Taxonomic and ecological studies of actinomycetes from Vietnam: Isolation and genus-level diversity

Journal of Antibiotics

Volumn 64, Issue 9, 2011, Pages 599-606

  Van Hop, Duong ^a   Sakiyama, Yayoi ^b   Binh, Chu Thi Thanh ^a   Otoguro, Misa ^b   Hang, Dinh Thuy ^a   Miyadoh, Shinji ^b   Luong, Dao Thi ^a   Ando, Katsuhiko ^b  

^a VIETNAM NATIONAL UNIVERSITY   (Viet Nam)

^b NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

Author keywords

actinomycete ecology; taxonomic diversity; Vietnamese actinomycetes

Indexed keywords

AGAR; DODECYL SULFATE SODIUM; HUMIC ACID; OIL; RNA 16S; VITAMIN;

ACTINOBACTERIA; ACTINOPLANES; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CELL STRUCTURE; CENTRIFUGATION; CONVERGENT EVOLUTION; CRYPTOSPORANGIUM; CULTURE MEDIUM; GENE SEQUENCE; GENUS; HEATING; KINEOSPORIA; LEAF LITTER; MICROBIAL DIVERSITY; MICROMONOSPORACEAE; NEW GENUS; NEW HIGHER TAXON; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; REHYDRATION CENTRIFUGATION; RNA GENE; SEPARATION TECHNIQUE; SOIL MICROFLORA; STREPTOMYCES; STREPTOMYCETACEAE; STREPTOSPORANGIACEAE; TAXONOMIC IDENTIFICATION; TAXONOMY; UNINDEXED SEQUENCE; VIET NAM;

ACTINOBACTERIA; BACTERIAL TYPING TECHNIQUES; PLANT LEAVES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; SOIL MICROBIOLOGY; VIETNAM;

ACTINOBACTERIA (CLASS); ACTINOPLANES; CRYPTOSPORANGIUM; KINEOSPORIA; MICROMONOSPORACEAE; STREPTOMYCES; STREPTOMYCETACEAE; STREPTOMYCINEAE; STREPTOSPORANGIACEAE; STREPTOSPORANGINEAE;

EID: 80053374353     PISSN: 00218820     EISSN: 18811469     Source Type: Journal    
DOI: 10.1038/ja.2011.40     Document Type: Article

References (35)

1. Thanh, V. N. Yeast, biodiversiy and promises. Proc. Natl Conf. Basic Biotechnol., Vietnam 118-123 (2005).
2. Bérdy, J. Bioactive microbial metabolites. J. Antibiot. 58, 1-26 (2005).
3. Sezaki, M. &Miyadoh, S. Practically used antibiotics and their related substrates. In Identification Manual of Actinomycetes (ed. Miyadoh, S.) 349-389 (Mainichi Academic Forum, Tokyo, 2002).
4. Xu, L. H., Li, Q. R. &Jiang, C. L. Diversity of soil actinomycetes in Yunnan, China. Appl. Environ. Microbiol. 62, 244-248 (1996).
5. Wang, Y., Zhang, J. S., Ruan, J. S., Wang, Y. M. &Ali, S. M. Inveatigation of actinomycete diversity in the tropical rainforests of Singapore. J. Ind. Microbiol. Biotechnol. 23, 178-187 (1999).
6. Muramatsu, H., Shahab, N., Tsurumi, Y. &Hino, M. A comparative study of Malaysian and Japanese actinomycetes using a simple identification method based on partial 16S rDNA sequence. Actinomycetologica 17, 33-43 (2003).
7. Ara, I. &Kudo, T. Krasilnikovia gen. nov., a new member of the family Micromonosporaceae and description of Krasilnikovia cinnamonea sp. nov. Actinomycetologica 21, 1-10 (2007).
8. Ara, I. &Kudo, T. Luedemannella gen. nov., a new member of the family Micromonosporaceae and description of Luedemannella helvata sp. nov. and Luedemannella flava sp. nov. J. Gen. Appl. Microbiol. 53, 39-51 (2007). (Pubitemid 351659029)
9. Ara, I. &Kudo, T. Sphaerosporangium gen. nov., a new member of the family. Streptosporangiaceae. Actinomycetologica 21, 11-21 (2007).
10. Hayakawa, M. et al. Diversity analysis of actinomycetes assemblages isolated from soils in cool-temperate and subtropical areas of Japan. Actinomycetologica 24, 1-11 (2010).
11. Hayakawa, M., Otoguro, M., Takeuchi, T., Yamazaki, T. &Iimura, Y. Application of a method incorporating differential centrifugation for selective isolation of motile actinomycetes in soil and plant litter. Antonie Van Leeuwenhoek 78, 171-185 (2000). (Pubitemid 32046759)
12. Hayakawa, M. &Nonomura, H. A new method for the intensive isolation of actinomycetes from soil. Actinomycetologica 3, 95-104 (1989).
13. Hayakawa, M., Sadataka, T., Kajiura, T. &Nonomura, H. New methods for the highly selective isolation of Micromonospora and Microbispora from soil. J. Fermen. Bioeng. 72, 320-326 (1991).
14. Hayakawa, M. &Nonomura, H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J. Ferment. Technol. 65, 501-509 (1987).
15. Tamura, T. &Hatano, K. Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and 'Actinoplanes aurantiacus' to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov. Int. J. Syst. Evol. Microbiol. 51, 2119-2125 (2001). (Pubitemid 33107433)
16. Chun, J. et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences (www.eztaxon.org). Int. J. Syst. Evol. Microbiol. 57, 2259-2261 (2007).
17. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. And Evol. (in press).
18. Saitou, N. &Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987).
19. Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 (1985).
20. Zhi, X. Y., Li, W. J. &Stackebrandt, E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria. Int. J. Syst. Evol. Microbiol. 59, 589-608 (2009).
21. Euzéby, J. P. List of Procaryoteic names with standing in nomenclature. (http://www.bacterio.cict.fr/index.html).
22. Pagani, H. &Parenti, F. Kineosporia, a new genus of the order Actinomycetales. Int. J. Syst. Bacteriol. 28, 401-406 (1978). (Pubitemid 8400125)
23. Itoh, T., Kudo, T., Parenti, F. &Seino, A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int. J. Syst. Bacteriol. 39, 168-173 (1989). (Pubitemid 19104416)
24. Kudo, T., Matsushima, K., Itoh, T., Sasaki, J. &Suzuki, K. Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia. Int. J. Syst. Bacteriol. 48, 1245-1255 (1998). (Pubitemid 28523337)
25. Tamura, T., Hayakawa, M. &Hatano, K. A new genus of the order Actinomycetales, Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov. Int. J. Syst. Bacteriol. 48, 995-1005 (1998). (Pubitemid 28394683)
26. Makkar, N. S. &Cross, T. Actinoplanes in soil and on plant-litter from freshwater habitats. J. Appl. Bacteriol. 52, 209-218 (1982). (Pubitemid 12066081)
27. Willoughby, L. G. A study on aquatic actinomycetes, the allochthonous leaf component. Nova Hedwigia 18, 45-113 (1969).
28. Hirsch, C. F. &Christensen, D. L. Novel method for selective isolation of actinomycetes. Appl. Environ. Microbiol. 46, 925-929 (1983). (Pubitemid 14236286)
29. Lisdiyanti, P. &Otoguro, M. The number of isolates based on genera of Indonesian actinomycetes. in Taxonomic and Ecological Studies of Fungi and Actinomycetes in Indonesia (eds Windyasturi, Y. &Ando, K.) 601-602 (2010).
30. Ohno, M. &Harayama, S. Isolation of actinomycetes from Japanese soil. in Explaration of Microorganisms in Diverse Environments (article in Japanese, ed. Harayama, S.) 154-162 (2008).
31. Sakiyama, Y. et al. Kineosporia babensis sp. nov., isolated from plant litter in Vietnam. Int. J. Syst. Evol. Microbiol. 59, 550-554 (2009).
32. Sakiyama, Y. et al. Pseudonocardia babensis sp. nov., isolated from plant litter in Vietnam. Int. J. Syst. Evol. Microbiol. 60, 2336-2340 (2010).
33. Drancourt, M. et al. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38, 3623-3630 (2006).
34. Stackebrandt, E. &Ebers, J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 33, 152-155 (2006).
35. Kim, S. J. &Lee, S. S. Amnibacterium kyonggiense gen. nov., sp. nov., a novel genus of the family Microbaceriaceae. Int. J. Syst. Evol. Microbiol. 61, 155-159 (2011).