1887

Abstract

A novel Gram-staining-negative bacterium, designated DH-5, was isolated from a farmland soil in Chuzhou, Anhui province, China. Cells of strain DH-5 were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 20–37 °C, pH 6.0–9.0 and with 0–5 % NaCl (w/v). The DNA G+C content was 42.8 mol%. The major fatty acids (>5 %) were iso-C, summed feature 3 (Cω7 and/or Cω6), iso-C 3-OH and C. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DH-5 was a member of the genus and shared the highest similarity with H7 (96.0 %), followed by H-12 (94.5 %). Strain DH-5 exhibited low DNA–DNA relatedness with H7 (35.1±1.4 %) and H-12 (21.4±1.0 %). On the basis of phenotypic, genotypic and phylogenetic evidence, DH-5 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DH-5 (=ACCC 19856=KCTC 42746).

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2016-12-01
2020-01-22
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References

  1. Ahmed I., Ehsan M., Sin Y., Paek J., Khalid N., Hayat R., Chang Y. H.. 2014; Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie van Leeuwenhoek105:325–333 [CrossRef][PubMed]
    [Google Scholar]
  2. Albert R. A., Waas N. E., Pavlons S. C., Pearson J. L., Ketelboeter L., Rosselló-Móra R., Busse H. J.. 2013; Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol63:952–958 [CrossRef][PubMed]
    [Google Scholar]
  3. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K.. (editors) 1995; Short Protocols in Molecular Biology: A Compendium of Methods From Current Protocols in Molecular Biology, 3rd edn.. New York: Wiley;
    [Google Scholar]
  4. Beveridge T. J., Lawrence J. R., Murray R. G. E.. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd edn. pp.19–33 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder R. L.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  5. Breznak J. A., Costilow R. N.. 1994; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, pp.137–154 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  6. Choi H. A., Lee S. S.. 2012; Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii. Int J Syst Evol Microbiol62:2559–2564 [CrossRef][PubMed]
    [Google Scholar]
  7. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E.. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  8. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–142[PubMed][CrossRef]
    [Google Scholar]
  9. Dong X. Z., Cai M. Y.. 2001; Determinative Manual for Routine Bacteriology Beijing: Scientific Press;
    [Google Scholar]
  10. Du J., Singh H., Won K., Yang J. E., Jin F., Yi T. H.. 2015; Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose. Int J Syst Evol Microbiol65:2949–2954 [CrossRef][PubMed]
    [Google Scholar]
  11. Ebersole L. L.. 1992; Acid-fast stain procedures. In Clinical Microbiology Procedures Handbook pp.3.5.1–3.5.3 Edited by Isenberg H. D.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  12. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  13. Feng H., Zeng Y., Huang Y.. 2014; Sphingobacterium paludis sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol64:3453–3458 [CrossRef][PubMed]
    [Google Scholar]
  14. Fitch W. M.. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool20:406–416 [CrossRef]
    [Google Scholar]
  15. Groth I., Schumann P., Weiss N., Martin K., Rainey F. A.. 1996; Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol46:234–239 [CrossRef][PubMed]
    [Google Scholar]
  16. Jiang S., Chen M., Su S., Yang M., Li A., Zhang C., Lin M., Zhang W., Luo X.. 2014; Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol64:248–253 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  18. Kimura M.. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  19. Lane D. L.. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp.115–175 Edited by Stackebrandt E. R., Goodfellow M.. Chichester, United Kingdom: Wiley;
    [Google Scholar]
  20. Lee D. H., Hur J. S., Kahng H. Y.. 2013; Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol63:755–760 [CrossRef][PubMed]
    [Google Scholar]
  21. Liu J., Yang L. L., Xu C. K., Xi J. Q., Yang F., Zhou F., Zhou Y., Mo M. H., Li W. J.. 2012; Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol62:1809–1813 [CrossRef][PubMed]
    [Google Scholar]
  22. Liu H., Zhang J., Chen D., Cao L., Lu P., Wu Z., Yang F., Li S., Hong Q.. 2013; Sphingobacterium changzhouense sp. nov., a bacterium isolated from a rice field. Int J Syst Evol Microbiol63:4515–4518 [CrossRef][PubMed]
    [Google Scholar]
  23. Ludwig W., Euzeby J., Whitman W. B.. 2008; Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. In Bergey’s Manual of Systematic Bacteriology, 2nd edn.vol. 4 pp.21–24 Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B., Paster B. J., Ward N., Ludwig W., Whitman W. B.. New York: Springer;
    [Google Scholar]
  24. Marqués A. M., Burgos-Díaz C., Aranda F. J., Teruel J. A., Manresa À., Ortiz A., Farfán M.. 2012; Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil. Int J Syst Evol Microbiol62:3036–3041 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 Bacteriol39:159–167 [CrossRef]
    [Google Scholar]
  26. Peng S., Hong D. D., Xin Y. B., Jun L. M., Hong W. G.. 2014; Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol64:3862–3866 [CrossRef][PubMed]
    [Google Scholar]
  27. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  28. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newslett20:1–6
    [Google Scholar]
  29. Schmidt V. S. J., Wenning M., Scherer S.. 2012; Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol62:1506–1511 [CrossRef][PubMed]
    [Google Scholar]
  30. 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]
  31. Son H. M., Yang J. E., Kook M. C., Shin H. S., Park S. Y., Lee D. G., Yi T. H.. 2013; Sphingobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field. J Gen Appl Microbiol59:345–352 [CrossRef][PubMed]
    [Google Scholar]
  32. 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 Bacteriol44:846–849 [CrossRef]
    [Google Scholar]
  33. 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 Bacteriol48:165–177 [CrossRef][PubMed]
    [Google Scholar]
  34. Sun L. N., Zhang J., Chen Q., He J., Li S. P.. 2013; Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol63:2260–2264 [CrossRef][PubMed]
    [Google Scholar]
  35. Sun L. N., Zhang J., Gong F. F., Wang X., Hu G., Li S. P., Hong Q.. 2014; Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim. Int J Syst Evol Microbiol64:2047–2052 [CrossRef][PubMed]
    [Google Scholar]
  36. Suzuki M., Nakagawa Y., Harayama S., Yamamoto S.. 2001; Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol51:1639–1652 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 Microbiol38:465–482 [CrossRef]
    [Google Scholar]
  38. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  39. Thompson, 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 Res25:4876–4882 [CrossRef]
    [Google Scholar]
  40. Xiao T., He X., Cheng G., Kuang H., Ma X., Yusup K., Hamdun M., Gulsimay A., Fang C., Rahman E.. 2013; Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense. Int J Syst Evol Microbiol63:815–820 [CrossRef][PubMed]
    [Google Scholar]
  41. Yabe S., Aiba Y., Sakai Y., Hazaka M., Kawahara K., Yokota A.. 2013; Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol63:1584–1588 [CrossRef][PubMed]
    [Google Scholar]
  42. 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 Bacteriol33:580–598 [CrossRef]
    [Google Scholar]
  43. Zhang J., Zheng J. W., Cho B. C., Hwang C. Y., Fang C., He J., Li S. P.. 2012; Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. Int J Syst Evol Microbiol62:683–687 [CrossRef][PubMed]
    [Google Scholar]
  44. Zhang H., Cheng M. G., Sun B., Guo S. H., Song M., Li Q., Huang X.. 2015; Flavobacterium suzhouense sp. nov., isolated from farmland river sludge. Int J Syst Evol Microbiol65:370–374 [CrossRef][PubMed]
    [Google Scholar]
  45. Zhao P., Zhou Z., Chen M., Lin W., Zhang W., Wei G.. 2014; Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. Int J Syst Evol Microbiol64:3931–3935 [CrossRef][PubMed]
    [Google Scholar]
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