1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 60, Issue 3

sp. nov., isolated from root nodules of (Willd.) Ohwi Free

Abstract

A Gram-negative, strictly aerobic bacterium, comprising non-endospore-forming motile rods (1.2–2.0 μm × 0.4–0.6 μm) with polar flagellae was isolated from root nodules of the leguminous plant (Willd.) Ohwi growing on the coast of Yakushima Island, Kagoshima Prefecture, Japan. The novel strain, designated Yak96B, grew at an optimum pH of 7.0 and an optimum temperature of 28 °C. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the new strain was closely related to J1 and IPL18, with sequence similarities of 98.1 % and 97.8 %, respectively. However, the DNA–DNA relatedness values of strain Yak96B with LMG 21357 and CCM 7426 were 53.6 % and 34 %, respectively. The DNA G+C content of strain Yak96B was 65.3 mol%, the predominant isoprenoid quinone was Q10 (85 %) and the polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>5 %) were 11-methyl C 7 (35.0 %), C (22.4 %), C 7 (21.8 %), C cyclo 8 (6.8 %) and C (5.4 %). The infection/nodulation test was negative and and genes were not detected. Based on its chemotaxonomic and physiological characteristics, strain Yak96B represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Yak96B (=KCTC 22147=NBRC 103855=LMG 24299).

  • Published Online:
SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.011254-0
2010-03-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/3/627.html?itemId=/content/journal/ijsem/10.1099/ijs.0.011254-0&mimeType=html&fmt=ahah

References

  1. Abaidoo R. C., Keyser H. H., Singleton P. W., Borthakur D. 2000; Bradyrhizobium spp. (TGx) isolates nodulating the new soybean cultivars in Africa are diverse and distinct from bradyrhizobia that nodulate North American soybeans. Int J Syst Evol Microbiol 50:225–234
     [Google Scholar]
  2. 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
     [Google Scholar]
  3. Collins M. D., Jones D. 1981; A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51:129–134 [CrossRef]
     [Google Scholar]
  4. 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]
  5. Germano M. G., Menna P., Mostasso F. L., Hungria M. 2006; RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species. Int J Syst Evol Microbiol 56:217–229
     [Google Scholar]
  6. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
     [Google Scholar]
  7. Heimbrook M. E., Wang W. L. L., Campbell G. 1989; Staining bacterial flagella easily. J Clin Microbiol 27:2612–2615
     [Google Scholar]
  8. Hiraishi A. 1992; Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15:210–213 [CrossRef]
     [Google Scholar]
  9. Jukes T., 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]
  10. Kimura M. 1983 In The Neutral Theory of Molecular Evolution pp 41–46 London: Cambridge University Press;
     [Google Scholar]
  11. Kumar M., Verma M., Lal R. 2008; Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int J Syst Evol Microbiol 58:861–865 [CrossRef]
     [Google Scholar]
  12. Kurahashi M., Yokota A. 2002; A preliminary report of phylogenetic diversity of bacterial strains isolated from marine creatures. J Gen Appl Microbiol 48:251–259 [CrossRef]
     [Google Scholar]
  13. Kwon S.-W., Park J.-Y., Kim J.-S., Kang J.-W., Cho Y.-H., Lim C.-K., Parker M. A., Lee G.-B. 2005; Phylogenetic analysis of the genera Bradyrhizobium , Mesorhizobium , Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences. Int J Syst Evol Microbiol 55:263–270
     [Google Scholar]
  14. Lee S. D. 2007; Devosia subaequoris sp. nov., isolated from beach sediment. Int J Syst Evol Microbiol 57:2212–2215 [CrossRef]
     [Google Scholar]
  15. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [CrossRef]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Nakagawa Y., Sakane T., Yokota A. 1996; Transfer of “ Pseudomonas riboflavina ” (Foster 1944), a Gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen nov., nom. rev. Int J Syst Bacteriol 4616–22
     [Google Scholar]
  19. Rivas R., Velázquez E., Willems A., Vizcanino N., Subba-Rao N. S., Mateos P. F., Gillis M., Dazzo F. B., Martinez-Molina E. 2002; A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce. Appl Environ Microbiol 68:5217–5222 [CrossRef]
     [Google Scholar]
  20. Rivas R., Willems A., Subba-Rao N. S., Vizcanino N., Mateos P. F., Dazzo F. B., Kroppenstedt R. M., Martinez-Molina E., Gillis M., Velázquez E. 2003; Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans , an aquatic legume from India. Syst Appl Microbiol 26:47–53 [CrossRef]
     [Google Scholar]
  21. Ryu S. H., Chung B. S., Le N. T., Jang H. H., Yun P.-Y., Park W., Jeon C. O. 2008; Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea. Int J Syst Evol Microbiol 58:633–636 [CrossRef]
     [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. Somasegaran P., Hoben H. J. 1994 Handbook for Rhizobia: Methods in Legume-Rhizobium Technology New York: Springer;
     [Google Scholar]
  24. 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
     [Google Scholar]
  25. 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]
  26. 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]
  27. Vanparys B., Heylen K., Lebbe L., Vos P. D. 2005; Devosia limi sp. nov., isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 55:1997–2000 [CrossRef]
     [Google Scholar]
  28. Vincent J. M. 1970; A Manual for the Practical Study of the Root Nodule Bacteria . IBP Handbook no:15 Oxford: Blackwell Scientific;
     [Google Scholar]
  29. Yoo S.-H., Weon H.-Y., Kim B.-Y., Hong S.-B., Kwon S.-W., Cho Y.-H., Go S.-J., Stackebrandt E. 2006; Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56:2689–2692 [CrossRef]
     [Google Scholar]
  30. Yoon J.-H., Kang S.-J., Park S. 2007; Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia . Int J Syst Evol Microbiol 57:1310–1314 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.011254-0
Loading
Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi
Int J Syst Evol Microbiol 60, 627 (2010); https://doi.org/10.1099/ijs.0.011254-0
/content/journal/ijsem/10.1099/ijs.0.011254-0
/content/journal/ijsem/10.1099/ijs.0.011254-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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