Cellulose-and xylan-degrading thermophilic anaerobic bacteria from biocompost

Applied and Environmental Microbiology

Volumn 77, Issue 7, 2011, Pages 2282-2291

  Sizova, M V ^a,b,c   Izquierdo, J A ^a,b   Panikov, N S ^a,b,c   Lynd, L R ^a,b  

^a DARTMOUTH COLLEGE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c NORTHEASTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; BACTERIAL ISOLATES; CELLULASE ACTIVITY; CELLULOSE DEGRADATION; ENRICHMENT CULTURE; ENZYMATIC ACTIVITIES; FERMENTATION PRODUCTS; GENE SEQUENCES; GLYCOSYL HYDROLASES; GROWTH CESSATION; LAG PHASE; MICROCRYSTALLINE CELLULOSE; MINOR PRODUCTS; PHYLOGENETIC ANALYSIS; SYNERGISTIC EFFECT; THERMOPHILIC ANAEROBIC BACTERIA; XYLANASE ACTIVITY;

BACTERIA; BACTERIOLOGY; CELLULOSE; DEGRADATION; ETHANOL; FERMENTATION; GENES; GLYCEROL; HYDROLASES; RNA; VOLATILE FATTY ACIDS;

WOOD;

ACETIC ACID; ALCOHOL; BACTERIAL DNA; CELLULOSE; FORMIC ACID; FORMIC ACID DERIVATIVE; GLYCEROL; GLYCOSIDASE; LACTIC ACID; RIBOSOME DNA; RNA 16S; XYLAN;

ANOXIC CONDITIONS; CELLULOSE; COMPOST; DEGRADATION; ENZYME ACTIVITY; ETHANOL; FERMENTATION; PHYLOGENETICS; THERMOPHILIC BACTERIUM;

ANAEROBIC BACTERIUM; ARTICLE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; HEAT; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOIL;

ACETIC ACID; BACTERIA, ANAEROBIC; CELLULOSE; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; ETHANOL; FORMIC ACIDS; GLYCEROL; GLYCOSIDE HYDROLASES; HOT TEMPERATURE; LACTIC ACID; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; XYLANS;

BACTERIA; BACTERIOLOGY; CELLULOSE; DEGRADATION; ETHANOL; FATTY ACIDS; FERMENTATION; GENES; GLYCEROL; NUCLEIC ACIDS; WOOD;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM;

EID: 79953285101     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01219-10     Document Type: Article

References (46)

1. Adelsberger, H., C. Hertel, E. Glawischnig, V. V. Zverlov, and W. H. Schwarz. 2004. Enzyme system of Clostridium stercorarium for hydrolysis of arabinoxylan: reconstitution of the in vivo system from recombinant enzymes. Microbiology 150:2257-2266.
2. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Atlas, R. M. 1996. Handbook of microbiological media, 2nd ed. CRC Press LLC, Boca Raton, FL.
4. Beg, Q. K., M. Kapoor, L. Mahajan, and G. S. Hoondal. 2001. Microbial xylanases and their industrial applications: a review. Appl. Microbiol. Biotechnol. 56:326-338.
5. Burrell, P. C., C. O'Sullivan, H. Song, W. P. Clarke, and L. L. Blackall. 2004. Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor. Appl. Environ. Microbiol. 70:2414-2419.
6. Coleman, D. J., M. J. Studler, and J. J. Naleway. 2007. A long-wavelength fluorescent substrate for continuous fluorometric determination of cellulase activity: resorufin-beta-D-cellobioside. Anal. Biochem. 371:146-153.
7. Drent, W. J., G. A. Lahpor, W. M. Wiegant, and J. C. Gottschal. 1991. Fermentation of inulin by Clostridium thermosuccinogenes sp. nov., a thermophilic anaerobic bacterium isolated from various habitats. Appl. Environ. Microbiol. 57:455-462.
8. Freier, D., C. P. Mothershed, and J. Wiegel. 1988. Characterization of Clostridium thermocellum JW20. Appl. Environ. Microbiol. 54:204-211.
9. Ge, Y., E. G. Antoulinakis, K. R. Gee, and I. Johnson. 2007. An ultrasensitive, continuous assay for xylanase using the fluorogenic substrate 6,8-difluoro-4-methylumbelliferyl [beta]-d-xylobioside. Anal. Biochem. 362:63-68.
10. Gilbert, H. J., and G. P. Hazelwood. 1993. Bacterial cellulases and xylanases. J. Gen. Microbiol. 139:187-194.
11. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
12. Hamilton-Brehm, S. D., et al. 2010. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl. Environ. Microbiol. 76: 1014-1020.
13. Izquierdo, J. A., M. V. Sizova, and L. R. Lynd. 2010. Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl. Environ. Microbiol. 76:3545-3553.
14. Junge, K., F. Imhoff, T. Staley, and J. W. Deming. 2002. Phylogenetic diversity of numerically important arctic sea-ice bacteria cultured at subzero temperature. Microb. Ecol. 43:315-328.
15. Kato, S., et al. 2004. Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community. Int. J. Syst. Evol. Microbiol. 54:2043-2047.
16. Kato, S., S. Haruta, Z. J. Cui, M. Ishii, and Y. Igarashi. 2005. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 71:7099-7106.
17. Kosugi, A., K. Murashima, and R. H. Doi. 2001. Characterization of xylanolytic enzymes in Clostridium cellulovorans: expression of xylanase activity dependent on growth substrates. J. Bacteriol. 183:7037-7043.
18. Kulkarni, N., A. Shendye, and M. Rao. 1999. Molecular and biotechnological aspects of xylanases. FEMS Microbiol. Rev. 23:411-456.
19. Lu, Y., Y. H. Zhang, and L. R. Lynd. 2006. Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum. Proc. Natl. Acad. Sci. U. S. A. 103:16165-16169.
20. Lynd, L. R., D. Currie, N. Ciazza, C. Herring, and N. Orem. 2008. Consolidated bioprocessing of cellulosic biomass to ethanol using thermophilic bacteria, p. 55-74. In J. D. Wall et al. (ed.), Bioenergy. ASM Press, Washington, DC.
21. Lynd, L. R., et al. 2008. How biotech can transform biofuels. Nat. Biotechnol. 26:169-172.
22. Lynd, L. R., P. J. Weimer, W. H. van Zyl, and I. S. Pretorius. 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66:506-577.
23. Madden, R. H. 1983. Isolation and characterization of Clostridium stercorarium sp. nov., cellulolytic thermophile. Int. J. Syst. Bacteriol. 33:837-840.
24. Morag, E., E. A. Bayer, and R. Lamed. 1990. Relationship of cellulosomal and noncellulosomal xylanases of Clostridium thermocellum to cellulosedegrading enzymes. J. Bacteriol. 172:6098-6105.
25. Ozkan, M., et al. 2001. Characterization of 13 newly isolated strains of anaerobic, cellulolytic, thermophilic bacteria. J. Ind. Microbiol. Biotechnol. 27:275-280.
26. Panikov, N. S., and L. R. Lynd. 2010. Physiological and methodological aspects of cellulolytic microbial cultures, p 644-656. In R. H. Baltz et al. (ed.), Manual of industrial microbiology and biotechnology, 3rd ed. ASM Press, Washington, DC.
27. Rainey, F. A., et al. 1994. Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium. FEMS Microbiol. Lett. 120:263-266.
28. Rzhetsky, A., and M. Nei. 1992. Statistical properties of the ordinary leastsquares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J. Mol. Evol. 35:367-375.
29. Saha, B. C. 2003. Hemicellulose bioconversion. J. Ind. Microbiol. Biotechnol. 30:279-291.
30. Shiratori, H., et al. 2006. Isolation and characterization of a new Clostridium sp. that performs effective cellulosic waste digestion in a thermophilic methanogenic bioreactor. Appl. Environ. Microbiol. 72:3702-3709.
31. Shiratori, H., et al. 2008. Lutispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming bacterium isolated from a thermophilic methanogenic bioreactor digesting municipal solid wastes. Int. J. Syst. Evol. Microbiol. 58:964-969.
32. Shiratori, H., et al. 2009. Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge. Int. J. Syst. Evol. Microbiol. 59:1764-1770.
33. Sizova, M. V., N. S. Panikov, T. P. Tourova, and P. W. Flanagan. 2003. Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol. Ecol. 45:301-315.
34. Sleat, R., R. A. Mah, and R. Robinson. 1984. Isolation and characterization of an anaerobic, cellulolytic bacterium, Clostridium cellulovorans sp. nov. Appl. Environ. Microbiol. 48:88-93.
35. Staley, J. T., and J. J. Gosink. 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53:189-215.
36. Svetlichny, V. A., T. P. Svetlichnaya, N. Chernykh, and G. A. Zavarzin. 1990. Anaerocellum thermophilum gen. nov. sp. nov, an extreme thermophilic celluloselytic eubacterium isolated from hot springs in the Valley of Geysers. Microbiology (Moscow) 59:871-879.
37. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
38. Tang, Y. Q., T. Matsui, S. Morimura, X. L. Wu, and K. Kida. 2008. Effect of temperature on microbial community of a glucose-degrading methanogenic consortium under hyperthermophilic chemostat cultivation. J. Biosci. Bioeng. 106:180-187.
39. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
40. Thomson, J. A. 1993. Molecular biology of xylan degradation. FEMS Microbiol. Rev. 10:65-82.
41. U.S. Environmental Protection Agency. 2007. Biomass conversion: emerging technologies, feedstocks, and products. EPA/600/R-07/144. U.S. Environmental Protection Agency, Washington, DC.
42. van de Werken, H. J. G., et al. 2008. Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl. Environ. Microbiol. 74:6720-6729.
43. Warnick, T. A., B. A. Methe, and S. B. Leschine. 2002. Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int. J. Syst. Evol. Microbiol. 52:1155-1160.
44. Wiegel, J., and M. Dykstra. 1984. Clostridium thermocellum: adhesion and sporulation while adhered to cellulose and hemicellulose. Appl. Microbiol. Biotechnol. 20:59-65.
45. Yang, S.-J., et al. 2009. Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Appl. Environ. Microbiol. 75:4762-4769.
46. Zverlov, V. V., and W. H. Schwarz. 2008. Bacterial cellulose hydrolysis in anaerobic environmental subsystems-Clostridium thermocellum and Clostridium stercorarium, thermophilic plant-fiber degraders. Ann. N. Y. Acad. Sci. 1125:298-307.