Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa)

International Journal of Systematic and Evolutionary Microbiology

Volumn 60, Issue 12, 2010, Pages 2818-2822

  Kaewkla, Onuma ^a   Franco, Christopher M M ^a  

^a FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DIAMINOPIMELIC ACID; FATTY ACID; MENAQUINONE; RNA 16S; BACTERIAL DNA; FARNOQUINONE; VITAMIN MK 8;

AEROBIC BACTERIUM; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; BACTERIUM ISOLATION; CHEMOTAXONOMY; DNA DNA HYBRIDIZATION; ENDOPHYTE; EUCALYPTUS; GENE SEQUENCE; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PSEUDONOCARDIA ADELAIDENSIS; PSEUDONOCARDIACEAE; ACTINOMYCETALES; ANALOGS AND DERIVATIVES; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; PLANT STEM;

ACTINOBACTERIA; EUCALYPTUS MICROCARPA; PSEUDONOCARDIA; PSEUDONOCARDIA ZIJINGENSIS; PSEUDONOCARDIACEAE;

ACTINOMYCETALES; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DIAMINOPIMELIC ACID; DNA, BACTERIAL; EUCALYPTUS; FATTY ACIDS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; PLANT STEMS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; VITAMIN K 2;

EID: 78650051604     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.019208-0     Document Type: Article

References (34)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
2. Atlas, R. M. (1993). Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
3. Bousfield, I. J., Keddie, R. M., Dando, T. R. & Shaw, S. (1985). Simple rapid methods of cell wall analysis as an aid in the identification of aerobic coryneform bacteria. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series, vol. 20), pp. 221-236. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
4. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221-230.
5. Conn, V. M. & Franco, C. M. M. (2004). Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism (T-RFLP) and sequencing of 16S rRNA clones. Appl Environ Microbiol 70, 1787-1794.
6. Coombs, J. T. & Franco, C. M. M. (2003). Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 69, 5603-5608.
7. Euzéby, J. P. (1997). List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47, 590-592. http://www.bacterio.cict.fr
8. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
9. Gonzalez, J. M. & Saiz-Jimenez, C. (2005). A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 9, 75-79.
10. Gordon, R. E., Barnett, D. A., Handerhan, J. E. & Pang, C. H.-N. (1974). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24, 54-63.
11. Hasegawa, T., Takizawa, M. & Tanida, S. (1983). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319-322. (Pubitemid 14176930)
12. Henssen, A. (1957). Beitrage zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26, 373-414 (in German).
13. Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. (2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69, 7210-7215.
14. Kaewkla, O. & Franco, C. M. M. (2010). Nocardia callistridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree. Int J Syst Evol Microbiol 60, 1532-1536.
15. Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
16. Kluge, A. G. & Farris, J. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1-32.
17. Kornerup, A. & Wanscher, J. H. (1978). Methuen Handbook of Colour, 3rd edn. Edited by D. Pavey. Fakenham, UK: Cox & Wyman.
18. Kurup, P. V. & Schmitt, J. A. (1973). Numerical taxonomy of Nocardia. Can J Microbiol 19, 1035-1048.
19. Lee, S. D., Kim, E. S. & Hah, Y. C. (2000). Phylogenetic analysis of the genera Pseudonocardia and Actinobispora based on 16S ribosomal DNA sequences. FEMS Microbiol Lett 182, 125-129.
20. McVeigh, H. P., Munro, J. & Embley, T. M. (1994). The phylogenetic position of Pseudomycolata halophobica (Akimov et al. 1989) and a proposal to reclassify it as Pseudonocardia halophobica. Int J Syst Bacteriol 44, 300-302. (Pubitemid 24116299)
21. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
22. Minnikin, D. E., Alshamaony, L. & Goodfellow, M. (1975). Differentiation of Mycobacterium, Nocardia and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88, 200-204.
23. Minnikin, D. E., Hutchinson, I. G. & Caldicott, A. B. (1980). Thin layer chromatography of methanolysates of mycolic acid containing bacteria. J Chromatogr A 188, 221-233.
24. Reichert, K., Lipski, A., Pradella, S., Stackebrandt, E. & Altendorf, K. (1998). Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Bacteriol 48, 441-449.
25. Rosselló-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39-67.
26. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
27. Sasser, M. (2001). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
28. Schoenborn, L., Yates, P. S., Grinton, B. E., Hugenholtz, P. & Janssen, P. H. (2004). Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol 70, 4363-4366.
29. Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313-340.
30. 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. (Pubitemid 47236692)
31. 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.
32. Uchida, K., Kudo, T., Suzuki, K. & Nakase, T. (1999). A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45, 49-56.
33. Warwick, S., Bowen, T., McVeigh, H. & Embley, T. M. (1994). A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44, 293-299. (Pubitemid 24116298)
34. 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. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.