1887

Abstract

A yellow pigmented, Gram-negative, rod-shaped bacterium designated FNE08-7 was isolated from subsurface water of the north-east basin of the bog lake Grosse Fuchskuhle (Brandenburg, Germany). A first analysis of the nearly full-length 16S rRNA gene sequence analysis including environmental 16S rRNA gene sequences derived from freshwater ecosystems showed that strain FNE08-7 is the first cultured representative, to our knowledge, of the freshwater tribe Novo-A2. Further analysis indicates highest 16S rRNA gene sequence similarities to the type strains of (98.0 %) and (97.4 %) and between 94.0 % and 96.9 % sequence similarity to other members of the genus . Reconstruction of phylogenetic trees showed that strain FNE08-7 formed a distinct cluster with the type strains of and supported by high bootstrap values. DNA–DNA hybridization of strain FNE08-7 with SMCC B0712 and DSM 17507 revealed low similarity values of 18.4 % (reciprocal: 11.4 %) and 23.1 % (reciprocal: 54.2 %), respectively. The predominant fatty acid of the isolate is Cω7 (56.4 %) and two characteristic 2-hydroxy fatty acids, C 2-OH (16.5 %) and C 2-OH (3.3 %) occur. Ubiquinone Q-10 is the major respiratory quinone. The predominant polar lipids are phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine and minor amounts of diphosphatidylglycerol. Spermidine is the predominant polyamine. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicate that strain FNE08-7 represents a novel species of the genus within the . Therefore, we propose the species sp. nov., with FNE08-7 ( = DSM 25065 = CCM 7978 = CCUG 61508) as the type strain.

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2013-02-01
2019-10-22
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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. Allgaier M. , Grossart H.-P. . ( 2006; ). Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany. . Aquat Microb Ecol 45:, 115–128. [CrossRef]
    [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. Brosius J. , Palmer M. L. , Kennedy P. J. , Noller H. F. . ( 1978; ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . . Proc Natl Acad Sci U S A 75:, 4801–4805. [CrossRef] [PubMed]
    [Google Scholar]
  6. Burkert U. , Warnecke F. , Babenzien D. , Zwirnmann E. , Pernthaler J. . ( 2003; ). Members of a readily enriched β-proteobacterial clade are common in surface waters of a humic lake. . Appl Environ Microbiol 69:, 6550–6559. [CrossRef] [PubMed]
    [Google Scholar]
  7. Busse H.-J. , Auling G. . ( 1988; ). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11:, 1–8. [CrossRef]
    [Google Scholar]
  8. Button D. K. . ( 1993; ). Nutrient-limited microbial growth kinetics: overview and recent advances. . Antonie van Leeuwenhoek 63:, 225–235. [CrossRef] [PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. Felsenstein J. . ( 1985; ). Confidence limits of phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  12. Felsenstein J. . ( 2005; ). phylip (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  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. Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . (editors) ( 1994; ). Methods for General and Molecular Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  15. 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]
  16. Glöckner F. O. , Zaichikov E. , Belkova N. , Denissova L. , Pernthaler J. , Pernthaler A. , Amann R. . ( 2000; ). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. . Appl Environ Microbiol 66:, 5053–5065. [CrossRef] [PubMed]
    [Google Scholar]
  17. Groth I. , Schumann P. , Weiss N. , Martin K. , Rainey F. A. . ( 1996; ). Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. . Int J Syst Bacteriol 46:, 234–239. [CrossRef] [PubMed]
    [Google Scholar]
  18. 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]
  19. Hobot J. A. , Carlemalm E. , Villiger W. , Kellenberger E. . ( 1984; ). Periplasmic gel: new concept resulting from the reinvestigation of bacterial cell envelope ultrastructure by new methods. . J Bacteriol 160:, 143–152.[PubMed]
    [Google Scholar]
  20. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of the protein molecule. . In Mammalian Protein Metabolism, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  21. 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]
  22. 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]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Lane D. J. . ( 1991; ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E. , Goodfellow M. . . London:: Wiley;.
    [Google Scholar]
  26. 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]
  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. Newton R. J. , Jones S. E. , Eiler A. , McMahon K. D. , Bertilsson S. . ( 2011; ). A guide to the natural history of freshwater lake bacteria. . Microbiol Mol Biol Rev 75:, 14–49. [CrossRef] [PubMed]
    [Google Scholar]
  31. 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]
  32. Pruesse E. , Quast C. , Knittel K. , Fuchs B. M. , Ludwig W. , Peplies J. , Glöckner F. O. . ( 2007; ). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. . Nucleic Acids Res 35:, 7188–7196. [CrossRef] [PubMed]
    [Google Scholar]
  33. 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]
  34. 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]
  35. Stolz A. , Busse H.-J. , Kämpfer P. . ( 2007; ). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57:, 572–576. [CrossRef] [PubMed]
    [Google Scholar]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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.[PubMed] [CrossRef]
    [Google Scholar]
  41. Yabuuchi E. , Kosako Y. , Fujiwara N. , Naka T. , Matsunaga I. , Ogura H. , Kobayashi K. . ( 2002; ). Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola . . Int J Syst Evol Microbiol 52:, 1485–1496. [CrossRef] [PubMed]
    [Google Scholar]
  42. Yarza P. , Richter M. , Peplies J. , Euzeby J. , Amann R. , Schleifer K. H. , Ludwig W. , Glöckner F. O. , Rosselló-Móra R. . ( 2008; ). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. . Syst Appl Microbiol 31:, 241–250. [CrossRef] [PubMed]
    [Google Scholar]
  43. 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]
  44. Ziemke F. , Höfle M. G. , Lalucat J. , Rosselló-Mora R. . ( 1998; ). Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. nov.. Int J Syst Bacteriol 48:, 179–186. [CrossRef] [PubMed]
    [Google Scholar]
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