1887

Abstract

A Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14 was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14 could grow at 10–40 °C (optimally at 30 °C), pH 6.0–10.0 (optimally at pH 8.0), and in the presence of 0–6.0 % (w/v) NaCl (optimally with 0–2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B () gene sequences revealed that strain Y3L14 clustered with strains belonging to the genus , sharing the highest 16S rRNA gene sequence similarity with WCC 4512 (94.99 %). Its major cellular fatty acids contained iso-C, C, iso-C 3-OH and summed feature 3 (iso-C 2-OH and/or Cω7). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14 contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14 was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14 represents a novel species within the genus , for which sp. nov. is proposed; the type strain is Y3L14 (=CGMCC 1.15782=KCTC 52379).

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2017-06-01
2024-12-04
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References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. 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 1983; 33:580–598 [View Article]
    [Google Scholar]
  2. Lai W-A, Hameed A, Liu Y-C, Hsu Y-H, Lin S-Y et al. Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium thermophilum Yabe et al. 2013. Int J Syst Evol Microbiol 2016; 66:5344 [View Article]
    [Google Scholar]
  3. Li Y, Song LM, Guo MW, Wang LF, Liang WX. Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2016; 66:3456–3462 [View Article][PubMed]
    [Google Scholar]
  4. Sun JQ, Liu M, Wang XY, Xu L, Wu XL. Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata. Int J Syst Evol Microbiol 2015; 65:4508–4513 [View Article][PubMed]
    [Google Scholar]
  5. Wang X, Zhang CF, Yu X, Hu G, Yang HX et al. Sphingobacterium chuzhouense sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:4968–4974 [View Article][PubMed]
    [Google Scholar]
  6. Albert RA, Waas NE, Pavlons SC, Pearson JL, Ketelboeter L et al. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from lake Michigan water. Int J Syst Evol Microbiol 2013; 63:952–958 [View Article][PubMed]
    [Google Scholar]
  7. Kim KH, Ten LN, Liu QM, Im WT, Lee ST. Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 2006; 56:2031–2036 [View Article][PubMed]
    [Google Scholar]
  8. Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW et al. Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 2007; 57:1590–1593 [View Article][PubMed]
    [Google Scholar]
  9. Choi HA, Lee SS. Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii. Int J Syst Evol Microbiol 2012; 62:2559–2564 [View Article][PubMed]
    [Google Scholar]
  10. Feng H, Zeng Y, Huang Y. Sphingobacterium paludis sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2014; 64:3453–3458 [View Article][PubMed]
    [Google Scholar]
  11. He X, Xiao T, Kuang H, Lan X, Tudahong M et al. Sphingobacterium shayense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2010; 60:2377–2381 [View Article][PubMed]
    [Google Scholar]
  12. Liu R, Liu H, Zhang CX, Yang SY, Liu XH et al. Sphingobacterium siyangense sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2008; 58:1458–1462 [View Article][PubMed]
    [Google Scholar]
  13. Liu H, Zhang J, Chen D, Cao L, Lu P et al. Sphingobacterium changzhouense sp. nov., a bacterium isolated from a rice field. Int J Syst Evol Microbiol 2013; 63:4515–4518 [View Article][PubMed]
    [Google Scholar]
  14. Peng S, Hong DD, Xin YB, Jun LM, Hong WG. Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 2014; 64:3862–3866 [View Article][PubMed]
    [Google Scholar]
  15. Teng C, Zhou Z, Molnár I, Li X, Tang R et al. Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the western desert of China. PLoS One 2015; 10:e0122254 [View Article][PubMed]
    [Google Scholar]
  16. Wei W, Zhou Y, Wang X, Huang X, Lai R. Sphingobacterium anhuiense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2008; 58:2098–2101 [View Article][PubMed]
    [Google Scholar]
  17. Xiao T, He X, Cheng G, Kuang H, Ma X et al. 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 Microbiol 2013; 63:815–820 [View Article][PubMed]
    [Google Scholar]
  18. Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K et al. Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol 2013; 63:1584–1588 [View Article][PubMed]
    [Google Scholar]
  19. Zhao P, Zhou Z, Chen M, Lin W, Zhang W et al. Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. Int J Syst Evol Microbiol 2014; 64:3931–3935 [View Article]
    [Google Scholar]
  20. Schmidt VS, Wenning M, Scherer S. Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 2012; 62:1506–1511 [View Article][PubMed]
    [Google Scholar]
  21. Sun LN, Zhang J, Chen Q, He J, Li SP. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260–2264 [View Article][PubMed]
    [Google Scholar]
  22. Zhang J, Zheng JW, Cho BC, Hwang CY, Fang C et al. Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. Int J Syst Evol Microbiol 2012; 62:683–687 [View Article][PubMed]
    [Google Scholar]
  23. Lee DH, Hur JS, Kahng HY. Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol 2013; 63:755–760 [View Article][PubMed]
    [Google Scholar]
  24. Liu J, Yang LL, Xu CK, Xi JQ, Yang FX et al. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 2012; 62:1809–1813 [View Article][PubMed]
    [Google Scholar]
  25. Ahmed I, Ehsan M, Sin Y, Paek J, Khalid N et al. Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie Van Leeuwenhoek 2014; 105:325–333 [View Article][PubMed]
    [Google Scholar]
  26. Ali A, Khalid R, Ali S, Akram Z, Hayat R. Characterization of plant growth promoting rhizobacteria isolated from chickpea (Cicer arietinum). Br Microbiol Res J 2015; 6:32–40 [View Article]
    [Google Scholar]
  27. Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S et al. Endophytic bacteria and their potential applications. Crit Rev Plant Sci 2002; 21:583–606 [View Article]
    [Google Scholar]
  28. Mehnaz S, Weselowski B, Lazarovits G. Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 2007; 30:519–524 [View Article][PubMed]
    [Google Scholar]
  29. Sun JQ, Xu L, Liu M, Wang XY, Wu XL. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata. Int J Syst Evol Microbiol 2016; 66:1943–1949 [View Article][PubMed]
    [Google Scholar]
  30. Sun JQ, Xu L, Wu XL. Lysinibacillus alkalisoli sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:71 [View Article][PubMed]
    [Google Scholar]
  31. Wang YN, Cai H, Yu SL, Wang ZY, Liu J et al. Halomonas gudaonensis sp. nov., isolated from a saline soil contaminated by crude oil. Int J Syst Evol Microbiol 2007; 57:911–915 [View Article][PubMed]
    [Google Scholar]
  32. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  33. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  35. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  36. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  37. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095[PubMed]
    [Google Scholar]
  38. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  39. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2016 In press
    [Google Scholar]
  40. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
    [Google Scholar]
  41. Yamamoto S, Harayama S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 1995; 61:1104–1109[PubMed]
    [Google Scholar]
  42. Mandel M, Marmur J. Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. In: Methods Enzymol vol. 12B 1968 p. 195
    [Google Scholar]
  43. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
  44. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  45. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [CrossRef]
    [Google Scholar]
  46. Takeuchi M, Yokota A. 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 1992; 38:465–482 [View Article]
    [Google Scholar]
  47. Smibert RM, Krieg NR. Phenotypic characterization. In: Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  48. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741[PubMed]
    [Google Scholar]
  49. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  50. Kim BC, Jeong WJ, Kim DY, Oh HW, Kim H et al. Paenibacillus pueri sp. nov., isolated from Pu'er tea. Int J Syst Evol Microbiol 2009; 59:1002–1006 [View Article][PubMed]
    [Google Scholar]
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