1887

International Journal of Systematic and Evolutionary Microbiology

Volume 59, Issue 3

sp. nov., an actinomycete isolated from an ocean sediment Free

Abstract

A Gram-positive, aerobic, non-motile actinobacterium, designated strain Ms392A, was isolated from an ocean-sediment sample collected from the South China Sea. The isolate contained chemical markers that supported chemotaxonomic assignment to the genus . On the basis of an analysis of 16S rRNA gene sequence similarities, strain Ms392A represents a novel subclade within the genus , with 1BDZ as its closest phylogenetic neighbour (99.4 % similarity). However, DNA–DNA hybridization demonstrated that strain Ms392A was distinct from AS 4.1729 (48.6 % relatedness). The polyphasic analysis demonstrated that the ocean isolate can be clearly distinguished from recognized species of the genus . Therefore, strain Ms392A represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Ms392A (=CGMCC 4.3568 =NBRC 104263).

  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000026-0
2009-03-01
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/59/3/477.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000026-0&mimeType=html&fmt=ahah

References

  1. Carlsohn, M. R., Groth, I., Tan, G. Y. A., Schütze, B., Saluz, H. P., Munder, T., Yang, J., Wink, J. & Goodfellow, M. ( 2007; ). Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57, 1640–1646.[CrossRef]
    [Google Scholar]
  2. 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.[CrossRef]
    [Google Scholar]
  3. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef]
    [Google Scholar]
  4. Demain, A. L. & Zhang, L. ( 2005; ). Natural products and drug discovery. In Natural Products: Drug Discovery and Therapeutic Medicine, pp. 3–32. Edited by L. Zhang & A. L. Demain. Totowa, NJ: Humana Press.
  5. Embley, T. M., Smida, J. & Stackebrandt, E. ( 1988; ). The phylogeny of mycolate-less wall chemotype IV actinomycetes and the description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 11, 44–52.[CrossRef]
    [Google Scholar]
  6. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  7. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  8. Goodfellow, M., Kim, S. B., Minnikin, D. E., Whitehead, D., Zhou, Z. H. & Mattinson-Rose, A. D. ( 2001; ). Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int J Syst Evol Microbiol 51, 187–193.
     [Google Scholar]
  9. 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.[CrossRef]
    [Google Scholar]
  10. Groth, I., Rodriguez, C., Schütze, B., Schmitz, P., Leistner, E. & Goodfellow, M. ( 2004; ). Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 54, 2121–2129.[CrossRef]
    [Google Scholar]
  11. Groth, I., Tan, G. Y. A., Gonzales, J. M., Laiz, L., Carlsohn, M. R., Schütze, B., Wink, J. & Goodfellow, M. ( 2007; ). Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb. Int J Syst Evol Microbiol 57, 513–519.[CrossRef]
    [Google Scholar]
  12. 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.[CrossRef]
    [Google Scholar]
  13. Henssen, A., Kothe, H. W. & Kroppenstedt, R. M. ( 1987; ). Transfer of Pseudonocardia azurea and “Pseudonocardia fastidiosa” to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 37, 292–295.[CrossRef]
    [Google Scholar]
  14. Huang, Y., Paściak, M., Liu, Z. H., Xie, Q. & Gamian, A. ( 2004; ). Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source. Int J Syst Evol Microbiol 54, 359–363.[CrossRef]
    [Google Scholar]
  15. Kawato, M. & Shinobu, R. ( 1959; ). On Streptomyces herbaricolor nov. sp. Supplement: a simple technique for the microscopic observation. Mem Osaka Univ Lib Arts Educ B 8, 114–119.
     [Google Scholar]
  16. Kim, S. B. & Goodfellow, M. ( 1999; ). Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Bacteriol 49, 507–512.[CrossRef]
    [Google Scholar]
  17. Kim, B., Sahin, N., Tan, G. Y. A., Zakrzewska-Czerwinska, J. & Goodfellow, M. ( 2002; ). Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil. Int J Syst Evol Microbiol 52, 889–894.[CrossRef]
    [Google Scholar]
  18. 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.[CrossRef]
    [Google Scholar]
  19. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  20. Kovács, N. ( 1956; ). Identification of Pseudomonas pyocyanea by oxidase reaction. Nature 178, 703–704.
     [Google Scholar]
  21. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  22. Labeda, D. P., Donahue, J. M., Williams, N. M., Sells, S. F. & Henton, M. M. ( 2003; ). Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas. Int J Syst Evol Microbiol 53, 1601–1605.[CrossRef]
    [Google Scholar]
  23. Lechevalier, H. A. & Lechevalier, M. P. ( 1980; ). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, pp. 277–284. Society for Industrial Microbiology Special Publication no. 6. Edited by A. Dietz & D. W. Thayer. Arlington, VA: Society for Industrial Microbiology.
  24. Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A. ( 1977; ). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249–260.[CrossRef]
    [Google Scholar]
  25. Lechevalier, M. P., Prauser, H., Labeda, D. P. & Ruan, J.-S. ( 1986; ). Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36, 29–37.[CrossRef]
    [Google Scholar]
  26. Lee, S. D., Kinkel, L. L. & Samac, D. A. ( 2006; ). Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil. Int J Syst Evol Microbiol 56, 265–269.[CrossRef]
    [Google Scholar]
  27. 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.[CrossRef]
    [Google Scholar]
  28. MacFaddin, J. F. ( 1980; ). Biochemical Tests for the Identification of Medical Bacteria, 2nd edn. Baltimore: Williams & Wilkins.
  29. Mertz, F. P. & Yao, R. C. ( 1993; ). Amycolatopsis alba sp. nov., isolated from soil. Int J Syst Bacteriol 43, 715–720.[CrossRef]
    [Google Scholar]
  30. 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.[CrossRef]
    [Google Scholar]
  31. 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.[CrossRef]
    [Google Scholar]
  32. Saintpierre-Bonaccio, D., Amir, H., Pineau, R., Tan, G. Y. A. & Goodfellow, M. ( 2005; ). Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. Int J Syst Evol Microbiol 55, 2057–2061.[CrossRef]
    [Google Scholar]
  33. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
     [Google Scholar]
  34. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  35. Staneck, J. L. & Roberts, G. D. ( 1974; ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231.
     [Google Scholar]
  36. Tamaoka, J., Katayama-Fujimura, Y. & Kuraishi, H. ( 1983; ). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54, 31–36.[CrossRef]
    [Google Scholar]
  37. Tan, G. Y. A., Robinson, S., Lacey, E. & Goodfellow, M. ( 2006a; ). Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils. Int J Syst Evol Microbiol 56, 2297–2301.[CrossRef]
    [Google Scholar]
  38. Tan, G. Y. A., Ward, A. C. & Goodfellow, M. ( 2006b; ). Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 29, 557–569.[CrossRef]
    [Google Scholar]
  39. Tang, S.-K., Li, W.-J., Wang, D., Zhang, Y.-G., Xu, L.-H. & Jiang, C.-L. ( 2003; ). Studies of the biological characteristics of some halophilic and halotolerant actinomycetes isolated from saline and alkaline soils. Actinomycetologica 17, 6–10.[CrossRef]
    [Google Scholar]
  40. 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.[CrossRef]
    [Google Scholar]
  41. Warwick, S., Bowen, T., McVeigh, H. P. & 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.[CrossRef]
    [Google Scholar]
  42. 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.[CrossRef]
    [Google Scholar]
  43. Yassin, A. F., Haggenei, B., Budzikiewicz, H. & Schaal, K. P. ( 1993; ). Fatty acid and polar lipid composition of the genus Amycolatopsis: application of fast atom bombardment-mass spectrometry to the structure analysis of underivatized phospholipids. Int J Syst Bacteriol 43, 414–420.[CrossRef]
    [Google Scholar]
  44. Zhang, L., An, R., Wang, J., Sun, N., Zhang, S., Hu, J. & Kuai, J. ( 2005; ). Exploring novel bioactive compounds from marine microbes. Curr Opin Microbiol 8, 276–281.[CrossRef]
    [Google Scholar]
  45. Zhang, L., Yan, K., Zhang, Y., Huang, R., Bian, J., Zheng, C., Sun, H., Chen, Z., Sun, N. & other authors ( 2007; ). High-throughput synergy screening identifies microbial metabolites as combination agents for the treatment of fungal infections. Proc Natl Acad Sci U S A 104, 4606–4611.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000026-0
Loading
Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment
Int J Syst Evol Microbiol 59, 477 (2009); https://doi.org/10.1099/ijs.0.000026-0
/content/journal/ijsem/10.1099/ijs.0.000026-0
/content/journal/ijsem/10.1099/ijs.0.000026-0
Loading

Data & Media loading...

Most cited articles

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