Bioprospecting metagenomics of decaying wood: Mining for new glycoside hydrolases

Biotechnology for Biofuels

Volumn 4, Issue , 2011, Pages

  Li, Luen Luen ^a,b   Taghavi, Safiyh ^a,b   McCorkle, Sean M ^a,b   Zhang, Yian Biao ^a   Blewitt, Michael G ^a   Brunecky, Roman ^b,c   Adney, William S ^b,c   Himmel, Michael E ^b,c   Brumm, Phillip ^d,e   Drinkwater, Colleen ^d,e   Mead, David A ^d,e   Tringe, Susannah G ^f   Lelie, Daniel Van Der ^a,b,g  

^a BROOKHAVEN NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

^d LUCIGEN CORPORATION   (United States)

^e UNIVERSITY OF WISCONSIN MADISON   (United States)

^f DOE JOINT GENOME INSTITUTE   (United States)

^g RTI INTERNATIONAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANAEROBIC MICROBIAL COMMUNITY; CELLULOLYTIC ENZYME; DECAYING WOOD; DEGRADING ENZYMES; FERMENTABLE SUGARS; GENETIC DIVERSITY; GLYCOSIDE HYDROLASES; INDUSTRIAL PROCESSS; LOWER COST; METAGENOMES; METAGENOMICS; MICROBIAL BIOMASS; PLANT BIOMASS; POTENTIAL APPLICATIONS;

BAST FIBERS; BIOMASS; CATALYSTS; CLONING; ENZYME ACTIVITY; ESCHERICHIA COLI; HYDROLASES; IONS; MICROORGANISMS; PLANTS (BOTANY); SUGARS;

IONIC LIQUIDS;

BIODEGRADATION; BIOMASS; BIOTECHNOLOGY; ENZYME ACTIVITY; GENOMICS; MICROBIAL COMMUNITY; MICROORGANISM; WOOD;

BIOMASS; CATALYSTS; CLONES; IONS; MICROORGANISMS; PLANTS; POPULUS; SUGARS;

ESCHERICHIA COLI;

EID: 79961101712     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/1754-6834-4-23     Document Type: Article

References (30)

1. Himmel ME, Ed, Biomass Recalcitrance-Deconstructing the Plant Cell Wall for Bioenergy Chichester, UK: Wiley 2008
2. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Bayer EA, Belaich J-P, Shoham Y, Lamed R, Ann Rev Microbiol 2004 58 521 554 10.1146/annurev.micro.57.030502.091022 (Pubitemid 39551996)
3. Cellulosomes-structure and ultrastructure. Bayer EA, Shimon LJ, Shoham Y, Lamed R, J Struct Biol 1998 124 221 234 10.1006/jsbi.1998.4065 10049808 (Pubitemid 29143062)
4. Fuels and chemicals from biomass. Saha BC, Woodward J, Eds, American Chemical Society Symposium Series (ACS, Washington, DC, 1997) Washington, DC: American Chemical Society 1997 2 45
5. Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Feng Y, Duan C, Pang H, Mo X, Wu C, Yu Y, Appl Microbiol Biotechnol 2007 75 319 328 10.1007/s00253-006-0820-9 17216439 (Pubitemid 46866527)
6. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN, Environ Microbiol 2005 7 1966 2010
7. Metagenomics in animal gastrointestinal ecosystem: potential biotechnological prospects. Singh B, Gautam SK, Verma V, Kumar M, Singh B, Anaerobe 2008 14 138 144 10.1016/j.anaerobe.2008.03.002 18457965
8. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA, Nat Rev Microbiol 2008 6 121 131 10.1038/nrmicro1817 18180751
9. Symbioses of flagellates and prokaryotes in the gut of lower termites. Ohkuma M, Trends Microbiol 2008 16 345 352 10.1016/j.tim.2008.04.004 18513972
10. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. 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, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR, Nature 2007 450 560 565 10.1038/nature06269 18033299 (Pubitemid 350190243)
11. Termite digestomes as sources for novel lignocellulases. Scharf ME, Tartar A, Biofuel Bioprod Biorefin 2008 2 540 552 10.1002/bbb.107
12. Gut-associated microflora of Limnoria tripunctata in marine creosote-treated wood pilings. Zachary A, Colwell RR, Nature 1979 282 716 717 10.1038/282716a0
13. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P, PLoS ONE 2010 5 8812 10.1371/journal.pone.0008812 20098679
14. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A, J Biotechnol 2008 136 77 90 10.1016/j.jbiotec.2008. 05.008 18597880
15. Microbial community succession and lignocellulose degradation during agricultural waste composting. Yu H, Zeng G, Huang H, Xi X, Wang R, Huang D, Huang G, Li J, Biodegradation 2007 18 793 802 10.1007/s10532-007-9108-8 17308882 (Pubitemid 47624342)
16. Prokaryotes: the unseen majority. Whitman WB, Coleman DC, Wiebe WJ, Proc Natl Acad Sci USA 1998 95 6578 6583 10.1073/pnas.95.12.6578 9618454 (Pubitemid 28278022)
17. Combination of 16S rRNA targeted oligonucleotide probes with flow-cemetry for analysing mixed microbial populations. Amann RJ, Binder BL, Chisholm SW, Devereux R, Stahl DA, Appl Environ Microbiol 1990 56 1910 1925
18. Epstein SS, Ed, Uncultivated Microorganisms New York: Springer-Verlag 2009
19. The metagenomics of soil. Daniel R, Nat Rev Microbiol 2005 3 470 478 10.1038/nrmicro1160 15931165 (Pubitemid 40716173)
20. Metagenomics and industrial applications. Lorenz P, Eck J, Nature 2005 3 510 516 (Pubitemid 40716178)
21. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Li LL, McCorkle S, Monchy S, Taghavi S, van der Lelie D, Biotechnol Biofuel 2009 2 10 10.1186/1754-6834-2-10
22. Community structure and metabolism through reconstruction of microbial genomes from the environment. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF, Nature 2004 428 37 43 10.1038/nature02340 14961025 (Pubitemid 38332350)
23. Enzyme catalysis with small ionic liquid quantities. Fischer F, Mutschler J, Zufferey D, J Ind Microbiol Biotechnol 2011 38 477 487 10.1007/s10295-010- 0908-1 21107639
24. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW, Foust TD, Science 2007 315 804 807 10.1126/science.1137016 17289988
25. Dissolution of cellulose with ionic liquids. Swatloski RP, Spear SK, Holbrey JD, Rogers RD, J Am Chem Soc 2002 124 4974 4975 10.1021/ja025790m 11982358 (Pubitemid 34495887)
26. Mechanism of cellulose dissolution in the ionic liquid 1-n-butyl-3-methylimidazolium chloride: a 13C and 35/37Cl NMR relaxation study on model systems. Remsing RC, Swatloski RP, Rogers RD, Moyna G, Chem Commun (Camb) 2006 12 1271 1273
27. Applications of ionic liquids in carbohydrate chemistry: a window of opportunities. El Seoud OA, Koschella A, Fidale LC, Dorn S, Heinze T, Biomacromolecules 2007 8 2629 2647 10.1021/bm070062i 17691840 (Pubitemid 47516909)
28. Ionic liquid salt-induced inactivation and unfolding of cellulase from Trichoderma reesei. Turner MB, Spear SK, Huddleston JG, Holbrey JD, Rogers RD, Green Chem 2003 5 447
29. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Schmidt TM, DeLong EF, Pace NR, J Bacteriol 1991 173 4371 4378 2066334
30. Microbial enzyme systems for biomass conversion: emerging paradigms. Himmel ME, Xu Q, Luo Y, Ding S-Y, Lamed R, Bayer EA, Biofuels 2010 1 323 341 10.4155/bfs.09.25