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Ye Y, Liu H, Wang Z, Qi Q, Du J, Tian S. A cellulosomal yeast reaction system of lignin-degrading enzymes for cellulosic ethanol fermentation. Biotechnol Lett 2024; 46:531-543. [PMID: 38607604 DOI: 10.1007/s10529-024-03485-0] [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: 12/08/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
Biofuel production from lignocellulose feedstocks is sustainable and environmentally friendly. However, the lignocellulosic pretreatment could produce fermentation inhibitors causing multiple stresses and low yield. Therefore, the engineering construction of highly resistant microorganisms is greatly significant. In this study, a composite functional chimeric cellulosome equipped with laccase, versatile peroxidase, and lytic polysaccharide monooxygenase was riveted on the surface of Saccharomyces cerevisiae to construct a novel yeast strain YI/LVP for synergistic lignin degradation and cellulosic ethanol production. The assembly of cellulosome was assayed by immunofluorescence microscopy and flow cytometry. During the whole process of fermentation, the maximum ethanol concentration and cellulose conversion of engineering strain YI/LVP reached 8.68 g/L and 83.41%, respectively. The results proved the availability of artificial chimeric cellulosome containing lignin-degradation enzymes for cellulosic ethanol production. The purpose of the study was to improve the inhibitor tolerance and fermentation performance of S. cerevisiae through the construction and optimization of a synergistic lignin-degrading enzyme system based on cellulosome.
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Affiliation(s)
- Yutong Ye
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Han Liu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Zhipeng Wang
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Qi Qi
- Beijing Chaoyang Foreign Language School, Beijing, 100012, China
| | - Jiliang Du
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Shen Tian
- College of Life Science, Capital Normal University, Beijing, 100048, China.
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2
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Haidar R, Compant S, Robert C, Antonielli L, Yacoub A, Grélard A, Loquet A, Brader G, Guyoneaud R, Attard E, Rey P. Two Paenibacillus spp. strains promote grapevine wood degradation by the fungus Fomitiporia mediterranea: from degradation experiments to genome analyses. Sci Rep 2024; 14:15779. [PMID: 38982270 PMCID: PMC11233627 DOI: 10.1038/s41598-024-66620-x] [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: 01/11/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.
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Affiliation(s)
- Rana Haidar
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France.
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France.
| | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Coralie Robert
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Livio Antonielli
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Amira Yacoub
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Günter Brader
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Rémy Guyoneaud
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Eléonore Attard
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
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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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Yu L, An Z, Xie D, Yin D, Xie G, Gao X, Xiao Y, Liu J, Fang Z. From waste to protein: a new strategy of converting composted distilled grain wastes into animal feed. Front Microbiol 2024; 15:1405564. [PMID: 38881654 PMCID: PMC11176434 DOI: 10.3389/fmicb.2024.1405564] [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: 03/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Distilled grain waste (DGW) is rich in nutrients and can be a potential resource as animal feed. However, DGW contains as much as 14% lignin, dramatically reducing the feeding value. White-rot fungi such as Pleurotus ostreatus could preferentially degrade lignin with high efficiency. However, lignin derivatives generated during alcohol distillation inhibit P. ostreatus growth. Thus, finding a new strategy to adjust the DGW properties to facilitate P. ostreatus growth is critical for animal feed preparation and DGW recycling. In this study, three dominant indigenous bacteria, including Sphingobacterium thermophilum X1, Pseudoxanthomonas byssovorax X3, and Bacillus velezensis 15F were chosen to generate single and compound microbial inoculums for DGW composting to prepare substrates for P. ostreatus growth. Compared with non-inoculated control or single microbial inoculation, all composite inoculations, especially the three-microbial compound, led to faster organic metabolism, shorter composting process, and improved physicochemical properties of DGW. P. ostreatus growth assays showed the fastest mycelial colonization (20.43 μg·g-1 ergosterol) and extension (9 mm/d), the highest ligninolytic enzyme activities (Lac, 152.68 U·g-1; Lip, 15.56 U·g-1; MnP, 0.34 U·g-1; Xylanase, 10.98 U·g-1; FPase, 0.71 U·g-1), and the highest lignin degradation ratio (30.77%) in the DGW sample after 12 h of composting with the three-microbial compound inoculation when compared to other groups. This sample was relatively abundant in bacteria playing critical roles in amino acid, carbohydrate, energy metabolism, and xenobiotic biodegradation, as suggested by metagenomic analysis. The feed value analysis revealed that P. ostreatus mycelia full colonization in composted DGW led to high fiber content retention and decreased lignin content (final ratio of 5% lignin) but elevated protein concentrations (about 130 g·kg-1 DM). An additional daily weight gain of 0.4 kg/d was shown in cattle feeding experiments by replacing 60% of regular feed with it. These findings demonstrate that compound inoculant consisting of three indigenous microorganisms is efficient to compost DGW and facilitate P. ostreatus growth. P. ostreatus decreased the lignin content of composted DGW during its mycelial growth, improving the quality of DGW for feeding cattle.
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Affiliation(s)
- Lei Yu
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Zichao An
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Dengdeng Xie
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Diao Yin
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Guopai Xie
- Anhui Golden Seed Winery Co., Ltd., Fuyang, China
| | - Xuezhi Gao
- Anhui Golden Seed Winery Co., Ltd., Fuyang, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, China
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Ali NS, Thakur S, Ye M, Monteil-Rivera F, Pan Y, Qin W, Yang TC. Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 2024; 24:181. [PMID: 38789935 PMCID: PMC11127350 DOI: 10.1186/s12866-024-03331-3] [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: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.
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Affiliation(s)
- Nadia Sufdar Ali
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Subarna Thakur
- Department of Bioinformatics, University of North Bengal, Siliguri, India
| | - Mengwei Ye
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- BioWise Technologies Inc, Ottawa, Canada.
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Fall I, Doumèche B, Abdellaoui S, Rémond C, Rakotoarivonina H, Ochs M. Paper-based electrodes as a tool for detecting ligninolytic enzymatic activities. Bioelectrochemistry 2024; 156:108609. [PMID: 37995505 DOI: 10.1016/j.bioelechem.2023.108609] [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: 09/16/2022] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Lignin is the most important natural source of aromatic compounds. The valorisation of lignin into aromatics requires fractionation steps that can be catalysed by ligninolytic enzymes. However, one of the main limitations of biological lignin fractionation is the low efficiency of biocatalysts; it is therefore crucial to enhance or to identify new ligninolytic enzymes. Currently, the screening of ligninolytic activities on lignin polymers represents a technological bottenleck and hinders the characterization and the discovery of efficient ligninolytic biocatalysts. An efficient and fast method for the measurement of such enzymatic activities is therefore required. In this work, we present a new electrochemical tool based on lignin-coated paper electrodes for the detection and the characterization of ligninolytic activity. The suitability of this method is demonstrated using a catalase-peroxidase isolated from Thermobacillus xylanilyticus.
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Affiliation(s)
- Issa Fall
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, AFERE, Reims, France
| | - Bastien Doumèche
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA, CPE-Lyon, UMR 5246, ICBMS (Institut de Chimie et Biochimie Moléculaires et Supramoléculaires), F-69622, Villeurbanne, France
| | - Sofiene Abdellaoui
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, AFERE, Reims, France
| | - Caroline Rémond
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, AFERE, Reims, France
| | | | - Marjorie Ochs
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INSA, CPE-Lyon, UMR 5246, ICBMS (Institut de Chimie et Biochimie Moléculaires et Supramoléculaires), F-69622, Villeurbanne, France.
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Zhao XQ, Liu CG, Bai FW. Making the biochemical conversion of lignocellulose more robust. Trends Biotechnol 2024; 42:418-430. [PMID: 37858385 DOI: 10.1016/j.tibtech.2023.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Lignocellulose is an alternative to fossil resources, but its biochemical conversion is not economically competitive. While decentralized processing can reduce logistical cost for this feedstock, sugar platforms need to be developed with energy-saving pretreatment technologies and cost-effective cellulases, and products must be selected correctly. Anaerobic fermentation with less energy consumption and lower contamination risk is preferred, particularly for producing biofuels. Great effort has been devoted to producing cellulosic ethanol, but CO2 released with large quantities during ethanol fermentation must be utilized in situ for credit. Unless titer and yield are improved substantially, butanol cannot be produced as an advanced biofuel. Microbial lipids produced through aerobic fermentation with low yield and intensive energy consumption are not affordable as feedstocks for biodiesel production.
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Affiliation(s)
- Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Kato H, Takahashi Y, Suzuki H, Ohashi K, Kawashima R, Nakamura K, Sakai K, Hori C, Takasuka TE, Kato M, Shimizu M. Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium. Appl Environ Microbiol 2024; 90:e0175323. [PMID: 38259078 PMCID: PMC10880611 DOI: 10.1128/aem.01753-23] [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: 10/03/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.
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Affiliation(s)
- Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | | | | | - Keisuke Ohashi
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Koki Nakamura
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Kiyota Sakai
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Chiaki Hori
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | | | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
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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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Vilbert AC, Kontur WS, Gille D, Noguera DR, Donohue TJ. Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics. Appl Environ Microbiol 2024; 90:e0166023. [PMID: 38117061 PMCID: PMC10807440 DOI: 10.1128/aem.01660-23] [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: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.
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Affiliation(s)
- Avery C. Vilbert
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wayne S. Kontur
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Derek Gille
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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11
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Wang Z, Jiang D, Wang X, Jiang Y, Sun Q, Ling W, An X, Ji C, Li S, Qi Y, Kang B. Spermidine improves the antioxidant capacity and morphology of intestinal tissues and regulates intestinal microorganisms in Sichuan white geese. Front Microbiol 2024; 14:1292984. [PMID: 38293560 PMCID: PMC10824853 DOI: 10.3389/fmicb.2023.1292984] [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: 10/04/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction Intestinal health is very important to the health of livestock and poultry, and is even a major determining factor in the performance of livestock and poultry production. Spermidine is a type of polyamine that is commonly found in a variety of foods, and can resist oxidative stress, promote cell proliferation and regulate intestinal flora. Methods In this study, we explored the effects of spermidine on intestinal health under physiological states or oxidative stress conditions by irrigation with spermidine and intraperitoneal injection of 3-Nitropropionic acid (3-NPA) in Sichuan white goose. Results and discussion Our results showed that spermidine could increase the ratio of intestinal villus to crypt and improve intestinal morphology. In addition, spermidine can also reduce malondialdehyde (MDA) accumulation caused by 3-NPA by increasing superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) enzyme activity, thus alleviating intestinal damage. Furthermore, spermidine can regulate intestinal digestive enzyme activities and affect intestinal digestion and absorption ability. Spermidine can also promote an increase in intestinal microbial diversity and abundance and alleviate the change of microflora structure caused by 3-NPA. In conclusion, spermidine promotes the production of beneficial intestinal metabolites such as Wikstromol, Alpha-bisabolol and AS 1-5, thus improving the level of intestinal health. Taken together, these results indicate that spermidine can improve intestinal health by improving intestinal morphology, increasing antioxidant capacity and regulating intestinal flora structure.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bo Kang
- State Key Laboratory of Swine and Poultry Breeding Industry, Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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12
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Liu D, Gong H, Li J, Liu Z, Wang L, Ouyang Z, Xu L, Wang T. Continuous crop rotation increases soil organic carbon stocks in river deltas: A 40-year field evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167749. [PMID: 37838062 DOI: 10.1016/j.scitotenv.2023.167749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/23/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
River deltas, as important food production centers, support 66 % of the world's population, together with other coastal areas. However, agriculture in river deltas is negatively affected by soil salinization and agricultural intensification. Improving the soil carbon pool is a mutually beneficial solution for maximizing crop production and improving climate resilience to secure food production. In this study, long-term croplands in the Yellow River Delta (YRD), with a wheat-maize (WM) rotation system and a single cotton (SC) cropping system, were selected to explore the changes in soil organic carbon (SOC) stocks and the driving mechanisms at 0-20 cm depth from 1980 to 2020. We found that, over the past 40 years, the SOC stocks in WM and SC croplands had increased by 10.05 Mg C ha-1 and 7.44 Mg C ha-1, respectively. The Random forest model revealed that in the WM croplands, soil N stock and available K were the most important driving factors of SOC stocks, while in SC croplands, soil type and salinity were the most important driving factors of SOC stock dynamics. An increase in soil salinity to 2.0 ‰ caused a 17.5 % loss in SOC stocks in SC croplands. Our results show that, in the long run, croplands with a WM rotation system have stronger carbon sequestration potential. Depending on the planting system, promoting crop carbon input under high soil nutrients and affecting SOC decomposition by soil salinity are two different pathways of SOC sequestration in delta croplands. We propose that nutrient management and organic fertilizer application are crucial for increasing SOC stocks in the WM and SC croplands, respectively. This study confirms that it is of practical significance to take measures to promote soil carbon sequestration at the farmland scale and to provide scientific guidance for the sustainable development of river delta agriculture.
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Affiliation(s)
- Deyao Liu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huarui Gong
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Yellow River Delta Modern Agricultural Engineering Laboratory, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhen Liu
- Yellow River Delta Modern Agricultural Engineering Laboratory, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingqing Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhu Ouyang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Yellow River Delta Modern Agricultural Engineering Laboratory, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Xu
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Tieyu Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
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Xu L, Liaqat F, Sun J, Khazi MI, Xie R, Zhu D. Advances in the vanillin synthesis and biotransformation: A review. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2024; 189:113905. [DOI: 10.1016/j.rser.2023.113905] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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14
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Peng Z, Jiang X, Si C, Joao Cárdenas-Oscanoa A, Huang C. Advances of Modified Lignin as Substitute to Develop Lignin-Based Phenol-Formaldehyde Resin Adhesives. CHEMSUSCHEM 2023; 16:e202300174. [PMID: 37338272 DOI: 10.1002/cssc.202300174] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Indexed: 06/21/2023]
Abstract
Traditionally, phenols used to prepare phenol-formaldehyde (PF) resin adhesives are obtained from phenolic compounds and various chemicals, which are extracted from petroleum-based raw materials. Lignin, a sustainable phenolic macromolecule in the cell wall of biomass with an aromatic ring and a phenolic hydroxyl group similar to those of phenol, can be an ideal substitute for phenol in PF resin adhesives. However, only a few lignin-based adhesives are produced on a large scale in industry, mainly because of the low activity of lignin. Preparing lignin-based PF resin adhesives with exceptional achievements by modifying lignin instead of phenol is an efficient method to improve the economic benefits and protect the environment. In this review, the latest progress in the preparation of PF resin adhesives via lignin modification, including chemical, physical, and biological modifications, is discussed. In addition, the advantages and disadvantages of different lignin modification methods for adhesives are compared and discussed, and future research directions for the synthesis of lignin-based PF resin adhesives are proposed.
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Affiliation(s)
- Zhenwen Peng
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P. R. China
| | - Xiao Jiang
- Department of Forestry Biomaterials, North Carolina State University Campus Box 8005, Raleigh, NC 27695-8005, USA
| | - Chuanling Si
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P. R. China
- Tianjin Key Laboratory of Pulp and Paper, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Aldo Joao Cárdenas-Oscanoa
- Forest Industry Department, Faculty of Forest Science, Universidad Nacional Agraria La Molina, Lima, 15024, Perú
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P. R. China
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15
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Duran K, Magnin J, America AH, Peng M, Hilgers R, de Vries RP, Baars JJ, van Berkel WJ, Kuyper TW, Kabel MA. The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation. iScience 2023; 26:107087. [PMID: 37426348 PMCID: PMC10329178 DOI: 10.1016/j.isci.2023.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6-15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Joris Magnin
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Antoine H.P. America
- Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roelant Hilgers
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Johan J.P. Baars
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, the Netherlands
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Thomas W. Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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Zhang Y, Wang R, Liu L, Wang E, Yang J, Yuan H. Distinct lignocellulolytic enzymes produced by Trichoderma harzianum in response to different pretreated substrates. BIORESOURCE TECHNOLOGY 2023; 378:128990. [PMID: 37003454 DOI: 10.1016/j.biortech.2023.128990] [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: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce β-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China; Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China.
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17
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Ferreira P, Carro J, Balcells B, Martínez AT, Serrano A. Expanding the Physiological Role of Aryl-Alcohol Flavooxidases as Quinone Reductases. Appl Environ Microbiol 2023; 89:e0184422. [PMID: 37154753 DOI: 10.1128/aem.01844-22] [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: 05/10/2023] Open
Abstract
Aryl-alcohol oxidases (AAOs) are members of the glucose-methanol-choline oxidase/dehydrogenase (GMC) superfamily. These extracellular flavoproteins have been described as auxiliary enzymes in the degradation of lignin by several white-rot basidiomycetes. In this context, they oxidize fungal secondary metabolites and lignin-derived compounds using O2 as an electron acceptor, and supply H2O2 to ligninolytic peroxidases. Their substrate specificity, including mechanistic aspects of the oxidation reaction, has been characterized in Pleurotus eryngii AAO, taken as a model enzyme of this GMC superfamily. AAOs show broad reducing-substrate specificity in agreement with their role in lignin degradation, being able to oxidize both nonphenolic and phenolic aryl alcohols (and hydrated aldehydes). In the present work, the AAOs from Pleurotus ostreatus and Bjerkandera adusta were heterologously expressed in Escherichia coli, and their physicochemical properties and oxidizing abilities were compared with those of the well-known recombinant AAO from P. eryngii. In addition, electron acceptors different from O2, such as p-benzoquinone and the artificial redox dye 2,6-Dichlorophenolindophenol, were also studied. Differences in reducing-substrate specificity were found between the AAO enzymes from B. adusta and the two Pleurotus species. Moreover, the three AAOs oxidized aryl alcohols concomitantly with the reduction of p-benzoquinone, with similar or even higher efficiencies than when using their preferred oxidizing-substrate, O2. IMPORTANCE In this work, quinone reductase activity is analyzed in three AAO flavooxidases, whose preferred oxidizing-substrate is O2. The results presented, including reactions in the presence of both oxidizing substrates-benzoquinone and molecular oxygen-suggest that such aryl-alcohol dehydrogenase activity, although less important than its oxidase activity in terms of maximal turnover, may have a physiological role during fungal decay of lignocellulose by the reduction of quinones (and phenoxy radicals) from lignin degradation, preventing repolymerization. Moreover, the resulting hydroquinones would participate in redox-cycling reactions for the production of hydroxyl free radical involved in the oxidative attack of the plant cell-wall. Hydroquinones can also act as mediators for laccases and peroxidases in lignin degradation in the form of semiquinone radicals, as well as activators of lytic polysaccharide monooxygenases in the attack of crystalline cellulose. Moreover, reduction of these, and other phenoxy radicals produced by laccases and peroxidases, promotes lignin degradation by limiting repolymerization reactions. These findings expand the role of AAO in lignin biodegradation.
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Affiliation(s)
- Patricia Ferreira
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Juan Carro
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Beatriz Balcells
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
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Lan HN, Liu RY, Liu ZH, Li X, Li BZ, Yuan YJ. Biological valorization of lignin to flavonoids. Biotechnol Adv 2023; 64:108107. [PMID: 36758651 DOI: 10.1016/j.biotechadv.2023.108107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
Lignin is the most affluent natural aromatic biopolymer on the earth, which is the promising renewable source for valuable products to promote the sustainability of biorefinery. Flavonoids are a class of plant polyphenolic secondary metabolites containing the benzene ring structure with various biological activities, which are largely applied in health food, pharmaceutical, and medical fields. Due to the aromatic similarity, microbial conversion of lignin derived aromatics to flavonoids could facilitate flavonoid biosynthesis and promote the lignin valorization. This review thereby prospects a novel valorization route of lignin to high-value natural products and demonstrates the potential advantages of microbial bioconversion of lignin to flavonoids. The biodegradation of lignin polymers is summarized to identify aromatic monomers as momentous precursors for flavonoid synthesis. The biosynthesis pathways of flavonoids in both plants and strains are introduced and compared. After that, the key branch points and important intermediates are clearly discussed in the biosynthesis pathways of flavonoids. Moreover, the most significant enzyme reactions including Claisen condensation, cyclization and hydroxylation are demonstrated in the biosynthesis pathways of flavonoids. Finally, current challenges and potential future strategies are also discussed for transforming lignin into various flavonoids. The holistic microbial conversion routes of lignin to flavonoids could make a sustainable production of flavonoids and improve the feasibility of lignin valorization.
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Affiliation(s)
- Hai-Na Lan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Ruo-Ying Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xia Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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Silva D, Rodrigues F, Lorena C, Borges PT, Martins LO. Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases. Biotechnol Adv 2023; 65:108153. [PMID: 37044267 DOI: 10.1016/j.biotechadv.2023.108153] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H2O2 to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H2O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.
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Affiliation(s)
- Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - F Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Constança Lorena
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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Lignin Valorization: Production of High Value-Added Compounds by Engineered Microorganisms. Catalysts 2023. [DOI: 10.3390/catal13030555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Lignin is the second most abundant polymer in nature, which is also widely generated during biomass fractionation in lignocellulose biorefineries. At present, most of technical lignin is simply burnt for energy supply although it represents the richest natural source of aromatics, and thus it is a promising feedstock for generation of value-added compounds. Lignin is heterogeneous in composition and recalcitrant to degradation, with this substantially hampering its use. Notably, microbes have evolved particular enzymes and specialized metabolic pathways to degrade this polymer and metabolize its various aromatic components. In recent years, novel pathways have been designed allowing to establish engineered microbial cell factories able to efficiently funnel the lignin degradation products into few metabolic intermediates, representing suitable starting points for the synthesis of a variety of valuable molecules. This review focuses on recent success cases (at the laboratory/pilot scale) based on systems metabolic engineering studies aimed at generating value-added and specialty chemicals, with much emphasis on the production of cis,cis-muconic acid, a building block of recognized industrial value for the synthesis of plastic materials. The upgrade of this global waste stream promises a sustainable product portfolio, which will become an industrial reality when economic issues related to process scale up will be tackled.
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Noroozi K, Jarboe LR. Strategic nutrient sourcing for biomanufacturing intensification. J Ind Microbiol Biotechnol 2023; 50:kuad011. [PMID: 37245065 PMCID: PMC10549214 DOI: 10.1093/jimb/kuad011] [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: 01/04/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
The successful design of economically viable bioprocesses can help to abate global dependence on petroleum, increase supply chain resilience, and add value to agriculture. Specifically, bioprocessing provides the opportunity to replace petrochemical production methods with biological methods and to develop novel bioproducts. Even though a vast range of chemicals can be biomanufactured, the constraints on economic viability, especially while competing with petrochemicals, are severe. There have been extensive gains in our ability to engineer microbes for improved production metrics and utilization of target carbon sources. The impact of growth medium composition on process cost and organism performance receives less attention in the literature than organism engineering efforts, with media optimization often being performed in proprietary settings. The widespread use of corn steep liquor as a nutrient source demonstrates the viability and importance of "waste" streams in biomanufacturing. There are other promising waste streams that can be used to increase the sustainability of biomanufacturing, such as the use of urea instead of fossil fuel-intensive ammonia and the use of struvite instead of contributing to the depletion of phosphate reserves. In this review, we discuss several process-specific optimizations of micronutrients that increased product titers by twofold or more. This practice of deliberate and thoughtful sourcing and adjustment of nutrients can substantially impact process metrics. Yet the mechanisms are rarely explored, making it difficult to generalize the results to other processes. In this review, we will discuss examples of nutrient sourcing and adjustment as a means of process improvement. ONE-SENTENCE SUMMARY The potential impact of nutrient adjustments on bioprocess performance, economics, and waste valorization is undervalued and largely undercharacterized.
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Affiliation(s)
- Kimia Noroozi
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
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Randazzo A, Zorzi F, Venturi S, Bicocchi G, Viti G, Tatàno F, Tassi F. Degradation of biogas in a simulated landfill cover soil at laboratory scale: Compositional changes of main components and volatile organic compounds. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 157:229-241. [PMID: 36577274 DOI: 10.1016/j.wasman.2022.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
A laboratory experiment lasting 28 days was run to simulate a typical landfill system and to investigate the compositional changes affecting the main components (CH4, CO2, and H2) and nonmethane volatile organic compounds from biogas generated by anaerobic digestion of food waste and passing through a soil column. Gas samples were periodically collected from both the digester headspace and the soil column at increasing distances from the biogas source. CH4 and H2 were efficiently degraded along the soil column. The isotopic values of δ13C measured in CH4 and CO2 from the soil column were relatively enriched in 13C compared to the biogas. Aromatics and alkanes were the most abundant groups in the biogas samples. Among these compounds, alkylated benzenes and long-chain C3+ alkanes were significantly degraded within the soil column, whereas benzene and short-chain alkanes were recalcitrant. Terpene and O-substituted compounds were relatively stable under oxidising conditions. Cyclic, alkene, S-substituted, and halogenated compounds, which exhibited minor amounts in the digester headspace, were virtually absent in the soil column. These results pointed out how many recalcitrant potentially toxic and polluting compounds tend to be relatively enriched along the soil column, claiming action to minimise diffuse landfill gas (LFG) emissions. The proposed experimental approach represents a reliable tool for investigating the attenuation capacities of landfill cover soils for LFG components and developing optimised covers by adopting proper soil treatments and operating conditions to improve their degradation efficiencies.
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Affiliation(s)
- Antonio Randazzo
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy; IGG - Institute of Geosciences and Earth Resources, CNR - National Research Council of Italy, Via G. La Pira 4, 50121 Firenze, Italy.
| | - Francesca Zorzi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy
| | - Stefania Venturi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy; IGG - Institute of Geosciences and Earth Resources, CNR - National Research Council of Italy, Via G. La Pira 4, 50121 Firenze, Italy
| | - Gabriele Bicocchi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy
| | - Gregorio Viti
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy
| | - Fabio Tatàno
- DiSPeA - Department of Pure and Applied Sciences, Section ChEM - Chemistry, Environment, and Materials, University of Urbino "Carlo Bo", Campus Scientifico "E. Mattei", 61029 Urbino, Italy
| | - Franco Tassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Firenze, Italy; IGG - Institute of Geosciences and Earth Resources, CNR - National Research Council of Italy, Via G. La Pira 4, 50121 Firenze, Italy
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Pan S, Wang G, Fan Y, Wang X, Liu J, Guo M, Chen H, Zhang S, Chen G. Enhancing the compost maturation of deer manure and corn straw by supplementation via black liquor. Heliyon 2023; 9:e13246. [PMID: 36755604 PMCID: PMC9900273 DOI: 10.1016/j.heliyon.2023.e13246] [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: 10/13/2022] [Revised: 12/06/2022] [Accepted: 01/23/2023] [Indexed: 01/29/2023] Open
Abstract
In this paper, the relationship between black liquor and microbial growth, enzymatic secretion and humus formation in composting was studied. The results showed that black liquor inoculation is an effective way to promote fermentation process. After black liquor inoculation, the abundance of Corynebacterium, Aequorivita, and Pedobacter, which have the catalase and oxidase activity, has been significantly increased. The enzymatic activity of alkaline phosphatase, catalase, peroxidase and invertase was 40 mg/(g·24h), 6.5 mg/(g·20 min), 13 100 mg/(g·24h), and 6100 mg/(g·24h) respectively at day 18. Humic acid and fulvic acid concentration was 12 g/kg and 11 g/kg which is higher than that of the treatments of no black liquor inoculation. The results suggested that black liquor inoculation was beneficial to indigenous microorganisms reproduce efficiently, then the secretion of enzymes related to cellulose, hemicellulose, and lipid hydrolysis, and the formation of humic substances.
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Affiliation(s)
- Shijun Pan
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
| | - Gang Wang
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
- Key Laboratory of Straw Comprehensive Utilization and Black Land Conservation, Education Ministry of China, Jilin Agricultural University, Jilin, 130118, China
| | - Yide Fan
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
| | - Xiqing Wang
- College of Food Science Technology and Chemical Engineering, Hubei University of Arts and Science, Hubei, 430000, China
| | - Juan Liu
- Sericultural Research Institute of Jilin Province, Jilin, China
| | | | - Huan Chen
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Jilin, 130118, China
- Key Laboratory of Straw Comprehensive Utilization and Black Land Conservation, Education Ministry of China, Jilin Agricultural University, Jilin, 130118, China
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Rodriguez A, Hirakawa MP, Geiselman GM, Tran-Gyamfi MB, Light YK, George A, Sale KL. Prospects for utilizing microbial consortia for lignin conversion. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2023.1086881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Naturally occurring microbial communities are able to decompose lignocellulosic biomass through the concerted production of a myriad of enzymes that degrade its polymeric components and assimilate the resulting breakdown compounds by members of the community. This process includes the conversion of lignin, the most recalcitrant component of lignocellulosic biomass and historically the most difficult to valorize in the context of a biorefinery. Although several fundamental questions on microbial conversion of lignin remain unanswered, it is known that some fungi and bacteria produce enzymes to break, internalize, and assimilate lignin-derived molecules. The interest in developing efficient biological lignin conversion approaches has led to a better understanding of the types of enzymes and organisms that can act on different types of lignin structures, the depolymerized compounds that can be released, and the products that can be generated through microbial biosynthetic pathways. It has become clear that the discovery and implementation of native or engineered microbial consortia could be a powerful tool to facilitate conversion and valorization of this underutilized polymer. Here we review recent approaches that employ isolated or synthetic microbial communities for lignin conversion to bioproducts, including the development of methods for tracking and predicting the behavior of these consortia, the most significant challenges that have been identified, and the possibilities that remain to be explored in this field.
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25
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Wu L, Che S, Qin X, Xu Y, Tian S, Zhu Y, Song J, Guan Y, Wang D, Wu M, Yang X, Wu Z, Yang M. Identification, characteristics and rice growth promotion of a highly efficient cellulolytic bacterial strain, Cellulomonas iranensis ZJW-6, isolated from paddy soil in central China. Front Microbiol 2023; 14:1152966. [PMID: 37032857 PMCID: PMC10073736 DOI: 10.3389/fmicb.2023.1152966] [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: 01/28/2023] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
The microbial degradation of lignocellulose is the best way to treat straw, which has a broad application prospect. It is consistent with the idea of agricultural sustainable development and has an important impact on the utilization of biomass resources. To explore and utilize the microbial resources of lignocellulose degradation, 27 lignocellulose degrading strains were screened from 13 regions in China. ZJW-6 was selected because of its 49.6% lignocellulose weight loss rate. According to the theoretical analysis of the experimental results, the following straw degradation conditions were obtained by ZJW-6: nitrogen source input of 8.45 g/L, a pH of 8.57, and a temperature of 31.63°C, the maximum weight loss rate of rice straw could reach 54.8%. It was concluded that ZJW-6 belonged to Cellulomonas iranensis according to 16S rRNA-encoding gene sequence comparison and identification. ZJW-6 is a Gram-positive bacterium that grows slowly and has a small yellowish green colony. To explain the degradation mechanism of lignocellulose, the experiment of enzymatic properties of the strain was prepared and carried out. It was discovered that ZJW-6 has an excellent ability to degrade cellulose, hemicellulose, and lignin, with cellulose and hemicellulose loss rates reaching almost 50% in 4 days and lignin loss rates reaching nearly 30%. Furthermore, ZJW-6 demonstrated lignocellulose degradation under aerobic and anaerobic conditions, indicating the strain's broad application potential. ZJW-6 was found to be more effective than ordinary humic acid in improving rice soil (available phosphorus, available nitrogen, organic matter) and promoting rice growth in a rice pot experiment (increasing root-shoot ratio, root activity, chlorophyll content and net photosynthetic rate). ZJW-6 plays an important role in promoting the development and utilization of straw resources. It has important significance for the advancement of green agriculture.
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Affiliation(s)
- Lei Wu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Songhao Che
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Xueting Qin
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yufeng Xu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Shiqi Tian
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuan Zhu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jian Song
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yunpeng Guan
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Dongchao Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Meikang Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xue Yang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhihai Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Meiying Yang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- *Correspondence: Meiying Yang,
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Suzuki H, Mori R, Kato M, Shimizu M. Biochemical characterization of hydroquinone hydroxylase from Phanerochaete chrysosporium. J Biosci Bioeng 2023; 135:17-24. [PMID: 36344390 DOI: 10.1016/j.jbiosc.2022.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The white-rot fungus Phanerochaete chrysosporium can degrade lignin polymers using extracellular, non-specific, one-electron oxidizing enzymes. This results in the formation of guaiacyl (G), syringyl (S), and hydroxyphenyl (H) units, such as vanillic acid, syringic acid, and p-hydroxybenzoic acid (p-HBA) and the corresponding aldehydes, which are further metabolized intracellularly. Therefore, the aim of this study was to identify proteins involved in the hydroxylation of H-unit fragments such as p-HBA and its decarboxylated product hydroquinone (HQ) in P. chrysosporium. A flavoprotein monooxygenase (FPMO), PcFPMO2, was identified and its activity was characterized. Recombinant PcFPMO2 with an N-terminal polyhistidine tag was produced in Escherichia coli and purified. In the presence of NADPH, PcFPMO2 used six phenolic compounds as substrates. PcFPMO2 catalyzed the hydroxylation of the H-unit fragments such as p-HBA and HQ, and the G-unit derivative methoxyhydroquinone (MHQ). The highest catalytic efficiency (kcat/Km) was observed with HQ, indicating that PcFPMO2 could be involved in HQ hydroxylation in vivo. Additionally, PcFPMO2 converted MHQ to 3-, 5-, and 6-methoxy-1,2,4-trihydroxybenzene (3-, 5-, and 6-MTHB), respectively, suggesting that PcFPMO2 might partially be involved in MHQ degradation, following aromatic ring fission, via three MTHBs. FPMOs are divided into eight groups (groups A to H). This is the first study to show MHQ hydroxylase activity of a FPMO-group A superfamily member. These findings highlight the unique substrate spectrum of PcFPMO2, making it an attractive candidate for biotechnological applications.
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Affiliation(s)
- Hiromitsu Suzuki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Reini Mori
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Masashi Kato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Motoyuki Shimizu
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan.
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Tan F, Cheng J, Zhang Y, Jiang X, Liu Y. Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:78. [PMID: 35831866 PMCID: PMC9277890 DOI: 10.1186/s13068-022-02175-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/01/2022] [Indexed: 11/27/2022]
Abstract
Background Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study. Results A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL−1 and 1265.58 UL−1, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL−1 on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography–mass spectrometry (GC–MS), including 9 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted. Conclusions Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions, gentisate pathway, anthranilate pathway, homogentisic pathway, and catabolic pathway for resorcinol. Two other pathways, the phenylacetate–CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02175-1.
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Li F, Zhao Y, Xue L, Ma F, Dai SY, Xie S. Microbial lignin valorization through depolymerization to aromatics conversion. Trends Biotechnol 2022; 40:1469-1487. [PMID: 36307230 DOI: 10.1016/j.tibtech.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022]
Abstract
Lignin is the most abundant source of renewable aromatic biopolymers and its valorization presents significant value for biorefinery sustainability, which promotes the utilization of renewable resources. However, it is challenging to fully convert the structurally complex, heterogeneous, and recalcitrant lignin into high-value products. The in-depth research on the lignin degradation mechanism, microbial metabolic pathways, and rational design of new systems using synthetic biology have significantly accelerated the development of lignin valorization. This review summarizes the key enzymes involved in lignin depolymerization, the mechanisms of microbial lignin conversion, and the lignin valorization application with integrated systems and synthetic biology. Current challenges and future strategies to further study lignin biodegradation and the trends of lignin valorization are also discussed.
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Affiliation(s)
- Fei Li
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiquan Zhao
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Le Xue
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fuying Ma
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Susie Y Dai
- Department of Plant Pathology and Microbiology, Texas A&M University, College station, TX 77843, USA.
| | - Shangxian Xie
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Liu ZH, Li BZ, Yuan JS, Yuan YJ. Creative biological lignin conversion routes toward lignin valorization. Trends Biotechnol 2022; 40:1550-1566. [PMID: 36270902 DOI: 10.1016/j.tibtech.2022.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
Abstract
Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.
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Affiliation(s)
- Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Joshua S Yuan
- Department of Energy, Environmental, and Chemical Engineering, The McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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A thermostable bacterial catalase-peroxidase oxidizes phenolic compounds derived from lignins. Appl Microbiol Biotechnol 2022; 107:201-217. [DOI: 10.1007/s00253-022-12263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022]
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Arentshorst M, Reijngoud J, van Tol DJC, Reid ID, Arendsen Y, Pel HJ, van Peij NNME, Visser J, Punt PJ, Tsang A, Ram AFJ. Utilization of ferulic acid in Aspergillus niger requires the transcription factor FarA and a newly identified Far-like protein (FarD) that lacks the canonical Zn(II) 2Cys 6 domain. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:978845. [PMID: 37746181 PMCID: PMC10512302 DOI: 10.3389/ffunb.2022.978845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/17/2022] [Indexed: 09/26/2023]
Abstract
The feruloyl esterase B gene (faeB) is specifically induced by hydroxycinnamic acids (e.g. ferulic acid, caffeic acid and coumaric acid) but the transcriptional regulation network involved in faeB induction and ferulic acid metabolism has only been partially addressed. To identify transcription factors involved in ferulic acid metabolism we constructed and screened a transcription factor knockout library of 239 Aspergillus niger strains for mutants unable to utilize ferulic acid as a carbon source. The ΔfarA transcription factor mutant, already known to be involved in fatty acid metabolism, could not utilize ferulic acid and other hydroxycinnamic acids. In addition to screening the transcription factor mutant collection, a forward genetic screen was performed to isolate mutants unable to express faeB. For this screen a PfaeB-amdS and PfaeB-lux613 dual reporter strain was engineered. The rationale of the screen is that in this reporter strain ferulic acid induces amdS (acetamidase) expression via the faeB promoter resulting in lethality on fluoro-acetamide. Conidia of this reporter strain were UV-mutagenized and plated on fluoro-acetamide medium in the presence of ferulic acid. Mutants unable to induce faeB are expected to be fluoro-acetamide resistant and can be positively selected for. Using this screen, six fluoro-acetamide resistant mutants were obtained and phenotypically characterized. Three mutants had a phenotype identical to the farA mutant and sequencing the farA gene in these mutants indeed showed mutations in FarA which resulted in inability to growth on ferulic acid as well as on short and long chain fatty acids. The growth phenotype of the other three mutants was similar to the farA mutants in terms of the inability to grow on ferulic acid, but these mutants grew normally on short and long chain fatty acids. The genomes of these three mutants were sequenced and allelic mutations in one particular gene (NRRL3_09145) were found. The protein encoded by NRRL3_09145 shows similarity to the FarA and FarB transcription factors. However, whereas FarA and FarB contain both the Zn(II)2Cys6 domain and a fungal-specific transcription factor domain, the protein encoded by NRRL3_09145 (FarD) lacks the canonical Zn(II)2Cys6 domain and possesses only the fungal specific transcription factor domain.
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Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jos Reijngoud
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Daan J. C. van Tol
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Yvonne Arendsen
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | - Herman J. Pel
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | | | - Jaap Visser
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Fungal Genetics and Technology Consultancy, Wageningen, AJ, Netherlands
| | - Peter J. Punt
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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32
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Xu Z, Peng B, Kitata RB, Nicora CD, Weitz KK, Pu Y, Shi T, Cort JR, Ragauskas AJ, Yang B. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:117. [PMID: 36316752 PMCID: PMC9620641 DOI: 10.1186/s13068-022-02214-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. RESULTS This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography-mass spectrometry (GC-MS) and two-dimensional 1H-13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C-C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C-O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. CONCLUSIONS Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.
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Affiliation(s)
- Zhangyang Xu
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Bo Peng
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Reta Birhanu Kitata
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Carrie D. Nicora
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Karl K. Weitz
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Yunqiao Pu
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - John R. Cort
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Arthur J. Ragauskas
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ,grid.411461.70000 0001 2315 1184Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA ,grid.411461.70000 0001 2315 1184Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Bin Yang
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
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33
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Wang J, Zheng F, Yu Z, Chen J, Lu H. Dissolved organic nitrogen derived from wastewater denitrification: Composition and nitrogenous disinfection byproduct formation. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129775. [PMID: 35994914 DOI: 10.1016/j.jhazmat.2022.129775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/23/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Microbially derived dissolved organic nitrogen (mDON) is a major fraction of effluent total nitrogen at wastewater treatment plants with enhanced nutrient removal, which stimulates phytoplankton blooms and formation of toxic nitrogenous disinfection by-products (N-DBPs). This study identified denitrifiers as major contributors to mDON synthesis, and further revealed the molecular composition, influential factors and synthetic microorganisms of denitrification-derived mDON compounds leading to N-DBP formation. The maximum mDON accumulated during denitrification was 8.92% of converted inorganic nitrogen, higher than that of anammox (4.24%) and nitrification (2.76%). Sodium acetate addition at relatively high C/N ratio (5-7) favored mDON formation, compared with methanol and low C/N (1-3). Different from acetate, methanol-facilitated denitrification produced 13-69% more lignin-like compounds than proteins using Orbitrap LC-MS. The most abundant N-DBPs formed from denitrification-derived mDON were N-nitrosodibutylamine and dichloroacetonitrile (13.32 μg/mg mDON and 12.21 μg/mg mDON, respectively). Major amino acids, aspartate, glycine, and alanine were positively correlated with typical N-DBPs. Biosynthesis and degradation pathways of these N-DBP precursors were enriched in denitrifiers belonging to Rhodocyclaceae, Mycobacteriaceae and Hyphomicrobiaceae. As intensive disinfection is applied at worldwide wastewater treatment plants during COVID-19, carbon source facilitated denitrification should be better managed to reduce both effluent inorganic nitrogen and DON, mitigating DON and N-DBP associated ecological risks in receiving waters.
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Affiliation(s)
- Jie Wang
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Fang Zheng
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Zhaoniao Yu
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Jinrong Chen
- Zhejiang Fuchun Ziguang Environmental Protection Co., Ltd., 310000 Hangzhou, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China.
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34
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Cai C, Xu Z, Li J, Zhou H, Jin M. Developing
Rhodococcus opacus
and
Sphingobium
sp. co‐culture systems for valorization of lignin‐derived dimers. Biotechnol Bioeng 2022; 119:3162-3177. [DOI: 10.1002/bit.28215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Chenggu Cai
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Zhaoxian Xu
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Jie Li
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Huarong Zhou
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
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35
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Zhao X, Zhang C, Dang Q, Xi B. Insights into phenol monomers in response to electron transfer capacity of humic acid during corn straw composting process. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119548. [PMID: 35644430 DOI: 10.1016/j.envpol.2022.119548] [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: 03/23/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Quinone is the important redox functional group for electron transfer capacity (ETC) of humic acid (HA). Lignin, as major component in corn straw, can be decomposed into phenol monomers, then oxidation into quinones for synthesis of HA during composting process. However, it is still unclear that the effects of type and variation characteristics of phenol monomers on redox characteristics of HA during straw composting process. In this study, p-hydroxybenzoic acid (P1), vanillic acid (P2), syringic acid (P3), p-hydroxy benzaldehyde (P4), 4-coumaric acid (P5), 4-hydroxyacetophenone (P6), ferulic acid (P7) and 4-hydroxy-3-methylacetophenone (P8) were recognized and clustered into three groups. The concentration of polyphenol presented a significant downward trend during the straw composting process. Based on the relationships among phenol monomers to ETC, electron donating capacity (EDC), electron accepting capacity (EAC) and quinone, we found that P1, P2, P3, P5 and P7 were significantly related to ETC, EDC and EAC of HA (P < 0.05). Furthermore, NH4+-N and NO3--N were the main micro-environmental factors linking to ETC-related phenol monomers and redox characteristics of HA in straw composts (P < 0.05). Finally, two groups of core microflora that promoting the ETC-related phenol monomers and NH4+-N, and ETC-related phenol monomers and NO3--N were identified by Mantel test, respectively. This study contributes a new insight for polyphenol way for redox capacity of HA in traditional composting and utilization of straw compost in contaminated environments.
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Affiliation(s)
- Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Chuanyan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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36
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Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr 2022; 10:e0234621. [PMID: 35579457 PMCID: PMC9241852 DOI: 10.1128/spectrum.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
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Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Jacob Ford
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Wing Yin Tam
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Meghan Whalen
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Marcel Huntemann
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alex Spunde
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - I-Min Chen
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T. B. K Reddy
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Ronan O’Malley
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos C. Kyrpides
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
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37
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Garrison CE, Roozbehi S, Mitra S, Corbett DR, Field EK. Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina. Front Microbiol 2022; 13:816573. [PMID: 35756005 PMCID: PMC9218724 DOI: 10.3389/fmicb.2022.816573] [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: 11/16/2021] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Hurricane frequencies and intensities are expected to increase under warming climate scenarios, increasing potential to disrupt microbial communities from steady-state conditions and alter ecosystem function. This study shows the impact of hurricane season on microbial community dynamics within the barrier island system of Outer Banks, North Carolina. We found that the passage of two sequential energetic hurricanes in 2018 (Florence and Michael) were correlated with shifts in total and active (DNA and RNA) portions of bacterial communities but not in archaeal communities, and within surface waters but not within the sediment. These microbial community shifts were distinct from non-hurricane season conditions, suggesting significant implications for nutrient cycling in nearshore and offshore environments. Hurricane-influenced marine sites in the coastal North Atlantic region had lower microbial community evenness and Shannon diversity, in addition to increased relative abundance of copiotrophic microbes compared to non-hurricane conditions. The abundance of functional genes associated with carbon and nitrogen cycling pathways were also correlated with the storm season, potentially shifting microbial communities at offshore sites from autotroph-dominated to heterotroph-dominated and leading to impacts on local carbon budgets. Understanding the geographic- and system-dependent responses of coastal microbial communities to extreme storm disturbances is critical for predicting impacts to nutrient cycling and ecosystem stability in current and future climate scenarios.
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Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Sara Roozbehi
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Siddhartha Mitra
- Department of Geological Sciences, East Carolina University, Greenville, NC, United States.,Integrated Coastal Programs, East Carolina University, Greenville, NC, United States
| | - D Reide Corbett
- Integrated Coastal Programs, East Carolina University, Greenville, NC, United States
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, NC, United States
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38
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Zhu Y, Hu Y, Yan Y, Du S, Pan F, Li S, Xu H, Luo Z. Metabolic Engineering of Bacillus amyloliquefaciens to Efficiently Synthesize L-Ornithine From Inulin. Front Bioeng Biotechnol 2022; 10:905110. [PMID: 35757793 PMCID: PMC9214239 DOI: 10.3389/fbioe.2022.905110] [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: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens is the dominant strain used to produce γ-polyglutamic acid from inulin, a non-grain raw material. B. amyloliquefaciens has a highly efficient tricarboxylic acid cycle metabolic flux and glutamate synthesis ability. These features confer great potential for the synthesis of glutamate derivatives. However, it is challenging to efficiently convert high levels of glutamate to a particular glutamate derivative. Here, we conducted a systematic study on the biosynthesis of L-ornithine by B. amyloliquefaciens using inulin. First, the polyglutamate synthase gene pgsBCA of B. amyloliquefaciens NB was knocked out to hinder polyglutamate synthesis, resulting in the accumulation of intracellular glutamate and ATP. Second, a modular engineering strategy was applied to coordinate the degradation pathway, precursor competition pathway, and L-ornithine synthesis pathway to prompt high levels of intracellular precursor glutamate for l-ornithine synthesis. In addition, the high-efficiency L-ornithine transporter was further screened and overexpressed to reduce the feedback inhibition of L-ornithine on the synthesis pathway. Combining these strategies with further fermentation optimizations, we achieved a final L-ornithine titer of 31.3 g/L from inulin. Overall, these strategies hold great potential for strengthening microbial synthesis of high value-added products derived from glutamate.
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Affiliation(s)
- Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yifan Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Shanshan Du
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Fei Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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39
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Characterization of two 1,2,4-trihydroxybenzene 1,2-dioxygenases from Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2022; 106:4499-4509. [PMID: 35687156 DOI: 10.1007/s00253-022-12007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/21/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
Lignin is the most abundant aromatic compound in nature, and it plays an important role in the carbon cycle. White-rot fungi are microbes that are capable of efficiently degrading lignin. Enzymes from these fungi possess exceptional oxidative potential and have gained increasing importance for improving bioprocesses, such as the degradation of organic pollutants. The aim of this study was to identify the enzymes involved in the ring cleavage of the lignin-derived aromatic 1,2,4-trihydroxybenzene (THB) in Phanerochaete chrysosporium, a lignin-degrading basidiomycete. Two intradiol dioxygenases (IDDs), PcIDD1 and PcIDD2, were identified and produced as recombinant proteins in Escherichia coli. In the presence of O2, PcIDD1 and PcIDD2 acted on eight and two THB derivatives, respectively, as substrates. PcIDD1 and PcIDD2 catalyze the ring cleavage of lignin-derived fragments, such as 6-methoxy-1,2,4-trihydroxybenzene (6-MeOTHB) and 3-methoxy-1,2-catechol. The current study also revealed that syringic acid (SA) was converted to 5-hydroxyvanillic acid, 2,6-dimethoxyhydroquinone, and 6-MeOTHB by fungal cells, suggesting that PcIDD1 and PcIDD2 may be involved in aromatic ring fission of 6-MeOTHB for SA degradation. This is the first study to show 6-MeOTHB dioxygenase activity of an IDD superfamily member. These findings highlight the unique and broad substrate spectra of PcIDDs, rendering it an attractive candidate for biotechnological application. KEY POINTS: • Novel intradiol dioxygenases (IDD) in lignin degradation were characterized. • PcIDDs acted on lignin-derived fragments and catechol derivatives. • Dioxygenase activity on 6-MeOTHB was identified in IDD superfamily enzymes.
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40
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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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41
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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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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Gu D, Xiang X, Wu Y, Zeng J, Lin X. Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127958. [PMID: 34894508 DOI: 10.1016/j.jhazmat.2021.127958] [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: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO2, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.
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Affiliation(s)
- Decheng Gu
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China; Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China
| | - Yucheng Wu
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China.
| | - Jun Zeng
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xiangui Lin
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
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44
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Zhao ZM, Meng X, Scheidemantle B, Pu Y, Liu ZH, Li BZ, Wyman CE, Cai CM, Ragauskas AJ. Cosolvent enhanced lignocellulosic fractionation tailoring lignin chemistry and enhancing lignin bioconversion. BIORESOURCE TECHNOLOGY 2022; 347:126367. [PMID: 34801717 DOI: 10.1016/j.biortech.2021.126367] [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: 09/23/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Cosolvent Enhanced Lignocellulosic Fractionation (CELF) is an emerging solvolysis pretreatment to fractionate lignocellulosic biomass. Herein, the bioconversion performance of CELF lignin was fully evaluated for the first time. Results showed that CELF lignin possessed higher content of carboxylic acid OH, lower molecular weight, and disappeared β-O-4 and β-5 linkages compared to other two technical lignins including a conventional ethanol organosolv lignin (EOL) and a kraft lignin (KL). Rhodococcus opacus PD630 cell count from CELF lignin fermentation reached the highest value of 3.9 × 107 CFU/mL, representing a 62.5% and 77.3% improvement over EOL and KL, respectively. Correspondingly, lipid yield reached 143 mg/L from CELF lignin, which was 36.2% and 26.5% higher than from EOL and KL, respectively. Principal component analysis (PCA) revealed that more carboxylic acid groups and lower molecular weight contributed to the enhanced bioconversion performance of CELF lignin. This study demonstrates that CELF lignin is a promising candidate for bioconversion.
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Affiliation(s)
- Zhi-Min Zhao
- School of Ecology and Environment, Inner Mongolia Key Laboratory of Environmental Pollution Control & Wastes Reuse, Inner Mongolia University, Hohhot 010021, China; Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Xianzhi Meng
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Brent Scheidemantle
- Bourns College of Engineering-Center for Environmental Research and Technology (CE-CERT), University of California, Riverside, CA 92507, United States
| | - Yunqiao Pu
- Center for Bioenergy Innovation (CBI), Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Zhi-Hua Liu
- School of Chemical Engineering and Technology, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Bing-Zhi Li
- School of Chemical Engineering and Technology, Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Charles E Wyman
- Bourns College of Engineering-Center for Environmental Research and Technology (CE-CERT), University of California, Riverside, CA 92507, United States
| | - Charles M Cai
- Bourns College of Engineering-Center for Environmental Research and Technology (CE-CERT), University of California, Riverside, CA 92507, United States
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, United States; Center for Bioenergy Innovation (CBI), Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, United States.
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Wang L, Xue C, Owens G, Chen Z. Artificial intelligence modeling and molecular docking to analyze the laccase delignification process of rice straw by Comamonas testosteroni FJ17. BIORESOURCE TECHNOLOGY 2022; 345:126565. [PMID: 34921918 DOI: 10.1016/j.biortech.2021.126565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The laccase enzymatic characteristics and delignification processes of rice straw by Comamonas testosteroni FJ17 were investigated. Artificial intelligence modeling and molecular docking revealed the specific functional properties involved in the interaction between laccase and lignin compounds with a maximum laccase activity of 2016.7 U L-1 at 24 h. Scanning electron microscopy and X-ray diffractometer analysis confirmed that laccase caused fractures and holes on the surface of rice straw, where crystallinity decrease from 45.3 to 39.9%, and lignin content decreased from 19.0 to 10.3%. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analysis showed that the main delignification process for laccase was via β-o-4 and α-aryl ether cleavage, which generated several small molecular products. The laccase gene was cloned and bioinformatics analysis presented 317 amino acids with a predicted molecular weight of 33.13 kDa. Finally, laccase protein was found to have low binding energies with all lignin compounds tested, and lignin compounds were oxidized by laccase through hydrogen-bonding interactions with the amino acid residues.
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Affiliation(s)
- Lijie Wang
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China
| | - Chao Xue
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China.
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australian, Mawson Lakes, SA 5095, Australia
| | - Zuliang Chen
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China
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46
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Banu Jamaldheen S, Kurade MB, Basak B, Yoo CG, Oh KK, Jeon BH, Kim TH. A review on physico-chemical delignification as a pretreatment of lignocellulosic biomass for enhanced bioconversion. BIORESOURCE TECHNOLOGY 2022; 346:126591. [PMID: 34929325 DOI: 10.1016/j.biortech.2021.126591] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Effective pretreatment of lignocellulosic biomass (LCB) is one of the most important steps in biorefinery, ensuring the quality and commercial viability of the overall bioprocess. Lignin recalcitrance in LCB is a major bottleneck in biological conversion as the polymerization of lignin with hemicellulose hinders enzyme accessibility and further bioconversion to fuels and chemicals. Therefore, there is a need to delignify LCB to ease further bioprocessing. The efficiency of delignification, quality and quantity of the desired products, and generation of inhibitors depend upon the type of pretreatment employed. This review summarizes different single and integrated physicochemical pretreatments for delignification. Additionally, conditions required for effective delignification and the advantages and drawbacks of each method were evaluated. Advances in overcoming the recalcitrance of residual lignin to saccharification and the methods to recover lignin after delignification are also discussed. Efficient lignin recovery and valorization strategies provide an avenue for the sustainable lignocellulose biorefinery.
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Affiliation(s)
- Sumitha Banu Jamaldheen
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Bikram Basak
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Chang Geun Yoo
- Department of Chemical Engineering, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Kyeong Keun Oh
- Department of Chemical Engineering, Dankook University, Youngin 16890, Gyeonggi-do, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Tae Hyun Kim
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea.
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47
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Screening and Application of Ligninolytic Microbial Consortia to Enhance Aerobic Degradation of Solid Digestate. Microorganisms 2022; 10:microorganisms10020277. [PMID: 35208731 PMCID: PMC8878073 DOI: 10.3390/microorganisms10020277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
Recirculation of solid digestate through digesters has been demonstrated to be a potential simple strategy to increase continuous stirred-tank reactor biogas plant efficiency. This study extended this earlier work and investigated solid digestate post-treatment using liquid isolated ligninolytic aerobic consortia in order to increase methane recovery during the recirculation. Based on sampling in several natural environments, an enrichment and selection method was implemented using a Lab-scale Automated and Multiplexed (an)Aerobic Chemostat system to generate ligninolytic aerobic consortia. Then, obtained consortia were further cultivated under liquid form in bottles. Chitinophagia bacteria and Sordariomycetes fungi were the two dominant classes of microorganisms enriched through these steps. Finally, these consortia where mixed with the solid digestate before a short-term aerobic post-treatment. However, consortia addition did not increase the efficiency of aerobic post-treatment of solid digestate and lower methane yields were obtained in comparison to the untreated control. The main reason identified is the respiration of easily degradable fractions (e.g., sugars, proteins, amorphous cellulose) by the selected consortia. Thus, this paper highlights the difficulties of constraining microbial consortia to sole ligninolytic activities on complex feedstock, such as solid digestate, that does not only contain lignocellulosic structures.
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48
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Reshmy R, Athiyaman Balakumaran P, Divakar K, Philip E, Madhavan A, Pugazhendhi A, Sirohi R, Binod P, Kumar Awasthi M, Sindhu R. Microbial valorization of lignin: Prospects and challenges. BIORESOURCE TECHNOLOGY 2022; 344:126240. [PMID: 34737164 DOI: 10.1016/j.biortech.2021.126240] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Lignin is the world's second most prevalent biomaterial, but its effective value-added product valorization methods are still being developed. The most common preparation processes for converting lignin to platform chemicals and biofuels are fragmentation and depolymerization. Due to its structural diversity, fragmentation generally produces a variety of products, necessitating tedious separation and purifying methods to isolate the desired products. Bacterial-based techniques are commonly utilized for lignin fragmentation due to their high metabolitic activity. Recent advancements in lignin valorization utilizing bacteria, such as lignin decomposing microbes and major pathways involved that can breakdown lignin into various valuable products namely lipids, furfural, vanillin, polyhydroxybutyrate, poly lactic acid blends were discussed in this review. This review also covers the genetic and fermentation methodologies to enhance lignin decomposition, challenges and future trends of microbe based lignin valorization.
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Affiliation(s)
- R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Palanisamy Athiyaman Balakumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - K Divakar
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur 602 117, Tamil Nadu, India
| | - Eapen Philip
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - Arivalagan Pugazhendhi
- School of Renewable Energy, Maejo University, Chiang Mai 50290, Thailand; College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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49
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A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement. Sci Rep 2021; 11:23982. [PMID: 34907211 PMCID: PMC8671467 DOI: 10.1038/s41598-021-03144-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/26/2021] [Indexed: 12/03/2022] Open
Abstract
Identification of novel enzymes from lignin degrading microorganisms will help to develop biotechnologies for biomass valorization and aromatic hydrocarbons degradation. Bacillus ligniniphilus L1 grows with alkaline lignin as the single carbon source and is a great candidate for ligninolytic enzyme identification. The first dioxygenase from strain L1 was heterologously expressed, purified, and characterized with an optimal temperature and pH of 32.5 °C and 7.4, respectively. It showed the highest activity with 3-ethylcatechol and significant activities with other substrates in the decreasing order of 3-ethylcatechol > 3-methylcatechol > 3-isopropyl catechol > 2, 3-dihydroxybiphenyl > 4-methylcatechol > catechol. It did not show activities against other tested substrates with similar structures. Most reported catechol 2,3-dioxygenases (C23Os) are Fe2+-dependent whereas Bacillus ligniniphilus catechol 2,3-dioxygenase (BLC23O) is more Mn2+- dependent. At 1 mM, Mn2+ led to 230-fold activity increase and Fe2+ led to 22-fold increase. Sequence comparison and phylogenetic analyses suggested that BL23O is different from other Mn-dependent enzymes and uniquely grouped with an uncharacterized vicinal oxygen chelate (VOC) family protein from Paenibacillus apiaries. Gel filtration analysis showed that BLC23O is a monomer under native condition. This is the first report of a C23O from Bacillus ligniniphilus L1 with unique substrate preference, metal-dependency, and monomeric structure.
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50
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Atiwesh G, Parrish CC, Banoub J, Le TAT. Lignin degradation by microorganisms: A review. Biotechnol Prog 2021; 38:e3226. [PMID: 34854261 DOI: 10.1002/btpr.3226] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/09/2022]
Abstract
Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.
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Affiliation(s)
- Ghada Atiwesh
- Environmental Science Program, Memorial University of Newfoundland. St. John's, St. John's, Newfoundland, Canada
| | - Christopher C Parrish
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Department of Ocean Sciences, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada
| | - Joseph Banoub
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Fisheries and Oceans Canada, Science Branch, Special Projects, St John's, Newfoundland, Canada
| | - Tuyet-Anh T Le
- School of Science and the Environment, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Environmental Policy Institute, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Forestry Economics Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
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