Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum

International Journal of Systematic and Evolutionary Microbiology

Volumn 65, Issue , 2015, Pages 1160-1166

  Zhu, Lingfang ^a   Si, Meiru ^a   Li, Changfu ^a   Xin, Kaiyun ^a   Chen, Chaoqiong ^a   Shi, Xu ^a   Huang, Ruijun ^a   Zhao, Liang ^a   Shen, Xihui ^a   Zhang, Lei ^a  

^a NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CARDIOLIPIN; ETHANOLAMINE; FATTY ACID; GLYCOLIPID; GLYCOSPHINGOLIPID; LIPID; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHOLIPID; POLYAMINE; QUINONE DERIVATIVE; RNA 16S; SPERMIDINE DERIVATIVE; UBIDECARENONE; SPERMIDINE; SYM-HOMOSPERMIDINE; UBIQUINONE; UBIQUINONE Q2;

ARTICLE; BACTERIAL CAPSULE; BACTERIAL CELL; BACTERIAL FLAGELLUM; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CHINA; CONCENTRATION (PARAMETERS); GENE SEQUENCE; GEUM; GEUM ALEPPICUM; GRAM NEGATIVE FACULTATIVELY ANAEROBIC RODS; NONHUMAN; PHYLOGENY; PLANT ROOT; PRIORITY JOURNAL; SPHINGOMONAS; SPHINGOMONAS ASACCHAROLYTICA; SPHINGOMONAS KYEONGGIENSE; SPHINGOMONAS LEIDYI; SPHINGOMONAS NAASENSIS; TAXONOMIC IDENTIFICATION; TYPE STRAIN; ANALOGS AND DERIVATIVES; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; PIGMENTATION;

BACTERIA (MICROORGANISMS); GEUM ALEPPICUM; SPHINGOMONAS; SPHINGOMONAS ASACCHAROLYTICA;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CHINA; DNA, BACTERIAL; FATTY ACIDS; GEUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHOSPHOLIPIDS; PHYLOGENY; PIGMENTATION; PLANT ROOTS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPERMIDINE; SPHINGOMONAS; UBIQUINONE;

EID: 84929009017     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.000074     Document Type: Article

References (40)

1. An, H., Xu, M., Dai, J., Wang, Y., Cai, F., Qi, H., Peng, F. & Fang, C. (2011). Sphingomonas xinjiangensis sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 61, 1865–1869.
2. An, D.-S., Liu, Q.-M., Lee, H.-G., Jung, M.-S., Kim, S.-C., Lee, S.-T. & Im, W.-T. (2013). Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. Int J Syst Evol Microbiol 63, 496–501.
3. Busse, H.-J. & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1–8.
4. Busse, H.-J., Denner, E. B. M., Buczolits, S., Salkinoja-Salonen, M., Bennasar, A. & Ka¨ mpfer, P. (2003). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air-and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 53, 1253–1260.
5. Chen, H., Jogler, M., Rohde, M., Klenk, H. P., Busse, H. J., Tindall, B. J., Spröer, C. & Overmann, J. (2012). Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int J Syst Evol Microbiol 62, 2835–2843.
6. Cleenwerck, I., Vandemeulebroecke, K., Janssens, D. & Swings, J. (2002). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52, 1551–1558.
7. Doetsch, R. N. (1981). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 21–33. Edited by P. Gerdhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
8. Euzéby, J. P. (2014). List of bacterial names with standing in nomenclature: a folder available on the Internet. [Last full update 7 November 2014]. http://www.bacterio.cict.fr/
9. 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.
10. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.
11. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.
12. Fitch, W. M. (1971). Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.
13. Huang, H. Y., Li, J., Zhao, G. Z., Zhu, W. Y., Yang, L. L., Tang, H. Y., Xu, L. H. & Li, W. J. (2012). Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. Int J Syst Evol Microbiol 62, 1576–1580.
14. Kim, B.-C., Poo, H., Lee, K. H., Kim, M. N., Kwon, O.-Y. & Shin, K.-S. (2012a). Mucilaginibacter angelicae sp. nov., isolated from the rhizosphere of Angelica polymorpha Maxim. Int J Syst Evol Microbiol 62, 55–60.
15. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (2012b). Introducing EzTaxone: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716–721.
16. Kim, S.-J., Moon, J.-Y., Lim, J.-M., Ahn, J.-H., Weon, H.-Y., Ahn, T.-Y. & Kwon, S.-W. (2014). Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 64, 926–932.
17. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.
18. Lane, D. J. (1991). 16S–23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 125–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
19. Lee, J.-S., Shin, Y. K., Yoon, J.-H., Takeuchi, M., Pyun, Y.-R. & Park, Y.-H. (2001). Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 51, 1491–1498.
20. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
21. Romanenko, L. A., Uchino, M., Frolova, G. M., Tanaka, N., Kalinovskaya, N. I., Latyshev, N. & Mikhailov, V. V. (2007). Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity. Int J Syst Evol Microbiol 57, 358–363.
22. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
23. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
24. Schenkel, E., Berlaimont, V., Dubois, J., Helson-Cambier, M. & Hanocq, M. (1995). Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 668, 189–197.
25. Son, H.-M., Kook, M. C., Tran, H. T. H., Kim, K.-Y., Park, S.-Y., Kim, J.-H. & Yi, T.-H. (2014). Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field. Antonie van Leeuwenhoek 105, 791–797.
26. Takeuchi, M., Kawai, F., Shimada, Y. & Yokota, A. (1993). Taxonomic study of polyethylene glycerol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol 16, 227–238.
27. Takeuchi, M., Sakane, T., Yanagi, M., Yamasato, K., Hamana, K. & Yokota, A. (1995). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 45, 334–341.
28. Takeuchi, M., Hamana, K. & Hiraishi, A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 1405–1417.
29. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731–2739.
30. 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.
31. Tindall, B. J. (1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128–130.
32. Tindall, B. J. (1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199–202.
33. 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.
34. Wilson, K. (1987). Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology, pp. 241–245. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Greene Publishing and Wiley Interscience.
35. Xie, C. H. & Yokota, A. (2003). Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49, 345–349.
36. Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T. & Yamamoto, H. (1990). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34, 99–119.
37. Yabuuchi, E., Kosako, Y., Fujiwara, N., Naka, T., Matsunaga, I., Ogura, H. & Kobayashi, K. (2002). Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobiumand Sphingopyxis, inconjunction with Blastomonas ursincola. Int J Syst EvolMicrobiol 52, 1485–1496.
38. Yang, D. C., Im, W. T., Kim, M. K., Ohta, H. & Lee, S. T. (2006). Sphingomonas soli sp. nov., a b-glucosidase-producing bacterium in the family Sphingomonadaceae in the a-4 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 56, 703–707.
39. Zhang, L., Wang, Y., Wei, L., Wang, Y., Shen, X. & Li, S. (2013). Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 63, 3769–3776.
40. Zhang, L., Wei, L., Zhu, L., Li, C., Wang, Y. & Shen, X. (2014). Pseudoxanthomonas gei sp. nov., a novel endophytic bacterium isolated from the stem of Geum aleppicum. Antonie van Leeuwenhoek 105, 653–661.