Sphingopyxis granuli sp. nov., a -Glucosidase-Producing Bacterium in the Family Sphingomonadaceae in -4 Subclass of the Proteobacteria |
Kim Myung Kyum
(Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST))
Im Wan Taek (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) Ohta Hiroyuki (Department of Bioresource Science, Ibaraki University College of Agriculture) Lee Myung Jin (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), NeoPharm Co., Ltd) Lee Sung Taik (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) |
1 | Buck, J.D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44, 992-993 PUBMED |
2 | de Zeeuw, W.J. and G. Lettinga. 1980. Use of anaerobic digestion for wastewater treatment. Antonie van Leeuwenhoek. 46, 110-112 DOI ScienceOn |
3 | Fujii, K., M. Satomi, N. Morita, T. Motomura, T. Tanaka, and S. Kikuchi. 2003. Novosphingobium tardaugens sp. nov., and oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int. J. Syst. Evol. Microbiol. 53, 47-52 DOI ScienceOn |
4 | Fukuzaki, S., Y.J. Chang, N. Nishio, and S. Nagai. 1991. Characteristics of granular methanogenic sludges grown on lactate in a UASB reactor. J. Ferm. Bioeng. 72,465-472 DOI ScienceOn |
5 | Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, Cambridge, New York |
6 | Kumar, S., K. Tamura, LB. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244-1245 DOI ScienceOn |
7 | MacLeod, F.A., S.R. Guiot, and J.W. Costerton. 1990. Layered structure of biological aggregates produced in an upflow sludge bed and filter reactor. Appl. Environ. Microbiol. 56, 1598-1607 PUBMED |
8 | Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc |
9 | Shen, C.F., N. Kosaric, and R. Blaszczyk. 1993. The effect of selected heavy metals (Ni, Co and Fe) on anaerobic granules and their extracellular polymeric substance (EPS). Water Res. 27, 25-33 DOI ScienceOn |
10 | Shin, Y.K., J.-S. Lee, C.O. Chun, H.-J. Kim. and Y.-H. Park. 1996. Isoprenoid quinine profiles of the Leclercia adecarboxylata KCTC J. Micorobiol. Biotechnol. 6, 68-69 |
11 | 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 DOI ScienceOn |
12 | Takeuchi, M., F. Kawai, Y. Shimada, and A. Yokota. 1993. Taxonomic study of polyethylene glycol-utilizing bacteria: emended description ofthe 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 DOI ScienceOn |
13 | Takeuchi, M., K. Hamana, and A. Hiraishi. 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 PUBMED |
14 | Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882 |
15 | Tiirola, M.A., H.-J. Busse, P. Kampfer, and M.K. Mannisto. 2005. Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int. J. Syst. Evol. Microbiol. 55, 583-588 DOI ScienceOn |
16 | Ushiba, Y., Y. Takahara, and H. Ohta. 2003. Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. Int. J. Syst. Evol. Microbiol. 53, 2045-2048 DOI ScienceOn |
17 | Vancanneyt, M., F. Schut, C. Snauwaert, J. Goris, J. Swings, and J.C. Gottschal. 2001. Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int. J. Syst. Evol. Microbiol. 51, 73-79 PUBMED |
18 | Weisburg, W.G, S.M. Barns, D.A. Pelletier, and D.J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol 173, 697-703 PUBMED |
19 | Yoon, J.-H. and T.-K. Oh. 2005. Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 55, 369-373 DOI ScienceOn |
20 | 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 DOI |
21 | Busse, H.-J., E.B.M. Denner, S. Buczolits, M. Salkinoja-Salonen, A. Bennasar, and P. Kampfer. 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 DOI ScienceOn |
22 | Yabuuchi, E., I. Yano, H. Oyaizu, Y. Hashimoto, T. Ezaki, and H. Yamamoto. 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 PUBMED |
23 | Yabuuchi, E., Y. Kosako, N. Fujiwara, T. Naka, I. Matsunaga, H. Ogura, and K. Kobayashi. 2002. Emendation of the genus Sphingomonas Yabuuuchi 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 DOI ScienceOn |
24 | Kampfer, P., R. Witzenberger, E.B.M. Denner, H.-J. Busse, and A. Neef. 2002. Sphingopyxis witflariensls sp. nov. isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 52, 2029-2034 DOI ScienceOn |
25 | Ezaki, T., Y. Hashimoto, and E. Yabuuchi. 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 DOI |
26 | Godoy, F., M. Vancanneyt, M. Martinez, A. Steinblichel, J. Swings, and B.H.A. Rehm. 2003. Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int. J. Syst. Evol. Microbiol. 53, 473-477 DOI ScienceOn |
27 | Cappuccino, J.G. and N. Sherman. 2002. Microbiology: a laboratory manual, 6th ed. Pearson Education, Inc., California |
28 | Li, Y., Y. Kawamura, N. Fujiwara, T. Naka, H. Liu, X. Huang, K. Kobayashi, and T. Ezaki. 2004. Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir. Int. J. Syst. Evol. Microbiol. 54, 819-825 DOI ScienceOn |
29 | Schmidt, J.E. and B.K. Ahring. 1996. Acetate and hydrogen metabolism in intact and disintegrated granules from an acetate-fed, , UASC reactor. Biotechnol. Bioeng. 49, 229-246 DOI ScienceOn |
30 | Rivas, R., A. Abril, M.E. Trujillo, and E. Velazquez. 2004. Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int. J. Syst. Evol. Microbiol. 54, 2147-2150 DOI ScienceOn |
31 | Collins, M.D. and D. Jones. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45, 316-354 PUBMED |
32 | Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98 |
33 | Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Bio. Evol. 4, 406-425 |
34 | Tamaoka, J. and K. Komagata. 1984. Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25, 125-128 DOI ScienceOn |
35 | Sohn, J.H., K.K. Kwon, J.-H. Kang, H-B. Jung, and S.-J. Kim. 2004. Novosphingobium pentaromativorans sp. nov., a highmolecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Evol. Syst. Microbiol. 54, 1483-1487 DOI ScienceOn |
36 | Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 DOI ScienceOn |