Identification of cellulolytic bacteria in soil by stable isotope probing

Environmental Microbiology

Volumn 9, Issue 3, 2007, Pages 625-634

  Haichar, Feth El Zahar ^a   Achouak, Wafa ^a   Christen, Richard ^b   Heulin, Thierry ^a   Marol, Christine ^a   Marais, Marie France ^c   Mougel, Christophe ^d   Ranjard, Lionel ^d   Balesdent, Jérôme ^a,e   Berge, Odile ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b CENTRE DE BIOCHIMIE   (France)

^c CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

^d UNIVERSITÉ DE BOURGOGNE   (France)

^e CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARBON; CELLULOSE; RIBOSOMAL SPACER DNA; RNA 16S;

ARTICLE; BACTERIUM; CLASSIFICATION; DENSITY GRADIENT CENTRIFUGATION; DNA SEQUENCE; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BACTERIA; CARBON ISOTOPES; CELLULOSE; CENTRIFUGATION, DENSITY GRADIENT; DNA, BACTERIAL; DNA, RIBOSOMAL SPACER; ECOSYSTEM; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); GLUCONACETOBACTER XYLINUS;

EID: 33846990441     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2006.01182.x     Document Type: Article

References (51)

1. An, D.S., Im, W.T., Yang, H.C., Yang, D.C., and Lee, S.T. (2005) Dyella koreensis sp. nov., a beta-glucosidase-producing bacterium. Int J Syst Evol Microbiol 55: 1625-1628.
2. Barr, B.K., Hsieh, Y.L., Ganem, B., and Wilson, D.B. (1996) Identification of two functionally different classes of exocellulases. Biochemistry 35: 586-592.
3. Béguin, P., and Aubert, J.P. (1994) The biological degradation of cellulose. FEMS Microbiol Rev 13: 25-58.
4. Bera-Maillet, C., Arthaud, L., Abad, P., and Rosso, M.N. (2000) Biochemical characterization of MI-ENG1, a family 5-endoglucanase secreted by the root-knot nematode Meloidogyne incognita. Eur J Biochem 267: 3255-3263.
5. Coughlan, M.P., and Mayer, F. (1992) The cellulose-decomposing bacteria and their enzyme systems. In The Prokaryotes: A Handbook on the Biology of Bacteria, 2nd edn. Balows, A., Trüper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds). New York, USA: Springer-Verlag, pp. 460-516.
6. 13C natural abundance. Eur J Soil Sci 57: 547-557.
7. Dumont, M.G., and Murrell, J.C. (2005) Stable isotope probing linking microbial identity to function. Nat Rev Microbiol 3: 499-504.
8. Freitag, T.E., Chang, L., and Prosser, J.I. (2005) Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ Microbiol 8: 684-696.
9. Friedrich, M.W. (2006) Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol 17: 59-66.
10. Friedrich, U., Prior, K., Altendorf, K., and Lipski, A. (2002) High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library. Environ Microbiol 4: 721-734.
11. Galtier, N., Gouy, M., and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
12. Gascuel, O. (1997) BIONJ, an improved version of the NJ algorithm based on a simple method of sequence data. Mol Biol Evol 14: 685-695.
13. Germida, J.J. (1988) Growth of indigenous Rhizobium leguminosarum and Rhizobium meliloti in soils amended with organic nutrients. Appl Environ Microbiol 54: 257-263.
14. Goellner, M., Wang, X., and Davis, E.L. (2001) Endo-beta-1,4-glucanase expression in compatible plant-nematode interactions. Plant Cell 13: 2241-2255.
15. Gromet-Elhanan, Z., and Hestrin, S. (1962) Synthesis of cellulose by Acetobacter xylinum. J Bacteriol 85: 284-292.
16. Higashi, S., and Abe, M. (1980) Scanning electron microscopy of Rhizobium trifolii infection sites on root hairs of white clover. Appl Environ Microbiol 40: 1094-1099.
17. Holben, W.E., Feris, K.P., Kettunen, A., and Apajalahti, J.H. (2004) GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol 70: 2263-2270.
18. Hubbell, D.H., Morales, V.M., and Umali-Garcia, M. (1978) Pectolytic enzymes in Rhizobium. Appl Environ Microbiol 35: 210-213.
19. Kato, S., Haruta, S., Cui, Z.J., Ishii, M., and Igarashi, Y. (2005) Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl Environ Microbiol 71: 7099-7106.
20. Kelley, S.T., Theisen, U., Angenent, L.T., St Amand, A., and Pace, N.R. (2004) Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol 70: 4187-4192.
21. Lednicka, D., Mergaert, J., Cnockaert, M.C., and Swings, J. (2000) Isolation and identification of cellulolytic bacteria involved in the degradation of natural cellulosic fibres. Syst Appl Microbiol 23: 292-299.
22. Lueders, T., Manefield, M., and Friedrich, M.W. (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73-78.
23. Lynd, L.R., Weimer, P.J., Van Zyl, W.H., and Pretorius, I.S. (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506-577.
24. McCaig, A.E., Glover, L.A., and Prosser, J.I. (2001) Numerical analysis of grassland bacterial community structure under different land management regimes by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol 67: 4554-4559.
25. Mahmood, S., Paton, G.I., and Prosser, J.I. (2005) Cultivation independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 7: 1349-1360.
26. Manefield, M., Whiteley, A.S., Griffiths, R.I., and Bailey, M.J. (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367-5373.
27. Männistö, M.K., and Häggblom, M.M. (2006) Characterization of psychrotolerant heterotrophic bacteria from Finnish Lapland. Syst Appl Microbiol 29: 229-243.
28. Mateos, P.F., Jimenez-Zurdo, J.I., Chen, J., Squartini, A.S., Haack, S.K., Martinez-Molina, E., et al. (1992) Cell-associated pectinolytic and cellulolytic enzymes in Rhizobium leguminosarum biovar trifolii. Appl Environ Microbiol 58: 1816-1822.
29. Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
30. Navarrete-Bolanos, J.L., Jimenez-Islas, H., Botello-Alvarez, E., and Rico-Martinez, R. (2003) Mixed culture optimization for marigold flower ensilage via experimental design and response surface methodology. J Agric Food Chem 51: 2206-2211.
31. Olson, R.A., and Bakken, L.R. (1987) Viability of soil bacteria: optimization of plate-counting technique and comparison between total counts and plate counts within different size groups. Microbiol Ecol 13: 59-74.
32. 13C-labeled soil DNA. Appl Environ Microbiol 69: 1614-1622.
33. Paul, E.A., and Clark, F.E. (1989) Soil Microbiology and Biochemistry. London, UK: Academic Press, pp. 93-97.
34. Radajewski, S., Ineson, P., Parekh, N.R., and Murell, J.C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646-649.
35. Rangel-Castro, J.I., Killham, K., Ostle, N., Nicol, G.W., Anderson, I.C., Scrimgeour, C.M., et al. (2005) Stable isotope probing analysis of the influence of liming on root exudates utilization by soil microorganisms. Environ Microbiol 7: 828-838.
36. Ranjard, L., Poly, F., Lata, J.C., Mougel, C., Thioulouse, J., and Nazaret, S. (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67: 4479-4487.
37. Ranjard, L., Lejon, D.P.H., Mougel, C., Schehrer, L., Merdinoglu, D., and Chaussod, R. (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 11: 1111-1120.
38. Reese, E.T., Siu, R.G.H., and Levinson, H.S. (1950) The biological degradation of soluble cellulose derivatives and its relationship to the mechanism of cellulose hydrolysis. J Bacteriol 59: 485-497.
39. Semêdo, L.T., Gomes, R.C., Bon, E.P., Soares, R.M., Linhares, L.F., and Coelho, R.R. (2000) Endocellulase and exocellulase activities of two Streptomyces strains isolated from a forest soil. Appl Biochem Biotechnol 84-86: 267-276.
40. Singh, A., and Hayashi, K. (1995) Microbial cellulases: protein architecture, molecular properties, and biosynthesis. Adv Appl Microbiol 40: 1-44.
41. Singleton, D.R., Powell, S.N., Sangaiah, R., Gold, A., Ball, L.M., and Aitken, M.D. (2005) Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl Environ Microbiol 71: 1202-1209.
42. Thioulouse, J., Chessel, D., Dolédec, S., and Olivier, J.M. (1997) ADE-4: a multivariate analysis and graphical display software. Stat Comput 7: 75-83.
43. Vandekerckhove, T.T., Willems, A., Gillis, M., and Coomans, A. (2000) Occurrence of novel Verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae). Int J Syst Evol Microbiol 50: 2197-2205.
44. Wachinger, G., Bronnenmeier, K., Staudenbauer, W.L., and Schrempf, H. (1989) Identification of mycelium-associated cellulase from Streptomyces reticuli. Appl Environ Microbiol 55: 2653-2657.
45. Wang, Y., and Hsieh, Y.P. (2002) Uncertainties and novel prospects in the study of the soil carbon dynamics. Chemosphere 49: 791-804.
46. Warnick, T.A., Methe, B.A., and Leschine, S.B. (2002) Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int J Syst Evol Microbiol 52: 1155-1160.
47. Wirth, S., and Ulrich, A. (2002) Cellulose degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil. Syst Appl Microbiol 25: 584-591.
48. Wong, H.C., Fear, A.L., Calhoon, R.D., Eichinger, G.H., Mayer, R., Amikam, D., et al. (1990) Genetic organization of the cellulose synthase operon in Acetobacter xylinum. Proc Natl Acad Sci USA 87: 8130-8134.
49. Wood, T.M., McCrae, S.I., and Bhat, K.M. (1989) The mechanism of fungal cellulase action. Synergism between enzyme components of Penicillium pinophilum cellulase in solubilizing hydrogen bond-ordered cellulose. Biochem J 260: 37-43.
50. Yan, Z.C., Wang, B., Li, Y.Z., Gong, X., Zhang, H.Q., and Gao, P.J. (2003) Morphologies and phylogenetic classification of cellulolytic Myxobacteria. Syst Appl Microbiol 26: 104-109.
51. Zhou, S., and Ingram, L.O. (2000) Synergistic hydrolysis of carboxymethyl cellulose and acid-swollen cellulose by two endoglucanases (CelZ and CelY) from Erwinia chrysanthemi. J Bacteriol 182: 5676-5682.