Analysis of a change in bacterial community in different environments with addition of chitin or chitosan

Journal of Bioscience and Bioengineering

Volumn 109, Issue 5, 2010, Pages 472-478

  Sato, Kazuaki ^a   Azama, Yasuhito ^a   Nogawa, Masahiro ^a   Taguchi, Goro ^a   Shimosaka, Makoto ^a  

^a SHINSHU UNIVERSITY   (Japan)

Author keywords

16S rRNA gene; Bacterial community; Chitin; Chitosan; PCR DGGE; Unculturable bacteria

Indexed keywords

16S RRNA GENE; 16S RRNA SEQUENCES; BACTERIAL CELLS; BACTERIAL COMMUNITY; BAND PATTERNS; CHITIN-CHITOSAN; DENATURING GRADIENT GEL ELECTROPHORESIS; NATURAL ENVIRONMENTS; NUCLEOTIDE SEQUENCES; PCR-DGGE; PROTEOBACTERIA; TEMPORAL CHANGE;

BACTERIOLOGY; CHITOSAN; ELECTROPHORESIS; RNA; SOILS;

CHITIN;

BACTERIAL DNA; BACTERIAL RNA; CHITIN; CHITOSAN; RIBOSOME RNA;

ARTICLE; BACTERIUM IDENTIFICATION; BIODEGRADATION; BIODIVERSITY; CELLVIBRIO; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; GENE TARGETING; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; RIVER; RNA SEQUENCE; SOIL MICROFLORA;

ADAPTATION, PHYSIOLOGICAL; CHITIN; CHITOSAN; ENVIRONMENT; PROTEOBACTERIA; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); CELLVIBRIO; PROTEOBACTERIA; UNIDENTIFIED BACTERIUM;

EID: 77949910288     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2009.10.021     Document Type: Article

References (44)

1. Tharanathan R.N., and Kittur F.S. Chitin-the undisputed biomolecule of great potential. Crit. Rev. Food Sci. Nutr. 43 (2003) 61-87
2. Synowiecki J., and Al-Khateeb N.A. Production, properties, and some new applications of chitin and its derivatives. Crit. Rev. Food Sci. Nutr. 43 (2003) 145-171
3. Chandy T., and Sharma C.P. Chitosan-as a biomaterial. Biomater. Artif. Cells Artif. Organs 18 (1990) 1-24
4. Raafat D., von Bargen K., Haas A., and Sahl H.G. Insights into the mode of action of chitosan as an antibacterial compound. Appl. Environ. Microbiol. 74 (2008) 3764-3773
5. Cohen-Kupiec R., and Chet I. The molecular biology of chitin digestion. Curr. Opin. Biotechnol. 9 (1998) 270-277
6. Ueno H., Mori T., and Fujinaga T. Topical formulations and wound healing applications of chitosan. Adv. Drug Deliv. Rev. 52 (2001) 105-115
7. Masotti A., and Ortaggi G. Chitosan micro- and nanospheres: fabrication and applications for drug and DNA delivery. Mini Rev. Med. Chem. 9 (2009) 463-469
8. Alves N.M., and Mano J.F. Chitosan derivatives obtained by chemical modifications for biomedical and environmental applications. Int. J. Biol. Macromol. 43 (2008) 401-414
9. Kobayashi D.Y., Reedy R.M., Bick J., and Oudemans P.V. Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control. Appl. Environ. Microbiol. 68 (2002) 1047-1054
10. Hjort K., Lembke A., Speksnijder A., Smalla K., and Jansson J.K. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. Microb. Ecol. 53 (2007) 399-413
11. Dahiya N., Tewari R., and Hoondal G.S. Biotechnological aspects of chitinolytic enzymes: a review. Appl. Microbiol. Biotechnol. 71 (2006) 773-782
12. Waniska R.D., Venkatesha R.T., Chandrashekar A., Krishnaveni S., Bejosano F.P., Jeoung J., Muthukrishnan S., and Liang G.H. Antifungal proteins and other mechanisms in the control of sorghum stalk rot and grain mold. J. Agric. Food Chem. 49 (2001) 4732-4742
13. Kaku H., Nishizawa Y., Ishii-Minami N., Akimoto-Tomiyama C., Dohmae N., Takio K., Minami E., and Shibuya N. Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 11086-11091
14. Ebel J. Oligoglucoside elicitor-mediated activation of plant defense. BioEssays 20 (1998) 569-576
15. Riesenfeld C.S., Schloss P.D., and Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38 (2004) 525-552
16. Singh J., Behal A., Singla N., Joshi A., Birbian N., Singh S., Bali V., and Batra N. Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol. J. 4 (2009) 480-494
17. Rappe M.S., and Giovannoni S.J. The uncultured microbial majority. Annu. Rev. Microbiol. 57 (2003) 369-394
18. Schloss P.D., and Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 6 (2005) 229
19. Rajendhran J., and Gunasekaren P. Strategies for accessing soil metagenome for desired applications. Biotechnol. Adv. 26 (2008) 576-590
20. Streit W.R., and Schmitz R.A. Metagenomics-the key to the uncultured microbes. Curr. Opin. Microbiol. 7 (2004) 492-498
21. Rodriguez-Valera F. Approaches to prokaryotic biodiversity: a population genetics perspective. Environ. Microbiol. 4 (2002) 628-633
22. Neefs J.M., Van de Peer Y., De Rijk P., Chapelle S., and De Wachter R. Comparison of small ribosomal subunit RNA structures. Nucleic Acids Res. 21 (1993) 3025-3049
23. Woodson S.A., and Leontis N.B. Structure and dynamics of ribosomal RNA. Curr. Opin. Struct. Biol. 8 (1998) 294-300
24. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
25. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
26. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
27. Rohland N., and Hofreiter M. Comparison and optimization of ancient DNA extraction. Biotechniques 42 (2007) 343-352
28. Wynne E.C., and Pemberton J.M. Cloning of a gene cluster from Cellvibrio mixtus which codes for cellulase, chitinase, amylase, and pectinase. Appl. Environ. Microbiol. 52 (1986) 1362-1367
29. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., Stackebrandt E., Starr M.P., and Truper H.G. Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37 (1987) 463-464
30. Stackebrandt E., and Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 33 (2006) 152-155
31. Frostegard A., Courtois S., Ramisse V., Clerc S., Bernillon D., Le Gall F., Jeannin P., Nesme X., and Simonet P. Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65 (1999) 5409-5420
32. Polz M.F., and Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64 (1998) 3724-3730
33. von Wintzingerode F., Gobel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21 (1997) 213-229
34. Vionis A.P., Niemeyer F., Karagouni A.D., and Schrempf H. Production and processing of a 59-kilodalton exochitinase during growth of Streptomyces lividans carrying pCHI012 in soil microcosms amended with crab or fungal chitin. Appl. Environ. Microbiol. 62 (1996) 1774-1780
35. Krsek M., and Wellington E.M. Assessment of chitin decomposer diversity within an upland grassland. Antonie Van Leeuwenhoek 79 (2001) 261-267
36. Gomes R.C., Semedo L.T., Soares R.M., Alviano C.S., Linhares L.F., and Coelho R.R. Chitinolytic activity of actinomycetes from a cerrado soil and their potential in biocontrol. Lett. Appl. Microbiol. 30 (2000) 146-150
37. Gomes R.C., Semedo L.T., Soares R.M., Linhares L.F., Ulhoa C.J., Alviano C.S., and Coelho R.R. Purification of a thermostable endochitinase from Streptomyces RC1071 isolated from a cerrado soil and its antagonism against phytopathogenic fungi. J. Appl. Microbiol. 90 (2001) 653-661
38. Williamson N., Brian P., and Wellington E.M. Molecular detection of bacterial and streptomycete chitinase in the environment. Antonie Van Leeuwenhoek 78 (2000) 315-321
39. In: Krieg N.R., and Holt J.G. (Eds). Bergey's manual of systematic bacteriology vol. 1 (1984), Williams & Wilkins, Baltimore, USA
40. In: Sneath P.H.A., Mair N.S., Sharpe M.E., and Holt J.G. (Eds). Bergey's manual of systematic bacteriology vol. 2 (1986), Williams & Wilkins, Baltimore, USA
41. In: Staley J.T., Bryant M.P., Pfennig N., and Holt J.G. (Eds). Bergey's manual of systematic bacteriology vol. 3 (1989), Williams & Wilkins, Baltimore, USA
42. In: Williams S.T., Sharpe M.E., and Holt J.G. (Eds). Bergey's manual of systematic bacteriology vol. 4 (1989), Williams & Wilkins, Baltimore, USA
43. Bergey's manual of systematic bacteriology. In: Boone D.R., Castenholz R.W., and Garrity G.M. (Eds). The Archaea and the deeply branching and phototrophic bacteria. 2nd ed. vol. 1 (2001), Springer, New York, USA
44. In: Brenner D.J., Krieg N.R., Staley J.T., and Garrity G.M. (Eds). Bergey's manual of systematic bacteriology. 2nd ed. vol. 2 (2005), Springer, New York, USA, The proteobacteria