1
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Silva JP, Frederico TD, Ticona ARP, Pinto OHB, Williams TCR, Krüger RH, Noronha EF. Insights on kraft lignin degradation in an anaerobic environment. Enzyme Microb Technol 2024; 179:110468. [PMID: 38850683 DOI: 10.1016/j.enzmictec.2024.110468] [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: 03/26/2024] [Revised: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Lignin is an aromatic macromolecule and one of the main constituents of lignocellulosic materials. Kraft lignin is generated as a residual by-product of the lignocellulosic biomass industrial process, and it might be used as a feedstock to generate low molecular weight aromatic compounds. In this study, we seek to understand and explore the potential of ruminal bacteria in the degradation of kraft lignin. We established two consortia, KLY and KL, which demonstrated significant lignin-degrading capabilities. Both consortia reached maximum growth after two days, with KLY showing a higher growth and decolorization rate. Additionally, SEM analysis revealed morphological changes in the residual lignin from both consortia, indicating significant degradation. This was further supported by FTIR spectra, which showed new bands corresponding to the C-H vibrations of guaiacyl and syringyl units, suggesting structural transformations of the lignin. Taxonomic analysis showed enrichment of the microbial community with members of the Dickeya genus. Seven metabolic pathways related to lignin metabolism were predicted for the established consortia. Both consortia were capable of consuming aromatic compounds such as 4-hydroxybenzoic acid, syringaldehyde, acetovanillone, and syringic acid, highlighting their capacity to convert aromatic compounds into commercially valuable molecules presenting antifungal activity and used as food preservatives as 4-hydroxyphenylacetic, 3-phenylacetic, and phenylacetic acids. Therefore, the microbial consortia shown in the present work are models for understanding the process of lignin degradation and consumption in bacterial anaerobic communities and developing biological processes to add value to industrial processes based on lignocellulosic biomass as feedstock.
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Affiliation(s)
- Jéssica P Silva
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Tayná D Frederico
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Alonso R P Ticona
- Enzyme Biotechnology Research Laboratory, Science Faculty, Universidad Nacional Jorge Basadre Grohmann, Tacna 23003, Peru
| | - Otávio H B Pinto
- Genomic for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Thomas C R Williams
- Plant Biochemistry Laboratory, Department of Botany, University of Brasilia, Brasília 70910-900, Brazil
| | - Ricardo H Krüger
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Eliane F Noronha
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil.
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2
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Edith Ayala-Rodríguez A, Valdés-Rodríguez S, Enrique Olalde-Mathieu V, Arias-Padró M, Reyes-Moreno C, Olalde-Portugal V. Extracellular ligninases production and lignin degradation by Paenibacillus polymyxa. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38104982 DOI: 10.2323/jgam.2023.12.001] [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] [Indexed: 12/19/2023]
Abstract
Bacteria represent an attractive source for the isolation and identification of potentially useful microorganisms for lignin depolymerization, a process required for the use of agricultural waste. In this work, ten autochthonous bacteria isolated from straw, cow manure, and composts were characterized for potential use in the biodelignification of the waste. A comparison of the ability to degrade lignin and the efficiency of ligninolytic enzymes was performed in bacteria grown in media with lignin as a sole carbon source (LLM, 3.5g/L lignin-alkali) and in complex media supplemented with All-Ban fiber (FLM, 1.5g/L). Bacterial isolates showed different abilities to degrade lignin, they decreased the lignin concentration from 7.6 to 18.6% in LLM and from 11.1 to 44.8% in FLM. They also presented the activity of manganese peroxidase, lignin peroxidases, and laccases with different specific activities. However, strain 26 identified as Paenibacillus polymyxa by sequencing the 16S rRNA showed the highest activity of lignin peroxidase and the ability to degrade efficiently lignocellulose. In addition, P. polymyxa showed the highest potential (desirability ≥ 0.795) related to the best combination of properties to depolymerize lignin from biomass. The results suggest that P. polymyxa has a coordinated lignin degradation system constituted of lignin peroxidase, manganese peroxidase, and laccase enzymes.
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Affiliation(s)
- Ana Edith Ayala-Rodríguez
- Programa Regional del Noroeste para el Doctorado en Biotecnología, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa
| | - Silvia Valdés-Rodríguez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Unidad Irapuato
| | | | - María Arias-Padró
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Unidad Irapuato
| | - Cuauhtémoc Reyes-Moreno
- Programa Regional del Noroeste para el Doctorado en Biotecnología, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Unidad Irapuato
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3
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Mubayi V, Ahern CB, Calusinska M, O’Malley MA. Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation. ACS Synth Biol 2024; 13:1978-1993. [PMID: 38918080 PMCID: PMC11264326 DOI: 10.1021/acssynbio.4c00077] [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: 02/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Polymer production is rapidly increasing, but there are no large-scale technologies available to effectively mitigate the massive accumulation of these recalcitrant materials. One potential solution is the development of a carbon-neutral polymer life cycle, where microorganisms convert plant biomass to chemicals, which are used to synthesize biodegradable materials that ultimately contribute to the growth of new plants. Realizing a circular carbon life cycle requires the integration of knowledge across microbiology, bioengineering, materials science, and organic chemistry, which itself has hindered large-scale industrial advances. This review addresses the biodegradation status of common synthetic polymers, identifying novel microbes and enzymes capable of metabolizing these recalcitrant materials and engineering approaches to enhance their biodegradation pathways. Design considerations for the next generation of biodegradable polymers are also reviewed, and finally, opportunities to apply findings from lignocellulosic biodegradation to the design and biodegradation of similarly recalcitrant synthetic polymers are discussed.
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Affiliation(s)
- Vikram Mubayi
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Colleen B. Ahern
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Magdalena Calusinska
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Environmental
Research and Innovation Department, Luxembourg
Institute of Science and Technology, L-4422 Belvaux, Luxembourg
| | - Michelle A. O’Malley
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Bioengineering, University of California, Santa Barbara, California 93106, United States
- Joint
BioEnergy Institute (JBEI), Emeryville, California 94608, United States
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4
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Gao J, Ali MY, Kamaraj Y, Zhang Z, Weike L, Sethupathy S, Zhu D. A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics. Microbiol Res 2024; 287:127835. [PMID: 39032264 DOI: 10.1016/j.micres.2024.127835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.
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Affiliation(s)
- Jiayue Gao
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mohamed Yassin Ali
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Yoganathan Kamaraj
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zhenghao Zhang
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Li Weike
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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5
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Tu Z, Geng A, Xiang Y, Zayas-Garriga A, Guo H, Zhu D, Xie R, Sun J. Lignin Degradation by Klebsiella aerogenes TL3 under Anaerobic Conditions. Molecules 2024; 29:2177. [PMID: 38792038 PMCID: PMC11124209 DOI: 10.3390/molecules29102177] [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: 04/06/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Lignin, the largest non-carbohydrate component of lignocellulosic biomass, is also a recalcitrant component of the plant cell wall. While the aerobic degradation mechanism of lignin has been well-documented, the anaerobic degradation mechanism is still largely elusive. In this work, a versatile facultative anaerobic lignin-degrading bacterium, Klebsiella aerogenes TL3, was isolated from a termite gut, and was found to metabolize a variety of carbon sources and produce a single kind or multiple kinds of acids. The percent degradation of alkali lignin reached 14.8% under anaerobic conditions, and could reach 17.4% in the presence of glucose within 72 h. Based on the results of infrared spectroscopy and 2D nuclear magnetic resonance analysis, it can be inferred that the anaerobic degradation of lignin may undergo the cleavage of the C-O bond (β-O-4), as well as the C-C bond (β-5 and β-β), and involve the oxidation of the side chain, demethylation, and the destruction of the aromatic ring skeleton. Although the anaerobic degradation of lignin by TL3 was slightly weaker than that under aerobic conditions, it could be further enhanced by adding glucose as an electron donor. These results may shed new light on the mechanisms of anaerobic lignin degradation.
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Affiliation(s)
- Zhuowei Tu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Alei Geng
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
- Changzhou Engineering and Technology Institute, Jiangsu University, Changzhou 214153, China
| | - Yuhua Xiang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Anaiza Zayas-Garriga
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Hao Guo
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Z.T.); (Y.X.); (A.Z.-G.); (H.G.); (D.Z.); (R.X.)
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6
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Kang J, La TV, Kim MJ, Bae JH, Sung BH, Kim S, Sohn JH. Secretory Production of the Hericium erinaceus Laccase from Saccharomyces cerevisiae. J Microbiol Biotechnol 2024; 34:930-939. [PMID: 38314447 DOI: 10.4014/jmb.2312.12043] [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: 12/28/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Mushroom laccases play a crucial role in lignin depolymerization, one of the most critical challenges in lignin utilization. Importantly, laccases can utilize a wide range of substrates, such as toxicants and antibiotics. This study isolated a novel laccase, named HeLac4c, from endophytic white-rot fungi Hericium erinaceus mushrooms. The cDNAs for this enzyme were 1569 bp in length and encoded a protein of 523 amino acids, including a 20 amino-acid signal peptide. Active extracellular production of glycosylated laccases from Saccharomyces cerevisiae was successfully achieved by selecting an optimal translational fusion partner. We observed that 5 and 10 mM Ca2+, Zn2+, and K+ increased laccase activity, whereas 5 mM Fe2+ and Al3+ inhibited laccase activity. The laccase activity was inhibited by the addition of low concentrations of sodium azide and L-cysteine. The optimal pH for the 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt was 4.4. Guaiacylglycerol-β-guaiacyl ether, a lignin model compound, was polymerized by the HeLac4c enzyme. These results indicated that HeLac4c is a novel oxidase biocatalyst for the bioconversion of lignin into value-added products for environmental biotechnological applications.
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Affiliation(s)
- Jin Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Thuat Van La
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Mi-Jin Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Hoon Bae
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Seonghun Kim
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jung-Hoon Sohn
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Cellapy Bio Inc., Daejeon 34141, Republic of Korea
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7
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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8
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Pereira AR, Assis NVD, Paranhos AGDO, Lima DRS, Baeta BEL, Aquino SFD, Silva SDQ. Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse. ENVIRONMENTAL TECHNOLOGY 2024; 45:2205-2217. [PMID: 36632771 DOI: 10.1080/09593330.2023.2166877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Nathália Vercelli de Assis
- Graduate Program in Biotechnology, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Diego Roberto Sousa Lima
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Bruno Eduardo Lobo Baeta
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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9
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Riyadi FA, Azman NF, Nadia Md Akhir F, Othman N, Hara H. Identification and characterization of lignin depolymerization enzymes in Bacillus subtilis strain S11Y isolated from a tropical environment in Malaysia. J GEN APPL MICROBIOL 2024; 69:278-286. [PMID: 37612074 DOI: 10.2323/jgam.2023.08.003] [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] [Indexed: 08/25/2023]
Abstract
Biological pretreatment using microbial enzymes appears to be the most promising pre-treatment technology for the breakdown of recalcitrant lignin structure. This research focuses on the identification and characterization of lignin-depolymerizing enzymes in Bacillus subtilis strain S11Y, previously isolated from palm oil wastes in Malaysia. The draft genome sequences of this highly lignin-depolymerizing strain revealed that the genome lacked any of the well-known dye-decolorizing peroxidase or catalase-peroxidase that are commonly reported to be involved in lignin depolymerization by bacteria, indicating that strain S11Y has distinct sets of potential lignin depolymerization genes. The oxidative stress-related enzymes Cu/Zn type-superoxide dismutase (Sod2) and a heme-containing monofunctional catalase (Kat2) were identified in the genome sequences that are of interest. Their lignin-depolymerizing ability were evaluated by treating Alkali lignin (AL) with each enzyme and their degradation ability were evaluated using gel-permeation chromatography (GPC), ultrahigh-pressure liquid chromatography-mass spectrometry (UHPLC/MS), and gas chromatography-mass spectrometry (GC/MS), which successfully proved lignin depolymerizing ability. Successful evaluation of lignin depolymerizing enzymes can be applicable for lignin pretreatment process in green energy production and generation of valuable chemicals in bio-refinery.
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Affiliation(s)
- Fatimah Azizah Riyadi
- Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nadia Farhana Azman
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Fazrena Nadia Md Akhir
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nor'azizi Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Hirofumi Hara
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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10
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Wang C, Kuzyakov Y. Mechanisms and implications of bacterial-fungal competition for soil resources. THE ISME JOURNAL 2024; 18:wrae073. [PMID: 38691428 PMCID: PMC11104273 DOI: 10.1093/ismejo/wrae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.
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Affiliation(s)
- Chaoqun Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Biogeochemistry of Agroecosystems, University of Göttingen, Göttingen 37077, Germany
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yakov Kuzyakov
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen 37077, Germany
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Han X, Ma Y, Ding S, Fang J, Liu G. Regulation of dietary fiber on intestinal microorganisms and its effects on animal health. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 14:356-369. [PMID: 37635930 PMCID: PMC10448034 DOI: 10.1016/j.aninu.2023.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 08/29/2023]
Abstract
The animal gut harbors diverse microbes that play an essential role in the well-being of their host. Specific diets, such as those rich in dietary fiber, are vital in disease prevention and treatment because they affect intestinal flora and have a positive impact on the metabolism, immunity, and intestinal function of the host. Dietary fiber can provide energy to colonic epithelial cells, regulate the structure and metabolism of intestinal flora, promote the production of intestinal mucosa, stimulate intestinal motility, improve glycemic and lipid responses, and regulate the digestion and absorption of nutrients, which is mainly attributed to short-chain fatty acids (SCFA), which is the metabolite of dietary fiber. By binding with G protein-coupled receptors (including GPR41, GPR43 and GPR109A) and inhibiting the activity of histone deacetylases, SCFA regulate appetite and glucolipid metabolism, promote the function of the intestinal barrier, alleviate oxidative stress, suppress inflammation, and maintain immune system homeostasis. This paper reviews the physicochemical properties of dietary fiber, the interaction between dietary fiber and intestinal microorganisms, the role of dietary fiber in maintaining intestinal health, and the function of SCFA, the metabolite of dietary fiber, in inhibiting inflammation. Furthermore, we consider the effects of dietary fiber on the intestinal health of pigs, the reproduction and lactation performance of sows, and the growth performance and meat quality of pigs.
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Affiliation(s)
- Xuebing Han
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, Hunan 410125, China
| | - Yong Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, Hunan 410125, China
| | - Sujuan Ding
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, Hunan 410125, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, Hunan 410125, China
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, Hunan 410125, China
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12
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Peng Q, Lin L, Tu Q, Wang X, Zhou Y, Chen J, Jiao N, Zhou J. Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates. mSystems 2023; 8:e0128322. [PMID: 37417747 PMCID: PMC10469889 DOI: 10.1128/msystems.01283-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/12/2023] [Indexed: 07/08/2023] Open
Abstract
Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
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Affiliation(s)
- Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Yueyue Zhou
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Joint Lab for Ocean Research and Education at Shandong University, Xiamen University and Dalhousie University, Qingdao, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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13
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Sarnaik AP, Shinde S, Mhatre A, Jansen A, Jha AK, McKeown H, Davis R, Varman AM. Unravelling the hidden power of esterases for biomanufacturing of short-chain esters. Sci Rep 2023; 13:10766. [PMID: 37402758 DOI: 10.1038/s41598-023-37542-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Microbial production of esters has recently garnered wide attention, but the current production metrics are low. Evidently, the ester precursors (organic acids and alcohols) can be accumulated at higher titers by microbes like Escherichia coli. Hence, we hypothesized that their 'direct esterification' using esterases will be efficient. We engineered esterases from various microorganisms into E. coli, along with overexpression of ethanol and lactate pathway genes. High cell density fermentation exhibited the strains possessing esterase-A (SSL76) and carbohydrate esterase (SSL74) as the potent candidates. Fed-batch fermentation at pH 7 resulted in 80 mg/L of ethyl acetate and 10 mg/L of ethyl lactate accumulation by SSL76. At pH 6, the total ester titer improved by 2.5-fold, with SSL76 producing 225 mg/L of ethyl acetate, and 18.2 mg/L of ethyl lactate, the highest reported titer in E. coli. To our knowledge, this is the first successful demonstration of short-chain ester production by engineering 'esterases' in E. coli.
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Affiliation(s)
- Aditya P Sarnaik
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Somnath Shinde
- Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, USA
| | - Apurv Mhatre
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Abigail Jansen
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Amit Kumar Jha
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, USA
| | - Haley McKeown
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Ryan Davis
- Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, USA.
| | - Arul M Varman
- Chemical Engineering Program, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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Mori T, Terashima T, Matsumura M, Tsuruta K, Dohra H, Kawagishi H, Hirai H. Construction of white-rot fungal-bacterial consortia with improved ligninolytic properties and stable bacterial community structure. ISME COMMUNICATIONS 2023; 3:61. [PMID: 37349534 PMCID: PMC10287725 DOI: 10.1038/s43705-023-00270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
It is believed that wood-rot fungi change their wood decay activities due to influences from co-existing bacterial communities; however, it is difficult to elucidate experimentally the interaction mechanisms in fungal-bacterial consortia because the bacterial community structure is quite unstable and readily changes. Indeed, the wood decay properties of fungal-bacterial consortia consisting of a white-rot fungus Phanerochaete sordida YK-624 and a natural bacterial community changed dramatically during several sub-cultivations on wood. Therefore, development of a sub-cultivation method that imparts stability to the bacterial community structure and fungal phenotype was attempted. The adopted method using agar medium enabled maintenance of fungal phenotypes relating to wood decay and the bacterial community even through dozens of repetitive sub-cultures. Some bacterial metabolic pathways identified based on gene predictions were screened as candidates involved in P. sordida-bacterial interactions. In particular, pathways related to prenyl naphthoquinone biosynthesis appeared to be involved in an interaction that promotes higher lignin degradation selectivity by the consortia, as naphthoquinone derivatives induced phenol-oxidizing activity. Based on these results, it is expected that detailed analyses of the relationship between the wood-degrading properties of white-rot fungal-bacterial consortia and bacterial community structures will be feasible using the sub-cultivation method developed in this study.
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Affiliation(s)
- Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan.
| | - Taiki Terashima
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Masaki Matsumura
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Koudai Tsuruta
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hideo Dohra
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
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15
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Ley Y, Cheng XY, Ying ZY, Zhou NY, Xu Y. Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions. Microbiol Spectr 2023; 11:e0442422. [PMID: 37042774 PMCID: PMC10269927 DOI: 10.1128/spectrum.04424-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.
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Affiliation(s)
- Yvette Ley
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yu Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Yue Ying
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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16
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Guo H, Zhao Y, Chang JS, Lee DJ. Lignin to value-added products: Research updates and prospects. BIORESOURCE TECHNOLOGY 2023; 384:129294. [PMID: 37311532 DOI: 10.1016/j.biortech.2023.129294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Due to the urgent need for renewable and clean energy, the efficient use of lignin is of wide interest. A comprehensive understanding of the mechanisms of lignin depolymerization and the generation of high-value products will contribute to the global control of the formation of efficient lignin utilization. This review explores the lignin value-adding process and discusses the link between lignin functional groups and value-added products. Mechanisms and characteristics of lignin depolymerization methods are presented, and challenges and prospects for future research are highlighted.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan.
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17
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Yadav S, Tripathi S, Purchase D, Chandra R. Development of a biofilm-forming bacterial consortium and quorum sensing molecules for the degradation of lignin-containing organic pollutants. ENVIRONMENTAL RESEARCH 2023; 226:115618. [PMID: 36921788 DOI: 10.1016/j.envres.2023.115618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The presence of lignin along with other pollutants makes effluent more complex when it is discharged from Pulp and paper mills. The present study investigates the use of biofilm-forming bacteria isolated from pulp paper mill effluent contaminated sites (PPMECSs) for lignin degradation. Isolated biofilm-forming and lignin-degrading bacteria were identified as Bacillus subtilis, Enterobacter cancerogenus, and Bacillus licheniformis by 16S rRNA gene sequencing. Thin liquid chromatography (TLC) analysis showed that the consortium of bacteria produced acyl-homoserine lactone (AHL) as quorum sensing molecules and extracellular polymeric substances (EPS) that protect the bacterial consortium under unfavorable conditions. The potential consortium was able to reduce lignin (900 ppm) by 73% after 8 days of incubation in a minimal salt medium containing kraft lignin and glucose at pH 7.0 and 37 °C as compared to individual strains. The degradation by-products were identified as amides, alcohols, and acids. The major organic pollutants in the effluent were reduced after treatment of the constructed consortium, thus confirming active biotransformation and biodegradation of the lignin. Microscopic examination also indicated the presence of lignin induced biofilm formation. Hence, the constructed biofilm-forming bacterial consortia based on quorum sensing offered a sustainable and effective solution to treat lignin-containing complex pollutants.
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Affiliation(s)
- Sangeeta Yadav
- Department of Microbiology, Dr. Shakuntala Misra National Rehabilitation University, Lucknow, 226017, Uttar Pradesh, India; Department of Botany, Vaishno Devi Prashikshan Mahavidyalaya, Godahi, Kunda, Pratapgarh, Uttar Pradesh, India.
| | - Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow, 226025, Uttar Pradesh, India
| | - Diane Purchase
- Department of Natural Sciences, Faculty of Science and Technology, Middlesex University, The Burroughs, Hendon, London, England, NW4 4BT, UK
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow, 226025, Uttar Pradesh, India.
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18
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Qin X, Yang K, Zou J, Wang X, Tu T, Wang Y, Su X, Yao B, Huang H, Luo H. Heterologous expression and characterization of novel GH12 β-glucanase and AA10 lytic polysaccharide monooxygenase from Streptomyces megaspores and their synergistic action in cellulose saccharification. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:89. [PMID: 37221623 DOI: 10.1186/s13068-023-02332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND The combination of cellulase and lytic polysaccharide monooxygenase (LPMO) is known to boost enzymatic saccharification of cellulose. Although the synergy between cellulases (GH5, 6 or 7) and LPMOs (AA9) has been extensively studied, the interplay between other glycoside hydrolase and LPMO families remains poorly understood. RESULTS In this study, two cellulolytic enzyme-encoding genes SmBglu12A and SmLpmo10A from Streptomyces megaspores were identified and heterologously expressed in Escherichia coli. The recombinant SmBglu12A is a non-typical endo-β-1,4-glucanase that preferentially hydrolyzed β-1,3-1,4-glucans and slightly hydrolyzed β-1,4-glucans and belongs to GH12 family. The recombinant SmLpmo10A belongs to a C1-oxidizing cellulose-active LPMO that catalyzed the oxidation of phosphoric acid swollen cellulose to produce celloaldonic acids. Moreover, individual SmBglu12A and SmLpmo10A were both active on barley β-1,3-1,4-glucan, lichenan, sodium carboxymethyl cellulose, phosphoric acid swollen cellulose, as well as Avicel. Furthermore, the combination of SmBglu12A and SmLpmo10A enhanced enzymatic saccharification of phosphoric acid swollen cellulose by improving the native and oxidized cello-oligosaccharides yields. CONCLUSIONS These results proved for the first time that the AA10 LPMO was able to boost the catalytic efficiency of GH12 glycoside hydrolases on cellulosic substrates, providing another novel combination of glycoside hydrolase and LPMO for cellulose enzymatic saccharification.
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Affiliation(s)
- Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahuan Zou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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Singh AK, Iqbal HMN, Cardullo N, Muccilli V, Fern'andez-Lucas J, Schmidt JE, Jesionowski T, Bilal M. Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review. Int J Biol Macromol 2023:124968. [PMID: 37217044 DOI: 10.1016/j.ijbiomac.2023.124968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Jesús Fern'andez-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanizaci'on El Bosque, 28670 Villaviciosa de Od'on, Spain; Grupo de Investigaci'on en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jens Ejbye Schmidt
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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Jain D, Navariya JK, Bhojiya AA, Singh A, Mohanty SR, Upadhyay SK. Bioprospecting of novel ligninolytic bacteria for effective bioremediation of agricultural by-product and synthetic pollutant dyes. Microbiol Res 2023; 270:127330. [PMID: 36848699 DOI: 10.1016/j.micres.2023.127330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/22/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Lignin is a significant renewable carbon source that needs to be exploited to manufacture bio-ethanol and chemical feedstocks. Lignin mimicking methylene blue (MB) dye is widely used in industries and causes water pollution. Using kraft lignin, methylene blue, and guaiacol as a full carbon source, 27 lignin-degrading bacteria (LDB) were isolated from 12 distinct traditional organic manures for the current investigation. The ligninolytic potential of 27 lignin-degrading bacteria was assessed by qualitative and quantitative assay. In a qualitative plate assay, the LDB-25 strain produced the largest zone, measuring 6.32 ± 0.297, on MSM-L-kraft lignin plates, while the LDB-23 strain produced the largest zone, measuring 3.44 ± 0.413, on MSM-L-Guaiacol plates. The LDB-9 strain in MSM-L-kraft lignin broth was able to decolorize lignin to a maximum of 38.327 ± 0.011% in a quantitative lignin degradation assay, which was later verified by FTIR assay. In contrast, LDB-20 produced the highest decolorization (49.633 ± 0.017%) in the MSM-L-Methylene blue broth. The highest manganese peroxidase enzyme activity, measuring 6322.314 ± 0.034 U L-1, was found in the LDB-25 strain, while the highest laccase enzyme activity, measuring 1.5105 ± 0.017 U L-1, was found in the LDB-23 strain. A preliminary examination into the biodegradation of rice straw using effective LDB was carried out, and efficient lignin-degrading bacteria were identified using 16SrDNA sequencing. SEM investigations also supported lignin degradation. LDB-8 strain had the highest percentage of lignin degradation (52.86%), followed by LDB-25, LDB-20, and LDB-9. These lignin-degrading bacteria have the ability to significantly reduce lignin and lignin-analog environmental contaminants, therefore they can be further researched for effective bio-waste management mediated breakdown.
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Affiliation(s)
- Devendra Jain
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India.
| | - Jitendra Kumar Navariya
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India
| | - Ali Asger Bhojiya
- All India Network Project on Soil Biodiversity and Biofertilizers, Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur 313001, India; Faculty of Science, US Ostwal Science, Arts and Commerce College, Mangalwad, Chittorgarh, Rajasthan 302024, India
| | - Abhijeet Singh
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Santosh Ranjan Mohanty
- All India Network Project on Soil Biodiversity-Biofertilizers, ICAR-Indian Institute of Soil Science, Bhopal 462038, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India.
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Ambika, Kumar V, Chandra D, Thakur V, Sharma U, Singh D. Depolymerization of lignin using laccase from Bacillus sp. PCH94 for production of valuable chemicals: A sustainable approach for lignin valorization. Int J Biol Macromol 2023; 234:123601. [PMID: 36775222 DOI: 10.1016/j.ijbiomac.2023.123601] [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: 11/30/2022] [Revised: 01/19/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Lignin is the most abundant aromatic polymer in nature, and its depolymerization offers excellent opportunities to develop renewable aromatic chemicals. In the present study, Bacillus sp. PCH94 was investigated for laccase production and lignin depolymerization. Maximum production of laccase enzyme was achieved within 6.0 h at 50 °C on a natural lignocellulosic substrate. Furthermore, Bacillus sp. PCH94 was used to bioconvert lignin dimeric and polymeric substrates, validated using FT-IR, NMR (1H, 13C), and LCMS. Genome mining of Bacillus sp. PCH94 revealed laccase gene (lacBl) as multicopper oxidase (spore coat CotA). Further, lacBl from Bacillus sp. PCH94 was cloned, expressed, and kinetically characterized. LacBl enzyme showed activity for substrates ABTS (40.64 IU/mg), guaiacol (5.43 IU/mg), and DMP (11.93 IU/mg). The LacBl was active in higher temperatures (10 to 100 °C) and showed a half-life of 36 and 27 h at 50 and 60 °C, respectively. The purified LacBl was able to depolymerize kraft lignin into valuable products (ferulic acid and acetovanillone), which have applications in the pharmaceutical and food industries. Overall, the current study demonstrated the role of bacterial laccase in the depolymerization of lignin and opened a promising prospect for the green production of valuable compounds from recalcitrant lignin.
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Affiliation(s)
- Ambika
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India.
| | - Devesh Chandra
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Vikas Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Upendra Sharma
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
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22
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Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks. BMC Microbiol 2023; 23:50. [PMID: 36859170 PMCID: PMC9979578 DOI: 10.1186/s12866-023-02798-w] [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: 04/09/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined. METHODS Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases. RESULTS Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis. CONCLUSION Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.
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An improved method for corn stalk in-situ degrading synthetic bacterial consortium construction in a cold region of China. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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24
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Ding Z, Kumar Awasthi S, Kumar M, Kumar V, Mikhailovich Dregulo A, Yadav V, Sindhu R, Binod P, Sarsaiya S, Pandey A, Taherzadeh MJ, Rathour R, Singh L, Zhang Z, Lian Z, Kumar Awasthi M. A thermo-chemical and biotechnological approaches for bamboo waste recycling and conversion to value added product: Towards a zero-waste biorefinery and circular bioeconomy. FUEL 2023; 333:126469. [DOI: 10.1016/j.fuel.2022.126469] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
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25
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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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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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27
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Metasecretome and biochemical analysis of consortium PM-06 during the degradation of nixtamalized maize pericarp. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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28
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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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Antony S, Antony S, Rebello S, George S, Biju DT, R R, Madhavan A, Binod P, Pandey A, Sindhu R, Awasthi MK. Bioremediation of Endocrine Disrupting Chemicals- Advancements and Challenges. ENVIRONMENTAL RESEARCH 2022; 213:113509. [PMID: 35660566 DOI: 10.1016/j.envres.2022.113509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/08/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Endocrine Disrupting Chemicals (EDCs), major group of recalcitrant compounds, poses a serious threat to the health and future of millions of human beings, and other flora and fauna for years to come. A close analysis of various xenobiotics undermines the fact that EDC is structurally diverse chemical compounds generated as a part of anthropogenic advancements as well as part of their degradation. Regardless of such structural diversity, EDC is common in their ultimate drastic effect of impeding the proper functioning of the endocrinal system, basic physiologic systems, resulting in deregulated growth, malformations, and cancerous outcomes in animals as well as humans. The current review outlines an overview of various EDCs, their toxic effects on the ecosystem and its inhabitants. Conventional remediation methods such as physico-chemical methods and enzymatic approaches have been put into action as some form of mitigation measures. However, the last decade has seen the hunt for newer technologies and methodologies at an accelerated pace. Genetically engineered microbial degradation, gene editing strategies, metabolic and protein engineering, and in-silico predictive approaches - modern day's additions to our armamentarium in combating the EDCs are addressed. These additions have greater acceptance socially with lesser dissonance owing to reduced toxic by-products, lower health trepidations, better degradation, and ultimately the prevention of bioaccumulation. The positive impact of such new approaches on controlling the menace of EDCs has been outlaid. This review will shed light on sources of EDCs, their impact, significance, and the different remediation and bioremediation approaches, with a special emphasis on the recent trends and perspectives in using sustainable approaches for bioremediation of EDCs. Strict regulations to prevent the release of estrogenic chemicals to the ecosystem, adoption of combinatorial methods to remove EDC and prevalent use of bioremediation techniques should be followed in all future endeavors to combat EDC pollution. Moreover, the proper development, growth and functioning of future living forms relies on their non-exposure to EDCs, thus remediation of such chemicals present even in nano-concentrations should be addressed gravely.
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Affiliation(s)
- Sherly Antony
- Department of Microbiology, Pushpagiri Institute of Medical Sciences and Research Centre, Thiruvalla, 689 101, Kerala, India
| | - Sham Antony
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Sharrel Rebello
- School of Food Science & Technology, Mahatma Gandhi University, Kottayam, India
| | - Sandhra George
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Devika T Biju
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Sciences and Research Centre, Thriuvalla, 689 101, Kerala, India
| | - Reshmy R
- Department of Science and Humanities, Providence College of Engineering, Chengannur, 689 122, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum, 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695 019, Kerala, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India; Centre for Energy and Environmental Sustainability, Lucknow, 226 029, Uttar Pradesh, India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, 691 505, Kerala, India.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186055. [PMID: 36144795 PMCID: PMC9500909 DOI: 10.3390/molecules27186055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/27/2022]
Abstract
The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.
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Isolation of functional ligninolytic Bacillus aryabhattai from paper mill sludge and its lignin degradation potential. BIOTECHNOLOGY REPORTS 2022; 35:e00755. [PMID: 35880093 PMCID: PMC9307452 DOI: 10.1016/j.btre.2022.e00755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Isolation of a functional lignin-degrading Bacillus aryabhattai. Production of growth-associated LiP and MnP enzymes. Almost 84% KL degradation at 500 mg L−1 KL concentration. KL biodegradation process was revealed by chemical analysis.
Kraft lignin (KL), is the major pollutant in pulp and paper effluent and due to its heterogeneous structure, it is resistant to the depolymerization process. It has drawn much attention from the researcher due to its challenging degradation process. In this study, a KL-degrading bacterium was isolated and screened from paper mill sludge. This bacterium was identified as ligninolytic Bacillus aryabhattai using biochemical and 16SrRNA gene analysis. B. aryabhattai showed maximum activities of lignin peroxidase-LiP (0.74 IU mL−1) and manganese peroxidase-MnP (9.2 IU mL−1) on the 4th day, and 5th day, respectively. A total 84% of KL (500 mg L−1) reduction was observed after 14 days. The KL bio-degradation was confirmed based on changes in chemical stracture of KL and new metabolites identification using FTIR and GC–MS, respectively. The study concluded that B. aryabhattai maybe becomes a potential biological agent in KL biodegradation and treatment of other lignin-containing industrial effluents.
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Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
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Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
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Mattoo AJ, Nonzom S. Endophytes in Lignin Valorization: A Novel Approach. Front Bioeng Biotechnol 2022; 10:895414. [PMID: 35928943 PMCID: PMC9343868 DOI: 10.3389/fbioe.2022.895414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lignin, one of the essential components of lignocellulosic biomass, comprises an abundant renewable aromatic resource on the planet earth. Although 15%––40% of lignocellulose pertains to lignin, its annual valorization rate is less than 2% which raises the concern to harness and/or develop effective technologies for its valorization. The basic hindrance lies in the structural heterogeneity, complexity, and stability of lignin that collectively makes it difficult to depolymerize and yield common products. Recently, microbial delignification, an eco-friendly and cheaper technique, has attracted the attention due to the diverse metabolisms of microbes that can channelize multiple lignin-based products into specific target compounds. Also, endophytes, a fascinating group of microbes residing asymptomatically within the plant tissues, exhibit marvellous lignin deconstruction potential. Apart from novel sources for potent and stable ligninases, endophytes share immense ability of depolymerizing lignin into desired valuable products. Despite their efficacy, ligninolytic studies on endophytes are meagre with incomplete understanding of the pathways involved at the molecular level. In the recent years, improvement of thermochemical methods has received much attention, however, we lagged in exploring the novel microbial groups for their delignification efficiency and optimization of this ability. This review summarizes the currently available knowledge about endophytic delignification potential with special emphasis on underlying mechanism of biological funnelling for the production of valuable products. It also highlights the recent advancements in developing the most intriguing methods to depolymerize lignin. Comparative account of thermochemical and biological techniques is accentuated with special emphasis on biological/microbial degradation. Exploring potent biological agents for delignification and focussing on the basic challenges in enhancing lignin valorization and overcoming them could make this renewable resource a promising tool to accomplish Sustainable Development Goals (SDG’s) which are supposed to be achieved by 2030.
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Affiliation(s)
| | - Skarma Nonzom
- *Correspondence: Skarma Nonzom, , orcid.org/0000-0001-9372-7900
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Mahuri M, Paul M, Sahu SK, Thatoi H. In silico homology modeling, docking and sequence analysis of some bacterial laccases to unravel enzymatic specificity towards lignin biodegradation. J Biomol Struct Dyn 2022:1-19. [PMID: 35838062 DOI: 10.1080/07391102.2022.2096117] [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: 10/17/2022]
Abstract
Laccase is a delignifying enzyme that belongs to the oxidoreductase family, and it has long been investigated as a pretreatment agent in biofuel production. In this study, amino acid sequences of five bacterial laccases from Bifidobacterium breve, Klebsiella pneumonia, Pseudodesulfovibrio hydrargyri, Pseudomonas aeruginosa and Veillonella rodentium have been retrieved from UniProtKB for sequence alignment, phylogenetic analysis using MEGA 7.0 and 3 D structure prediction by homology modeling in SWISS-MODEL. Multiple sequence alignment between all the bacterial laccase sequences revealed a similar structural fold, although the overall protein sequence varied greatly with the substrate binding sites. Further molecular docking in AutoDock Vina and MD stimulation (MDS) in GROMACS for those modelled enzymes were performed considering both apo and ligand bound structures considering both apo and its ligand bound form. Investigation of molecular interaction utilizing docking of five bacterial laccases with three substrates (ABTS, DMP and Guaiacol) revealed that ABTS with K. pneumoniae laccase had the highest binding energy of -7.00 kcal/mol. In the current MDS investigation, bacterial laccases demonstrated greater binding and substrate energy in the ligand bound complex than in the apo form for ABTS, DMP and Guaiacol. In most cases of bacterial laccase, MDS revealed that DMP bound complex was more stable within an average RMSD value lower than 0.5 nm throughout 100 ns time scale. Thus, in silico studies undertaken in this work will be useful in determining the stable enzyme-substrate complex which further might improve the enzymatic catalysis of bacterial laccases for lignin breakdown and biofuel generation.
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Affiliation(s)
- Monalisa Mahuri
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
| | - Sumanta Kumar Sahu
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
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Rammala B, Zhou N. Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:64. [PMID: 35689287 PMCID: PMC9188235 DOI: 10.1186/s13068-022-02159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.
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Affiliation(s)
- Bame Rammala
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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Brown B, Wilkins M, Saha R. Rhodopseudomonas palustris: A biotechnology chassis. Biotechnol Adv 2022; 60:108001. [PMID: 35680002 DOI: 10.1016/j.biotechadv.2022.108001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.
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Affiliation(s)
- Brandi Brown
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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Zuo K, Li H, Chen J, Ran Q, Huang M, Cui X, He L, Liu J, Jiang Z. Effective Biotransformation of Variety of Guaiacyl Lignin Monomers Into Vanillin by Bacillus pumilus. Front Microbiol 2022; 13:901690. [PMID: 35633711 PMCID: PMC9130762 DOI: 10.3389/fmicb.2022.901690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Biotransformation has gained increasing attention due to its being an eco-friendly way for the production of value-added chemicals. The present study aimed to assess the potential of Bacillus pumilus ZB1 on guaiacyl lignin monomers biotransformation for the production of vanillin. Consequently, isoeugenol, eugenol, and vanillyl alcohol could be transformed into vanillin by B. pumilus ZB1. Based on the structural alteration of masson pine and the increase of total phenol content in the supernatant, B. pumilus ZB1 exhibited potential in lignin depolymerization and valorization using masson pine as the substrate. As the precursors of vanillin, 61.1% of isoeugenol and eugenol in pyrolyzed bio-oil derived from masson pine could be transformed into vanillin by B. pumilus ZB1. Four monooxygenases with high specific activity were identified that were involved in the transformation process. Thus, B. pumilus ZB1 could emerge as a candidate in the biosynthesis of vanillin by using wide guaiacyl precursors as the substrates.
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Affiliation(s)
- Kangjia Zuo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Huanan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jianhui Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qiuping Ran
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Mengtian Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xinxin Cui
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lili He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jiashu Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhengbing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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Zhong H, Zhou J, Wang F, Wu W, Abdelrahman M, Li X. Whole-Genome Sequencing Reveals Lignin-Degrading Capacity of a Ligninolytic Bacterium (Bacillus cereus) from Buffalo (Bubalus bubalis) Rumen. Genes (Basel) 2022; 13:genes13050842. [PMID: 35627226 PMCID: PMC9140826 DOI: 10.3390/genes13050842] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 01/05/2023] Open
Abstract
The buffalo is an amazing ruminant. Its ability to degrade lignin, which has been recently reported, is most likely due to unique rumen microorganisms with lignin-degradation potential. Our goal was to explore the lignin-degradation potential of ruminal microorganisms, in which ligninolytic enzyme encoding genes were involved to provide ideas for revealing the mechanism of lignin degradation by buffalo. In this study, a bacterium strain identified as Bacillus cereus AH7-7 was isolated from the buffalo (Bubalus bubalis) rumen. After whole-genome sequencing, the results demonstrated that B. cereus AH7-7 had laccase, cytochrome P450 and vanillin alcohol oxidase-encoding genes. Sixty-four genes of B. cereus AH7-7 were involved in multiple aromatic metabolic pathways, such as phenylalanine metabolism and aminobenzoate degradation. A positive reaction resulting in guaiacol medium indicated that laccase secretion from B. cereus AH7-7 increased with time. A biodegradation experiment revealed that a significant reduction in kraft lignin content (25.9%) by B. cereus AH7-7 occurred at the end of 6 days of incubation, which confirmed its lignin-degradation capacity. Overall, this is the first report showing that B. cereus AH7-7 from the buffalo rumen can degrade lignin, and revealing the encoding genes of lignin-degrading enzymes from genome level.
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Affiliation(s)
- Huimin Zhong
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China; (H.Z.); (J.Z.); (F.W.); (W.W.)
| | - Jiayan Zhou
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China; (H.Z.); (J.Z.); (F.W.); (W.W.)
| | - Fan Wang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China; (H.Z.); (J.Z.); (F.W.); (W.W.)
| | - Wenqing Wu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China; (H.Z.); (J.Z.); (F.W.); (W.W.)
| | - Mohamed Abdelrahman
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Animal Production Department, Faculty of Agriculture, Assuit University, Asyut 71515, Egypt
| | - Xiang Li
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan 430070, China; (H.Z.); (J.Z.); (F.W.); (W.W.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-18995622055
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40
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Diet Fermentation Leads to Microbial Adaptation in Black Soldier Fly (Hermetia illucens; Linnaeus, 1758) Larvae Reared on Palm Oil Side Streams. SUSTAINABILITY 2022. [DOI: 10.3390/su14095626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Insects offer a promising alternative source of protein to mitigate the environmental consequences of conventional livestock farming. Larvae of the black soldier fly (Hermetia illucens; Linnaeus, 1758) efficiently convert a variety of organic side streams and residues into valuable proteins, lipids, and chitin. Here, we evaluated the suitability of two palm oil industry side streams—empty fruit bunches (EFB) and palm kernel meal (PKM)—as larval feed, and their impact on the larval gut microbiome. Among 69 fungal species we screened, Marasmius palmivorus, Irpex consors, and Bjerkandera adusta achieved the fastest growth and lignin degradation, so these fungi were used for the pretreatment of 7:3 mixtures of EFB and PKM. Larvae reared on the mixture pretreated with B. adusta (BAD) developed significantly more quickly and reached a higher final weight than those reared on the other pretreatments or the non-fermented reference (NFR). Amplicon sequencing of the BAD and NFR groups revealed major differences in the larval gut microbiome. The NFR group was dominated by facultatively anaerobic Enterobacteriaceae (typical of H. illucens larvae) whereas the BAD group favored obligately anaerobic, cellulolytic bacteria (Ruminococcaceae and Lachnospiraceae). We hypothesize that fungal lignin degradation led to an accumulation of mycelia and subsequent cellulolytic breakdown of fiber residues, thus improving substrate digestibility.
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41
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Hemati A, Nazari M, Asgari Lajayer B, Smith DL, Astatkie T. Lignocellulosics in plant cell wall and their potential biological degradation. Folia Microbiol (Praha) 2022; 67:671-681. [PMID: 35508797 DOI: 10.1007/s12223-022-00974-5] [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: 10/21/2021] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
Lignocellulosic materials are composed of three main structural polymers: hemicellulose, cellulose, and lignin. Cellulose is a long chain molecule of glucose requiring a small number of enzymes for degradation due to its simple structure while lignin is a complex polymer of phenylpropane making its biochemical decomposition difficult. Under anaerobic conditions, lignocellulose breakdown is much easier and more rapid than aerobic conditions. Various studies have been carried out to estimate the rate of degradation of lignocellulosic materials. Microorganisms play a key role in the degradation of lignocellulosic materials because they produce a variety of hydrolytic enzymes including cellulase, proteases, xylanases, lipases, laccase, and phosphatases during the degradation of lignocellulosic materials. Based on the body of literature, microorganismal activity can provide useful information about the process of organic matter decomposition.
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Affiliation(s)
- Arash Hemati
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mahtab Nazari
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Donald L Smith
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Tess Astatkie
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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42
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Wang H, Peng X, Li H, Giannis A, He C. Recent Biotechnology Advances in Bio-Conversion of Lignin to Lipids by Bacterial Cultures. Front Chem 2022; 10:894593. [PMID: 35494654 PMCID: PMC9039179 DOI: 10.3389/fchem.2022.894593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
The complexity and recalcitrance of the lignin structure is a major barrier to its efficient utilization and commercial production of high-value products. In recent years, the “bio-funneling” transformation ability of microorganisms has provided a significant opportunity for lignin conversion and integrated biorefinery. Based on the chemical structure of lignin, this mini-review introduces the recent advances of lignin depolymerization by bacterial strains and the application of microbial lignin degradation in lipids production. Furthermore, the current challenges, future trends and perspectives for microbe-based lignin conversion to lipids are discussed.
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Affiliation(s)
- Huan Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, China
- Guizhou Industry Polytechnic College, Guiyang, China
| | - Xiaodong Peng
- Guizhou Institute of Products Quality Inspection and Testing, Guiyang, China
| | - Hu Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, China
- *Correspondence: Hu Li, ; Chao He,
| | - Apostolos Giannis
- School of Chemical and Environmental Engineering, Technical University of Crete, University Campus, Chania, Greece
| | - Chao He
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
- *Correspondence: Hu Li, ; Chao He,
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43
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Schaefer A, Lee J, Soupir ML, Moorman TB, Howe A. Comparison of microbial communities in replicated woodchip bioreactors. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:205-215. [PMID: 34965312 DOI: 10.1002/jeq2.20320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Denitrification in woodchip bioreactors is a microbial process, but the effects of variations in bioreactors operation on microbial community structure are not well understood. Here, our goals were to understand hydraulic retention time (HRT) as a factor that influences woodchip bioreactor microbial community variation and structure in replicated field bioreactors and to evaluate relationships between microbial community membership and marker genes for denitrification. We used a combination of quantitative polymerase chain reaction of nirS, nirK, nosZI, and nosZII and 16S rRNA amplicon sequencing to characterize the microbial communities of nine pilot-scale woodchip bioreactors located at Iowa State University. Our results showed dynamic microbial communities but with persistent taxa between two sampling years and three HRTs. Similarities between functional gene copy numbers across sampling year and HRT indicate that the potential for denitrification is conserved despite differences in the microbial communities. These results are evidence that there are specific and persistent taxa within replicated bioreactors. Woodchip bioreactor microbial community membership is recommended to be the focus of future studies to better understand the relationship between microbial community functions and bioreactor management.
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Affiliation(s)
- Abby Schaefer
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Jaejin Lee
- Genomics and Environmental Research in Microbial Systems Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3346 Elings Hall, Ames, IA, 50011, USA
| | - Michelle L Soupir
- Water Quality Research Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3358 Elings Hall, Ames, IA, 50011, USA
| | - Thomas B Moorman
- USDA-ARS, National Laboratory for Agriculture and the Environment, 2110 University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Genomics and Environmental Research in Microbial Systems Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3346 Elings Hall, Ames, IA, 50011, USA
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Zovo K, Pupart H, Van Wieren A, Gillilan RE, Huang Q, Majumdar S, Lukk T. Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase from Streptomyces coelicolor A3(2). ACS OMEGA 2022; 7:6184-6194. [PMID: 35224382 PMCID: PMC8867573 DOI: 10.1021/acsomega.1c06668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Many industrial processes operate at elevated temperatures or within broad pH and salinity ranges. However, the utilization of enzymes to carry out biocatalysis in such processes is often impractical or even impossible. Laccases (EC 1.10.3.2), which constitute a large family of multicopper oxidases, have long been used in the industrial setting. Although fungal laccases are in many respects considered superior to their bacterial counterparts, the bacterial laccases have been receiving greater attention recently. Albeit lower in redox potential than fungal laccases, bacterial laccases are commonly thermally more stable, act within broader pH ranges, do not contain posttranslational modifications, and could therefore serve as a high potential scaffold for directed evolution for the production of enzymes with enhanced properties. Several examples focusing on the axial ligand mutations of the T1 copper site have been published in the past. However, structural evidence on the local and global changes induced by those mutations have thus far been of computational nature only. In this study, we set out to structurally and kinetically characterize a few of the most commonly reported axial ligand mutations of a bacterial small laccase (SLAC) from Streptomyces coelicolor. While one of the mutations (Met to Leu) equips the enzyme with better thermal stability, the other (Met to Phe) induces an opposite effect. These mutations cause local structural rearrangement of the T1 site as demonstrated by X-ray crystallography. Our analysis confirms past findings that for SLACs, single point mutations that change the identity of the axial ligand of the T1 copper are not enough to provide a substantial increase in the catalytic efficiency but can in some cases have a detrimental effect on the enzyme's thermal stability parameters instead.
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Affiliation(s)
- Kairit Zovo
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Hegne Pupart
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Arie Van Wieren
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Richard E. Gillilan
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Qingqiu Huang
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Sudipta Majumdar
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Tiit Lukk
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
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45
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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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Recent Advances in Synthesis and Degradation of Lignin and Lignin Nanoparticles and Their Emerging Applications in Nanotechnology. MATERIALS 2022; 15:ma15030953. [PMID: 35160893 PMCID: PMC8838035 DOI: 10.3390/ma15030953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/16/2023]
Abstract
Lignin is an important commercially produced polymeric material. It is used extensively in both industrial and agricultural activities. Recently, it has drawn much attention from the scientific community. It is abundantly present in nature and has significant application in the production of biodegradable materials. Its wide usage includes drug delivery, polymers and several forms of emerging lignin nanoparticles. The synthesis of lignin nanoparticles is carried out in a controlled manner. The traditional manufacturing techniques are costly and often toxic and hazardous to the environment. This review article highlights simple, safe, climate-friendly and ecological approaches to the synthesis of lignin nanoparticles. The changeable, complex structure and recalcitrant nature of lignin makes it challenging to degrade. Researchers have discovered a small number of microorganisms that have developed enzymatic and non-enzymatic metabolic pathways to use lignin as a carbon source. These microbes show promising potential for the biodegradation of lignin. The degradation pathways of these microbes are also described, which makes the study of biological synthesis much easier. However, surface modification of lignin nanoparticles is something that is yet to be explored. This review elucidates the recent advances in the biodegradation of lignin in the ecological system. It includes the current approaches, methods for modification, new applications and research for the synthesis of lignin and lignin nanoparticles. Additionally, the intricacy of lignin’s structure, along with its chemical nature, is well-described. This article will help increase the understanding of the utilization of lignin as an economical and alternative-resource material. It will also aid in the minimization of solid waste arising from lignin.
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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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48
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Liu ZC, Wang ZW, Gao S, Tong YX, Le X, Hu NW, Yan QS, Zhou XG, He YR, Wang L. Isolation and Fractionation of the Tobacco Stalk Lignin for Customized Value-Added Utilization. Front Bioeng Biotechnol 2021; 9:811287. [PMID: 34938726 PMCID: PMC8685371 DOI: 10.3389/fbioe.2021.811287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
The value-added utilization of tobacco stalk lignin is the key to the development of tobacco stalk resources. However, the serious heterogeneity is the bottleneck for making full use of tobacco stalk lignin. Based on this, lignin was separated from tobacco stalk through hydrothermal assisted dilute alkali pretreatment. Subsequently, the tobacco stalk alkaline lignin was fractionated into five uniform lignin components by sequential solvent fractionation. Advanced spectral technologies (FT-IR, NMR, and GPC) were used to reveal the effects of hydrothermal assisted dilute alkali pretreatment and solvent fractionation on the structural features of tobacco stalk lignin. The lignin fractions extracted with n-butanol and ethanol had low molecular weight and high phenolic hydroxyl content, thus exhibiting superior chemical reactivity and antioxidant capacity. By contrast, the lignin fraction extracted with dioxane had high molecular weight and low reactivity, nevertheless, the high residual carbon rate made it suitable as a precursor for preparing carbon materials. In general, hydrothermal assisted dilute alkali pretreatment was proved to be an efficient method to separate lignin from tobacco stalk, and the application of sequential solvent fractionation to prepare lignin fractions with homogeneous structural features has specific application prospect.
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Affiliation(s)
- Zhi Chang Liu
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Zi Wei Wang
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Song Gao
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Yu Xing Tong
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Xi Le
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Nian Wu Hu
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Qun Shan Yan
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Xian Gang Zhou
- China Tobacco Hubei Industrial Co., Ltd., Wuhan, China.,Hubei Xinye Reconstituted Tobacco Development Co., Ltd, Wuhan, China.,Applied Technology Research of Reconstituted Tobacco Hubei Province Key Laboratory, Wuhan, China
| | - Yan Rong He
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan, China
| | - Lei Wang
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan, China
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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: 5] [Impact Index Per Article: 1.7] [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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Agustin MB, de Carvalho DM, Lahtinen MH, Hilden K, Lundell T, Mikkonen KS. Laccase as a Tool in Building Advanced Lignin-Based Materials. CHEMSUSCHEM 2021; 14:4615-4635. [PMID: 34399033 PMCID: PMC8597079 DOI: 10.1002/cssc.202101169] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/09/2021] [Indexed: 05/22/2023]
Abstract
Lignin is an abundant natural feedstock that offers great potential as a renewable substitute for fossil-based resources. Its polyaromatic structure and unique properties have attracted significant research efforts. The advantages of an enzymatic over chemical or thermal approach to construct or deconstruct lignins are that it operates in mild conditions, requires less energy, and usually uses non-toxic chemicals. Laccase is a widely investigated oxidative enzyme that can catalyze the polymerization and depolymerization of lignin. Its dual nature causes a challenge in controlling the overall direction of lignin-laccase catalysis. In this Review, the factors that affect laccase-catalyzed lignin polymerization were summarized, evaluated, and compared to identify key features that favor lignin polymerization. In addition, a critical assessment of the conditions that enable production of novel lignin hybrids via laccase-catalyzed grafting was presented. To assess the industrial relevance of laccase-assisted lignin valorization, patented applications were surveyed and industrial challenges and opportunities were analyzed. Finally, our perspective in realizing the full potential of laccase in building lignin-based materials for advanced applications was deduced from analysis of the limitations governing laccase-assisted lignin polymerization and grafting.
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Affiliation(s)
- Melissa B. Agustin
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Danila Morais de Carvalho
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Maarit H. Lahtinen
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Kristiina Hilden
- Department of MicrobiologyFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
| | - Taina Lundell
- Department of MicrobiologyFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
| | - Kirsi S. Mikkonen
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
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