Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas

International Journal of Systematic and Evolutionary Microbiology

Volumn 57, Issue 8, 2007, Pages 1740-1746

  Wittich, Rolf Michael ^a,e   Busse, Hans Jürgen ^b   Kämpfer, Peter ^c   Macedo, Alexandre J ^a   Tiirola, Marja ^d   Wieser, Monika ^b   Abraham, Wolf Rainer ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b UNIVERSITY OF VETERINARY MEDICINE   (Austria)

^c JUSTUS LIEBIG UNIVERSITY   (Germany)

^d UNIVERSITY OF JYVÄSKYLÄ   (Finland)

^e CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CHLOROPHENOL; DRINKING WATER; FATTY ACID; GENOMIC DNA; LIPID; RNA 16S; UBIQUINONE; WELL WATER;

ARTICLE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CHEMOTAXONOMY; CONTAMINATION; CONTROLLED STUDY; FINLAND; GENE SEQUENCE; GENETIC SIMILARITY; GRAM NEGATIVE BACTERIUM; LIPID ANALYSIS; LIPID COMPOSITION; MOLECULAR PHYLOGENY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPHINGOMONAS; SPHINGOMONAS FENNICA; SPHINGOMONAS HALOAROMATICAMANS; SPHINGOMONAS WITTICHII; STRAIN DIFFERENCE; TYPE STRAIN;

BASE COMPOSITION; CHLOROPHENOLS; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SPHINGOMONAS;

BACTERIA (MICROORGANISMS); SPHINGOMONAS; SPHINGOMONAS WITTICHII;

EID: 34548171470     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64835-0     Document Type: Article

References (46)

1. Abraham, W.-R., Meyer, H., Lindholst, S., Vancanneyt, M. & Smit, J. (1997). Phospho- and sulfolipids as biomarkers of Caulobacter sensu lato, Brevundimonas and Hyphomonas. Syst Appl Microbiol 20, 522-539.
2. Abraham, W.-R., Stroempl, C., Meyer, H., Lindholst, S., Moore, E. R. B., Christ, R., Vancanneyt, M., Tindall, B., Bennasar, A. & other authors (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 49, 1053-1073.
3. Altenburger, P., Kämpfer, P., Makristathis, A., Lubitz, W. & Busse, H.-J. (1996). Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47, 39-52.
4. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
5. 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.
6. Blasco, R., Wittich, R.-M., Mallavarapu, M., Timmis, K. N. & Pieper, D. H. (1995). From xenobiotic to antibiotic, formation of proto-anemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway. J Biol Chem 270, 29229-29235.
7. 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.
8. Busse, H.-J. & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
9. Busse, H.-J., Kämpfer, P. & Denner, E. B. M. (1999). Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 23, 242-251.
10. Busse, H.-J., Hauser, E. & Kämpfer, P. (2005). Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni. sp. nov. Int J Syst Evol Microbiol 55, 2565-2569.
11. AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov. Int J Syst Bacteriol 49, 1103-1109.
12. Denner, E. B. M., Paukner, S., Kämpfer, P., Moore, E. R. B., Abraham, W. R., Busse, H.-J., Wanner, G. & Lubitz, W. (2001). Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan. Int J Syst Evol Microbiol 51, 827-841.
13. Fredrickson, H. L., Cappenberg, T. E. & De Leeuw, J. (1986). Polar lipid ester-linked fatty acid composition of Lake Vechten seston: an ecological application of lipid analysis. FEMS Microbiol Ecol 38, 381-396.
14. Geueke, B., Busse, H.-J., Fleischmann, T., Kämpfer, P. & Kohler, H.-P. E. (2007). Description of Sphingosinicella xenopeptidilytica sp. nov., a β-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans. Int J Syst Evol Microbiol 57, 107-113.
15. Johnson, J. L. (1994). Similarity analysis of DNAs. In Methods for General and Molecular Bacteriology, pp. 664-666. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
16. Junca, H. & Pieper, D. H. (2004). Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries. Environ Microbiol 6, 95-110.
17. Ka, J. O., Holben, W. E. & Tiedje, J. M. (1994). Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils. Appl Environ Microbiol 60, 1106-1115.
18. Kämpfer, P. & Altwegg, M. (1992). Numerical classification and identification of Aeromonas genospecies. J Appl Bacteriol 72, 341-351.
19. Kämpfer, P., Steiof, M. & Dott, W. (1991). Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21, 227-251.
20. Kämpfer, P., Bark, K., Busse, H.-J., Auling, G. & Dott, W. (1992). Numerical and chemotaxonomy of polyphosphate accumulating Acinetobacter strains with high polyphosphate: AMP phosphotransferase (PPAT) activity. Syst Appl Microbiol 15, 409-419.
21. Kämpfer, P., Denner, E. B. M., Meyer, S., Moore, E. R. B. & Busse, H.-J. (1997). Classification of 'Pseudomonas azotocolligans' Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov. Int J Syst Bacteriol 47, 577-583.
22. Kanz, C., Aldebert, P., Althorpe, N., Baker, W., Baldwin, A., Bates, K., Browne, P., van den Broek, A., Castro, M. & other authors (2005). The EMBL nucleotide sequence database. Nucleic Acids Res 33, D29-D33.
23. Karlson, U., Rojo, F., van Elsas, J. D. & Moore, E. (1996). Genetic and serological evidence for the recognition of four pentachlorophenol-degrading bacterial strains as a species of the genus Sphingomonas. Syst Appl Microbiol 18, 539-548.
24. Konig, C., Eulberg, D., Groning, J., Lakner, S., Seibert, V., Kaschabek, S. R. & Schlömann, M. (2004). A linear MEGAplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP. Microbiology 150, 3075-3087.
25. Kosako, Y., Yabuuchi, E., Naka, T., Fujiwara, N. & Kobayashi, K. (2000). Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990. Microbiol Immunol 44, 563-575.
26. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
27. Männistö, M. K., Tiirola, M. A., Salkinoja-Salonen, M. S., Kulomaa, M. S. & Puhakka, J. A. (1999). Diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater. Arch Microbiol 171, 189-197.
28. 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.
29. Moore, E. R. B., Wittich, R.-M., Fortnagel, P. & Timmis, K. N. (1993). 16S ribosomal RNA gene sequence characterization and phylogenetic analysis of a dibenzo-p-dioxin-degrading isolate within the new genus Sphingomonas. Lett Appl Microbiol 17, 115-118.
30. Nikodem, P., Hecht, V., Schlömann, M. & Pieper, D. H. (2003). New bacterial pathway for 4- and 5-chlorosalicylate degradation via 4-chlorocatechol and maleylacetate in Pseudomonas sp. strain MT1. J Bacteriol 185, 6790-6800.
31. T, KF3 and NKF1 as a new species of the genus Sphingomonas, Sphingomonas subarctica sp. nov. Int J Syst Bacteriol 46, 1042-1055.
32. Nohynek, L. J., Suhonen, E. L, Nurmiaho-Lassila, E.-L., Hantula, J. & Salkinoja-Salonen, M. S. (1996b). Description of four pentachlorophenol-degrading bacterial strains as Sphingomonas chlorophenolica sp. nov. Syst Appl Microbiol 18, 527-538.
33. Pal, R., Bhasin, V. K. & Lal, R. (2006). Proposal to reclassify [Sphingomonas] xenophaga Stolz et al. 2000 and [Sphingomonas] taejonensis Lee et al. 2001 as Sphingobium xenophagum comb. nov. and Sphingopyxis taejonensis comb. nov., respectively. Int J Syst Evol Microbiol 56, 667-670.
34. Schraa, G., Boone, M. L., Jetten, M. S. M., van Nerven, A. R. W., Colberg, P. J. & Zehnder, A. J. B. (1986). Degradation of 1,4-dichlorobenzene by Alcaligenes sp. strain A175. Appl Environ Microbiol 52, 1374-1381.
35. T and N,N which degrade xenobiotic aromatic compounds, Int J Syst Evol Microbiol 50, 35-41.
36. 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.
37. 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.
38. Tiirola, M. A., Busse, H.-J., Kämpfer, P. & Männistö, M. K. (2005). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 55, 583-588.
39. Tindall, B. J. (1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
40. Ventosa, A., Marquez, M. C., Kocur, M. & Tindall, B. J. (1993). Comparative study of 'Micrococcus sp.' strains CCM 168 and CCM 1405 and members of the genus Salinicoccus. Int J Syst Bacteriol 43, 245-248.
41. White, D. C., Sutton, S. D. & Ringelberg, D. B. (1996). The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7, 301-306.
42. Wilson, K. (1994). 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: John Wiley & Sons Inc.
43. Wittich, R.-M., Strömpl, C., Moore, E. R. B., Blasco, R. & Timmis, K. N. (1999). Interaction of Sphingomonas and Pseudomonas strains in the degradation of chlorinated dibenzofurans. J Ind Microbiol Biotechnol 23, 353-358.
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. T, known as a dibenzo-p-dioxin metabolizer. Int J Syst Evol Microbiol 51, 281-292.
46. Zipper, C., Nickel, K., Angst, W. & Kohler, H. P. (1996). Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy)-propionic acid] in an enantioselective manner by Sphingomonas herbicidovorans sp. nov. Appl Environ Microbiol 62, 4318-4322.