sp. nov., isolated from desert soil crusts, and emended description of the genus Indananda 2010 Free

Abstract

An actinomycete strain, designated I12A-02593, was isolated from a desert soil crust sample collected in the Shapotou region of Tengger Desert, north-west China. The isolate grew well on International Project (ISP) media 2, 3, 5 and 7, YS and Bennett’s agar; it produced spherical bodies and formed clumps on the aerial mycelia on ISP 5 agar plates. Chemotaxonomically, the strain contained -diaminopimelic acid as the diagnostic diamino acid, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, MK-9(H) as the sole isoprenoid quinone, and iso-C, iso-C 2-OH and iso-C H as the major cellular fatty acids, without mycolic acids. The profile of the phospholipids mainly comprised diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The genomic DNA G+C content was 70.1 mol%. The 16S rRNA gene sequence of strain I12A-02593 exhibited 96.4–97.4 % similarities with members of the genus . In the phylogenetic tree based on 16S rRNA gene sequences, the isolate formed a robust cluster with NBRC 105245, NBRC 105524, NBRC 105525, NBRC 105883and NBRC 106673. DNA–DNA hybridization values between strain I12A-02593 and the five species of the genus were all less than 70 %. On the basis of the polyphasic taxonomy evidence, a novel species of the genus is proposed, with the name sp. nov. The type strain is I12A-02593 ( = CPCC 203543 = DSM 45828 = NBRC 109453 = KCTC 29165). An emended description of the genus is also provided.

Funding
This study was supported by the:
  • National Infrastructure of Microbial Resources (NIMR)
  • National Natural Science Foundation of China (NSFC) (Award 81173026 and 30970008)
  • National S&T Major Special Project on Major New Drug Innovation (Award 2010ZX09401–403)
  • Special Fund for Health-scientific Research in the Public Interest (Award 201002021)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.061051-0
2014-09-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/9/3120.html?itemId=/content/journal/ijsem/10.1099/ijs.0.061051-0&mimeType=html&fmt=ahah

References

  1. Ara I., Tsetseg B., Daram D., Suto M., Ando K. ( 2011 ). Actinophytocola burenkhanensis sp. nov., isolated from Mongolian soil. . Int J Syst Evol Microbiol 61, 10331038. [View Article] [PubMed]
    [Google Scholar]
  2. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230. [View Article] [PubMed]
    [Google Scholar]
  3. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  4. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  5. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  6. Groth I., Schumann P., Rainey F. A., Martin K., Schuetze B., Augsten K. ( 1997 ). Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. . Int J Syst Bacteriol 47, 11291133. [View Article] [PubMed]
    [Google Scholar]
  7. Guo X.-X., Qiu D.-H., Ruan J.-S., Huang Y. ( 2011 ). Actinophytocola xinjiangensis sp. nov., isolated from virgin forest soil. . Int J Syst Evol Microbiol 61, 29282932. [View Article] [PubMed]
    [Google Scholar]
  8. Indananda C., Matsumoto A., Inahashi Y., Takahashi Y., Duangmal K., Thamchaipenet A. ( 2010 ). Actinophytocola oryzae gen. nov., sp. nov., isolated from the roots of Thai glutinous rice plants, a new member of the family Pseudonocardiaceae . . Int J Syst Evol Microbiol 60, 11411146. [View Article] [PubMed]
    [Google Scholar]
  9. Kellogg J. A., Bankert D. A., Withers G. S., Sweimler W., Kiehn T. E., Pfyffer G. E. ( 2001 ). Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory. . J Clin Microbiol 39, 964970. [View Article] [PubMed]
    [Google Scholar]
  10. Kim O. S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  11. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  12. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  13. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 132. [View Article]
    [Google Scholar]
  14. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics ( Society for Applied Bacteriology Technical Series vol. 20), pp. 173199. Edited by Goodfellow M., Minnikin D. E. . New York:: Academic Press;.
    [Google Scholar]
  15. Lechevalier H., Lechevalier M. P. ( 1965 ). Classification des actinomycètes aérobies basée sur leur morphologie et leur composition chimique. . Ann Inst Pasteur (Paris) 108, 662673. (in French).[PubMed]
    [Google Scholar]
  16. Lechevalier M. P., Lechevalier H. A. ( 1980 ). The chemotaxonomy of actinomycetes. . In Actinomycete Taxonomy ( Special Publication no. 6), pp. 227291. Edited by Dietz A., Thayer D. W. . Arlington, VA:: Society for Industrial Microbiology;.
    [Google Scholar]
  17. Li W.-J., Xu P., Schumann P., Zhang Y.-Q., Pukall R., Xu L.-H., Stackebrandt E., Jiang C.-L. ( 2007 ). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . . Int J Syst Evol Microbiol 57, 14241428. [View Article] [PubMed]
    [Google Scholar]
  18. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109118. [View Article] [PubMed]
    [Google Scholar]
  19. Meier A., Kirschner P., Schröder K. H., Wolters J., Kroppenstedt R. M., Böttger E. C. ( 1993 ). Mycobacterium intermedium sp. nov.. Int J Syst Bacteriol 43, 204209. [View Article] [PubMed]
    [Google Scholar]
  20. 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, 233241. [View Article]
    [Google Scholar]
  21. Otoguro M., Yamamura H., Tamura T., Irzaldi R., Ratnakomala S., Ridwan R., Kartina G., Triana E., Nurkanto A. & other authors ( 2011 ). Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil. . Int J Syst Evol Microbiol 61, 834838. [View Article] [PubMed]
    [Google Scholar]
  22. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  23. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  24. Smibert R. M., Krieg N. L. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  25. Stackebrandt E., Goebel B. M. ( 1994 ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44, 846849. [View Article]
    [Google Scholar]
  26. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  27. Yuan L.-J., Zhang Y.-Q., Guan Y., Wei Y.-Z., Li Q.-P., Yu L.-Y., Li W.-J., Zhang Y.-Q. ( 2008 ). Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil. . Int J Syst Evol Microbiol 58, 11801185. [View Article] [PubMed]
    [Google Scholar]
  28. Zhang Y. Q., Yu L. Y., Wang D., Liu H. Y., Sun C. H., Jiang W., Zhang Y. Q., Li W. J. ( 2008 ). Roseomonas vinacea sp. nov., a Gram-negative coccobacillus isolated from a soil sample. . Int J Syst Evol Microbiol 58, 20702074. [View Article] [PubMed]
    [Google Scholar]
  29. Zhou Z.-H., Liu Z.-H., Qian Y.-D., Kim S. B., Goodfellow M. ( 1998 ). Saccharopolyspora spinosporotrichia sp. nov., a novel actinomycete from soil. . Int J Syst Bacteriol 48, 5358. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.061051-0
Loading
/content/journal/ijsem/10.1099/ijs.0.061051-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed