Molecular Phylogenetic Classification of Streptomycetes Isolated from the Rhizosphere of Tropical Legume (Paraserianthes falcataria) (L.) Nielsen

HAYATI Journal of Biosciences

Volumn 16, Issue 3, 2009, Pages 100-108

  SEMBIRING, LANGKAH ^a  

^a GADJAH MADA UNIVERSITY   (Indonesia)

Author keywords

classification; molecular phylogenetic; Paraserianthes falcatharia; rhizosphere; streptomycetes

Indexed keywords

EID: 84887128682     PISSN: 19783019     EISSN: 20864094     Source Type: Journal    
DOI: 10.4308/hjb.16.3.100     Document Type: Article

References (64)

1. Arai, T, Nakada, T, Suzuki, M, Production of viomycin-like substance by a Streptomyces. Antibiotics Chemotherapy 7 (1957), 435–442.
2. Arcamone, FC, Bertazzoli, C, Ghione, M, Scotti, T, Melanosporin and elaiophylin, a new antibiotic from Streptomyces melanosporus (sive melanosporofaciens) n. sp. Giornale di Microbiologia 7 (1959), 207–216.
3. Atalan, E, Manfio, GP, Ward, AC, Kroppenstedt, RM, Goodfellow, M, Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek 77 (2000), 337–353.
4. Atmosuseno, BS, Budidaya, Kegunaan dan Prospek Sengon, 1997, Penebar Swadaya, Indonesi, Jakarta.
5. Baldacci, E, Farina, G, Locci, R, Emendation of the genus Streptoverticillium Baldacci 1958 and revision of some species. Giornale di Microbiologia 14 (1966), 153–171.
6. Bennedict, RG, Dvonch, W, Shotwell, O, Pridham, TG, Lindenfelser, LA, Cinnamycin, an antibiotic from Streptomyces cinnamoneus nov. sp. Antibiotics Chemotherapy 2 (1952), 591–594.
7. Benson, DA, Boguski, M, Lipman, DJ, Ostell, J, Oulette, BF, GenBank. Nucleic Acids Research 26 (1998), 1–7.
8. Chun, J, Computer Assisted Classification and Identification of Actinomycetes [thesis], 1995, University of Newcastle, Newcastle upon Tyne UK.
9. Chun J. 1999. Phylogenetic Editor (PHYDIT).
10. Chun, J, et al. Streptomyces seoulensis sp. nov. Int J Syst Bacteriol 47 (1997), 492–498.
11. Chun, J, et al. Amycolatopsis thermoflava sp. nov. a novel soil actinomycete from Hainan Island, China. International J Systematic Bacteriology 49 (1999), 1369–1373.
12. Esnard, J, Potter, T, Zuckerman, BM, Streptomyces costaricanus sp. nov. Int J Syst Bacteriol 45 (1995), 775–779.
13. Farina, G, Locci, R, Contributo allo studio di Streptoverticillium: descrizione di una nuovo specie (Streptoverticillium baldacci sp. nov.) ed esame di alcune specie precedentemente dilineate. Giornale di Microbiologia 14 (1966), 33–52.
14. Felsenstein, J, Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985), 783–791.
15. Felsenstein, J, PHYLIP (PHYLogeny Inference Package) version 3.5c. Distributed by the author, 1993, Department of Genetics, University of Washington, Seattle.
16. Fitch, WM, Margoliash, E, Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome C sequences is of general applicability. Science 155 (1967), 279–284.
17. Goodfellow, M, Haynes, JA, Actinomycetes in marine sediments. Ortiz-Ortiz, L, Bojalil, LF, Yakoleff, V, (eds.) Biological, Biochemical, and Biomedical Aspects of Actinomycetes, 1984, Acad Pr, New York, 452–472.
18. Goodfellow, M, Kumar, Y, Labeda, DP, Sembiring, L, The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Antonie van Leeuwenhoek 92 (2007), 173–199.
19. Goyer, C, Otrysko, B, Beaulieu, C, Taxonomic studies on streptomycetes causing popato common scab – A review. Can J Plant Pathol 18 (1996), 107–113.
20. Hain, T, Ward-Rainey, N, Kroppenstedt, RM, Stackebrandt, E, Rainey, FA, Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S – 23S rDNA intergenic spacers. Int J Syst Bacteriol 47 (1997), 202–206.
21. Jensen, HL, Contribution to our knowledge of the actinomycetales II. The definition and subdivision of the genus Actinomyces with a preliminary account of Australian soil actinomycetes. Proceedings of the Linnean Society of New South Wales 56 (1931), 345–370.
22. Jones, KL, Fresh isolates of actinomycetes in which the presence of sporo-genous aerial mycelia is a fluctuating characteristic. J Bacteriol 57 (1949), 141–145.
23. Jukes, TH, Cantor, CR, Evolution of protein molecules. Munro, HN, (eds.) Mammalian protein metabolism, Vol. 3, 1969, Acad Pr, New York, 21–132.
24. Kataoka, M, Ueda, K, Kudo, T, Seki, T, Yoshida, T, Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiol Lett 151 (1997), 249–255.
25. Kim, B, Al-Tai, AM, Kim, SB, Somarundaram, P, Goodfellow, M, Streptomyces thermocoprophilus sp. nov. a cellulase-free endoxylanase-producing streptomycete. Int J Syst Evol Microbiol 50 (2000), 505–509.
26. Kim, B, et al. Classification of thermophilic streptomycetes including the description of Streptomyces thermoalkalitolerans. Int J Syst Bacteriol 49 (1999), 7–17.
27. Kim, D, Chun, J, Sahin, N, Hah, Y-C, Goodfellow, M, Analysis of thermophilic clades within the genus Streptomyces by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 46 (1996), 581–587.
28. Kim, SB, Falconer, C, Williams, E, Goodfellow, M, Streptomyces thermocarboxydivorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol 48 (1998), 59–68.
29. Kluge, AG, Farris, FS, Quantitative phyletics and the evolution of anurans. Syst Zoo 18 (1969), 1–32.
30. Labeda, DP, DNA-DNA hybridization in the systematics of Streptomyces. Gene 115 (1992), 249–253.
31. Labeda, DP, DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. Int J Syst Bacteriol 43 (1993), 822–825.
32. Labeda, DP, DNA relatedness among verticill-forming Streptomyces species (formerly Streptoverticillium species). Int J Syst Bacteriol 46 (1996), 699–703.
33. Labeda, DP, DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. Int J Syst Bacteriol 48 (1998), 829–832.
34. Labeda, DP, Lechevalier, MP, Testa, RT, Streptomyces stamineus sp. nov., a new species of the verticillate streptomycetes. Int J Syst Bacteriol 47 (1997), 747–753.
35. Labeda, DP, Lyons, AJ, The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: emendation of the description of Streptomyces violaceusniger and Streptomyces hygroscopicus. Int J Syst Bacteriol 41 (1991), 398–401.
36. Labeda, DP, Lyons, AJ, Deoxyribonucleic acid relatedness among species of the Streptomyces cyaneus cluster. Syst Appl Microbiol 14 (1991), 158–164.
37. Labeda, DP, Lyons, AJ, DNA relatedness among strains of the sweet potato pathogen Streptomyces ipomoea (Person & Martin 1940) Waksman and Henrici 1948. Appl Environ Microbiol 58 (1992), 532–535.
38. Lane, DJ, 16S/23S rRNA sequencing. Stackebrandt, E, Goodfellow, M, (eds.) Nucleic Acid Techniques in Bacterial Systematic, 1991, John Wiley & Sons, New York, 115–175.
39. Li, L, Kato, C, Horikoshi, H, Bacterial diversity in deep-sea sediments from different depths. Biodiv Conserv 8 (1999), 659–677.
40. Maidak, BL, et al. The ribosomal database project (RDP). Nucleic Acid Research 25 (1997), 109–111.
41. Pernodet, JL, Boccard, F, Alegre, MT, Gagnat, J, Guerineau, M, Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene 79 (1989), 33–46.
42. Pitcher, DG, Saunders, NA, Owen, RJ, Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8 (1989), 151–156.
43. Saddler, GS, Selective Isolation and Rapid Identification of Streptomycetes [thesis], 1988, Univ of Newcastle, Newcastle upon Tyne, UK.
44. Sahin, N, Selective Isolation, Characterisation and Classification of Novel Alkaliphilic Streptomycetes [Thesis], 1995, Univ of Newcastle, Newcastle upon Tyne UK.
45. Saitou, N, Nei, M, The neighbor-joining method: a new mwthod for reconstructing phylogenetic trees. Mol Biol Evol 4 (1987), 406–425.
46. nd Edition., 1989, Cold Spring Harbor Lab Pr, New York.
47. Sanglier, JJ, Whitehead, D, Saddler, GS, Ferguson, EV, Goodfellow, M, Pyrolysis mass spectrometry as a method for the classification identification and selection of actinomycetes. Gene 115 (1992), 235–242.
48. Santoso, HB, Budidaya Sengon, 1992, Kanisius, Yogyakarta.
49. Shirling, EB, Gottlieb, D, Cooperative description of type cultures Streptomyces II. Species description from first study. Int J Syst Bacteriol 18 (1968), 69–189.
50. Shirling, EB, Gottlieb, D, Cooperative description of type cultures of Streptomyces III. Additional species descriptions from first and second studies. Int J Syst Bacteriol 18 (1968), 279–392.
51. Shirling, EB, Gottlieb, D, Cooperative description of type cultures of Streptomyces IV. Species Description from the second, the third, and the fourth studies. Int J Syst Bacteriol 19 (1969), 391–512.
52. Shirling, EB, Gottlieb, D, Cooperative description of type cultures of Streptomyces V. Additional descriptions. Int J Syst Bacteriol 22 (1972), 265–394.
53. Shojaei, H, Molecular Systematics of Some Medically Important Actinomy-cetes [thesis], 1997, University of Newcastle, Newcastle upon Tyne UK.
54. Stackebrandt, E, Ludwig, W, Seewal, Schleifer, KH, Phylogeny of sporeforming members of the order Actinomycetales. Int J Syst Bacteriol 33 (1983), 172–180.
55. Stackebrandt, E, Witt, D, Kemmerling, C, Kroppenstedt, R, Liesack, W, Designation of streptomycete 16S and 23S rRNA-base target region for oligonucleotide probes. Appl Environ Microbiol 57 (1991), 1468–1477.
56. Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG, The ClustalX Windows Interface: flexible strategies for multiple sequence alignment aided by quality analysis tool. Nucleic Acid Research 24 (1997), 4876–4882.
57. Takeuchi, T, Sawada, H, Tanaka, F, Matsuda, I, Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences. Int J Syst Bacteriol 46 (1996), 476–479.
58. Ueda K, Kudo T, Seki T, Yoshida T, Kataoka M. 1997. Phylogenetic analysis of Streptomyces by 16S rDNA partial sequence (Unpublished).
59. Umezawa, H, Tazaki, T, Fukuyama, S, On anti-viral substances abikoviromycin, produced by Streptomyces species. Japanaese Medical J 4 (1951), 331–346.
60. van de Peer, Y, De Wachter, R, TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computer Appl Biol Sci 10 (1994), 569–570.
61. Waksman, SA, Curtis, RE, The Actinomyces of the soil. Soil Science 1 (1916), 99–134.
62. Wayne, LG, et al. Report of the adhoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 (1987), 463–464.
63. Williams, ST, et al. Numerical Classification of Streptomyces and Related Genera. J General Microbiol 129 (1983), 1743–1813.
64. Williams, ST, Vickers, JC, Detection of actinomycetes in the natural environment: problems and prospectives. Okami, Y, Beppu, T, Ogawara, K, (eds.) Biology of Actinomycetes'88, 1988, Japan Scientific Societies Pr, Tokyo, 265–270.