1887

Abstract

A yellow, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1) was isolated from the rhizosphere of a field-grown plant in Auburn, AL, USA. 16S rRNA gene sequence analysis of strain JM-1 showed high sequence similarity to the type strains of (98.9 %), (97.4 %), (97.3 %) and (97.1 %); sequence similarities to all other type strains of species of the genus were below 97.0 %. DNA–DNA hybridizations of strain JM-1 and DSM 30196, SMCC F199 and SMCC B0478 showed low similarity values of 33 % (reciprocal: 21 %), 14 % (reciprocal 16 %) and 36 % (reciprocal 38 %), respectively. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid was Cω7 (71.0 %) and the typical 2-hydroxy fatty acid C 2-OH (11.7 %) was detected. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain JM-1 represents a novel species of the genus . For this species we propose the name sp. nov. with the type strain JM-1 ( = LMG 28479 = CCM 8547).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.070375-0
2015-01-01
2019-11-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/1/195.html?itemId=/content/journal/ijsem/10.1099/ijs.0.070375-0&mimeType=html&fmt=ahah

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. 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]
  3. 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]
  4. Brosius J., Dull T. J., Sleeter D. D., Noller H. F.. ( 1981;). Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. . J Mol Biol 148:, 107–127. [CrossRef][PubMed]
    [Google Scholar]
  5. Chen Q., Zhang J., Wang C.-H., Jiang J., Kwon S.-W., Sun L.-N., Shen W.-B., He J.. ( 2014;). Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge. . Int J Syst Evol Microbiol 64:, 2573–2578. [CrossRef][PubMed]
    [Google Scholar]
  6. 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]
  7. 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][PubMed]
    [Google Scholar]
  8. Felsenstein J.. ( 1985;). Confidence limits of phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Felsenstein J.. ( 2005;). phylip (Phylogeny Inference Package) version 3.6. Distributed by the author. . Department of Genome Sciences, University of Washington;, Seattle, USA:.
  10. 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]
  11. 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]
  12. Glaeser S. P., Bolte K., Busse H. J., Kämpfer P., Grossart H. P., Glaeser J.. ( 2013a;). 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]
  13. Glaeser S. P., Bolte K., Martin K., Busse H. J., Grossart H. P., Kämpfer P., Glaeser J.. ( 2013b;). 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]
  14. 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]
  15. Jukes T. H., Cantor C. R.. ( 1969;). Evolution of the protein molecules. . In Mammalian Protein Metabolism, pp. 21–132. Edited by Munro H. N... New York:: Academic Press;. [CrossRef]
    [Google Scholar]
  16. Kämpfer P.. ( 1990;). Evaluation of the Titertek-Enterobac-Automated System (TTE-AS) for identification of members of the family Enterobacteriaceae. . Zentralbl Bakteriol 273:, 164–172. [CrossRef][PubMed]
    [Google Scholar]
  17. Kämpfer P., Kroppenstedt R. M.. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42:, 989–1005. [CrossRef]
    [Google Scholar]
  18. Kämpfer P., Steiof M., Dott W.. ( 1991;). Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. . Microb Ecol 21:, 227–251. [CrossRef][PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Kim J. K., He D., Liu Q. M., Park H. Y., Jung M. S., Yoon M. H., Kim S. C., Im W. T.. ( 2013;). Novosphingobium ginsenosidimutans sp. nov., with the ability to convert ginsenoside. . J Microbiol Biotechnol 23:, 444–450. [CrossRef][PubMed]
    [Google Scholar]
  22. Lane D. J.. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M... Chichester:: Wiley;.
    [Google Scholar]
  23. Lee L.-H., Azman A.-S., Zainal N., Eng S.-K., Fang C.-M., Hong K., Chan K.-G.. ( 2014a;). Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. . Int J Syst Evol Microbiol 64:, 1194–1201. [CrossRef][PubMed]
    [Google Scholar]
  24. Lee J. C., Kim S. G., Whang K. S.. ( 2014b;). Novosphingobium aquiterrae sp. nov., isolated from ground water. . Int J Syst Evol Microbiol 64:, 3282–3287. [CrossRef][PubMed]
    [Google Scholar]
  25. 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]
  26. Lin S.-Y., Hameed A., Liu Y.-C., Hsu Y.-H., Lai W.-A., Huang H.-I., Young C.-C.. ( 2014;). Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. . Int J Syst Evol Microbiol 64:, 594–598. [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S.. & other authors ( 2004;). arb: a software environment for sequence data. . Nucleic Acids Res 32:, 1363–1371. [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. Neef A., Witzenberger R., Kämpfer P.. ( 1999;). Detection of sphingomonads and in situ identification in activated sludge using 16S rRNA-targeted oligonucleotide probes. . J Ind Microbiol Biotechnol 23:, 261–267. [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. Pitcher D. G., Saunders N. A., Owen R. J.. ( 1989;). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. . Lett Appl Microbiol 8:, 151–156. [CrossRef]
    [Google Scholar]
  33. Pruesse E., Peplies J., Glöckner F. O.. ( 2012;). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. . Bioinformatics 28:, 1823–1829. [CrossRef][PubMed]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Stamatakis A.. ( 2006;). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22:, 2688–2690. [CrossRef][PubMed]
    [Google Scholar]
  37. Stolz A., Busse H.-J., Kämpfer P.. ( 2007;). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57:, 572–576. [CrossRef][PubMed]
    [Google Scholar]
  38. 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]
  39. 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]
  40. 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]
  41. Tiirola M. A., Männistö M. K., Puhakka J. A., Kulomaa M. S.. ( 2002;). Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. . Appl Environ Microbiol 68:, 173–180. [CrossRef][PubMed]
    [Google Scholar]
  42. 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]
  43. Xie F., Quan S., Liu D., He W., Wang Y., Ma H., Chen G., Chao Y., Qian S.. ( 2014;). Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. . Int J Syst Evol Microbiol 64:, 2324–2329. [CrossRef][PubMed]
    [Google Scholar]
  44. 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]
  45. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.070375-0
Loading
/content/journal/ijsem/10.1099/ijs.0.070375-0
Loading

Data & Media loading...

Most Cited This Month

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