Four novel Arthrobacter species isolated from filtration substrate

International Journal of Systematic and Evolutionary Microbiology

Volumn 59, Issue 4, 2009, Pages 856-862

  Ding, Linxian ^a,b   Hirose, Taketo ^a,b   Yokota, Akira ^b  

^a Hirose Laboratory Environmental Microorganism   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID DERIVATIVE; FATTY ACID DERIVATIVE; LYSINE; MENAQUINONE; PEPTIDOGLYCAN; RNA 16S; AMINO ACID; BACTERIAL DNA; FARNOQUINONE; FATTY ACID; RIBOSOME DNA; SODIUM CHLORIDE;

ARTHROBACTER; ARTHROBACTER ALBIDUS; ARTHROBACTER ALKALIPHILUS; ARTHROBACTER ECHIGONENSIS; ARTHROBACTER GLOBIFORMIS; ARTHROBACTER NIIGATENSIS; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; CHEMOTAXONOMY; CONTROLLED STUDY; GENOTYPE; GENUS; GRAM POSITIVE BACTERIUM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PH MEASUREMENT; PHYLOGENETIC TREE; PRIORITY JOURNAL; RNA SEQUENCE; ROCK; TAXONOMIC IDENTIFICATION; TEMPERATURE MEASUREMENT; UNINDEXED SEQUENCE; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PH; PHYLOGENY; PHYSIOLOGY; SEQUENCE HOMOLOGY; TEMPERATURE;

ALKALIPHILUS; ARTHROBACTER; ARTHROBACTER GLOBIFORMIS; BACTERIA (MICROORGANISMS); POSIBACTERIA;

AMINO ACIDS; ARTHROBACTER; BACTERIAL TYPING TECHNIQUES; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SODIUM CHLORIDE; SOIL MICROBIOLOGY; TEMPERATURE; VITAMIN K 2;

EID: 66149158586     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65301-0     Document Type: Article

References (37)

1. Borodina, E., Kelly, D. P., Schumann, P., Rainey, F. A., Ward-Rainey, N. L. & Wood, A. P. (2002). Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch Microbiol 177, 173-183.
2. Carter, J. P., Hsiao, Y. H., Spiro, S. & Richardson, D. J. (1995). Soil and sediment bacteria capable of aerobic nitrate respiration. Appl Environ Microbiol 61, 2852-2858.
3. Conn, H. J. & Dimmick, I. (1947). Soil bacteria similar in morphology to Mycobacterium and Corynebacterium. J Bacteriol 54, 291-303.
4. Ding, L. & Yokota, A. (2002). Phylogenetic analysis of the genus Aquaspirillum based on 16S rRNA gene sequences. FEMS Microbiol Lett 212, 165-169.
5. Ding, L. & Yokota, A. (2004). Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol 54, 2223-2230.
6. Duarte, G. F., Rosado, A. S., Seldin, L., de Araujo, W. & van Elsas, J. D. (2001). Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl Environ Microbiol 67, 1052-1062.
7. 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.
8. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
9. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
10. Fukatsu, H., Goda, M., Hashimoto, Y., Higashibata, H. & Kobayashi, M. (2005). Optimum culture conditions for the production of N-substituted formamide deformylase by Arthrobacter pascens F164. Biosci Biotechnol Biochem 69, 228-230.
11. Harper, J. J. & Davis, G. H. G. (1979). Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 29, 56-58.
12. Heyrman, J., Verbeeren, J., Schumann, P., Swings, J. & Paul, D. V. (2005). Six novel Arthrobacter species isolated from deteriorated mural paintings. Int J Syst Evol Microbiol 55, 1457-1464.
13. Jussila, M. M., Jurgens, G., Lindstrom, K. & Suominen, L. (2006). Genetic diversity of culturable bacteria in oil-contaminated rhizosphere of Galega orientalis. Environ Pollut 139, 244-257.
14. AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 1288-1301. Edited by N. R. Klieg & J. G. Holt. Baltimore, MD: Williams & Wilkins.
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. Koch, C., Schmann, P. & Stackebrandt, E. (1995). Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter. Int J Syst Bacteriol 45, 837-839.
17. Kuhn, D. A. & Starr, M. P. (1960). Arthrobacter atrocyaneus, n. sp., and its blue pigment. Arch Mikrobiol 36, 175-181.
18. Li, Y., Kawamura, Y., Fujiwara, N., Naka, T., Liu, H., Huang, X., Kobayashi, K. & Ezaki, T. (2004). Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir. Int J Syst Evol Microbiol 54, 827-835.
19. Margesin, R., Schumann, P., Spröer, C. & Gounot, A. M. (2004). Arthrobacter psychrophenolicus sp. nov., isolated from an alpine ice cave. Int J Syst Evol Microbiol 54, 2067-2072.
20. Marks, T. S., Smith, A. R. & Quirk, A. V. (1984). Degradation of 4-chlorobenzoic acid by Arthrobacter sp. Appl Environ Microbiol 48, 1020-1025.
21. 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 Bacteriol 39, 159-167.
22. Rzechowska, E. (1976). Studies on the biodegradation of nonionic surfactants applied in the polyester fiber industry. I. Activated sludge bacteria degrading the surfactants. Acta Microbiol Pol 25, 211-217.
23. Saitou, N. & Nei, M. (1987). The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
24. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
25. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note, 101. Newark, DE: MIDI Inc.
26. Schleifer, K. H. & Kandler, O. (1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407-477.
27. Sguros, P. L. (1955). Microbial transformations of the tobacco alkaloids. I. Cultural and morphological characteristics of a nicotinophile. J Bacteriol 69, 28-37.
28. Singer, A. C., Gilbert, E. S., Luepromchai, E. & Crowley, D. E. (2000). Bioremediation of polychlorinated biphenyl-contaminated soil using carvone and surfactant-grown bacteria. Appl Microbiol Biotechnol 54, 838-843.
29. Skerman, V. B. D., McGowan, V. & Sneath, P. H. A. (editors) (1980). Approved lists of bacterial names. Int J Syst Bacteriol 30, 225-420.
30. 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 Bacteriol 44, 846-849.
31. Stackebrandt, E., Fowler, V. J., Fiedler, F. & Seiler, H. (1983). Taxonomic studies on Arthrobacter nicotianae and related taxa: description of Arthrobacter uratoxydans sp. nov. and Arthrobacter sulfureus sp. nov. and reclassification of Brevibacterium protophormiae as Arthrobacter protophormiae comb. nov. Syst Appl Microbiol 4, 470-486.
32. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kämpfer, P., Maiden, M. C., 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.
33. Takeuchi, M. & Yokota, A. (1991). Reclassification of strains of Flavobacterium-Cytophaga group in IFO culture collection. Inst Ferment Osaka Res Commun 15, 83-96.
34. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
35. 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.
36. Westerberg, K., Elvang, A. M., Stackebrandt, E. & Jansson, J. K. (2000). Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol. Int J Syst Evol Microbiol 50, 2083-2092.
37. Willems, A., Doignon, B. F., Goris, J., Coopman, R., Lajudie, P., Vos, D. P. & Gillis, M. (2001). DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51, 1315-1322.