sp. nov., isolated from an estuarine lake Free

Abstract

The taxonomic position of a novel actinomycete, strain RC 1831, isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus . The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with DSM 41689 (98.22 % similarity) and a subclade consisting of DSM 42065 (98.40 %), R97 DSM 41901 (98.27 %), GIMN4.003 (98.33 %), DSM 41926 (98.13 %), NBRC 14749 (97.37 %) and NBRC 14748 (98.22 %). However, the levels of DNA–DNA relatedness between strain RC 1831 and phylogenetically related strains DSM 42065 (28.75±3.25 %) and DSM 41689 (15±2.40 %) were significantly lower than the 70 % threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831 is therefore considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RC 1831 ( = JCM 18754 = DSM 42082).

Funding
This study was supported by the:
  • World Bank
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2014-04-01
2024-03-29
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [View Article] [PubMed]
    [Google Scholar]
  2. Bérdy J. ( 2005 ). Bioactive microbial metabolites. . J Antibiot (Tokyo) 58, 126. [View Article] [PubMed]
    [Google Scholar]
  3. Bligh E. G., Dyer W. J. ( 1959 ). A rapid method of total lipid extraction and purification. . Can J Biochem Physiol 37, 911917. [View Article] [PubMed]
    [Google Scholar]
  4. Chater K. F., Biró S., Lee K. J., Palmer T., Schrempf H. ( 2010 ). The complex extracellular biology of Streptomyces . . FEMS Microbiol Rev 34, 171198. [View Article] [PubMed]
    [Google Scholar]
  5. 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]
  6. Edwards U., Rogall T., Blöcker H., Emde M., Böttger E. C. ( 1989 ). Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. . Nucleic Acids Res 17, 78437853. [View Article] [PubMed]
    [Google Scholar]
  7. Embley T. M., Stackebrandt E. ( 1994 ). The molecular phylogeny and systematics of the actinomycetes. . Annu Rev Microbiol 48, 257289. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  9. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  10. Goodfellow M. ( 1971 ). Numerical taxonomy of some nocardioform bacteria. . J Gen Microbiol 69, 3380. [View Article] [PubMed]
    [Google Scholar]
  11. Goodfellow M., Ferguson E. V., Sanglier J. J. ( 1992 ). Numerical classification and identification of Streptomyces species – a review. . Gene 115, 225233. [View Article] [PubMed]
    [Google Scholar]
  12. Goodfellow M., Kumar Y., Labeda D. P., Sembiring L. ( 2007 ). The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. . Antonie van Leeuwenhoek 92, 173199. [View Article] [PubMed]
    [Google Scholar]
  13. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H. N. ( 1974 ). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Bacteriol 24, 5463. [View Article]
    [Google Scholar]
  14. Hain T., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E., Rainey F. A. ( 1997 ). Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S–23S ribosomal DNA intergenic spacers. . Int J Syst Bacteriol 47, 202206. [View Article] [PubMed]
    [Google Scholar]
  15. Hall T. A. ( 1999 ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41, 9598.
    [Google Scholar]
  16. Hatano K., Nishii T., Kasai H. ( 2003 ). Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA–DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.. Int J Syst Evol Microbiol 53, 15191529. [View Article] [PubMed]
    [Google Scholar]
  17. Hsu S. C., Lockwood J. L. ( 1975 ). Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. . Appl Microbiol 29, 422426.[PubMed]
    [Google Scholar]
  18. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  19. Kämpfer P. ( 2012 ). Genus I. Streptomyces Waksman and Henrici 1943, 339 emend. Witt and Stackebrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. . In Bergey’s Manual of Systematic Bacteriology, vol. 5, pp. 14551767. Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Suzuki K.-I. , Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  20. Kämpfer P., Labeda D. P. ( 2006 ). International Committee on Systematics of Prokaryotes; Subcommittee on the taxonomy of the Streptomycetaceae: Minutes of the meeting, 25 July 2005, San Francisco, CA, USA. . Int J Syst Evol Microbiol 56, 495. [View Article]
    [Google Scholar]
  21. Kämpfer P., Kroppenstedt R. M., Dott W. ( 1991 ). A numerical classification of the genera Streptomyces and Streptoverticellium using miniaturized physiological tests. . J Gen Microbiol 137, 18311891. [View Article]
    [Google Scholar]
  22. Kämpfer P., Huber B., Buczolits S., Thummes K., Grün-Wollny I., Busse H. J. ( 2008 ). Streptomyces specialis sp. nov.. Int J Syst Evol Microbiol 58, 26022606. [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. Kieser T., Bibb M. J., Buttner M. J., Chater K. F., Hopwood D. A. ( 2000 ). Practical Streptomyces Genetics, A Laboratory Manual. Norwich:: John Innes Foundation;.
    [Google Scholar]
  25. Kim S. B., Goodfellow M. ( 2002 ). Streptomyces avermitilis sp. nov., nom. rev., a taxonomic home for the avermectin-producing streptomycetes. . Int J Syst Evol Microbiol 52, 20112014. [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and realated organisms. . In Chemical Methods in Bacterial Systematics, pp. 173199. Edited by Goodfellow M., Minnikin D. E. . New York:: Academic Press;.
    [Google Scholar]
  29. Labeda D. P., Goodfellow M., Brown R., Ward A. C., Lanoot B., Vanncanneyt M., Swings J., Kim S. B., Liu Z. & other authors ( 2012 ). Phylogenetic study of the species within the family Streptomycetaceae . . Antonie van Leeuwenhoek 101, 73104. [View Article] [PubMed]
    [Google Scholar]
  30. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
    [Google Scholar]
  31. Lanoot B., Vancanneyt M., Cleenwerck I., Wang L., Li W., Liu Z., Swings J. ( 2002 ). The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus . . Int J Syst Evol Microbiol 52, 823829. [View Article] [PubMed]
    [Google Scholar]
  32. Lanoot B., Vancanneyt M., Dawyndt P., Cnockaert M., Zhang J., Huang Y., Liu Z., Swings J. ( 2004 ). BOX-pCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus . . Syst Appl Microbiol 27, 8492. [View Article] [PubMed]
    [Google Scholar]
  33. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. & other authors ( 2007 ). clustal w and clustal_x version 2. . Bioinformatics 23, 29472948. [View Article] [PubMed]
    [Google Scholar]
  34. Lechevalier M. P., Lechevalier H. A. ( 1970 ). Chemical composition as a criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20, 435443. [View Article]
    [Google Scholar]
  35. Lodders N., Kämpfer P. ( 2007 ). Streptomycetaceae: Phylogeny, Ecology and Pathogenicity. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [View Article]
    [Google Scholar]
  36. Madigan M. T., Martinko J. M., Parker J. ( 1997 ). Antibiotics: isolation and characterization. . In Brock Biology of Microorganisms, , 8th edn., pp. 440442, Prentice-Hall International Inc, Upper Saddle River:, New Jersey:.
    [Google Scholar]
  37. Mandel M., Marmur J. ( 1968 ). Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12, 195206. [View Article]
    [Google Scholar]
  38. Manfio G. P., Zakrzewska-Czerwinska J., Atlan E., Goodfellow M. ( 1995 ). Towards minimal standards for the description of Streptomyces species. . Biotechnologia 7–8, 242253.
    [Google Scholar]
  39. Ray L., Suar M., Pattnaik A. K., Raina V. ( 2013 ). Streptomyces chilikensis sp. nov., a halophilic streptomycete isolated from brackish water sediment. . Int J Syst Evol Microbiol 63, 27572764. [View Article] [PubMed]
    [Google Scholar]
  40. Rhuland L. E., Work E., Denman R. F., Hoare D. S. ( 1955 ). The behaviour of the isomers of 2,6-diaminopimelic acid on paper chromatograms. . J Am Chem Soc 77, 48444846. [View Article]
    [Google Scholar]
  41. Rong X., Huang Y. ( 2010 ). Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. . Int J Syst Evol Microbiol 60, 696703. [View Article] [PubMed]
    [Google Scholar]
  42. Rzhetsky A., Nei M. ( 1992 ). A simple methd for estimation and testing minimum evolution trees. . Mol Biol 9, 945967.
    [Google Scholar]
  43. Saintpierre D., Amir H., Pineau R., Sembiring L., Goodfellow M. ( 2003 ). Streptomyces yatensis sp. nov., a novel bioactive streptomycete isolated from a New-Caledonian ultramafic soil. . Antonie van Leeuwenhoek 83, 2126. [View Article] [PubMed]
    [Google Scholar]
  44. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  45. Santhanam R., Okoro C. K., Rong X., Huang Y., Bull A. T., Weon H. Y., Andrews B. A., Asenjo J. A., Goodfellow M. ( 2012 ). Streptomyces atacamensis sp. nov., isolated from an extreme hyper-arid soil of the Atacama Desert, Chile. . Int J Syst Evol Microbiol 62, 26802684. [View Article] [PubMed]
    [Google Scholar]
  46. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20, 16.
    [Google Scholar]
  47. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  48. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152155.
    [Google Scholar]
  49. 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]
  50. Staneck J. L., Roberts G. D. ( 1974 ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28, 226231.[PubMed]
    [Google Scholar]
  51. 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]
  52. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  53. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  54. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R. ( 2007 ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology (T. J. Beveridge, J.A Breznak, G. A. Marzluf, T. M. Schmidt, and L. R. Snyder, eds.), , 3rd edn., pp. 330393. ASM Press, Washington, D. C.
    [Google Scholar]
  55. Watve M. G., Tickoo R., Jog M. M., Bhole B. D. ( 2001 ). How many antibiotics are produced by the genus Streptomyces . ? Arch Microbiol 176, 386390. [View Article] [PubMed]
    [Google Scholar]
  56. 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 Bacterial Systematics. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  57. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. ( 1983 ). Numerical classification of Streptomyces and related genera. . J Gen Microbiol 129, 17431813.[PubMed]
    [Google Scholar]
  58. Williams S. T., Goodfellow M., Alderson G. ( 1989 ). Genus Streptomyces Waksman and Henrici 1943. 339 AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 4, pp. 24522492. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams &Wilkins;.
    [Google Scholar]
  59. Zhu H., Jiang S., Yao Q., Wang Y., Chen M., Chen Y., Guo J. ( 2011 ). Streptomyces fenghuangensis sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 61, 28112815. [View Article] [PubMed]
    [Google Scholar]
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