sp. nov., a nitrogen-fixing bacterium isolated from a freshwater lake Free

Abstract

A novel nitrogen-fixing strain, designated HL-12, was isolated from a freshwater lake in Taiwan. Cells of strain HL-12 were aerobic, Gram-negative, motile rods that were surrounded by a thick capsule, contained poly-β-hydroxybutyrate granules, and formed light-yellow to brownish-red colonies. Growth occurred at 15–40 °C (optimum 25–35 °C), at pH 6.0–7.0 (optimum pH 6.0) and with 0–4 % NaCl (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HL-12 belonged to the genus and exhibited 99.1 and 98.8 % 16S rRNA gene sequence similarity, respectively, with IAM 14990 and IAM 13946. The major fatty acids (>10 %) of strain HL-12 were summed feature 3 (comprising Cω7 and/or Cω6), C and Cω7. The cellular hydroxy fatty acids were C 3-OH, C 2-OH and C 3-OH. The isoprenoid quinone was Q-8 and the DNA G+C content was 72.0 mol%. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unknown aminophospholipids and phospholipids. DNA–DNA relatedness between strain HL-12 and LMG 3975 and LMG 3977 was <70 %. On the basis of the genotypic and phenotypic data, strain HL-12 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HL-12 ( = BCRC 80208  = KCTC 23311).

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2013-03-01
2024-03-29
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References

  1. Anzai Y., Kudo Y., Oyaizu H. ( 1997 ). The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. . Int J Syst Bacteriol 47, 249251. [View Article] [PubMed]
    [Google Scholar]
  2. Breznak J. A., Costilow R. N. ( 1994 ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  3. Chen W. M., Laevens S., Lee T. M., Coenye T., De Vos P., Mergeay M., Vandamme P. ( 2001 ). Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. . Int J Syst Evol Microbiol 51, 17291735. [View Article] [PubMed]
    [Google Scholar]
  4. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y.-W. ( 2007 ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57, 22592261. [View Article] [PubMed]
    [Google Scholar]
  5. Collins M. D. ( 1985 ). Isoprenoid quinone analysis in classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267287. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [Google Scholar]
  6. De Smedt J., Bauwens M., Tytgat R., De Ley J. ( 1980 ). Intra- and intergeneric similarities of ribosomal ribonucleic acid cistrons of free-living, nitrogen-fixing bacteria. . Int J Syst Bacteriol 30, 106122. [View Article]
    [Google Scholar]
  7. Elliott G. N., Chen W. M., Chou J. H., Wang H. C., Sheu S.-Y., Perin L., Reis V. M., Moulin L., Simon M. F. & other authors ( 2007 ). Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta. . New Phytol 173, 168180. [View Article] [PubMed]
    [Google Scholar]
  8. Embley T. M., Wait R. ( 1994 ). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121161. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: John Wiley & Sons;.
    [Google Scholar]
  9. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39, 224229. [View Article]
    [Google Scholar]
  10. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  11. Felsenstein, J. (1993). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  12. Garrity G. M., Bell J. A., Lilburn T. ( 2005 ). Order I. Burkholderiales ord. nov.. In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2, pp. 575763. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. . New York:: Springer;.
    [Google Scholar]
  13. 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]
  14. Jennsen H. L., Petersen E. J., De P. K., Bhattacharya R. ( 1960 ). A new nitrogen-fixing bacterium: Derxia gummosa nov. gen. nov.spec.. Arch Mikrobiol 36, 182195. [View Article] [PubMed]
    [Google Scholar]
  15. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  16. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 132. [View Article]
    [Google Scholar]
  17. Maidak B. L., Cole J. R., Lilburn T. G., Parker C. T. Jr, Saxman P. R., Farris R. J., Garrity G. M., Olsen G. J., Schmidt T. M., Tiedje J. M. ( 2001 ). The RDP-II (Ribosomal Database Project). . Nucleic Acids Res 29, 173174. [View Article] [PubMed]
    [Google Scholar]
  18. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the GC content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  19. Moulin L., Munive A., Dreyfus B., Boivin-Masson C. ( 2001 ). Nodulation of legumes by members of the β-subclass of Proteobacteria . . Nature 411, 948950. [View Article] [PubMed]
    [Google Scholar]
  20. Murray R. G. E., Doetsch R. N., Robinow C. F. ( 1994 ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 2141. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  21. Nokhal T. H., Schlegel H. G. ( 1983 ). Taxonomic study of Paracoccus denitrijicans . . Int J Syst Bacteriol 33, 2637. [View Article]
    [Google Scholar]
  22. Powers E. M. ( 1995 ). Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. . Appl Environ Microbiol 61, 37563758.[PubMed]
    [Google Scholar]
  23. Reinhold B., Hurek T., Niemann E. G., Fendrik I. ( 1986 ). Close association of Azospirillum and diazotrophic rods with different root zones of kallar grass. . Appl Environ Microbiol 52, 520526.[PubMed]
    [Google Scholar]
  24. Rosado A. S., Duarte G. F., Seldin L., Van Elsas J. D. ( 1998 ). Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. . Appl Environ Microbiol 64, 27702779.[PubMed]
    [Google Scholar]
  25. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  26. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc.;
  27. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  28. 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]
  29. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  30. 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 of bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  31. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697703.[PubMed]
    [Google Scholar]
  32. Xie C. H., Yokota A. ( 2004 ). Phylogenetic analyses of the nitrogen-fixing genus Derxia . . J Gen Appl Microbiol 50, 129135. [View Article] [PubMed]
    [Google Scholar]
  33. Young J. P. W. ( 1992 ). Phylogenetic classification of nitrogen-fixing organisms. . In Biological Nitrogen Fixation, pp. 4386. Edited by Stacey G., Burris R. H., Evans H. J. . New York:: Chapman & Hall;.
    [Google Scholar]
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