1887

Abstract

In this study, the taxonomic position of an actinobacterium, strain YIM M 10931, which was isolated from a mangrove sediment sample collected in Dugong Creek, Little Andaman, India, was determined by a polyphasic approach. This Gram-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, which differentiated into short, hooked or spiral spore chains. The organism contained -diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole cell sugars consisted of mannose, ribose, glucose, galactose and madurose. The cellular fatty acid profile mainly consisted of iso-C, 10-methyl C and C. The quinone system was predominantly composed of MK-9(H) (45.5 %) and MK-9(H) (39 %). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and two unknown phospholipids. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus . Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relatives as DSM 43676 (98.4 % sequence similarity), DSM 43936 (97.4 %) and IM17-1 (96.9 %). It was obvious from the resulting phylogenetic trees that strain YIM M 10931 belongs to a distinct subclade within the evolutionary radiation of the genus DNA–DNA hybridizations of strain YIM M 10931 with DSM 43676 and DSM 43936 were performed and further confirmed that the isolate represents a separate genomic species. Based on the phenotypic and genotypic characteristics presented, it is proposed that strain YIM M 10931 represents a novel species within the genus , for which the name sp. nov. is proposed; the type strain is YIM M 10931 ( = CCTCC AA 2010009 = DSM 45500).

Funding
This study was supported by the:
  • National Basic Research Program of China (Award 2010CB833801)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.032979-0
2012-05-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/5/1110.html?itemId=/content/journal/ijsem/10.1099/ijs.0.032979-0&mimeType=html&fmt=ahah

References

  1. Alongi D. M. 1988; Bacterial productivity and microbial biomass in tropical mangrove sediments. Microb Ecol 15:59–79 [View Article]
    [Google Scholar]
  2. Athalye M., Goodfellow M., Lacey J., White R. P. 1985; Numerical classification of Actinomadura and Nocardiopsis . Int J Syst Bacteriol 35:86–98 [View Article]
    [Google Scholar]
  3. Bauer A. W., Kirby W. M. M., Sherris J. C., Turck M. 1966; Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496[PubMed]
    [Google Scholar]
  4. Collins M. D., Jones D. 1980; Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470 [View Article]
    [Google Scholar]
  5. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230[PubMed] [CrossRef]
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  7. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  9. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  10. Goodfellow M. 1971; Numerical taxonomy of some nocardioform bacteria. J Gen Microbiol 69:33–80[PubMed] [CrossRef]
    [Google Scholar]
  11. He L., Li W., Huang Y., Wang L. M., Liu Z. H., Lanoot B. J., Vancanneyt M., Swings J. 2005; Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944 [View Article][PubMed]
    [Google Scholar]
  12. Holguin G., Vazquez P., Bashan Y. 2001; The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol Fertil Soils 33:265–278 [View Article]
    [Google Scholar]
  13. Holguin G., Gonzalez-Zamorano P., de-Bashan L. E., Mendoza R., Amador E., Bashan Y. 2006; Mangrove health in an arid environment encroached by urban development – a case study. Sci Total Environ 363:260–274 [View Article][PubMed]
    [Google Scholar]
  14. Kathiresan K., Bingham B. L. 2001; Biology of mangroves and mangrove ecosystems. Adv Mar Biol 40:81–251 [View Article]
    [Google Scholar]
  15. Kawato N., Shinobu R. 1959; On Streptomyces herbaricolor sp. nov. Supplement: a simple technique for the microscopic observation. Mem Osaka Univ Lib Arts Educ B Nat Sci 8:114–119
    [Google Scholar]
  16. Kelly K. L. 1964 Inter-Society Color Council – National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;
    [Google Scholar]
  17. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  18. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  19. Kroppenstedt R. M., Stackebrandt E., Goodfellow M. 1990; Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora . Syst Appl Microbiol 13:148–160 [View Article]
    [Google Scholar]
  20. Lechevalier H. A., Lechevalier M. P. 1968; A critical evaluation of the genera of aerobic actinomycetes. In The Actinomycetales pp. 393–405 Edited by Prauser H. Jena: VEB Gustav Fischer Verlag;
    [Google Scholar]
  21. Lee D. W., Lee S. D. 2010; Actinomadura scrupuli sp. nov., isolated from rock. Int J Syst Evol Microbiol 60:2647–2651 [View Article][PubMed]
    [Google Scholar]
  22. 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 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  23. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  24. 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 [View Article]
    [Google Scholar]
  25. Minnikin D. E., Collins M. D., Goodfellow M. 1979; Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95 [View Article]
    [Google Scholar]
  26. Pridham T. G., Gottlieb G. 1948; The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 56:107–114
    [Google Scholar]
  27. Promnuan Y., Kudo T., Ohkuma M., Chantawannakul P. 2011; Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov.. Int J Syst Evol Microbiol 61:2271–2277 [View Article][PubMed]
    [Google Scholar]
  28. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  29. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16
    [Google Scholar]
  30. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  31. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231[PubMed]
    [Google Scholar]
  32. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. 1983; Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36 [View Article]
    [Google Scholar]
  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 [View Article][PubMed]
    [Google Scholar]
  34. Tamura T., Ishida Y., Nozawa Y., Otoguro M., Suzuki K.-I. 2009; Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomuru s iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov.. Int J Syst Evol Microbiol 59:1867–1874 [View Article][PubMed]
    [Google Scholar]
  35. Tang S.-K., Wang Y., Chen Y., Lou K., Cao L.-L., Xu L.-H., Li W.-J. 2009; Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 59:2025–2033 [View Article][PubMed]
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
  37. Trujillo M. E., Goodfellow M. 2003; Numerical phenetic classification of clinically significant aerobic sporoactinomycetes and related organisms. Antonie van Leeuwenhoek 84:39–68 [View Article][PubMed]
    [Google Scholar]
  38. 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; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  39. Xu J., Wang Y., Xie S.-J., Xu J., Xiao J., Ruan J.-S. 2009; Streptomyces xiamenensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 59:472–476 [View Article][PubMed]
    [Google Scholar]
  40. Zhang Z., Wang Y., Ruan J. 1998; Reclassification of Thermomonospora and Microtetraspora . Int J Syst Bacteriol 48:411–422 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.032979-0
Loading
/content/journal/ijsem/10.1099/ijs.0.032979-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error