1
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Wang Q, Li X, Zhou K, Li Y, Wang Y, Zhang G, Guo H, Zhou J, Wang T. Mechanisms of conjugative transfer of antibiotic resistance genes induced by extracellular polymeric substances: Insights into molecular diversities and electron transfer properties. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135181. [PMID: 39003806 DOI: 10.1016/j.jhazmat.2024.135181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/29/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
Dissemination of antibiotic resistance genes (ARGs) has become a critical threat to public health. Activated sludge, rich in extracellular polymeric substances (EPS), is an important pool of ARGs. In this study, mechanisms of conjugation transfer of ARGs induced by EPS, including tightly bound EPS (TBEPS), soluble EPS (SEPS), and loosely bound EPS (LBEPS), were explored in terms of molecular diversities and electron transfer properties of EPS. Conjugation transfer frequency was increased by 9.98-folds (SEPS), 4.21-folds (LBEPS), and 15.75-folds (TBEPS) versus the control, respectively. Conjugation-related core genes involving SOS responses (9 genes), membrane permeability (18 genes), intercellular contact (17 genes), and energy metabolism pathways (13 genes) were all upregulated, especially in the presence of TBEPS. Carbohydrates and aliphatic substances in SEPS and LBEPS were contributors to ARG transfer, via influencing reactive oxygen species (ROS) formation (SEPS) and ROS and adenosine triphosphate (ATP) production (LBEPS). TBEPS had the highest redox potential and greatest lability and facilitated electron transfer and alternated respiration between cells, thus promoting ARG transfer by producing ATP. Generally, the chemical molecular characteristics and redox properties of EPS facilitated ARG transfer mainly by influencing lipid peroxidation and ATP, respectively.
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Affiliation(s)
- Qi Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Xiao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Keying Zhou
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Yutong Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Yanjie Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Guodong Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - He Guo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jian Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
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2
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Silverstein MR, Bhatnagar JM, Segrè D. Metabolic complexity drives divergence in microbial communities. Nat Ecol Evol 2024:10.1038/s41559-024-02440-6. [PMID: 38956426 DOI: 10.1038/s41559-024-02440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.
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Affiliation(s)
- Michael R Silverstein
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jennifer M Bhatnagar
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Daniel Segrè
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering and Department of Physics, Boston University, Boston, MA, USA.
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3
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Li H, Liu P, Li Z, Xu C, Pan J, Zhou Y, Hu Q, Zheng S, Zou Y. Valorization of Ginkgo biloba Leaf Powder as a Substrate in King Oyster Mushroom ( Pleurotus eryngii) Cultivation. Life (Basel) 2024; 14:639. [PMID: 38792659 PMCID: PMC11123215 DOI: 10.3390/life14050639] [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: 04/07/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Ginkgo biloba is widely planted as a colorful foliage tree, and its leaf can be used as a biomass energy source, but it has been underutilized for a long time. The aim of this study was to investigate the potential of garden waste as a substrate component in the cultivation process of the king oyster mushroom (Pleurotus eryngii), with the goal of enhancing both the yield of P. eryngii and the efficiency of energy use. The percentages of G. biloba leaf powder in the substrate were 10.5% and 21% to replace sawdust or sugarcane bagasse in a typical substrate. A substrate formulation that could completely replace sawdust and sugarcane bagasse was selected by analyzing mycelial growth rate, days of production, fruiting body length, biological efficiency, yield, stipe thickness, pileus diameter and laccase activity. The results showed that Y1 (treatment with 21% G. biloba leaf powder and sugarcane bagasse) had the highest yield (303.1 ± 31.9 g), which was higher than that of CK (control) (259.3 ± 37.4 g). The crude fiber content of the samples grown on substrate Y1 (as 7.43%) was higher than CK (7.37%). In addition, P. eryngii grown on substrate Y1 had the highest laccase activity for the complete colonization of the mycelium. Thus, these findings suggest that G. biloba leaf powder represents a viable and economical supplement for enhancing both the yield and quality of P. eryngii.
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Affiliation(s)
- Haikang Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Department of Gardens and Ecological Engineering, Hebei University of Engineering, Handan 056107, China;
| | - Peng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zihao Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Congtao Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinlong Pan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yi Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingxiu Hu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suyue Zheng
- Department of Gardens and Ecological Engineering, Hebei University of Engineering, Handan 056107, China;
| | - Yajie Zou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China; (H.L.); (P.L.); (Z.L.); (C.X.); (J.P.); (Y.Z.); (Q.H.)
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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Wang Q, Wang L, Li C, Jiang C, Hu J, Lv Y, Tao Y, Lu J, Pan G, Du J, Wang H. Biodegradable and multifunctional black mulch film decorated with darkened lignin induced by iron ions for "green" agriculture. Int J Biol Macromol 2024; 265:130981. [PMID: 38513894 DOI: 10.1016/j.ijbiomac.2024.130981] [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: 10/17/2023] [Revised: 03/08/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
High-value utilization of bleached lignin has been widely used in different fields, whereas the investigation on darkened lignin in composite materials was often ignored. In this work, a sort of eco-friendly and structurally robust sodium carboxymethyl cellulose (CMC)/polyvinyl alcohol (PVA)/sodium lignosulfonate (SLS) black composite mulch film was elaborately designed. The chelation and redox reaction effect between Fe ions and SLS lead to the formation of a more quinones structure on lignin, darkening both lignin and the mulch films. The chelation effect between Fe ions and biopolymer formed three-dimensional structures, which can be used as sacrifice bonds to dissipate energy and improve the mechanical properties of the composite films. In particular, the maximum elongation at break and toughness increased from 48.4 % and 1141 kJ/m3 for the CMC/PVA film to 210.9 % and 1426 kJ/m3 for the optimized CMC/PVA/SLS/Fe black mulch film, respectively. In addition, the optimized black mulch film also possesses good soil water retention, thermal preservation effect, controlled urea release, and well biodegradability. This work offered a novel strategy for designing eco-friendly black mulch with reinforced mechanical strength, slow-release urea, soil moisture retention, and heat preservation performances.
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Affiliation(s)
- Qiansen Wang
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Louyu Wang
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Chao Li
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Cong Jiang
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Jinwen Hu
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Yanna Lv
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Yehan Tao
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Jie Lu
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Gaofeng Pan
- Mudanjiang Hengfeng Paper CO., LTD, Mudanjiang 157013, China
| | - Jian Du
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China.
| | - Haisong Wang
- Liaoning Key Lab of Lignocellulose Chemistry and Biomaterials, Liaoning Collaborative Innovation Center for Lignocellulosic Biorefinery, College of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China.
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6
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Uddin N, Li X, Ullah MW, Sethupathy S, Ma K, Zahoor, Elboughdiri N, Khan KA, Zhu D. Lignin developmental patterns and Casparian strip as apoplastic barriers: A review. Int J Biol Macromol 2024; 260:129595. [PMID: 38253138 DOI: 10.1016/j.ijbiomac.2024.129595] [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: 07/03/2023] [Revised: 12/30/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024]
Abstract
Lignin and Casparian strips are two essential components of plant cells that play critical roles in plant development regulate nutrients and water across the plants cell. Recent studies have extensively investigated lignin diversity and Casparian strip formation, providing valuable insights into plant physiology. This review presents the established lignin biosynthesis pathway, as well as the developmental patterns of lignin and Casparian strip and transcriptional network associated with Casparian strip formation. It describes the biochemical and genetic mechanisms that regulate lignin biosynthesis and deposition in different plants cell types and tissues. Additionally, the review highlights recent studies that have uncovered novel lignin biosynthesis genes and enzymatic pathways, expanding our understanding of lignin diversity. This review also discusses the developmental patterns of Casparian strip in roots and their role in regulating nutrient and water transport, focusing on recent genetic and molecular studies that have identified regulators of Casparian strip formation. Previous research has shown that lignin biosynthesis genes also play a role in Casparian strip formation, suggesting that these processes are interconnected. In conclusion, this comprehensive overview provides insights into the developmental patterns of lignin diversity and Casparian strip as apoplastic barriers. It also identifies future research directions, including the functional characterization of novel lignin biosynthesis genes and the identification of additional regulators of Casparian strip formation. Overall, this review enhances our understanding of the complex and interconnected processes that drive plant growth, pathogen defense, regulation and development.
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Affiliation(s)
- Nisar Uddin
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xia Li
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Keyu Ma
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zahoor
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, Ha'il 81441, Saudi Arabia; Chemical Engineering Process Department, National School of Engineers Gabes, University of Gabes, Gabes 6029, Tunisia
| | - Khalid Ali Khan
- Applied College, Mahala Campus and the Unit of Bee Research and Honey Production/Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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7
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Li X, Li Z, Li M, Li J, Wang Q, Wang S, Li S, Li H. Transcriptomic and metabolomic analysis reveals the influence of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens. Front Microbiol 2024; 15:1224855. [PMID: 38333584 PMCID: PMC10850570 DOI: 10.3389/fmicb.2024.1224855] [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: 05/18/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction Ligninolytic bacteria can secrete extracellular enzymes to depolymerize lignin into small-molecular aromatics that are subsequently metabolized and funneled into the TCA cycle. Carbohydrates, which are the preferred carbon sources of bacteria, influence the metabolism of lignin-derived aromatics through bacteria. Methods In this study, untargeted metabolomics and transcriptomics analyses were performed to investigate the effect of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens MN-13, a strain with lignin-degrading activity that was isolated in our previous work. Results The results demonstrated that the cell growth of the MN-13 strain and lignin removal were promoted when carbohydrates such as glucose and sodium carboxymethyl cellulose were added to an alkaline lignin-minimal salt medium (AL-MSM) culture. Metabolomics analysis showed that lignin depolymerization took place outside the cells, and the addition of glucose regulated the uptake and metabolism of lignin-derived monomers and activated the downstream metabolism process in cells. In the transcriptomics analysis, 299 DEGs were screened after 24 h of inoculation in AL-MSM with free glucose and 2 g/L glucose, respectively, accounting for 8.3% of the total amount of annotated genes. These DEGs were primarily assigned to 30 subcategories, including flagellar assembly, the PTS system, RNA degradation, glycolysis/gluconeogenesis, the TCA cycle, pyruvate metabolism, and tryptophan metabolism. These subcategories were closely associated with the cell structure, generation of cellular energy, and precursors for biosynthetic pathways, based on a - log 10 (P adjust) value in the KEGG pathway analysis. Conclusion In summary, the addition of glucose increased lignin degradation mediated by the MN-13 strain through regulating glycolysis, TCA cycle, and central carbon metabolism.
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Affiliation(s)
- Xiaodan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhuofan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ming Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jingwen Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Quan Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuxiang Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuna Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Hongya Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
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8
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [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: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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9
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Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
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Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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10
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Wang J, Yin R, Hashizume Y, Todoroki Y, Mori T, Kawagishi H, Hirai H. Ergosterol and Its Metabolites Induce Ligninolytic Activity in the Lignin-Degrading Fungus Phanerochaete sordida YK-624. J Fungi (Basel) 2023; 9:951. [PMID: 37755059 PMCID: PMC10532932 DOI: 10.3390/jof9090951] [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: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
White-rot fungi are the most important group of lignin biodegraders. Phanerochaete sordida YK-624 has higher ligninolytic activity than that of model white-rot fungi. However, the underlying mechanism responsible for lignin degradation by white-rot fungi remains unknown, and the induced compounds isolated from white-rot fungi for lignin degradation have never been studied. In the present study, we tried to screen ligninolytic-inducing compounds produced by P. sordida YK-624. After large-scale incubation of P. sordida YK-624, the culture and mycelium were separated by filtration. After the separation and purification, purified compounds were analyzed by high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance. The sterilized unbleached hardwood kraft pulp was used for the initial evaluation of ligninolytic activity. Ergosterol was isolated and identified and it induced the lignin-degrading activity of this fungus. Moreover, we investigated ergosterol metabolites from P. sordida YK-624, and the ergosterol metabolites ergosta-4,7,22-triene-3,6-dione and ergosta-4,6,8(14),22-tetraen-3-one were identified and then chemically synthesized. These compounds significantly improved the lignin-degrading activity of the fungus. This is the first report on the ligninolytic-inducing compounds produced by white-rot fungi.
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Affiliation(s)
- Jianqiao Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China;
| | - Ru Yin
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Yuki Hashizume
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
| | - Yasushi Todoroki
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hirofumi Hirai
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Global Interdisciplinary Science and Innovation, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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11
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Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds. Int J Mol Sci 2023; 24:13115. [PMID: 37685920 PMCID: PMC10487439 DOI: 10.3390/ijms241713115] [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: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.
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Affiliation(s)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (K.V.M.); (O.S.S.); (T.V.F.)
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12
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Civzele A, Stipniece-Jekimova AA, Mezule L. Fungal Ligninolytic Enzymes and Their Application in Biomass Lignin Pretreatment. J Fungi (Basel) 2023; 9:780. [PMID: 37504768 PMCID: PMC10381709 DOI: 10.3390/jof9070780] [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: 06/01/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
Lignocellulosic biomass is a significant source of sustainable fuel and high-value chemical production. However, due to the complex cross-linked three-dimensional network structure, lignin is highly rigid to degradation. In natural environments, the degradation is performed by wood-rotting fungi. The process is slow, and thus, the use of lignin degradation by fungi has not been regarded as a feasible technology in the industrial lignocellulose treatment. Fungi produce a wide variety of ligninolytic enzymes that can be directly introduced in industrial processing of lignocellulose. Within this study, screening of ligninolytic enzyme production using decolorization of ABTS and Azure B dyes was performed for 10 fungal strains with potentially high enzyme production abilities. In addition to standard screening methods, media containing lignin and hay biomass as carbon sources were used to determine the change in enzyme production depending on the substrate. All selected fungi demonstrated the ability to adapt to a carbon source limitation; however, four strains indicated the ability to secrete ligninolytic enzymes in all experimental conditions-Irpex lacteus, Pleurotus dryinus, Bjerkandera adusta, and Trametes versicolor-respectively displayed a 100%, 82.7%, 82.7%, and 55% oxidation of ABTS on lignin-containing media and 100%, 87.9%, 78%, and 70% oxidation of ABTS on hay-containing media after 168 h of incubation. As a result, the most potent strains of fungi were selected to produce lignocellulose-degrading enzymes and to demonstrate their potential application in biological lignocellulose pretreatment.
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Affiliation(s)
- Anna Civzele
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
| | - Alise Anna Stipniece-Jekimova
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
| | - Linda Mezule
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
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13
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Qin X, Yang K, Wang X, Tu T, Wang Y, Zhang J, Su X, Yao B, Huang H, Luo H. Insights into the H 2O 2-Driven Lytic Polysaccharide Monooxygenase Activity on Efficient Cellulose Degradation in the White Rot Fungus Irpex lacteus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:8104-8111. [PMID: 37204864 DOI: 10.1021/acs.jafc.3c01777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In contrast to O2, H2O2 as the cosubstrate for lytic polysaccharide monooxygenases (LPMOs) exhibits great advantages in industrial settings for cellulose degradation. However, H2O2-driven LPMO reactions from natural microorganisms have not been fully explored and understood. Herein, secretome analysis unraveled the H2O2-driven LPMO reaction in the efficient lignocellulose-degrading fungus Irpex lacteus, including LPMOs with different oxidative regioselectivities and various H2O2-generating oxidases. Biochemical characterization of H2O2-driven LPMO catalysis showed orders of magnitude improvement in catalytic efficiency compared to that of O2-driven LPMO catalysis for cellulose degradation. Significantly, H2O2 tolerance of LPMO catalysis in I. lacteus was an order of magnitude higher than that in other filamentous fungi. In addition, natural reductants, gallic acid, in particular, presented in lignocellulosic biomass could sufficiently maintain LPMO catalytic reactions. Moreover, the H2O2-driven LPMO catalysis exhibited synergy with canonical endoglucanases for efficient cellulose degradation. Taken together, these findings demonstrate the great application potential of the H2O2-driven LPMO catalysis for upgrading cellulase cocktails to further improve cellulose degradation efficiency.
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Affiliation(s)
- Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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14
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Jain D, Navariya JK, Bhojiya AA, Singh A, Mohanty SR, Upadhyay SK. Bioprospecting of novel ligninolytic bacteria for effective bioremediation of agricultural by-product and synthetic pollutant dyes. Microbiol Res 2023; 270:127330. [PMID: 36848699 DOI: 10.1016/j.micres.2023.127330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/22/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Lignin is a significant renewable carbon source that needs to be exploited to manufacture bio-ethanol and chemical feedstocks. Lignin mimicking methylene blue (MB) dye is widely used in industries and causes water pollution. Using kraft lignin, methylene blue, and guaiacol as a full carbon source, 27 lignin-degrading bacteria (LDB) were isolated from 12 distinct traditional organic manures for the current investigation. The ligninolytic potential of 27 lignin-degrading bacteria was assessed by qualitative and quantitative assay. In a qualitative plate assay, the LDB-25 strain produced the largest zone, measuring 6.32 ± 0.297, on MSM-L-kraft lignin plates, while the LDB-23 strain produced the largest zone, measuring 3.44 ± 0.413, on MSM-L-Guaiacol plates. The LDB-9 strain in MSM-L-kraft lignin broth was able to decolorize lignin to a maximum of 38.327 ± 0.011% in a quantitative lignin degradation assay, which was later verified by FTIR assay. In contrast, LDB-20 produced the highest decolorization (49.633 ± 0.017%) in the MSM-L-Methylene blue broth. The highest manganese peroxidase enzyme activity, measuring 6322.314 ± 0.034 U L-1, was found in the LDB-25 strain, while the highest laccase enzyme activity, measuring 1.5105 ± 0.017 U L-1, was found in the LDB-23 strain. A preliminary examination into the biodegradation of rice straw using effective LDB was carried out, and efficient lignin-degrading bacteria were identified using 16SrDNA sequencing. SEM investigations also supported lignin degradation. LDB-8 strain had the highest percentage of lignin degradation (52.86%), followed by LDB-25, LDB-20, and LDB-9. These lignin-degrading bacteria have the ability to significantly reduce lignin and lignin-analog environmental contaminants, therefore they can be further researched for effective bio-waste management mediated breakdown.
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Affiliation(s)
- Devendra Jain
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India.
| | - Jitendra Kumar Navariya
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India
| | - Ali Asger Bhojiya
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India; Faculty of Science, US Ostwal Science, Arts and Commerce College, Mangalwad, Chittorgarh, Rajasthan 302024, India
| | - Abhijeet Singh
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Santosh Ranjan Mohanty
- All India Network Project on Soil Biodiversity-Biofertilizers, ICAR-Indian Institute of Soil Science, Bhopal 462038, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India.
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15
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Rodriguez-Yupanqui M, De La Cruz-Noriega M, Quiñones C, Otiniano NM, Quezada-Alvarez MA, Rojas-Villacorta W, Vergara-Medina GA, León-Vargas FR, Solís-Muñoz H, Rojas-Flores S. Lignin-Degrading Bacteria in Paper Mill Sludge. Microorganisms 2023; 11:1168. [PMID: 37317142 DOI: 10.3390/microorganisms11051168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
The effluents generated in the paper industry, such as black liquor, have a high content of lignin and other toxic components; however, they represent a source of lignin-degrading bacteria with biotechnological potential. Therefore, the present study aimed to isolate and identify lignin-degrading bacteria species in paper mill sludge. A primary isolation was carried out from samples of sludge present in environments around a paper company located in the province of Ascope (Peru). Bacteria selection was made by the degradation of Lignin Kraft as the only carbon source in a solid medium. Finally, the laccase activity (Um-L-1) of each selected bacteria was determined by oxidation of 2,2'-azinobis-(3-etilbencenotiazolina-6-sulfonate) (ABTS). Bacterial species with laccase activity were identified by molecular biology techniques. Seven species of bacteria with laccase activity and the ability to degrade lignin were identified. The bacteria Agrobacterium tumefasciens (2), Klebsiella grimontii (1), and Beijeinckia fluminensis (1) were reported for first time. K. grimowntii and B. fluminensis presented the highest laccase activity, with values of 0.319 ± 0.005 UmL-1 and 0.329 ± 0.004 UmL-1, respectively. In conclusion, paper mill sludge may represent a source of lignin-degrading bacteria with laccase activity, and they could have potential biotechnological applications.
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Affiliation(s)
- Magda Rodriguez-Yupanqui
- Escuela de Ingeniería Ambiental, Facultad de Ingeniería y Arquitectura, Universidad Cesar Vallejo, Trujillo 13007, Peru
| | | | - Claudio Quiñones
- Laboratorio de Biotecnología e Ingeniería Genética, Departamento de Microbiología y Parasitología, Universidad Nacional de Trujillo, Trujillo 13011, Peru
| | - Nélida Milly Otiniano
- Instituto de Investigación en Ciencia y Tecnología, Universidad César Vallejo, Trujillo 13001, Peru
| | | | | | - Gino A Vergara-Medina
- Facultad de Ingeniería Civil y Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas 01001, Peru
| | - Frank R León-Vargas
- Departamento de Ingeniería Química, Facultad de Ingeniería Química, Universidad Nacional de la Amazonia Peruana, Iquitos 16002, Peru
| | - Haniel Solís-Muñoz
- Escuela de Ingeniería Industrial, Facultad de Ingeniería, Universidad Cesar Vallejo, Trujillo 13007, Peru
| | - Segundo Rojas-Flores
- Vicerrectorado de Investigación, Universidad Autónoma del Perú, Lima 15842, Peru
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16
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Chen R, Gong Y, Xie M, Rao C, Zhou L, Pang Y, Lou H, Yang D, Qiu X. Functionalized Regulation of Metal Defects in ln 2S 3 of p-n Homojunctions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5065-5077. [PMID: 36972499 DOI: 10.1021/acs.langmuir.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The introduction of metal vacancies into n-type semiconductors could efficiently construct intimate contact interface p-n homojunctions to accelerate the separation of photogenerated carriers. In this work, a cationic surfactant occupancy method was developed to synthesize an indium-vacancy (VIn)-enriched p-n amorphous/crystal homojunction of indium sulfide (A/C-IS) for sodium lignosulfonate (SL) degradation. The amount of VIn in the A/C-IS could be regulated by varying the content of added cetyltrimethylammonium bromide (CTAB). Meanwhile, the steric hindrance of CTAB produced mesopores and macropores, providing transfer channels for SL. The degradation rates of A/C-IS to SL were 8.3 and 20.9 times higher than those of crystalline In2S3 and commercial photocatalyst (P25), respectively. The presence of unsaturated dangling bonds formed by VIn reduced the formation energy of superoxide radicals (•O2-). In addition, the inner electric field between the intimate contact interface p-n A/C-IS promoted the migration of electron-hole pairs. A reasonable degradation pathway of SL by A/C-IS was proposed based on the above mechanism. Moreover, the proposed method could also be applicable for the preparation of p-n homojunctions with metal vacancies from other sulfides.
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Affiliation(s)
- Runlin Chen
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yufeng Gong
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Maoliang Xie
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Cheng Rao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lan Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yuxia Pang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Hongming Lou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dongjie Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab of Green Chemical Product Technology, State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xueqing Qiu
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
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17
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Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives. Catalysts 2023. [DOI: 10.3390/catal13010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.
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18
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Gupta A, Tiwari A, Ghosh P, Arora K, Sharma S. Enhanced lignin degradation of paddy straw and pine needle biomass by combinatorial approach of chemical treatment and fungal enzymes for pulp making. BIORESOURCE TECHNOLOGY 2023; 368:128314. [PMID: 36375698 DOI: 10.1016/j.biortech.2022.128314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Paddy straw (PS) and pine needles (PN) are one of the challenging biomasses in terms of disposal and compost making due to their high silica and tannin contents. Particulate air pollution, loss of biodiversity and respiratory impairments are some of disastrous outcomes caused by burning. However, high percentage of cellulose and hemicellulose makes them potential substrate for paper and pulp industries. The main aim of work was to study and utilize a combinatorial approach of weak chemical treatment and lignin degrading fungal species as agents of effective production of lignin modifying enzymes (LME's) for lignin depolymerisation from the biomasses. Phanerochaete chrysosporium was found to be the best degrader of lignin (47.11 % in PS + PN in 28 days) with maximum LME's production between 10th-17th days. Efficient lignin degradation in the PS and PN biomass will aid further application in pulp production supporting the transition to a circular economy in a greener way.
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Affiliation(s)
- Akansha Gupta
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Abhay Tiwari
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pooja Ghosh
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Kalpana Arora
- Centre for Technology, Society of Economics and Social Science, India
| | - Satyawati Sharma
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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19
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Properties, Physiological Functions and Involvement of Basidiomycetous Alcohol Oxidase in Wood Degradation. Int J Mol Sci 2022; 23:ijms232213808. [PMID: 36430286 PMCID: PMC9699415 DOI: 10.3390/ijms232213808] [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: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive research efforts have been devoted to describing yeast alcohol oxidase (AO) and its promoter region, which is vastly applied in studies of heterologous gene expression. However, little is known about basidiomycetous AO and its physiological role in wood degradation. This review describes several alcohol oxidases from both white and brown rot fungi, highlighting their physicochemical and kinetic properties. Moreover, the review presents a detailed analysis of available AO-encoding gene promoter regions in basidiomycetous fungi with a discussion of the manipulations of culture conditions in relation to the modification of alcohol oxidase gene expression and changes in enzyme production. The analysis of reactions catalyzed by lignin-modifying enzymes (LME) and certain lignin auxiliary enzymes (LDA) elucidated the possible involvement of alcohol oxidase in the degradation of derivatives of this polymer. Combined data on lignin degradation pathways suggest that basidiomycetous AO is important in secondary reactions during lignin decomposition by wood degrading fungi. With numerous alcoholic substrates, the enzyme is probably engaged in a variety of catalytic reactions leading to the detoxification of compounds produced in lignin degradation processes and their utilization as a carbon source by fungal mycelium.
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Mattoo AJ, Nonzom S. Endophytes in Lignin Valorization: A Novel Approach. Front Bioeng Biotechnol 2022; 10:895414. [PMID: 35928943 PMCID: PMC9343868 DOI: 10.3389/fbioe.2022.895414] [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: 03/13/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lignin, one of the essential components of lignocellulosic biomass, comprises an abundant renewable aromatic resource on the planet earth. Although 15%––40% of lignocellulose pertains to lignin, its annual valorization rate is less than 2% which raises the concern to harness and/or develop effective technologies for its valorization. The basic hindrance lies in the structural heterogeneity, complexity, and stability of lignin that collectively makes it difficult to depolymerize and yield common products. Recently, microbial delignification, an eco-friendly and cheaper technique, has attracted the attention due to the diverse metabolisms of microbes that can channelize multiple lignin-based products into specific target compounds. Also, endophytes, a fascinating group of microbes residing asymptomatically within the plant tissues, exhibit marvellous lignin deconstruction potential. Apart from novel sources for potent and stable ligninases, endophytes share immense ability of depolymerizing lignin into desired valuable products. Despite their efficacy, ligninolytic studies on endophytes are meagre with incomplete understanding of the pathways involved at the molecular level. In the recent years, improvement of thermochemical methods has received much attention, however, we lagged in exploring the novel microbial groups for their delignification efficiency and optimization of this ability. This review summarizes the currently available knowledge about endophytic delignification potential with special emphasis on underlying mechanism of biological funnelling for the production of valuable products. It also highlights the recent advancements in developing the most intriguing methods to depolymerize lignin. Comparative account of thermochemical and biological techniques is accentuated with special emphasis on biological/microbial degradation. Exploring potent biological agents for delignification and focussing on the basic challenges in enhancing lignin valorization and overcoming them could make this renewable resource a promising tool to accomplish Sustainable Development Goals (SDG’s) which are supposed to be achieved by 2030.
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Affiliation(s)
| | - Skarma Nonzom
- *Correspondence: Skarma Nonzom, , orcid.org/0000-0001-9372-7900
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Lu Q, Jia L, Awasthi MK, Jing G, Wang Y, He L, Zhao N, Chen Z, Zhang Z, Shi X. Variations in lignin monomer contents and stable hydrogen isotope ratios in methoxy groups during the biodegradation of garden biomass. Sci Rep 2022; 12:8734. [PMID: 35610354 PMCID: PMC9130509 DOI: 10.1038/s41598-022-12689-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Lignin, a highly polymerized organic component of plant cells, is one of the most difficult aromatic substances to degrade. Selective biodegradation under mild conditions is a promising method, but the dynamic variations in lignin monomers during the biodegradation of lignocellulose are not fully understood. In this study, we evaluated the differences in lignin degradation under different microbial inoculation based on the lignin monomer content, monomer ratio, and stable hydrogen isotope ratio of lignin methoxy groups (δ2HLM). The weight loss during degradation and the net loss of lignocellulosic components improved dramatically with fungal inoculation. Syringyl monolignol (S-lignin), which contains two methoxy groups, was more difficult to degrade than guaiacyl (G-lignin), which contains only one methoxy group. The co-culture of Pseudomonas mandelii and Aspergillus fumigatus produced the greatest decrease in the G/S ratio, but δ2HLM values did not differ significantly among the three biodegradation experiments, although the enrichment was done within the fungal inoculation. The fluctuation of δ2HLM values during the initial phase of biodegradation may be related to the loss of pectic polysaccharides (another methoxy donor), which mainly originate from fallen leaves. Overall, the relative δ2HLM signals were preserved despite decreasing G/S ratios in the three degradation systems. Nevertheless, some details of lignin δ2HLM as a biomarker for biogeochemical cycles need to be explored further.
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Affiliation(s)
- Qiangqiang Lu
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
- School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Lili Jia
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Guanghua Jing
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Yabo Wang
- School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Liyan He
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Ning Zhao
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Zhikun Chen
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Zhao Zhang
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Xinwei Shi
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China.
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