1887

Abstract

Nitrogen-fixing bacteria, strains SA41, SA42 and SA53, were isolated from an aquatic plant, , that grows in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-negative, aerobic, non-spore-forming, rod-shaped bacteria, having a cell width of 0.6–0.7 μm and a length of 1.5–1.7 μm. They showed good growth between pH 3.0 and 7.0, and between 17 and 37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone, and C, C cyclo, C 7 and summed feature 3 (C 7 and/or iso-C 2-OH) as major fatty acids. Their fatty acid profiles are similar to those reported for other species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Although their calculated 16S rRNA gene sequence similarity values to and were 98.5, 98.2, 98.0 and 97.0 %, respectively, the isolates formed a distinct group in phylogenetic trees, and the DNA–DNA relatedness values of strain SA41 to these species were 39, 41, 39 and 33 %, respectively. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from the published species. Therefore, strains SA41, SA42 and SA53 represent a novel species for which the name sp. nov. is proposed. The type strain is SA41 (=NBRC 101817=VTCC-D6-7).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.015198-0
2010-05-01
2024-11-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/5/1152.html?itemId=/content/journal/ijsem/10.1099/ijs.0.015198-0&mimeType=html&fmt=ahah

References

  1. Aizawa T., Nguyen B. V., Kimoto K., Iwabuchi N., Sumida H., Hasegawa I., Sasaki S., Tamura T., Kudo T. other authors 2007; Curtobacterium ammoniigenes sp. nov., an ammonia-producing bacterium isolated from plants inhabiting acidic swamps in actual acid sulfate soil areas of Vietnam. Int J Syst Evol Microbiol 57:1447–1452 [CrossRef]
    [Google Scholar]
  2. Aizawa T., Urai M., Iwabuchi N., Nakajima M., Sunairi M. 2010; Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae ( Trypoxylus dichotomus septentrionalis. Int J Syst Evol Microbiol 60:61–66 [CrossRef]
    [Google Scholar]
  3. Bogan B. W., Sullivan W. R., Kayser K. J., Derr K. D., Aldrich H. C., Paterek J. R. 2003; Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. Int J Syst Evol Microbiol 53:1389–1395 [CrossRef]
    [Google Scholar]
  4. Burris R. H. 1972; Nitrogen fixation assay methods and techniques. Methods Enzymol 24:415–431
    [Google Scholar]
  5. Caballero-Mellado J., Martı'nez-Aguilar L., Paredes-Valdez G., Estrada-de los Santos P. 2004; Burkholderia unamae sp nov., an N2-fixing rhizospheric and endophytic species. Int J Syst Evol Microbiol 54:1165–1172 [CrossRef]
    [Google Scholar]
  6. Chen W. M., James E. K., Coenye T., Chou J. H., Barrios E., de Faria S. M., Elliott G. N., Sheu S. Y., Sprent J. I., Vandamme P. 2006; Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 56:1847–1851 [CrossRef]
    [Google Scholar]
  7. Chen W.-M., de Faria S. M., James E. K., Elliott G. N., Lin K.-Y., Chou J.-H., Sheu S.-Y., Cnockaert M., Sprent J. I., Vandamme P. 2007; Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella . Int J Syst Evol Microbiol 57:1055–1059 [CrossRef]
    [Google Scholar]
  8. Ezaki T., Hashimoto Y., Takeuchi N., Yamamoto H., Liu S. L., Miura H., Matsui K., Yabuuchi E. 1988; Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. J Clin Microbiol 26:1708–1713
    [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 39:224–229 [CrossRef]
    [Google Scholar]
  10. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [CrossRef]
    [Google Scholar]
  11. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  12. Felsenstein J. 2005 phylip (phylogeny inference package) version 3.65. Distributed by the author. Department of Genome Sciences University of Washington; Seattle, USA:
    [Google Scholar]
  13. Gillis M., Van Van T., Bardin R., Goor M., Hebbar P., Willems A., Segers P., Kersters K., Heulin T., Fernandez M. P. 1995; Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 45:274–289 [CrossRef]
    [Google Scholar]
  14. Goris J., De Vos P., Caballero-Mellado J., Park J.-H., Falsen E., Quensen J. F. III, Tiedje J. M., Vandamme P. 2004; Classification of the PCB- and biphenyl-degrading strain LB400 and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol 54:1677–1681 [CrossRef]
    [Google Scholar]
  15. Hashidoko Y., Tada M., Osaki M., Tahara S. 2002; Soft gel medium solidified with gellan gum for preliminary screening for root-associating, free-living nitrogen-fixing bacteria inhabiting the rhizoplane of plants. Biosci Biotechnol Biochem 66:2259–2263 [CrossRef]
    [Google Scholar]
  16. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol. 3 pp 21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  17. Kluge A. G., Farris J. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32 [CrossRef]
    [Google Scholar]
  18. Perin L., Martinez-Aguilar L., Paredes-Valdez G., Baldani J. I., Estrada-de los Santos P., Reis V. M., Caballero-Mellado J. 2006; Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. Int J Syst Evol Microbiol 56:1931–1937 [CrossRef]
    [Google Scholar]
  19. Pot B., Vandamme P., Kersters K. 1994; Analysis of electrophoretic whole-organism protein fingerprints. In Chemical Methods in Prokaryotic Systematics pp 493–521 Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;
    [Google Scholar]
  20. Reis V. M., Estrada-de los Santos P., Tenorio-Salgado S., Vogel J., Stoffels M., Guyon S., Mavingui P., Baldani V. L., Schmid M. other authors 2004; Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int J Syst Evol Microbiol 54:2155–2162 [CrossRef]
    [Google Scholar]
  21. Ryu E. 1938; On the Gram-differentiation of bacteria by the simplest method. J Jpn Soc Vet Sci 17:31
    [Google Scholar]
  22. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  23. Sasaki S., Ishii R., Hasegawa I. other authors 2008 Development of New Bioremediation Systems of Acid Sulfate Soil for Agriculture and Forestry Kyoto, Japan: Nakanishi Printing Co. Ltd;
    [Google Scholar]
  24. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  25. 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]
  26. Tamura T., Hatano K. 2001; Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. , 1986 and ‘ Actinoplanes aurantiacus ' to Cryptosporangium minutisporangium comb.nov. and Cryptosporangium aurantiacum sp. nov. Int J Syst Evol Microbiol 51:2119–2125 [CrossRef]
    [Google Scholar]
  27. Tamura T., Nakagaito Y., Nishii T., Hasegawa T., Stackebrandt E., Yokota A. 1994; A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky, 1986) comb.nov. and Couchioplanescaeruleus subsp. azureus subsp. nov.. Int J Syst Bacteriol 44:193–203 [CrossRef]
    [Google Scholar]
  28. Tamura T., Hayakawa M., Hatano K. 1999; Sporichthya brevicatena sp. nov. Int J Syst Bacteriol 49:1779–1784 [CrossRef]
    [Google Scholar]
  29. Tamura K., Dudley J., Nei M., Kumar S. 2007; MEGA4: Molecular Evolutionary Genetics Analysis (mega) Software Version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef]
    [Google Scholar]
  30. 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]
    [Google Scholar]
  31. Ueda T., Suga Y., Yahiro N., Matsuguchi T. 1995; Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414–1417
    [Google Scholar]
  32. Valdes M., Perez N.-O., Estrada-de los Santos P., Caballero-Mellado J., Pena-Cabriales J. J., Normand P., Hirsch A. M. 2005; Non- Frankia Actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen. Appl Environ Microbiol 71:460–466 [CrossRef]
    [Google Scholar]
  33. Valverde A., Delvasto P., Peix A., Velázquez E., Santa-Regina I., Ballester A., Rodríguez-Barrueco C., García-Balboa C., Igual J. M. 2006; Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil. Int J Syst Evol Microbiol 56:2421–2425 [CrossRef]
    [Google Scholar]
  34. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
  35. 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 to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  36. Yabuuchi E., Kosako Y., Oyaizu H., Yano I., Hotta H., Hashimoto Y., Ezaki T., Arakawa M. 1992; Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36:1251–1275 [CrossRef]
    [Google Scholar]
  37. Yamada Y., Takinami-Nakamura H., Tahara Y., Oyaizu H., Komagata K. 1982; The ubiquinone systems in the strains of Pseudomonas species. J Gen Appl Microbiol 28:7–12 [CrossRef]
    [Google Scholar]
  38. Yang H. C., Im W. T., Kim K. K., An D. S., Lee S. T. 2006; Burkholderia terrae sp. nov., isolated from a forest soil. Int J Syst Evol Microbiol 56:453–457 [CrossRef]
    [Google Scholar]
  39. Zhang H., Hanada S., Shigematsu T., Shibuya K., Kamagata Y., Kanagawa T., Kurane R. 2000; Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. Int J Syst Evol Microbiol 50:743–749 [CrossRef]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijs.0.015198-0
Loading
/content/journal/ijsem/10.1099/ijs.0.015198-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF

Supplementary material 4

PDF

Supplementary material 5

PDF
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