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Zhao S, Deng D, Wan T, Feng J, Deng L, Tian Q, Wang J, Aiman UE, Mukhaddi B, Hu X, Chen S, Qiu L, Huang L, Wei Y. Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:25. [PMID: 38360683 PMCID: PMC10870720 DOI: 10.1186/s13068-024-02470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. RESULTS Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47-69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography-mass spectrometry (LC-MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. CONCLUSIONS Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.
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Affiliation(s)
- Shuting Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dongtao Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Tianzheng Wan
- Vrije University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, Netherlands
| | - Jie Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lei Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qianyi Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiayu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Umm E Aiman
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Balym Mukhaddi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaofeng Hu
- Shanghai Personal Biotechnology Co., Ltd, Shanghai, 20030, People's Republic of China
| | - Shaolin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ling Qiu
- College of Mechanical and Electronic Engineering, The West Scientific Observing and Experimental Station of Rural Renewable Energy Exploitation and Utilization of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Yahong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Camargo FP, Sakamoto IK, Delforno TP, Midoux C, Duarte ICS, Silva EL, Bize A, Varesche MBA. Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment. ENVIRONMENTAL TECHNOLOGY 2023; 44:3141-3160. [PMID: 35298346 DOI: 10.1080/09593330.2022.2052361] [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: 12/05/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.
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Affiliation(s)
- Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | | | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
| | | | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos (UFSCar) São Carlos, Brazil
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
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Camargo FP, Sakamoto IK, Delforno TP, Mariadassou M, Loux V, Midoux C, Duarte ICS, Silva EL, Bize A, Varesche MBA. Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 291:112631. [PMID: 33932835 DOI: 10.1016/j.jenvman.2021.112631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Energy recovery from lignocellulosic waste has been studied as an alternative to the problem of inappropriate waste disposal. The present study aimed at characterizing the microbial community and the functional activity of reactors applied to H2 production through lignocellulosic waste fermentation in optimized conditions. The latter were identified by means of Rotational Central Composite Design (RCCD), applied to optimize allochthonous inoculum concentration (2.32-5.68 gTVS/L of granular anaerobic sludge), pH (4.32-7.68) and Citrus Peel Waste (CPW) concentration (1.55-28.45 g/L). After validation, the conditions identified for optimal H2 production were 4 gSTV/L of allochthonous inoculum, 29.8 g/L of CPW (substrate) and initial pH of 8.98. In these conditions, 48.47 mmol/L of H2 was obtained, which is 3.64 times higher than the concentration in unoptimized conditions (13.31 mmol H2/L using 15 g/L of CPW, 2 gTVS/L of allochthonous inoculum, pH 7.0). Acetogenesis was the predominant pathway, and maximal concentrations of 3,731 mg/L of butyric acid and 3,516 mg/L of acetic acid were observed. Regarding the metataxonomic profile, Clostridium genus was dramatically favored in the optimized condition (79.78%) when compared to the allochthonous inoculum (0.43%). It was possible to identify several genes related to H2 (i.e dehydrogenases) and volatile fatty acids (VFA) production and with cellulose degradation, especially some CAZymes from the classes Auxiliary Activities, Glycoside Hydrolases and Glycosyl Transferase. By means of differential gene expression it was observed that cellulose degradation and acetic acid production pathways were overabundant in samples from the optimized reactors, highlighting endo-β-1,4-glucanase/cellulose, endo-β-1,4-xylanase, β-glucosidase, β-mannosidase, cellulose β-1,4-cellobiosidase, cellobiohydrolase, and others, as main the functions.
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Affiliation(s)
- Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Tiago Palladino Delforno
- Department of Biology, Federal University of São Carlos (UFSCar), João Leme dos Santos Highway, Km 101, zipcode 18052-780, Sorocaba, São Paulo, Brazil
| | - Mahendra Mariadassou
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Valentin Loux
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350, Jouy-en-Josas, France; Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), 92761, Antony, France; Université Paris Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Iolanda Cristina Silveira Duarte
- Department of Biology, Federal University of São Carlos (UFSCar), João Leme dos Santos Highway, Km 101, zipcode 18052-780, Sorocaba, São Paulo, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos (UFSCar), Rod Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, SP, Brazil
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), 92761, Antony, France
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), Av. Trabalhador São Carlense, 400, 13566-590, São Carlos, SP, Brazil.
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Akita H, Fujimoto S, Wada K, Takeda N, Iwasaki Y, Fujii T, Matsushika A. Performance of Burkholderia multivorans CCA53 for ethyl red degradation. J GEN APPL MICROBIOL 2020; 66:220-227. [PMID: 32507782 DOI: 10.2323/jgam.2019.11.001] [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: 11/03/2022]
Abstract
The discharge of industrial dyes and their breakdown products are often environmentally harmful. Here, we describe a biodegradation method using Burkholderia multivorans CCA53, which exhibits a capacity to degrade azo dyes, particularly ethyl red. Under the optimized culture conditions, 100 μM ethyl red was degraded more than 99% after incubation for 8 h. Real-time PCR analysis of azoR1 and azoR2, encoding two azoreductases, revealed that transcription level of these genes is enhanced at early phase under the optimized conditions. For a more practical approach, hydrolysates were prepared from eucalyptus or Japanese cedar chips or rice straw, and rice straw hydrolysate was used as the best medium for ethyl red biodegradation. Under those conditions, ethyl red was also degraded with high efficiency (>91%). We have thus constructed a potentially economical method for the biodegradation of ethyl red.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shinji Fujimoto
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Keisuke Wada
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Noriyo Takeda
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yuki Iwasaki
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Akinori Matsushika
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST).,Graduate School of Advanced Sciences of Matter, Hiroshima University
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