DOI QR코드

DOI QR Code

Pedobacter xinjiangensis sp. nov., from the Desert, Xinjiang

  • Tang, Yali (College of Life Sciences, Wuhan University) ;
  • Wang, Yang (College of Life Sciences, Wuhan University) ;
  • Ji, Shanming (College of Life Sciences, Wuhan University) ;
  • Zhang, Kundi (College of Life Sciences, Wuhan University) ;
  • Dai, Jun (College of Life Sciences, Wuhan University) ;
  • Zhang, Lei (College of Life Sciences, Wuhan University) ;
  • Peng, Fang (College of Life Sciences, Wuhan University) ;
  • Fang, Chengxiang (College of Life Sciences, Wuhan University)
  • Published : 2010.02.28

Abstract

A Gram-negative, rod-shaped, gliding, aerobic bacterium, designated $12157^T$, was isolated from the desert of Xinjiang, China and subjected to a polyphasic taxonomic study. The strain $12157^T$ grew optimally at pH 7.0 and $30^{\circ}C$. MK-7 was the predominant respiratory menaquinone. The DNA G+C content was 42.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolate was mostly related to members of the genus Pedobacter, with similarities ranging from 90.0% to 93.7%. Phylogenetic evidence and the results of phenotypic and genotypic analyses support the establishment of a novel species, Pedobacter xinjiangensis sp. nov., with strain $12157^T$ (=CCTCC AB $208092^T$=NRRL B-$51338^T$) as the type strain.

Keywords

References

  1. An, D. S., S. G. Kim, L. N. Ten, and C. H. Cho. 2009. Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int. J. Syst. Evol. Microbiol. 59: 69-72. https://doi.org/10.1099/ijs.0.001529-0
  2. Baik, K. S., Y. D. Park, M. S. Kim, S. C. Park, E. Y. Moon, M. S. Rhee, J. H. Choi, and C. N. Seong. 2007. Pedobacter koreensis sp. nov., isolated from fresh water. Int. J. Syst. Evol. Microbiol. 57: 2079-2083. https://doi.org/10.1099/ijs.0.65186-0
  3. Bowman, J. P. 2000. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int. J. Syst. Evol. Microbiol. 50: 1861-1868.
  4. Buck, J. D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44: 992-993.
  5. Chanal, A., V. Chapon, K. Benzerara, M. Barakat, R. Christen, W. Achouak, F. Barras, and T. Heulin. 2006. The desert of Tataouine: An extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ. Microbiol. 8: 514-525. https://doi.org/10.1111/j.1462-2920.2005.00921.x
  6. Chun, J., J.-H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y. W. Lim. 2007. EzTaxon: A Web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57: 2259-2261. https://doi.org/10.1099/ijs.0.64915-0
  7. Collins, M. D., T. Pirouz, M. Goodfellow, and D. E. Minnikin. 1977. Distribution of menaquinones in Actinomycetes and Corynebacteria. J. Gen. Microbiol. 100: 221-230. https://doi.org/10.1099/00221287-100-2-221
  8. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791. https://doi.org/10.2307/2408678
  9. Gallego, V., M. T. García, and A. Ventosa. 2006. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int. J. Syst. Evol. Microbiol. 56: 1853-1858. https://doi.org/10.1099/ijs.0.64176-0
  10. Gordon, N. S., A. Valenzuela, S. M. Adams, P. W. Ramsey, J. L. Pollock, W. E. Holben, and J. E. Gannon. 2009. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int. J. Syst. Evol. Microbiol. 59: 1720-1726. https://doi.org/10.1099/ijs.0.000158-0
  11. Hwang, C. Y., D. H. Choi, and B. C. Cho. 2006. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int. J. Syst. Evol. Microbiol. 56: 1831-1836. https://doi.org/10.1099/ijs.0.64045-0
  12. Kwon, S. W., B. Y. Kim, K. H. Lee, K. Y. Jang, S. J. Seok, J. S. Kwon, W. G. Kim, and H. Y. Weon. 2007. Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int. J. Syst. Evol. Microbiol. 57: 480-484. https://doi.org/10.1099/ijs.0.64196-0
  13. Lee, H. G., S. G. Kim, W. T. Im, H. M. Oh, and S. T. Lee. 2009. Pedobacter composti sp. nov., isolated from compost. Int. J. Syst. Evol. Microbiol. 59: 345-349. https://doi.org/10.1099/ijs.0.003061-0
  14. Margesin, R., C. Spröer, P. Schumann, and F. Schinner. 2003. Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int. J. Syst. Evol. Microbiol. 53: 1291-1296. https://doi.org/10.1099/ijs.0.02436-0
  15. Mesbah, M., U. Premachandran, and W. B. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39: 159-167. https://doi.org/10.1099/00207713-39-2-159
  16. Muurholm, S., S. Cousin, O. Pauker, E. Brambilla, and E. Stackebrandt. 2007. Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int. J. Syst. Evol. Microbiol. 57: 2221-2227. https://doi.org/10.1099/ijs.0.65166-0
  17. Roh, S. W., Z. X. Quan, Y. D. Nam, H. W. Chang, K. H. Kim, M. K. Kim, et al. 2008. Pedobacter agri sp. nov., from soil. Int. J. Syst. Evol. Microbiol. 58: 1640-1643. https://doi.org/10.1099/ijs.0.65783-0
  18. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
  19. Shivaji, S., P. Chaturvedi, G. S. N. Reddy, and K. Suresh. 2005. Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int. J. Syst. Evol. Microbiol. 55: 1083-1088. https://doi.org/10.1099/ijs.0.63532-0
  20. Smibert, R. M. and N. R. Krieg. 1994. Phenotypic characterization, pp. 607-654. In P. Gerhardt, R. G. E. Murray, W. A. Woods, and N. R. Krieg (eds.). Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, DC.
  21. Stackebrandt, E. and B. M. Goebel. 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. https://doi.org/10.1099/00207713-44-4-846
  22. Steyn, P. L., P. Segers, M. Vancanneyt, P. Sandra, K. Kersters, and J. J. Joubert. 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. https://doi.org/10.1099/00207713-48-1-165
  23. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599. https://doi.org/10.1093/molbev/msm092
  24. Tindall, B. J. 1990. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol. Lett. 66: 199-202. https://doi.org/10.1111/j.1574-6968.1990.tb03996.x
  25. Ten, L. N., Q. M. Liu, W. T. Im, M. Lee, D. C. Yang, and S. T. Lee. 2006. Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int. J. Syst. Evol. Microbiol. 56: 2565-2570. https://doi.org/10.1099/ijs.0.64414-0
  26. Vanparys, B., K. Heylen, L. Lebbe, and P. De Vos. 2005. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int. J. Syst. Evol. Microbiol. 55: 1315-1318. https://doi.org/10.1099/ijs.0.63635-0
  27. Wilson, K. 1987. Preparation of genomic DNA from bacteria, pp. 2.4.1-2.4.5. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (eds.). Current Protocols in Molecular Biology. Greene Publishing and Wiley-Interscience, New York.
  28. Xie, C. H. and A. Yokota. 2003. Phylogenetic analysis of Lampropedia hyalina based on the 16S rRNA gene sequence. J. Gen. Appl. Microbiol. 49: 345-349. https://doi.org/10.2323/jgam.49.345
  29. Yoon, J.-H., M.-H. Lee, S.-J. Kang, S.-Y. Park, and T.-K. Oh. 2006. Pedobacter sandarakinus sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 56: 1273-1277. https://doi.org/10.1099/ijs.0.64148-0
  30. Yoon, J. H., S. J. Kang, H. W. Oh, and T. K. Oh. 2007. Pedobacter insulae sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 57: 1999-2003. https://doi.org/10.1099/ijs.0.64986-0
  31. Yoon, J. H., S. J. Kang, S. Park, and T. K. Oh. 2007. Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 57: 2089-2095. https://doi.org/10.1099/ijs.0.65146-0
  32. Yoon, J. H., S. J. Kang, and T. K. Oh. 2007. Pedobacter terrae sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 57: 2462-2466. https://doi.org/10.1099/ijs.0.64727-0
  33. Yoon, M. H., L. N. Ten, W. T. Im, and S. T. Lee. 2007. Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int. J. Syst. Evol. Microbiol. 57: 381-386. https://doi.org/10.1099/ijs.0.64693-0

Cited by

  1. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter , Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terr vol.62, pp.8, 2010, https://doi.org/10.1099/ijs.0.031104-0
  2. Pedobacter hainanensis sp. nov., Isolated from Seaside Soil vol.66, pp.5, 2010, https://doi.org/10.1007/s00284-013-0305-x
  3. Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica vol.65, pp.11, 2015, https://doi.org/10.1099/ijsem.0.000504
  4. Pedobacter mongoliensis sp. nov., isolated from grassland soil vol.68, pp.4, 2010, https://doi.org/10.1099/ijsem.0.002637
  5. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication vol.71, pp.3, 2021, https://doi.org/10.1099/ijsem.0.004688