Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil

International Journal of Systematic and Evolutionary Microbiology

Volumn 59, Issue 1, 2009, Pages 156-161

  Gupta, Sanjay Kumar ^a   Lal, Devi ^a   Lal, Rup ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; ETHANOLAMINE DERIVATIVE; OIL; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLDIMETHYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHATIDYLMETHYLETHANOLAMINE; RNA 16S; SPERMIDINE; SPHINGOLIPID; UNCLASSIFIED DRUG; FATTY ACID; RIBOSOME DNA;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL CELL WALL; BACTERIAL STRAIN; BACTERIUM ISOLATE; CELL WALL; CHEMOTAXONOMY; CLADISTICS; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; FATTY ACID ANALYSIS; GRAM NEGATIVE BACTERIUM; HALOPHILIC BACTERIUM; LIPID ANALYSIS; NEW SPECIES; NONHUMAN; NOVOSPHINGOBIUM MATHURENSE; NOVOSPHINGOBIUM PANIPATENSE; NOVOSPHINGOBIUM PENTAROMATIVORANS; NOVOSPHINGOBIUM RESINOVORUM; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY; SOIL POLLUTION; SPHINGOMONAS; STRAIN DIFFERENCE; TYPE STRAIN; BACTERIUM IDENTIFICATION; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; NUCLEIC ACID HYBRIDIZATION; RNA GENE; SOIL POLLUTANT; SPECIES DIFFERENCE; SPHINGOMONADACEAE;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; NOVOSPHINGOBIUM; NOVOSPHINGOBIUM PENTAROMATIVORANS;

BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; GENES, RRNA; NUCLEIC ACID HYBRIDIZATION; OILS; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SOIL POLLUTANTS; SPECIES SPECIFICITY; SPHINGOMONADACEAE;

EID: 60549114247     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65743-0     Document Type: Article

References (45)

1. Balkwill, D. L., Drake, G. R., Reeves, R. H., Fredrickson, J. K., White, D. C., Ringelberg, D. B., Chandler, D. P., Romine, M. F., Kennedy, D. W. & Spadoni, C.M. (1997). Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bacteriol 47, 191-201.
2. Beiss, U. (1964). Zur papierchromatographischen Auftrennung von Pflanzenlipiden. J Chromatogr 13, 104-110 (in German).
3. Bligh, E. G. & Dyer, W. J. (1959). A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37, 911-917.
4. Bruns, A., Rohde, M. & Berthe-Corti, L. (2001). Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51, 1997-2006.
5. Busse, H.-J. & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
6. Busse, H.-J., Bunka, S., Hensel, A. & Lubitz, W. (1997). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47, 698-708.
7. Consden, R. & Gordon, A. H. (1948). The effect of salt on partition chromatograms. Nature 162, 180.
8. Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
9. Dittmer, J. C. F. & Lester, R. L. (1964). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 5, 126-127.
10. Fujii, K., Urano, N., Ushio, H., Satomi, M., Iida, H., Ushio-Sata, N. & Kimura, S. (2000). Profile of a nonylphenol-degrading microflora and its potential for bioremedial applications. J Biochem 128, 909-916.
11. Gunstone, F. D. & Jacobsberg, F. R. (1972). Fatty acids, part 35: the preparation and properties of a complete series of methyl epoxyoctadecanoates. Chem Phys Lipids 9, 26-64.
12. Jacin, H. & Mishkin, A. R. (1965). Separation of carbohydrates on borate impregnated silica gel G plates. J Chromatogr 18, 170-173.
13. Jeffries, C. D., Holtmann, D. F. & Guse, D. G. (1957). Rapid method for determining the activity of microorganisms on nucleic acids. J Bacteriol 73, 590-591.
14. Kämpfer, P., Witzenberger, R., Denner, E. B. M., Busse, H.-J. & Neef, A. (2002). Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst Appl Microbiol 25, 37-45.
15. 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.
16. Kiyohara, H., Nagao, K. & Yana, K. (1982). Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl Environ Microbiol 43, 454-457.
17. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
18. Kushner, D. J. (1957). An evaluation of the egg-yolk reaction as a test for lecithinase activity. J Bacteriol 73, 297-302.
19. Kuykendall, L. D., Roy, M. A., O'Neill, J. J. & Devine, T. E. (1988). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38, 358-361.
20. Lal, R., Dogra, C., Malhotra, S., Sharma, P. & Pal, R. (2006). Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. Trends Biotechnol 24, 121-130.
21. Lányí, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1-67.
22. Leifson, E. (1962). The bacterial flora of distilled and stored water. III. New species of the genera Corynebacterium, Flavobacterium, Spirillum and Pseudomonas. Int Bull Bacteriol Nomencl Taxon 12, 161-170.
23. Lim, Y. W., Moon, E. Y. & Chun, J. (2007). Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym. Int J Syst Evol Microbiol 57, 1906-1908.
24. Liu, Z.-P., Wang, B.-J., Liu, Y.-H. & Liu, S.-J. (2005). Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 55, 1229-1232.
25. Maruyama, T., Park, H.-D., Ozawa, K., Tanaka, Y., Sumino, T., Hamana, K., Hiraishi, A. & Kato, K. (2006). Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 56, 85-89.
26. Miller, L. T. (1982). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16, 584-586.
27. Mohn, W. W., Mertens, B., Neufeld, J.D., Verstraete, W. & de Lorenzo, V. (2006). Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain. Environ Microbiol 8, 60-68.
28. Nei, M. & Kumar, S. (2000). Molecular Evolution and Phylogenetics. New York: Oxford University Press.
29. Pal, R., Bala, S., Dadhwal, M., Kumar, M., Dhingra, G., Prakash, O., Prabagaran, S. R., Shivaji, S., Cullum, J. & other authors (2005). Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Int J Syst Evol Microbiol 55, 1965-1972.
30. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444-2448.
31. Prakash, O., Kumari, K. & Lal, R. (2007). Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. Int J Syst Evol Microbiol 57, 527-531.
32. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
33. Sohn, J. H., Kwon, K. K., Kang, J.-H., Jung, H.-B. & Kim, S.-J. (2004). Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54, 1483-1487.
34. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
35. Stanier, R. Y., Palleroni, N. J. & Doudoroff, M. (1966). The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43, 159-271.
36. 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.
37. 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.
38. 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.
39. Tiirola, M. A., Busse, H.-J., Kämpfer, P. & Männistö, M. (2005). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 55, 583-588.
40. Tourova, T. P. & Antonov, A. S. (1987). Identification of microorganisms by rapid DNA-DNA hybridization. Methods Microbiol 19, 333-355.
41. Vanbroekhoven, K., Ryngaert, A., Bastiaens, L., Wattiau, P., Vancanneyt, M., Swings, J., De Mot, R. & Springael, D. (2004). Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples. Environ Microbiol 6, 1123-1136.
42. Wagner, H., Hörhammer, L. & Wolff, P. (1961). Dunnschicht-chromatographie von Phosphatiden und Glykolipiden. Biochem Z 334, 175-184 (in German).
43. 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.
44. 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.
45. 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, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52, 1485-1496.