Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia

Applied Microbiology and Biotechnology

Volumn 97, Issue 20, 2013, Pages 8941-8954

  Wongwilaiwalin, Sarunyou ^a   Laothanachareon, Thanaporn ^a   Mhuantong, Wuttichai ^a   Tangphatsornruang, Sithichoke ^a   Eurwilaichitr, Lily ^a   Igarashi, Yasuo ^b   Champreda, Verawat ^a  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Biorefinery; Glycosyl hydrolase; Lignocellulose; Metagenome; Microbial consortium

Indexed keywords

BIOREFINERIES; GLYCOSYL HYDROLASES; LIGNOCELLULOSE; METAGENOMES; MICROBIAL CONSORTIA;

AGRICULTURAL WASTES; BIOCONVERSION; BIOMASS; CELLULOSE; ENZYME ACTIVITY; GENES; HYDROLASES; INDUSTRY; LIGNIN; PAPER AND PULP MILLS; PULP REFINING; REFINING; RNA;

PILES;

BAGASSE; BETA GLUCAN HYDROLASE; GLYCOSIDASE; LIGNOCELLULOSE; RNA 16S; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ACTIVATED SLUDGE; ANOXIC CONDITIONS; BIOMASS; CARBON CYCLE; COEXISTENCE; DECOMPOSITION; ENZYME; ENZYME ACTIVITY; FERMENTATION; GENE; MICROCOSM; RELATIVE ABUNDANCE;

ACETANAEROBACTERIUM; ACTIVATED SLUDGE; ANAEROBIC BACTERIUM; ARTICLE; BACILLUS; CLOSTRIDIUM; COMMUNITY STRUCTURE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME DEGRADATION; FERMENTATION; FIRMICUTES; GENE MAPPING; METAGENOMICS; MICROBIAL BIOMASS; MICROBIAL COMMUNITY; MICROBIAL CONSORTIUM; MICROCOSM; NONHUMAN; PULP MILL; PYROSEQUENCING; RICE; RNA ISOLATION; SUGARCANE; UREIBACILLUS;

BIOMASS; ENZYMES; GENETIC ENGINEERING; LIGNOCELLULOSE; MICROSTRUCTURE; PULP MILLS; REFINERS;

ACETANAEROBACTERIUM; CLOSTRIDIUM; FIRMICUTES; UREIBACILLUS;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BACTERIAL PROTEINS; BIOMASS; CATTLE; CELLULASES; CELLULOSE; INDUSTRIAL WASTE; LIGNIN; METAGENOMICS; MICROBIAL CONSORTIA; RUMEN; SACCHARUM; SEWAGE; SYMBIOSIS;

EID: 84885387137     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-4699-y     Document Type: Article

References (42)

1. Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, Vander Gheynst JS, Hugenholtz P (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5:e8812
2. Alvira P, Negro MJ, Ballesteros M (2011) Effect of endoxylanase and α-L-arabinofuranosidase supplementation on the enzymatic hydrolysis of steam exploded wheat straw. Bioresour Technol 102:4552-4558
3. Brulc JM, Antonopoulos DA, Miller MEB, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frankh ED, Emersoni JB, Wacklini P, Coutinhoj PM, Henrissatj B, Nelsoni KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Nat Acad Sci USA 106:1946-1953
4. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233-238
5. Chen S, Dong X (2004) Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water. Inter J Sys Evol Microbiol 54:2257-2262
6. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676
7. Crespo CF, Badshah M, Alvarez MT, Mattiasson B (2012) Ethanol production by continuous fermentation of D-(+)-cellobiose, D-(+)-xylose and sugarcane bagasse hydrolysate using the thermoanaerobe Caloramator boliviensis. Bioresour Technol 103:186-191
8. Doi RH (2008) Cellulases of mesophilic microorganisms cellulosome and noncellulosome producers. Ann NY Acad Sci 1125:267-279
9. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200
10. FitzPatrick M, Champagne P, Cunningham MF, Whitney RA (2010) A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products. Bioresour Technol 101:8915-8922
11. Fengel D, Wegener G (1984) Wood: chemistry, ultrastructure, reactions. De Gruyter, Berlin, Germany
12. Feng Y, Yu Y, Wang X, Qu Y, Li D, He W, Kim BH (2011) Degradation of raw corn stover powder (RCSP) by an enriched microbial consortium and its community structure. Bioresour Technol 102:742-747
13. Fu Z, Holtzapple MT (2010) Consolidated bioprocessing of sugarcane bagasse and chicken manure to ammonium carboxylates by a mixed culture of marine microorganisms. Bioresour Technol 101:2825-2836
14. Guo P, Zhu W, Wang H, Lü Y, Wang X, Zheng D, Cui Z (2010) Functional characteristics and diversity of a novel lignocelluloses degrading composite microbial system with high xylanase activity. J Microbiol Biotechnol 20:254-264
15. Haruta S, Cui Z, Huang Z, Li M, Ishii M, Igarashi Y (2002) Construction of a stable microbial community with high cellulose-degradation ability. Appl Microbiol Biotechnol 59:529-534
16. He Q, Hemme CL, Jiang H, He Z, Zhou J (2011) Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresour Technol 102:9586-9592
17. Kanokratana P, Uengwetwanit T, Rattanachomsri U, Bunterngsook B, Nimchua T, Tangphatsornruang S, Plengvidhaya V, Champreda V, Eurwilaichitr L (2010) Metagenomic analysis on phylogenetics and metabolic potential of microbial community in primary tropical peat swamp forest. Microb Ecol 61:518-528
18. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2004) Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria. FEMS Microbiol Ecol 51:133-142
19. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2005) Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl Environ Microbiol 71:7099-7106
20. Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2008) Network relationships of bacteria in a stable mixed culture. Microb Ecol 56:403-411
21. Li L-L, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (2009) Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuel 2:10
22. Lu Y, Zhang Y, Lynd LR (2006) Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum. Proc Nat Acad Sci USA 103:16165-16169
23. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107-1115
24. Lynd LR, Weimer PJ, Van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66:506-739
25. Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3:267-278
26. Mitchell WJ (1998) Physiology of carbohydrate to solvent conversion by clostridia. Adv Microb Physiol 39:31-130
27. Narisawa N, Haruta S, Cui ZJ, Ishii M, Igarashi Y (2007) Effect of adding cellulolytic bacterium on stable cellulose-degrading microbial community. J Biosci Bioeng 104:432-434
28. Nimchua T, Thongaram T, Uengwetwanit T, Pongpattanakitshote S, Eurwilaichitr L (2011) Metagenomic analysis of novel lignocellulose-degrading enzymes from higher termite guts inhabiting microbes. J Microbiol Biotechnol 22:462-469
29. Okura N, Soneura M, Ninomiya K, Katakura Y, Shioya S (2008) Biological detoxification of waste house wood hydrolysate using Ureibacillus thermosphaericus for bioethanol production. J Biosci Bioeng 106:128-133
30. Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M (2010) Adaptation of herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Nat Acad Sci 107:14793-14798
31. Rattanachomsri U, Tanapongpipat S, Eurwilaichitr L, Champreda V (2009) Simultaneous non-thermal saccharification of cassava pulp by multi-enzyme activity and ethanol fermentation by Candida tropicalis. J Biosci Bioeng 107:488-493
32. Ren N, Xing D, Rittmann BE, Zhao L, Xie T, Zhao X (2007) Microbial community structure of ethanol type fermentation in bio-hydrogen production. Environ Microbiol 9:1112-1125
33. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-7541
34. TAPPI (1992) TAPPI test method: determination of cellulose and pentosan contents of wood. Technical Association of Pulp and Paper Industry (TAPPI) Press, Atlanta
35. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267
36. Wang W, Yan L, Cui Z, Gao Y, Wang Y, Jing R (2011) Characterization of a microbial consortium capable of degrading lignocellulose. Bioresour Technol 102:9321-9324
37. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernandez M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560-565
38. Weber CF, Stubner S, Conrad R (2001) Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl Environ Microbiol 67:1318-1327
39. Wongwilaiwalin S, Rattanachomsri U, Laothanachareon T, Eurwilaichitr L, Igarashi Y, Champreda V (2010) Analysis of a thermophilic lignocellulose degrading microbial consortium and multi-species lignocellulolytic enzyme system. Enzym Microb Technol 47:283-290
40. Zhang Q, He J, Tian M, Maoa Z, Tang L, Zhang J, Zhang H (2011) Enhancement of methane production from cassava residues by biological pretreatment using a constructed microbial consortium. Bioresour Technol 102:8899-8906
41. Zhu H, Qu F, Zhu LH (1993) Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucleic Acids Res 21:5278-5280
42. Zuroff TR, Curtis WR (2012) Developing symbiotic consortia for lignocellulosic biofuel production. Appl Microbiol Biotechnol 93:1423-1435