1887

Abstract

A novel bacterium, strain MUSC 273, was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273 was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus . The 16S rRNA gene sequence of strain MUSC 273 showed the highest sequence similarity to those of H25 (96.8 %), TUT562 (96.4 %) and CC-TPE-1 (95.9 %) and lower sequence similarity to members of all other species of the genus . Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273 formed a distinct cluster with members of the genus . DNA–DNA relatedness of strain MUSC 273 to the type strains of the most closely related species, MCCC 1A01080 and DSM 18518, was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were Cω7, Cω6, C, C 2-OH and Cω7. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273 represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MUSC 273 ( = DSM 27798 = MCCC 1A00645 = NBRC 109947).

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2014-04-01
2019-10-14
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References

  1. Addison S. L., Foote S. M., Reid N. M., Lloyd-Jones G.. ( 2007;). Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. . Int J Syst Evol Microbiol 57:, 2467–2471. [CrossRef][PubMed]
    [Google Scholar]
  2. Atlas R. M.. ( 1993;). Handbook of Microbiological Media. Edited by Parks L. C... Boca Raton, FL:: CRC Press;.
    [Google Scholar]
  3. Baek S.-H., Lim J. H., Jin L., Lee H.-G., Lee S.-T.. ( 2011;). Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. . Int J Syst Evol Microbiol 61:, 2464–2468. [CrossRef][PubMed]
    [Google Scholar]
  4. Balkwill D. L., Drake G. R., Reeves R. H., Fredrickson J. K., White D. C., Ringelberg D. B., Chandler D. P., Romine M. F., Kennedy D. W., Spadoni C. M.. ( 1997;). Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.. Int J Syst Bacteriol 47:, 191–201. [CrossRef][PubMed]
    [Google Scholar]
  5. Busse H.-J., Auling G.. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11:, 1–8. [CrossRef]
    [Google Scholar]
  6. Busse H.-J., Bunka S., Hensel A., Lubitz W.. ( 1997;). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Bacteriol 47:, 698–708. [CrossRef]
    [Google Scholar]
  7. Carillo P. G., Mardaraz C., Pitta-Alvarez S. I., Giulietti A. M.. ( 1996;). Isolation and selection of biosurfactant producing bacteria. . World J Microbiol Biotechnol 12:, 82–84. [CrossRef]
    [Google Scholar]
  8. Cashion P., Holder-Franklin M. A., McCully J., Franklin M.. ( 1977;). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81:, 461–466. [CrossRef][PubMed]
    [Google Scholar]
  9. Cerny G.. ( 1978;). Studies on aminopeptidase for the distinction of gram-negative from gram-positive bacteria. . Eur J Appl Microbiol Biotechnol 5:, 113–122. [CrossRef]
    [Google Scholar]
  10. De Ley J., Cattoir H., Reynaerts A.. ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef][PubMed]
    [Google Scholar]
  11. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  12. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–789. [CrossRef]
    [Google Scholar]
  13. Fujii K., Satomi M., Morita N., Motomura T., Tanaka T., Kikuchi S.. ( 2003;). Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. . Int J Syst Evol Microbiol 53:, 47–52. [CrossRef][PubMed]
    [Google Scholar]
  14. Glaeser S. P., Kämpfer P., Busse H.-J., Langer S., Glaeser J.. ( 2009;). Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. . Int J Syst Evol Microbiol 59:, 323–330. [CrossRef][PubMed]
    [Google Scholar]
  15. Glaeser S. P., Bolte K., Martin K., Busse H.-J., Grossart H.-P., Kämpfer P., Glaeser J.. ( 2013a;). Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle. . Int J Syst Evol Microbiol 63:, 586–592. [CrossRef][PubMed]
    [Google Scholar]
  16. Glaeser S. P., Bolte K., Busse H.-J., Kämpfer P., Grossart H.-P., Glaeser J.. ( 2013b;). Novosphingobium aquaticum sp. nov., isolated from the humic-matter-rich bog lake Grosse Fuchskuhle. . Int J Syst Evol Microbiol 63:, 2630–2636. [CrossRef][PubMed]
    [Google Scholar]
  17. Gupta S. K., Lal D., Lal R.. ( 2009;). Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. . Int J Syst Evol Microbiol 59:, 156–161. [CrossRef][PubMed]
    [Google Scholar]
  18. Hong K., Gao A. H., Xie Q. Y., Gao H., Zhuang L., Lin H. P., Yu H. P., Li J., Yao X. S.. & other authors ( 2009;). Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China. . Mar Drugs 7:, 24–44. [CrossRef][PubMed]
    [Google Scholar]
  19. 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:, 184–192. [CrossRef][PubMed]
    [Google Scholar]
  20. Kämpfer P., Witzenberger R., Denner E. B. M., Busse H.-J., Neef A.. ( 2002;). Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. . Syst Appl Microbiol 25:, 37–45. [CrossRef][PubMed]
    [Google Scholar]
  21. Kämpfer P., Young C.-C., Busse H.-J., Lin S.-Y., Rekha P. D., Arun A. B., Chen W.-M., Shen F.-T., Wu Y.-H.. ( 2011;). Novosphingobium soli sp. nov., isolated from soil. . Int J Syst Evol Microbiol 61:, 259–263. [CrossRef][PubMed]
    [Google Scholar]
  22. Kates M.. ( 1986;). Techniques of Lipidology, , 2nd edn.. Amsterdam:: Elsevier;.
    [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. 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:, 716–721. [CrossRef][PubMed]
    [Google Scholar]
  25. 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][PubMed]
    [Google Scholar]
  26. Küster E., Williams S. T.. ( 1964;). Selection of media for isolation of streptomycetes. . Nature 202:, 928–929. [CrossRef][PubMed]
    [Google Scholar]
  27. Lal R., Dogra C., Malhotra S., Sharma P., Pal R.. ( 2006;). Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. . Trends Biotechnol 24:, 121–130. [CrossRef][PubMed]
    [Google Scholar]
  28. Li H. F., Zou Z. T., Li B. Z., Wang X., Yang J. S., Yuan H. L.. ( 2012;). Novosphingobium sediminis sp. nov., isolated from the sediment of a eutrophic lake. . J Gen Appl Microbiol 58:, 357–362. [CrossRef][PubMed]
    [Google Scholar]
  29. Lim Y. W., Moon E. Y., Chun J.. ( 2007;). Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym. . Int J Syst Evol Microbiol 57:, 1906–1908. [CrossRef][PubMed]
    [Google Scholar]
  30. Lin S. Y., Hameed A., Liu Y. C., Hsu Y. H., Lai W. A., Huang H. I., Young C. C.. ( 2013;). Novosphingobium arabidopsis sp. nov., a novel DDT-resistant bacterium isolated from the Arabidopsis thaliana rhizosphere. . Int J Syst Evol Microbiol 64: (in press) [CrossRef][PubMed]
    [Google Scholar]
  31. Liu Z.-P., Wang B.-J., Liu Y.-H., Liu S.-J.. ( 2005;). Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. . Int J Syst Evol Microbiol 55:, 1229–1232. [CrossRef][PubMed]
    [Google Scholar]
  32. MacFaddin J. F.. ( 2000;). Biochemical Tests for Identification of Medical Bacteria, , 3rd edn.. Baltimore:: Lippincott, Williams & Wilkins;.
    [Google Scholar]
  33. Meena B., Rajan L. A., Vinithkumar N. V., Kirubagaran R.. ( 2013;). Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts. . BMC Microbiol 13:, 145. [CrossRef][PubMed]
    [Google Scholar]
  34. 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]
  35. Niharika N., Moskalikova H., Kaur J., Sedlackova M., Hampl A., Damborsky J., Prokop Z., Lal R.. ( 2013;). Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. . Int J Syst Evol Microbiol 63:, 667–672. [CrossRef][PubMed]
    [Google Scholar]
  36. 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]
  37. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  38. Saxena A., Anand S., Dua A., Sangwan N., Khan F., Lal R.. ( 2013;). Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. . Int J Syst Evol Microbiol 63:, 2160–2167. [CrossRef][PubMed]
    [Google Scholar]
  39. Shieh W. Y., Chen Y.-W., Chaw S.-M., Chiu H.-H.. ( 2003;). Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. . Int J Syst Evol Microbiol 53:, 479–484. [CrossRef][PubMed]
    [Google Scholar]
  40. Shirling E. B., Gottlieb D.. ( 1966;). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16:, 313–340. [CrossRef]
    [Google Scholar]
  41. Sohn J. H., Kwon K.-K., Kang J.-H., Jung H.-B., Kim S.-J.. ( 2004;). Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. . Int J Syst Evol Microbiol 54:, 1483–1487. [CrossRef][PubMed]
    [Google Scholar]
  42. 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:, 846–849. [CrossRef]
    [Google Scholar]
  43. Suzuki S., Hiraishi A.. ( 2007;). Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. . J Gen Appl Microbiol 53:, 221–228. [CrossRef][PubMed]
    [Google Scholar]
  44. Takeuchi M., Sakane T., Yanagi M., Yamasato K., Hamana K., Yokota A.. ( 1995;). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.. Int J Syst Bacteriol 45:, 334–341. [CrossRef][PubMed]
    [Google Scholar]
  45. Takeuchi M., Hamana K., Hiraishi A.. ( 2001;). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. . Int J Syst Evol Microbiol 51:, 1405–1417.[PubMed]
    [Google Scholar]
  46. 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:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  47. 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][PubMed]
    [Google Scholar]
  48. Tiirola M. A., Busse H.-J., Kämpfer P., Männistö M. K.. ( 2005;). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. . Int J Syst Evol Microbiol 55:, 583–588. [CrossRef][PubMed]
    [Google Scholar]
  49. Versalovic J., Koeuth T., Lupski J. R.. ( 1991;). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. . Nucleic Acids Res 19:, 6823–6831. [CrossRef][PubMed]
    [Google Scholar]
  50. 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. [CrossRef]
    [Google Scholar]
  51. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H.. ( 1990;). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. . Microbiol Immunol 34:, 99–119. [CrossRef][PubMed]
    [Google Scholar]
  52. Yuan J., Lai Q., Zheng T., Shao Z.. ( 2009;). Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. . Int J Syst Evol Microbiol 59:, 2084–2088. [CrossRef][PubMed]
    [Google Scholar]
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