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Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
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3
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Evaluation of natural materials as exogenous carbon sources for biological treatment of low carbon-to-nitrogen wastewater. BIOMED RESEARCH INTERNATIONAL 2015; 2015:754785. [PMID: 26495313 PMCID: PMC4606129 DOI: 10.1155/2015/754785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/19/2015] [Accepted: 03/30/2015] [Indexed: 11/17/2022]
Abstract
In the bacterial processes involved in the mitigation of nitrogen pollution, an adequately high carbon-to-nitrogen (C : N) ratio is key to sustain denitrification. We evaluated three natural materials (woodchips, barley grains, and peanut shells) as carbon sources for low C : N wastewater. The amount of organic matter released from these materials to aqueous media was evaluated, as well as their pollution swapping potential by measuring the release of total Kjeldahl nitrogen, N-NH4 (+), NO2 (-), and NO3 (-), and total phosphorous. Barley grains yielded the highest amount of organic matter, which also showed to be the most easily biodegradable. Woodchips and peanut shells released carbon rather steadily and so they would not require frequent replenishment from biological reactors. These materials produced eluates with lower concentrations of nutrients than the leachates from barley grains. However, as woodchips yielded lower amounts of suspended solids, they constitute an adequate exogenous source for the biological treatment of carbon-deficient effluents.
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 2014; 98:9527-44. [PMID: 25343973 DOI: 10.1007/s00253-014-6142-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/24/2022]
Abstract
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, 35044, Rennes, France
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6
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Větrovský T, Steffen KT, Baldrian P. Potential of cometabolic transformation of polysaccharides and lignin in lignocellulose by soil Actinobacteria. PLoS One 2014; 9:e89108. [PMID: 24551229 PMCID: PMC3923840 DOI: 10.1371/journal.pone.0089108] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 11/25/2022] Open
Abstract
While it is known that several Actinobacteria produce enzymes that decompose polysaccharides or phenolic compounds in dead plant biomass, the occurrence of these traits in the environment remains largely unclear. The aim of this work was to screen isolated actinobacterial strains to explore their ability to produce extracellular enzymes that participate in the degradation of polysaccharides and their ability to cometabolically transform phenolic compounds of various complexities. Actinobacterial strains were isolated from meadow and forest soils and screened for their ability to grow on lignocellulose. The potential to transform 14C-labelled phenolic substrates (dehydrogenation polymer (DHP), lignin and catechol) and to produce a range of extracellular, hydrolytic enzymes was investigated in three strains of Streptomyces spp. that possessed high lignocellulose degrading activity. Isolated strains showed high variation in their ability to produce cellulose- and hemicellulose-degrading enzymes and were able to mineralise up to 1.1% and to solubilise up to 4% of poplar lignin and to mineralise up to 11.4% and to solubilise up to 64% of catechol, while only minimal mineralisation of DHP was observed. The results confirm the potential importance of Actinobacteria in lignocellulose degradation, although it is likely that the decomposition of biopolymers is limited to strains that represent only a minor portion of the entire community, while the range of simple, carbon-containing compounds that serve as sources for actinobacterial growth is relatively wide.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Praha, Czech Republic
| | - Kari Timo Steffen
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki, Finland
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Praha, Czech Republic
- * E-mail:
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7
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Brown ME, Chang MCY. Exploring bacterial lignin degradation. Curr Opin Chem Biol 2013; 19:1-7. [PMID: 24780273 DOI: 10.1016/j.cbpa.2013.11.015] [Citation(s) in RCA: 283] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/26/2013] [Accepted: 11/29/2013] [Indexed: 12/18/2022]
Abstract
Plant biomass represents a renewable carbon feedstock that could potentially be used to replace a significant level of petroleum-derived chemicals. One major challenge in its utilization is that the majority of this carbon is trapped in the recalcitrant structural polymers of the plant cell wall. Deconstruction of lignin is a key step in the processing of biomass to useful monomers but remains challenging. Microbial systems can provide molecular information on lignin depolymerization as they have evolved to break lignin down using metalloenzyme-dependent radical pathways. Both fungi and bacteria have been observed to metabolize lignin; however, their differential reactivity with this substrate indicates that they may utilize different chemical strategies for its breakdown. This review will discuss recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
| | - Michelle C Y Chang
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-1460, USA.
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Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MCY. Discovery and characterization of heme enzymes from unsequenced bacteria: application to microbial lignin degradation. J Am Chem Soc 2011; 133:18006-9. [PMID: 21671563 DOI: 10.1021/ja203972q] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria and other living organisms offer a potentially unlimited resource for the discovery of new chemical catalysts, but many interesting reaction phenotypes observed at the whole organism level remain difficult to elucidate down to the molecular level. A key challenge in the discovery process is the identification of discrete molecular players involved in complex biological transformations because multiple cryptic genetic components often work in concert to elicit an overall chemical phenotype. We now report a rapid pipeline for the discovery of new enzymes of interest from unsequenced bacterial hosts based on laboratory-scale methods for the de novo assembly of bacterial genome sequences using short reads. We have applied this approach to the biomass-degrading soil bacterium Amycolatopsis sp. 75iv2 ATCC 39116 (formerly Streptomyces setonii and S. griseus 75vi2) to discover and biochemically characterize two new heme proteins comprising the most abundant members of the extracellular oxidative system under lignin-reactive growth conditions.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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Manangeeswaran M, Ramalingam VV, Kumar K, Mohan N. Degradation of indulin, a kraft pine lignin, by Serratia marcescens. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2007; 42:321-7. [PMID: 17454386 DOI: 10.1080/03601230701229320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Serratia marcescens isolated from decaying coconut pith exhibited high lignolytic activity. Growth on indicator medium, analysis of residual indulin, and infra-red spectroscopic analysis indicated the lignolytic potential of the isolate. Ortho-Coumaric acid, ferulic acid, 2,3-dihydroxy cinnamic acid and protocatechuic acid were identified as intermediates involved in indulin degradation by S. marcescens. Qualitative confirmation and quantitative estimation of the intermediates were carried out by high performance thin layer chromatography (HPTLC).
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Perestelo F, Falcón MA, Carnicero A, Rodríguez A, de la Fuente G. Limited degradation of industrial, synthetic and natural lignins by Serratia marcescens. Biotechnol Lett 1994. [DOI: 10.1007/bf00134629] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Swanson CL, Shogren RL, Fanta GF, Imam SH. Starch-plastic materials?Preparation, physical properties, and biodegradability (a review of recent USDA research). ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01418208] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ghosh P, Singh A. Physicochemical and Biological Treatments for Enzymatic/Microbial Conversion of Lignocellulosic Biomass. ADVANCES IN APPLIED MICROBIOLOGY 1993. [DOI: 10.1016/s0065-2164(08)70598-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Vasudevan N, Mahadevan A. Utilization of complex phenolic compounds by Acinetobacter sp. Appl Microbiol Biotechnol 1992. [DOI: 10.1007/bf00211002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Protein enrichment of lignocellulose resulting from the growth of two Streptomyces strains. World J Microbiol Biotechnol 1991; 7:624-5. [DOI: 10.1007/bf00452846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/1991] [Revised: 04/02/1991] [Indexed: 10/26/2022]
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Pasti MB, Pometto AL, Nuti MP, Crawford DL. Lignin-solubilizing ability of actinomycetes isolated from termite (Termitidae) gut. Appl Environ Microbiol 1990; 56:2213-8. [PMID: 2167628 PMCID: PMC184585 DOI: 10.1128/aem.56.7.2213-2218.1990] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The lignocellulose-degrading abilities of 11 novel actinomycete strains isolated from termite gut were determined and compared with that of the well-characterized actinomycete, Streptomyces viridosporus T7A. Lignocellulose bioconversion was followed by (i) monitoring the degradation of [14C]lignin- and [14C]cellulose-labeled phloem of Abies concolor to 14CO2 and 14C-labeled water-soluble products, (ii) determining lignocellulose, lignin, and carbohydrate losses resulting from growth on a lignocellulose substrate prepared from corn stalks (Zea mays), and (iii) quantifying production of a water-soluble lignin degradation intermediate (acid-precipitable polymeric lignin). The actinomycetes were all Streptomyces strains and could be placed into three groups, including a group of five strains that appear superior to S. viridosporus T7A in lignocellulose-degrading ability, three strains of approximately equal ability, and three strains of lesser ability. Strain A2 was clearly the superior and most effective lignocellulose decomposer of those tested. Of the assays used, total lignocellulose weight loss was most useful in determining overall bioconversion ability but not in identifying the best lignin-solubilizing strains. A screening procedure based on 14CO2 evolution from [14C-lignin]lignocellulose combined with measurement of acid-precipitable polymeric lignin yield was the most effective in identifying lignin-solubilizing strains. For the termite gut strains, the pH of the medium showed no increase after 3 weeks of growth on lignocellulose. This is markedly different from the pattern observed with S. viridosporus T7A, which raises the medium pH considerably. Production of extracellular peroxidases by the 11 strains and S. viridosporus T7A was followed for 5 days in liquid cultures.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M B Pasti
- Department of Bacteriology and Biochemistry, University of Idaho, Moscow 83843
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20
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Imam SH, Gould JM. Adhesion of an Amylolytic
Arthrobacter
sp. to Starch-Containing Plastic Films. Appl Environ Microbiol 1990; 56:872-6. [PMID: 16348173 PMCID: PMC184314 DOI: 10.1128/aem.56.4.872-876.1990] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells of the amylolytic bacterium KB-1 (thought to be an
Arthrobacter
sp.) adhered (∼70%) to the surface of plastic films composed of starch-poly (methylacrylate) graft copolymer (starch-PMA), but did not adhere (<10%) to films composed of polymethylacrylate (PMA), polyethylene (PE), carboxymethyl cellulose, or a mixture of PE plus poly (ethylene-coacrylic acid) (EAA), starch plus PE, or starch plus PE and EAA. About 30% of the cells adhered to gelatinized insoluble starch. Dithiothreitol (5 mM), EDTA (5 mM), and soluble starch (1%, wt/vol) had little effect on the adhesion of KB-1 cells to starch-PMA films. However, glutaraldehyde-fixed cells, azide-treated cells, and heat-killed cells did not bind to starch-PMA plastic, suggesting that the observed adhesion required cell viability. Culture supernatant from 5-day-old KB-1 cultures contained a proteolytic enzyme that inhibited cell adhesion to starch-PMA plastics. Trypsin-treated KB-1 cells also lost their ability to bind to starch-PMA plastic. When washed free of trypsin and suspended in fresh medium, trypsin-treated bacteria were able to recover adhesion activity in the absence, but not in the presence, of the protein synthesis inhibitor chloramphenicol. These results suggested that adhesion of KB-1 to starch-PMA plastic may be mediated by a cell surface protein. Although KB-1 bacteria bound to starch-PMA plastic, they did not appear to degrade starch in these films. Evidence of starch degradation was observed for starch-PE-EAA plastics, where <10% of the bacteria was bound, suggesting that cell adhesion may not be a prerequisite for degradation of some starch-containing plastics.
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Affiliation(s)
- S H Imam
- Northern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
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Monitoring bacterial consumption of low molecular weight lignin derivatives by high performance liquid chromatography. Enzyme Microb Technol 1986. [DOI: 10.1016/0141-0229(86)90090-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kerr TJ, Windham WR, Benner R. Chemical and Bacterial Pretreatment of Lignocellulosic Material to Increase Ruminant Digestibility. Nat Biotechnol 1984. [DOI: 10.1038/nbt0984-805] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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