Analysis of Molecular Diversity of Bacterial Chitinase Genes in the Maize Rhizosphere Using Culture-Independent Methods

Microbes and Environments

Volumn 22, Issue 1, 2007, Pages 71-77

  Ikeda, Seishi ^a,d   Ytow, Nozomi ^a   Ezura, Hiroshi ^a   Minamisawa, Kiwamu ^b   Miyashita, Kiyotaka ^c   Fujimura, Tatsuhito ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b TOHOKU UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE FOR AGRO ENVIRONMENTAL SCIENCES   (Japan)

^d NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

Author keywords

chitinase; maize; rhizosphere; Streptomyces avermitilis; T RFLP

Indexed keywords

EID: 60249092998     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.22.71     Document Type: Article

References (28)

1. Akutsu, K., A. Hirata, M. Yamamoto, K. Hirayae, S. Okuyama and T. Hibi. 1993. Growth inhibition of Botrytis spp. by Serratia marcescens B2 isolated from tomato phylloplane. Ann. Phytopath. Soc. Jpn. 59: 18–25.
2. Amann, R.I., W. Ludwig and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.
3. Cohen-Kupiec, R. and I. Chet. 1998. The molecular biology of chitin digestion. Curr. Opin. Biotechnol. 51: 270–277.
4. Cottrell, M.T., J.A. Moore and D.L. Kirchman. 1999. Chitinases from uncultured marine microorganisms. Appl. Envrion. Microbiol. 65: 2553–2557.
5. Cottrell, M.T., D.N. Wood, L. Yu and D.L. Kirchman. 2000. Selected chitinase genes in cultured and uncultured marine bacteria in the alpha- and gamma-subclasses of the proteobacteria. Appl. Environ. Microbiol. 66: 1195–1201.
6. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39: 783–791.
7. Felske, P.A. and T. Panda. 1999. Regulation and cloning of microbial chitinase genes. Appl. Environ. Microbiol. 65: 141–151.
8. Fuchs, R.L., S.A. McPherson and D.J. Drahos. 1986. Cloning of a Serratia marcescens gene encoding chitinase. Appl. Envrion. Microbiol. 51: 504–509.
9. Gonzalez-Franco, A.C., L.A. Deobald, A. Spivak and D.L. Crawford. 2003. Actinobacterial chitinase-like enzymes: profiles of rhizosphere versus non-rhizosphere isolates. Can. J. Microbiol. 49: 683–698.
10. Gooday, G.W. 1990. The ecology of chitin degradation. Adv. Microb. Ecol. 11: 387–430.
11. Ikeda, S., T. Fujimura and N. Ytow. 2005. Potential application of ribosomal intergenic spacer analysis to the microbial community analysis of agronomic products. J. Agric. Food Chem. 53: 5604–5611.
12. Ikeda, H., J. Ishikawa, A. Hanamoto, M. Shinose, H. Kikuchi, T. Shiba, Y. Sasaki, M. Hattori and S. Ōmura. 2003. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat. Biotechnol. 21: 526–531.
13. Ikeda, S., D.M. Roberts, K.N. Watanabe and N. Ytow. 2004. Microbial community analyses using a simple, rapid detection method for DNA fingerprints with a fluorescence scanner. J. Biosci. Bioeng. 98: 500–503.
14. Ikeda, S., K.N. Watanabe, K. Minamisawa and N. Ytow. 2004. Evaluation of soil DNA from arable land in Japan using a modified direct-extraction method. Microbes Environ. 19: 301–309.
15. Jack, G., S. Logemann, G. Wolf, A. Oppenheim, I. Chet, J. Schell and J. Logemann. 1992. Expression of a bacterial chitinase leads to improved resistance of transgenic tobacco plants against fungal infection. Biopractice 1: 33–41.
16. Metcalfe, A.C., M. Kresk, G.W. Gooday, J.I. Prosser and E.M.H. Wellington. 2002. Molecular analysis of a bacterial chitinolytic community in an upland pasture. Appl. Envrion. Microbiol. 68: 5042–5050.
17. Miyashita, K., T. Fujii and Y. Sawada. 1991. Molecular cloning and characterization of chitinase genes from Streptomyces lividans 66. J. Gen. Microbiol. 137: 2065–2072.
18. Newman, T., F.J. de Bruijin, P. Green, K. Keegstra, H. Kende, L. Mcintosh, J. Ohlrogge, N. Raikhel, S. Somerville, M. Thomashow, E. Retzel and C. Somerville. 1994. Gene Galore: a summary of methods for accessing results from large-scale sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 103: 359–370.
19. Nishimura, T., K. Toyota and M. Mochizuki. 2005. Predominant culturalbe Bacillus species in Japanese arable soils and their potential as biocotrol agents. Microbes Environ. 20: 61–68.
20. Ramaiah, N., R.T. Hill, J. Chun, J. Ravel, M.H. Matte, W.L. Straube and R.R. Colwell. 2000. Use of a chiA probe for detection of chitinase genes in bacteria from the Chesapeake Bay. FEMS Microbiol. Ecol. 34: 63–71.
21. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
22. Singh, B.K., P. Millard, A.S. Whiteley and J.C. Murrell. 2004. Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol. 12: 386–393.
23. Suzuki, K., M. Taiyoji, N. Sugawara, N. Nikaidou, B. Henrissat and T. Watanabe. 1999. The third chitinase gene (chiC) of Serratia marcescens 2170 and the relationship of its product to other bacterial chitinases. Biochem. J. 343: 587–596.
24. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLASTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
25. Tokala, R.K., J.L. Strap, C.M. Jung, D.L. Crawford, M.H. Salove, L.A. Deobald, J.F. Bailey and M.J. Morra. 2002. Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC 108 and the pea plant (Pisum sativum). Appl. Environ. Microbiol. 68: 2161–2171.
26. Watanabe, T., W. Oyanagi, K. Suzuki and H. Tanaka. 1990. Chitinases system of Bacillus circulans WL-12 and importance of chitinase A1 in chitin degradation. J. Bacteriol. 172: 4017–4022.
27. Watanabe, T., K. Suzuki, W. Oyanagi, K. Ohnishi and H. Tanaka. 1990. Gene cloning of chitinase A1 from Bacillus circulans WL-12 revealed its evolutionary relationship to Serratia chitinase and to the type III homology units of fibronectin. J. Biol. Chem. 265: 15659–15665.
28. Williamson, N., P. Brian and E.M.H. Wellington. 2001. Molecular detection of bacterial and stremptomycete chitinases in the environment. Antonie van Leeuwenhoek 78: 315–321.