Metagenomic SMRT Sequencing-Based Exploration of Novel Lignocellulose-Degrading Capability in Wood Detritus from Torreya nucifera in Bija Forest on Jeju Island
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초록
Lignocellulose, composed mostly of cellulose, hemicellulose, and lignin generated through secondary growth of woody plant, is considered as promising resources for biofuel. In order to use lignocellulose as a biofuel, biodegradation besides high-cost chemical treatments were applied, but knowledge on the decomposition of lignocellulose occurring in a natural environment is insufficient. We analyzed the 16S rRNA gene and metagenome to understand how the lignocellulose is decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment. A total of 464,360 reads were obtained from 16S rRNA gene sequencing, representing diverse phyla; Proteobacteria (51%), Bacteroidetes (11%) and Actinobacteria (10%). The metagenome analysis using single molecules real-time sequencing revealed that the assembled contigs determined originated from Proteobacteria (58%) and Actinobacteria (10.3%). Carbohydrate Active enZYmes (CAZy)- and Protein families (Pfam)-based analysis showed that Proteobacteria was involved in degrading whole lignocellulose, and Actinobacteria played a role only in a part of hemicellulose degradation. Combining these results, it suggested that Proteobacteria and Actinobacteria had selective biodegradation potential for different lignocellulose substrates. Thus, it is considered that understanding of the systemic microbial degradation pathways may be a useful strategy for recycle of lignocellulosic biomass, and the microbial enzymes in Bija forest can be useful natural resources in industrial processes.
Abstract
Lignocellulose, composed mostly of cellulose, hemicellulose, and lignin generated through secondary growth of woody plant, is considered as promising resources for biofuel. In order to use lignocellulose as a biofuel, biodegradation besides high-cost chemical treatments were applied, but knowledge on the decomposition of lignocellulose occurring in a natural environment is insufficient. We analyzed the 16S rRNA gene and metagenome to understand how the lignocellulose is decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment. A total of 464,360 reads were obtained from 16S rRNA gene sequencing, representing diverse phyla; Proteobacteria (51%), Bacteroidetes (11%) and Actinobacteria (10%). The metagenome analysis using single molecules real-time sequencing revealed that the assembled contigs determined originated from Proteobacteria (58%) and Actinobacteria (10.3%). Carbohydrate Active enZYmes (CAZy)- and Protein families (Pfam)-based analysis showed that Proteobacteria was involved in degrading whole lignocellulose, and Actinobacteria played a role only in a part of hemicellulose degradation. Combining these results, it suggested that Proteobacteria and Actinobacteria had selective biodegradation potential for different lignocellulose substrates. Thus, it is considered that understanding of the systemic microbial degradation pathways may be a useful strategy for recycle of lignocellulosic biomass, and the microbial enzymes in Bija forest can be useful natural resources in industrial processes.
참고문헌 (49)
- Lynd LR, "Microbial cellulose utilization: fundamentals and biotechnology", Microbiol. Mol. Biol. Rev, 66, pp.506~577 (2002)
- Lee H, "Conversion of lignocellulosic biomass to nanocellulose: structure and chemical process", ScientificWorldJournal, 2014, pp.631013~ (2014)
- Himmel ME, "Biomass recalcitrance: engineering plants and enzymes for biofuels production", Science, 315, pp.804~807 (2007)
- Gallezot P., "Conversion of biomass to selected chemical products", Chem. Soc. Rev, 41, pp.1538~1558 (2012)
- Kato DM, "Pretreatment of lignocellulosic biomass using Fenton chemistry", Bioresour. Technol, 162, pp.273~278 (2014)
- Iqbal HMN, "Advances in the valorization of lignocellulosic materials by biotechnology:an overview", BioResources, 8, pp.3157~3176 (2013)
- Mhuantong W, "Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities", Biotechnol. Biofuels, 8, pp.16~ (2015)
- Kanokratana P, "Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis", Microb. Ecol, 61, pp.518~528 (2011)
- Woo HL, "Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils", Syst. Appl. Microbiol, 37, pp.60~67 (2014)
- Aylward FO, "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens", ISME J, 6, pp.1688~1701 (2012)
- Scully ED, "Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle", PLoS One, 8, pp.e73827~ (2013)
- Metzker ML, "Sequencing technologies — the next generation", Nat. Rev. Genetics, 11, pp.31~46 (2010)
- Roberts RJ, "The advantages of SMRT sequencing", Genome Biol, 14, pp.405~ (2013)
- Qin W., "Recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms", Int. J. Biol. Sci, 12, pp.156~ (2016)
- Kim DS, "Plant Community Dynamics", 107~135 (2010)
- Caporaso JG, "Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms", ISME J, 6, pp.1621~1624 (2012)
- Caporaso JG, "QIIME allows analysis of high-throughput community sequencing data", Nat. Methods, 7, pp.335~336 (2010)
- Eren AM, "A filtering method to generate high quality short reads using Illumina paired-end technology", PLoS One, 8, pp.e66643~ (2013)
- Edgar RC, "Search and clustering orders of magnitude faster than BLAST", Bioinformatics, 26, pp.2460~2461 (2010)
- Cole JR, "The ribosomal database project: improved alignments and new tools for rRNA analysis", Nucleic Acids Res, 37, pp.D141~D145 (2009)
- Caporaso JG, "PyNAST: a flexible tool for aligning sequences to a template alignment", Bioinformatics, 26, pp.266~267 (2010)
- Sakai H, "The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome", Sci. Rep, 5, pp.16780~ (2015)
- Seemann T, "Prokka: rapid prokaryotic genome annotation", Bioinformatics, 30, pp.2068~2069 (2014)
- Hyatt D, "Prodigal: prokaryotic gene recognition and translation initiation site identification", BMC Bioinformatics, 11, pp.119~ (2010)
- Camacho C, "BLAST+: architecture and applications", BMC Bioinformatics, 10, pp.421~ (2009)
- Li P-E, "Enabling the democratization of the genomics revolution with a fully integrated Web-based bioinformatics platform", Nucleic Acids Res, 45, pp.67~80 (2017)
- Li H, "Fast and accurate long-read alignment with Burrows-Wheeler transform", Bioinformatics, 26, pp.589~595 (2010)
- O’Leary N A, "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation", Nucleic Acids Res, 44, pp.D733~D745 (2016)
- Cantarel BL, "The carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics", Nucleic Acids Res, 37, pp.D233~D238 (2009)
- Lombard V, "The carbohydrate-active enzymes database (CAZy) in 2013", Nucleic Acids Res, 42, pp.D490~D495 (2014)
- Park BH, "CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database", Glycobiology, 20, pp.1574~1584 (2010)
- Finn RD, "The Pfam protein families database:towards a more sustainable future", Nucleic Acids Res, 44, pp.D279~D285 (2016)
- Aziz RK, "The RAST server: rapid annotations using subsystems technology", BMC Genomics, 9, pp.75~ (2008)
- Huerta-Cepas J, "eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences", Nucleic Acids Res, 44, pp.D286~D293 (2016)
- Kanehisa M, "BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences", J. Mol. Biol, 428, pp.726~731 (2016)
- Konietzny SG, "Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders", Biotechnol. Biofuels, 7, pp.124~ (2014)
- Zhu D, "Biodegradation of alkaline lignin by Bacillus ligniniphilus L1", Biotechnol. Biofuels, 10, pp.44~ (2017)
- Zhang J, "Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta", Proc. Natl. Acad. Sci. USA, 113, pp.10968~10973 (2016)
- Horn SJ, "Novel enzymes for the degradation of cellulose", Biotechnol. Biofuels, 5, pp.45~ (2012)
- Kameshwar AKS, "Recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms", Int. J. Biol. Sci, 12, pp.156~171 (2016)
- 한송이, "상수리림 부식층으로부터 방향족 화합물 분해세균의 분리 및 세균군집의 계통학적 특성", 미생물학회지, 52(2), pp.175~182 (2016), 한국미생물학회[DOI]
- Jimenez DJ, "Characterization of three plant biomass-degrading microbial consortia by metagenomicsand metasecretomics-based approaches", Appl. Microbiol. Biotechnol, 100, pp.10463~10477 (2016)
- Folman LB, "Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil", FEMS Microbiol. Ecol, 63, pp.181~191 (2008)
- Lacerda Junior GV, "Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes", FEMS Microbiol. Ecol, 93, pp.fiw248~ (2017)
- Kim Y, "Differential assemblage of functional units in paddy soil microbiomes", PLoS One, 10, pp.e0122221~ (2015)
- Cragg SM, "Lignocellulose degradation mechanisms across the Tree of Life", Curr. Opin. Chem. Biol, 29, pp.108~119 (2015)
- Wang C, "Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition", Biotechnol. Biofuels, 9, pp.22~ (2016)
- Warnecke F, "Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite", Nature, 450, pp.560~565 (2007)
- Lopez-Mondejar R, "Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems", Sci. Rep, 6, pp.25279~ (2016)