Qin
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
- Trent Chunzhong Yang
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41
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Rai R, Dhar P. Biomedical engineering aspects of nanocellulose: a review. NANOTECHNOLOGY 2022; 33:362001. [PMID: 35576914 DOI: 10.1088/1361-6528/ac6fef] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Cellulose is one of the most abundant renewable biopolymer in nature and is present as major constituent in both plant cell walls as well as synthesized by some microorganisms as extracellular products. In both the systems, cellulose self-assembles into a hierarchical ordered architecture to form micro to nano-fibrillated structures, on basis of which it is classified into various forms. Nanocellulose (NCs) exist as rod-shaped highly crystalline cellulose nanocrystals to high aspect ratio cellulose nanofibers, micro-fibrillated cellulose and bacterial cellulose (BC), depending upon the origin, structural and morphological properties. Moreover, NCs have been processed into diversified products ranging from composite films, coatings, hydrogels, aerogels, xerogels, organogels, rheological modifiers, optically active birefringent colored films using traditional-to-advanced manufacturing techniques. With such versatility in structure-property, NCs have profound application in areas of healthcare, packaging, cosmetics, energy, food, electronics, bioremediation, and biomedicine with promising commercial potential. Herein this review, we highlight the recent advancements in synthesis, fabrication, processing of NCs, with strategic chemical modification routes to tailor its properties for targeted biomedical applications. We also study the basic mechanism and models for biosynthesis of cellulose in both plant and microbial systems and understand the structural insights of NC polymorphism. The kinetics study for both enzymatic/chemical modifications of NCs and microbial growth behavior of BC under various reactor configurations are studied. The challenges associated with the commercial aspects as well as industrial scale production of pristine and functionalized NCs to meet the growing demands of market are discussed and prospective strategies to mitigate them are described. Finally, post chemical modification evaluation of biological and inherent properties of NC are important to determine their efficacy for development of various products and technologies directed for biomedical applications.
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Affiliation(s)
- Rohit Rai
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh-221005, India
| | - Prodyut Dhar
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh-221005, India
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42
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Kuthiala T, Thakur K, Sharma D, Singh G, Khatri M, Arya SK. The eco-friendly approach of cocktail enzyme in agricultural waste treatment: A comprehensive review. Int J Biol Macromol 2022; 209:1956-1974. [PMID: 35500773 DOI: 10.1016/j.ijbiomac.2022.04.173] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/17/2022] [Accepted: 04/24/2022] [Indexed: 12/26/2022]
Abstract
Agricultural development over the past decade has majorly contributed to the world's bioeconomy, but is the rise in agricultural activities just resulting in the best? Farming, food processing, livestock handling and other agro-based actions show an incremental rise in environmental deterioration by generating millions of tonnes of organic and inorganic solid waste across the globe. Incautious waste handling practices (incineration and landfilling) is resulting in greenhouse gas emissions, land pollution, groundwater contamination, soil erosion and chronic health hazards. Lately the concept of bioconversion has gained importance in valorising agro-waste (lignocellulosic biomasses) into value added products like biofuels, biogas, single cell proteins and biochar to effectively control waste and reduce the dependency on non-renewable feedstocks (fossil fuels). Biomass hydrolysis via enzymes is improved in terms of cost, efficiency, catalysis, stability and specificity by enrolling the use of enzyme cocktails to synergistically degrade lignocellulose into monomeric sugars and further into valued products. Enzyme blends like that of Xylanase + Pectinase + Cellulase shows 76.5% fermentation within 30 h by using banana peel as substrate for biofuel production. Other sectors like paper industries have also explored the use of enzyme blends of Xylanase + Pectinase + α-amylase + Protease+ lipase for bio-bleaching showing reduction in 50% chemical usage and 19.5% kappa number with adjacent increase in tensile strength by 23.55%. The scope of the present review is to highlight the technicalities of the concepts mentioned above, include qualitative data from different relatable studies and prove how the use of enzyme cocktails is an eco-friendly approach towards agro-waste management.
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Affiliation(s)
- Tanya Kuthiala
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, INDIA
| | - Kritika Thakur
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, INDIA
| | - Dharini Sharma
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, INDIA
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Madhu Khatri
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, INDIA
| | - Shailendra Kumar Arya
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, INDIA.
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Mao Z, Yang P, Liu H, Mao Y, Lei Y, Hou D, Ma H, Liao X, Jiang W. Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis. Front Microbiol 2022; 13:880946. [PMID: 35685935 PMCID: PMC9171200 DOI: 10.3389/fmicb.2022.880946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Ceriporia lacerata is an endophytic white-rot fungus that has lignocellulolytic and terpenoid-biosynthetic abilities. However, little is known about the genomic architecture of this fungus, even at the genus level. In this study, we present the first de novo genome assembly of C. lacerata (CGMCC No. 10485), based on PacBio long-read and Illumina short-read sequencing. The size of the C. lacerata genome is approximately 36 Mb (N50, 3.4 Mb). It encodes a total of 13,243 genes, with further functional analysis revealing that these genes are primarily involved in primary metabolism and host interactions in this strain's saprophytic lifestyle. Phylogenetic analysis based on ITS demonstrated a primary evolutionary position for C. lacerata, while the phylogenetic analysis based on orthogroup inference and average nucleotide identity revealed high-resolution phylogenetic details in which Ceriporia, Phlebia, Phlebiopsis, and Phanerochaete belong to the same evolutionary clade within the order Polyporales. Annotation of carbohydrate-active enzymes across the genome yielded a total of 806 genes encoding enzymes that decompose lignocellulose, particularly ligninolytic enzymes, lytic polysaccharides monooxygenases, and enzymes involved in the biodegradation of aromatic components. These findings illustrate the strain's adaptation to woody habitats, which requires the degradation of lignin and various polycyclic aromatic hydrocarbons. The terpenoid-production potential of C. lacerata was evaluated by comparing the genes of terpenoid biosynthetic pathways across nine Polyporales species. The shared genes highlight the major part of terpenoid synthesis pathways, especially the mevalonic acid pathway, as well as the main pathways of sesquiterpenoid, monoterpenoid, diterpenoid, and triterpenoid synthesis, while the strain-specific genes illustrate the distinct genetic factors determining the synthesis of structurally diverse terpenoids. This is the first genomic analysis of a species from this genus that we are aware of, and it will help advance functional genome research and resource development of this important fungus for applications in renewable energy, pharmaceuticals, and agriculture.
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Affiliation(s)
- Zhitao Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ping Yang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Lei
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongwei Hou
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wenxia Jiang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Recent advances in the treatment of lignin in papermaking wastewater. World J Microbiol Biotechnol 2022; 38:116. [PMID: 35593964 DOI: 10.1007/s11274-022-03300-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
More than 695.7 million m3 of papermaking wastewater is discharged globally. It contains a mixture of complex pollutants, of which lignin is the major constituent (600-1000 mg/L) of papermaking black liquor, making it the second-largest energy-containing biomass globally and accounting for 47.4% and 59.4% of chemical oxygen demand (16,400 ± 120 mg/L) and chroma (3100 ± 22.32 mg/L) of papermaking wastewater. The complex process and dissolved pollutants are responsible for high pH, biochemical oxygen demand, chemical oxygen demand, total suspended solids, dark color, and toxicity. Papermaking wastewater has emerged as a substantial source of environmental pollution as the conventional wastewater treatment processes are high cost and seldom efficacious. This work introduces the shortcomings of the common treatment methods for papermaking wastewater and lignin, focusing on lignin biodegradation and discussing the metabolic pathways and application prospects of lignin-degrading microbial species. A comprehensive review of the existing lignin treatment methods has proposed that the reasonable amalgamation of biodegradation and various physicochemical techniques are environmentally friendly, sustainable, and economical. Lignin extraction from papermaking wastewater by technology combination is an effective approach to recover valuable organic materials and detoxify wastewater. This review focuses on recent breakthroughs and future trends in papermaking wastewater treatment and lignin removal, with special emphasis on biodegradation, recovery, and utilization of lignin, providing guidance for the mechanism exploration of lignin-degrading microorganisms and the optimization of high-value chemical production.
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Broda M, Popescu CM, Curling SF, Timpu DI, Ormondroyd GA. Effects of Biological and Chemical Degradation on the Properties of Scots Pine Wood-Part I: Chemical Composition and Microstructure of the Cell Wall. MATERIALS 2022; 15:ma15072348. [PMID: 35407682 PMCID: PMC9000077 DOI: 10.3390/ma15072348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/11/2022] [Accepted: 03/19/2022] [Indexed: 11/16/2022]
Abstract
Research on new conservation treatment for archaeological wood requires large amounts of wooden material. For this purpose, artificial wood degradation (biological-using brown-rot fungus Coniophora puteana, and chemical-using NaOH solution) under laboratory conditions was conducted to obtain an abundance of similar samples that mimic naturally degraded wood and can serve for comparative studies. However, knowledge about its properties is necessary to use this material for further study. In this study, the chemical composition and microstructure of degraded cell walls were investigated using FT-IR, XRD, helium pycnometry and nitrogen absorption methods. The results show that biological degradation caused the loss of hemicelluloses and celluloses, including the reduction in cellulose crystallinity, and led to lignin modification, while chemical degradation mainly depleted the amount of hemicelluloses and lignin, but also affected crystalline cellulose. These changes affected the cell wall microstructure, increasing both surface area and total pore volume. However, the chemical degradation produced a greater number of mesopores of smaller size compared to fungal decomposition. Both degradation processes weakened the cell wall's mechanical strength, resulting in high shrinkage of degraded wood during air-drying. The results of the study suggest that degraded wood obtained under laboratory conditions can be a useful material for studies on new consolidants for archaeological wood.
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Affiliation(s)
- Magdalena Broda
- Department of Wood Science and Thermal Techniques, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, ul. Wojska Polskiego 38/42, 60-637 Poznan, Poland
- Correspondence: ; Tel.: +48-61-848-7448
| | - Carmen-Mihaela Popescu
- Petru Poni Institute of Macromolecular Chemistry of the Romanian Academy, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (C.-M.P.); (D.I.T.)
- Centre of Wood Science and Technology, Edinburgh Napier University, 37 Bankhead Crossway South, Edinburgh EH14EP, UK
| | - Simon F. Curling
- BioComposites Centre, Bangor University, Deiniol Road, Bangor LL57 2UW, Gwynedd, UK; (S.F.C.); (G.A.O.)
| | - Daniel Ilie Timpu
- Petru Poni Institute of Macromolecular Chemistry of the Romanian Academy, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (C.-M.P.); (D.I.T.)
| | - Graham A. Ormondroyd
- BioComposites Centre, Bangor University, Deiniol Road, Bangor LL57 2UW, Gwynedd, UK; (S.F.C.); (G.A.O.)
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Frey B, Varliero G, Qi W, Stierli B, Walthert L, Brunner I. Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. Front Microbiol 2022; 13:828977. [PMID: 35300488 PMCID: PMC8921678 DOI: 10.3389/fmicb.2022.828977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Gilda Varliero
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,Centre for Microbial Ecology and Genomics, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Weihong Qi
- Functional Genomics Center Zurich (FGCZ), ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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47
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Gao Y, Shah K, Kwok I, Wang M, Rome LH, Mahendra S. Immobilized fungal enzymes: Innovations and potential applications in biodegradation and biosynthesis. Biotechnol Adv 2022; 57:107936. [PMID: 35276253 DOI: 10.1016/j.biotechadv.2022.107936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 01/10/2023]
Abstract
Microbial enzymes catalyze various reactions inside and outside living cells. Among the widely studied enzymes, fungal enzymes have been used for some of the most diverse purposes, especially in bioremediation, biosynthesis, and many nature-inspired commercial applications. To improve their stability and catalytic ability, fungal enzymes are often immobilized on assorted materials, conventional as well as nanoscale. Recent advances in fungal enzyme immobilization provide effective and sustainable approaches to achieve improved environmental and commercial outcomes. This review aims to provide a comprehensive overview of commonly studied fungal enzymes and immobilization technologies. It also summarizes recent advances involving immobilized fungal enzymes for the degradation or assembly of compounds used in the manufacture of products, such as detergents, food additives, and fossil fuel alternatives. Furthermore, challenges and future directions are highlighted to offer new perspectives on improving existing technologies and addressing unexplored fields of applications.
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Affiliation(s)
- Yifan Gao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Kshitjia Shah
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Ivy Kwok
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Meng Wang
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Leonard H Rome
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, United States; California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States; California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States.
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Suryadi H, Judono JJ, Putri MR, Eclessia AD, Ulhaq JM, Agustina DN, Sumiati T. Biodelignification of lignocellulose using ligninolytic enzymes from white-rot fungi. Heliyon 2022; 8:e08865. [PMID: 35141441 PMCID: PMC8814692 DOI: 10.1016/j.heliyon.2022.e08865] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/17/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
Lignocellulose is the most abundant biomass available on earth, including wood and agricultural wastes such as rice straw, corn cobs, and oil palm empty bunches. The biopolymer content in lignocellulose has a great potential as feedstock for producing industrial raw materials such as glucose, sorbitol, xylose, xylitol, and other pharmaceutical excipients. Currently, scientists and governments agree that the enzymatic delignification method is an environmentally friendly green method to be applied. This review attempts to explain the proper preparation of the enzymes laccase, lignin peroxidase, and manganese peroxidase, as well as the important factors influencing their activity. The recent applications of the enzymes for detoxification of hazardous substances, proper enzyme immobilization technique, and future prospect combination with DESs extraction of lignin are also discussed.
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Huang C, Wu X, Liu X, Fang Y, Liu L, Wu C. Functional fungal communities dominate wood decomposition and are modified by wood traits in a subtropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151377. [PMID: 34740660 DOI: 10.1016/j.scitotenv.2021.151377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Wood decomposition is a fundamental process of the carbon cycle in forest ecosystems and differs under varying environmental conditions. However, it remains unclear whether exposure situation and litter removal affect wood decomposition, especially in subtropical forests. Therefore, we chose wood from four dominant species and carried out an experiment with treatments consisting of placing wood in ground contact with and without litter input and above ground exposure. The experiment was performed for 2.5 consecutive years in the subtropical forest of Southwest China to reveal the potential effects of microenvironmental changes due to above ground exposure and nutrient input changes due to litter removal. In this study, neither above ground exposure nor litter removal significantly changed the fungal communities, microbial respiration rates or decomposition rates of the wood, but significant differences among tree species were observed. The abundance of Ascomycota (70.2%) was higher than that of Basidiomycota (24.3%), and there was a significant negative relationship between their abundances, suggesting competition. Moreover, negative (Ascomycota) and positive (Basidiomycota) relationships with microbial respiration and explained 21.5 and 25.5% of the variation in microbial respiration, respectively. The wood density was directly controlled by the sugar, cellulose, and lignin contents and influenced the water content in the wood. The abundances of saprotrophic and pathotrophic fungi were significantly and directly regulated by the water content of the wood. The abundance of pathotrophic fungi was unaffected by wood traits, but these fungi may limit saprotrophic fungal colonization, thereby affecting microbial respiration and decomposition processes. We confirmed that the saprotrophic fungal abundance, rather than fungal diversity, determined wood microbial respiration. These results are of great significance for the comprehensive assessment of wood decomposition and the carbon cycle in subtropical forests, although long-term fungal community dynamics and decomposition rates under different conditions require further study.
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Affiliation(s)
- Changjiang Huang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Xiaoqing Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China.
| | - Xiaoyu Liu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Yuting Fang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Lei Liu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China.
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50
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Lou X, Zhao J, Lou X, Xia X, Feng Y, Li H. The Biodegradation of Soil Organic Matter in Soil-Dwelling Humivorous Fauna. Front Bioeng Biotechnol 2022; 9:808075. [PMID: 35083207 PMCID: PMC8784593 DOI: 10.3389/fbioe.2021.808075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Soil organic matter contains more carbon than global vegetation and the atmosphere combined. Gaining access to this source of organic carbon is challenging and requires at least partial removal of polyphenolic and/or soil mineral protections, followed by subsequent enzymatic or chemical cleavage of diverse plant polysaccharides. Soil-feeding animals make significant contributions to the recycling of terrestrial organic matter. Some humivorous earthworms, beetles, and termites, among others, have evolved the ability to mineralize recalcitrant soil organic matter, thereby leading to their tremendous ecological success in the (sub)tropical areas. This ability largely relies on their symbiotic associations with a diverse community of gut microbes. Recent integrative omics studies, including genomics, metagenomics, and proteomics, provide deeper insights into the functions of gut symbionts. In reviewing this literature, we emphasized that understanding how these soil-feeding fauna catabolize soil organic substrates not only reveals the key microbes in the intestinal processes but also uncovers the potential novel enzymes with considerable biotechnological interests.
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Affiliation(s)
- Xuliang Lou
- Zhuji Real Estate Management Service Center, Shaoxing, China
| | - Jianming Zhao
- Zhuji Real Estate Management Service Center, Shaoxing, China
| | - Xiangyang Lou
- Zhuji Real Estate Management Service Center, Shaoxing, China
| | - Xiejiang Xia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yilu Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hongjie Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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