Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.)

International Journal of Systematic and Evolutionary Microbiology

Volumn 62, Issue 12, 2012, Pages 3030-3035

  Chung, Eu Jin ^a   Park, Tae Soon ^b   Jeon, Che Ok ^c   Chung, Young Ryun ^b  

^a JGreen Inc   (South Korea)

^b Gyeongsang National University   (South Korea)

^c Chung Ang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACID; GENOMIC DNA; HOMOSPERMIDINE; MENAQUINONE; PHOSPHATIDYLETHANOLAMINE; POLYAMINE; RNA 16S; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; CHITINOPHAGA ORYZITARRAE; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; KOREA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RHIZOSPHERE; RICE;

BACTERIAL TYPING TECHNIQUES; BACTEROIDETES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; REPUBLIC OF KOREA; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPERMIDINE; VITAMIN K 2;

BACTERIA (MICROORGANISMS); CHITINOPHAGA; CHITINOPHAGA PINENSIS; NEGIBACTERIA; ORYZA SATIVA;

EID: 84870865570     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.036442-0     Document Type: Article

References (37)

1. Alloway, B. J. (2009). Soil factors associated with zinc deficiency in crops and humans. Environ Geochem Health 31, 537-548.
2. Atlas, R. M. (1993). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
3. Ausubel, F. W., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1995). Current Protocols in Molecular Biology. New York: Wiley.
4. Bernardet, J. F., Nakagawa, Y., Holmes, B. & Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049-1070.
5. Brown, A. E. (2007). Benson's Microbiological Applications: Laboratory Manual in General Microbiology. New York: McGraw-Hill.
6. Busse, H. J. & Auling, G. (1988). Polyamine pattern as a chemotaxo-nomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
7. Busse, H. J., Bunka, S., Hensel, A. & Lubitz, W. (1997). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47, 698-708.
8. Cappuccino, J. G. & Sherman, N. (2002). Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
9. Chen, Z., Ma, S. & Liu, L. L. (2008). Studies on phosphorus solubilizing activity of a strain of phosphobacteria isolated from chestnut type soil in China. Bioresour Technol 99, 6702-6707.
10. Dittmer, J. C. & Lester, R. L. (1964). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 15, 126-127.
11. Fautz, E. & Reichenbach, H. (1980). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8, 87-91.
12. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
13. 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.
14. Hendricks, C. W., Doyle, J. D. & Hugley, B. (1995). A new solid medium for enumerating cellulose-utilizing bacteria in soil. Appl Environ Microbiol 61, 2016-2019.
15. Jacin, H. & Mishkin, A. R. (1965). Separation of carbohydrates on borate impregnated silica gel G plates. J Chromatogr A 18, 170-173.
16. Kämpfer, P., Young, C. C., Sridhar, K. R., Arun, A. B., Lai, W. A., Shen, F. T. & Rekha, P. D. (2006). Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arven-sicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 56, 2223-2228.
17. Kämpfer, P., Lodders, N. & Falsen, E. (2011). Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumi-bacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61, 518-523.
18. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H., Yi, H., Won, S. & Chun, J. (2012). IntroducingEzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716-721.
19. Kroppenstedt, R. M. (1982). Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5, 2359-2367.
20. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. New York: Wiley.
21. Lee, H. G., An, D. S., Im, W. T., Liu, Q. M., Na, J. R., Cho, D. H., Jin, C. W., Lee, S. T. & Yang, D. C. (2007). Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 57, 1396-1401.
22. Lee, D. W., Lee, J. E. & Lee, S. D. (2009). Chitinophaga rupis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59, 2830-2833.
23. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
24. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233-241.
25. Nautiyal, C. S. (1999). An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 170, 265-270.
26. Park, M. S., Park, Y. J., Jung, J. Y., Lee, S. H., Park, W. J., Lee, K. S. & Jeon, C. O. (2011). Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas. Int J Syst Evol Microbiol 61, 2901-2906.
27. Ross, H. N. M., Grant, W. D. & Harris, J. E. (1985). Lipids in archaebacterial taxonomy. In Chemical Methods in Bacterial Systematics, pp. 289-300. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
28. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method forreconstructingphylogenetic trees. Mol Biol Evol 4, 406-425.
29. Sangkhobol, V. & Skerman, V. B. D. (1981). Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 31, 285-293.
30. Saravanan, V. S., Subramoniam, S. R. & Raj, S. A. (2004). Assessing in vitro solubilization potential of different zinc solubilizing bacterial isolates. Braz J Microbiol 35, 121-125.
31. Saravanan, V. S., Madhaiyan, M. & Thangaraju, M. (2007). Solubilization of zinc compounds by the diazotrophic, plant growth promoting bacterium Gluconacetobacter diazotrophicus. Chemosphere 66, 1794-1798.
32. Singh, P. P., Shin, Y. C., Park, C. S. & Chung, Y. R. (1999). Biological control of fusarium wilt of cucumber by chitinolytic bacteria. Phytopathology 89, 92-99.
33. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24, 1596-1599.
34. Ten, L. N., Im, W. T., Kim, M. K., Kang, M. S. & Lee, S. T. (2004). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromo-genic substrates. J Microbiol Methods 56, 375-382.
35. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
36. Weon, H. Y., Yoo, S. H., Kim, Y. J., Son, J. A., Kim, B. Y., Kwon, S. W. & Koo, B. S. (2009). Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59, 1267-1271.
37. Yasir, M., Chung, E. J., Song, G. C., Bibi, F., Jeon, C. O. & Chung, Y. R. (2011). Chitinophaga eiseniae sp. nov., isolated from vermicompost. Int J Syst Evol Microbiol 61, 2373-2378.