1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 6

sp. nov., isolated from farm soil Free

Abstract

The taxonomic position of a novel Gram-negative strain, designated SY1, isolated from a farm-soil sample obtained from Jiangsu Province, PR China, was characterized by using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30–37 °C and at pH 6.0–8.0. Based on 16S rRNA gene sequence analysis, strain SY1 is a member of the genus ; JCM 21156 was the nearest relative (98.5 % sequence similarity). The predominant fatty acids of strain SY1 were iso-C (32.9 %), C (10.9 %) and summed feature 3 (iso-C 2-OH and/or C 7; 24.1 %). The DNA G+C content was 38.5 mol%. The low level of DNA–DNA relatedness (2.2 %) to JCM 21156 in combination with differential morphological and biochemical properties demonstrated that strain SY1 (=KCTC 22131=CGMCC 1.6855) should be classified as representing a novel species of the genus for which the name sp. nov. is proposed.

  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65696-0
2008-06-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/58/6/1458.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65696-0&mimeType=html&fmt=ahah

References

  1. Cui, X. L., Mao, P. H., Tseng, M., Li, W. J., Zhang, L. P., Xu, L. H. & Jiang, C. L.(2001).Streptomonospora salina gen. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51, 357–363. [Google Scholar]
  2. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  3. Escara, J. F. & Hutton, J. R.(1980). Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: acceleration of renaturation rate. Biopolymers 19, 1315–1327.[CrossRef] [Google Scholar]
  4. Euzéby, J. P.(1998). Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int J Syst Bacteriol 48, 1073–1075.[CrossRef] [Google Scholar]
  5. Felsenstein, J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef] [Google Scholar]
  6. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  7. Felsenstein, J.(1993).phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  8. 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.
  9. Holmes, B., Weaver, R. E., Steigerwalt, A. G. & Brenner, D. J.(1988). A taxonomic study of Flavobacterium spiritivorum and Sphingobacterium mizutae: proposal of Flavobacterium yabuuchiae sp. nov. and Flavobacterium mizutaii comb. nov. Int J Syst Bacteriol 38, 348–353.[CrossRef] [Google Scholar]
  10. Huß, V. A. R., Festl, H. & Schleifer, K. H.(1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef] [Google Scholar]
  11. Jahnke, K. D.(1992).basic computer program for evaluation of spectroscopic DNA renaturation data from GILFORD SYSTEM 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61–73.[CrossRef] [Google Scholar]
  12. Kim, K.-H., Ten, L. N., Liu, Q.-M., Im, W.-K. & Lee, S.-T.(2006).Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56, 2031–2036.[CrossRef] [Google Scholar]
  13. Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J Mol Evol 16, 111–120.[CrossRef] [Google Scholar]
  14. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  15. Kumar, S., Tamura, K., Jakobsen, I.-B. & Nei, M.(2001).mega2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244–1245.[CrossRef] [Google Scholar]
  16. Lányí, B.(1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67. [Google Scholar]
  17. Mandel, M. & Marmur, J.(1968). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B, 195–206. [Google Scholar]
  18. Nedashkovskaya, O. I., Kim, S. B., Suzuki, M., Shevchenko, L. S., Lee, M. S., Lee, K. H., Park, M. S., Frolova, G. M., Oh, H. W. & other authors(2005).Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evol Microbiol 55, 2583–2588.[CrossRef] [Google Scholar]
  19. Park, M., Ryu, S. H., Thi Vu, T.-H., Ro, H.-S., Yun, P.-Y. & Jeon, C. O.(2007).Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 57, 233–237.[CrossRef] [Google Scholar]
  20. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  21. Sasser, M.(1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16 [Google Scholar]
  22. Shivaji, S., Ray, M. K., Rao, N. S., Saisree, L., Jagannadham, M. V., Kumar, G. S., Reddy, G. S. N. & Bhargava, P. M.(1992).Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. Int J Syst Bacteriol 42, 102–106.[CrossRef] [Google Scholar]
  23. 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]
  24. Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K. & Joubert, J. J.(1998). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48, 165–177.[CrossRef] [Google Scholar]
  25. Takeuchi, M. & Yokota, A.(1992). Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 38, 465–482.[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, 4876–4888.[CrossRef] [Google Scholar]
  27. 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]
  28. Xu, P., Li, W.-J., Tang, S.-K., Zhang, Y.-Q., Chen, G.-Z., Chen, H.-H., Xu, L.-H. & Jiang, C.-L.(2005).Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55, 1149–1153.[CrossRef] [Google Scholar]
  29. Yabuuchi, E., Kaneko, T., Yano, I., Moss, C. W. & Miyoshi, N.(1983).Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Bacteriol 33, 580–598.[CrossRef] [Google Scholar]
  30. Yamaguchi, S. & Yokoe, M.(2000). A novel protein-deamidating enzyme from Chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil. Appl Environ Microbiol 66, 3337–3343.[CrossRef] [Google Scholar]
  31. Yoo, S.-H., Weon, H.-Y., Jang, H.-B., Kim, B.-Y., Kwon, S.-W., Go, S.-J. & Stackebrandt, E.(2007).Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 57, 1590–1593.[CrossRef] [Google Scholar]
  32. Yoon, J.-H., Kim, H., Kim, S.-B., Kim, H.-J., Kim, W. Y., Lee, S. T., Goodfellow, M. & Park, Y.-H.(1996). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46, 502–505.[CrossRef] [Google Scholar]
  33. Zhou, Y., Dong, J., Wang, X., Huang, X., Zhang, K.-Y., Zhang, Y.-Q., Guo, Y.-F., Lai, R. & Li, W.-J.(2007).Chryseobacterium flavum sp. nov., isolated from a polluted soil. Int J Syst Evol Microbiol 57, 1765–1769.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65696-0
Loading
Sphingobacterium siyangense sp. nov., isolated from farm soil
Int J Syst Evol Microbiol 58, 1458 (2008); https://doi.org/10.1099/ijs.0.65696-0
/content/journal/ijsem/10.1099/ijs.0.65696-0
/content/journal/ijsem/10.1099/ijs.0.65696-0
Loading

Data & Media loading...

Supplements

vol. , part 6, pp. 1458 - 1462

Transmission electron micrographs of cells of strain SY1 grown on Luria-Bertani agar. [PDF](275 KB)

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