Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART2, 2013, Pages 735-743

  Chen, Hong ^a,b   Jogler, Mareike ^a,b   Rohde, Manfred ^c   Klenk, Hans Peter ^b   Busse, Hans Jürgen ^d   Tindall, Brian J ^b   Spröer, Cathrin ^b   Overmann, Jörg ^a,b  

^a UNIVERSITY OF MUNICH   (Germany)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^d UNIVERSITY OF VETERINARY MEDICINE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMPICILLIN; AZTREONAM; BACITRACIN; CEFALOTIN; CEFAZOLIN; CEFOTAXIME; CEFTRIAXONE; CHLORAMPHENICOL; CLINDAMYCIN; COLISTIN; DOXYCYCLINE; ERYTHROMYCIN; GENTAMICIN; IMIPENEM; KANAMYCIN; LINCOMYCIN; MEZLOCILLIN; NEOMYCIN; NITROFURANTOIN; NORFLOXACIN; OFLOXACIN; OXACILLIN; PENICILLIN G; PIPEMIDIC ACID; POLYMYXIN B; TETRACYCLINE; TICARCILLIN; UNINDEXED DRUG; VANCOMYCIN;

AEROBIC BACTERIUM; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIOPLANKTON; BACTERIUM ISOLATION; CHEMOHETEROTROPH; CLASSIFICATION; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; FRESHWATER SPECIES; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SPHINGOBIUM AMIENSE; SPHINGOBIUM BOECKII; SPHINGOBIUM LIMNETICUM; SPHINGOBIUM SCIONENSE; SPHINGOBIUM SUBERIFACIENS; SPHINGOBIUM VERMICOMPOSTI; SPHINGOBIUM YANOIKUYAE; SPHINGOMONADACEAE; SPHINGOMONAS; SPHINGOMONAS SUBERIFACIENS; TEMPERATURE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; FRESH WATER; MOLECULAR SEQUENCE DATA; MYRISTIC ACIDS; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; QUINONES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPHINGOMONADACEAE; WATER MICROBIOLOGY;

EID: 84868001106     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.040105-0     Document Type: Article

References (39)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
2. Bartscht, K., Cypionka, H. & Overmann, J. (1999). Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. FEMS Microbiol Ecol 28, 249-259.
3. Bruns, A., Cypionka, H. & Overmann, J. (2002). Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl Environ Microbiol 68, 3978-3987.
4. Busse, H. J. & Auling, G. (1988). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
5. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. (1977). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461-466.
6. Chen, C., Zheng, Q., Wang, Y.-N., Yan, X.-J., Hao, L.-K., Du, X. & Jiao, N. (2010). Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. Int J Syst Evol Microbiol 60, 2857-2861.
7. CLSI (2007). Performance Standards for Antimicrobial Disk Diffusion Susceptibility Tests; Approved Standard, 17th Informational Supplement M100-S17. Wayne, PA: Clinical and Laboratory Standards Institute.
8. De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
9. Gich, F., Schubert, K., Bruns, A., Hoffelner, H. & Overmann, J. (2005). Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl Environ Microbiol 71, 5908-5919.
10. Huss, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
11. Jaspers, E., Nauhaus, K., Cypionka, H. & Overmann, J. (2001). Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol Ecol 36, 153-164.
12. Jogler, M., Siemens, H., Chen, H., Bunk, B., Sikorski, J. & Overmann, J. (2011). Identification and targeted cultivation of abundant novel freshwater sphingomonads and analysis of their population substructure. Appl Environ Microbiol 77, 7355-7364.
13. Judicial Commission (1954). Opinions 4, 6, 7, 8, 9, 10, 11, 12, 13, 14. Int Bull Bacteriol Nomencl Taxon 4, 141-158.
14. Kampfer, P., Arun, A. B., Young, C.-C., Busse, H.-J., Kassmannhuber, J., Rosselló-Móra, R., Geueke, B., Rekha, P. D. & Chen, W.-M. (2012). Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 62, 1326-1330.
15. Kawahara, K., Seydel, U., Matsuura, M., Danbara, H., Rietschel, E. T. & Zahringer, U. (1991). Chemical structure of glycosphingolipids isolated from Sphingomonas paucimobilis. FEBS Lett 292, 107-110.
16. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
17. Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R. & Clark, W. A. (editors) (1992). International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology.
18. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, H., Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
19. 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.
20. 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.
21. Naka, T., Fujiwara, N., Yabuuchi, E., Doe, M., Kobayashi, K., Kato, Y. & Yano, I. (2000). A novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of Sphingomonas yanoikuyae. J Bacteriol 182, 2660-2663.
22. Overmann, J., Tuschak, C., Sass, H. & Frostl, J. (1998). The ecological niche of the consortium "Pelochromatium roseum". Arch Microbiol 169, 120-128.
23. Pfennig, N. & Wagener, S. (1986). An improved method of preparing wet mounts for photomicrographs of microorganisms. J Microbiol Methods 4, 303-306.
24. Reasoner, D. J. & Geldreich, E. E. (1985). A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49, 1-7.
25. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
26. Stolz, A., Busse, H.-J. & Kampfer, P. (2007). Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57, 572-576.
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 analysis. Int J Syst Evol Microbiol 51, 1405-1417.
29. Tindall, B. J. (1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128-130.
30. Tindall, B. J. (1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
31. Tindall, B. J. (1996). Respiratory lipoquinones as biomarkers. In Molecular Microbial Ecology Manual, pp. 4.1.5 (Suppl. 1). Edited by A. Akkermans, F. de Bruijn & D. van Elsas. Dordrecht: Kluwer.
32. Tindall, B. J. (2005). Respiratory lipoquinones as biomarkers. In Molecular Microbial Ecology Manual, 2nd edn, pp. 4.1.5 (Suppl. 1). Edited by A. Akkermans, F. de Bruijn & D. van Elsas. Dordrecht: Kluwer.
33. Tindall, B. J. (2008). Are the concepts of legitimate and illegitimate names necessary under the current International Code of Nomenclature of Bacteria? A proposal to make changes to the Code. Int J Syst Evol Microbiol 58, 1979-1986.
34. van Bruggen, A. H. C., Jochimsen, K. N. & Brown, P. R. (1990). Rhizomonas suberifaciens gen. nov., sp. nov., the causal agent of corky root of lettuce. Int J Syst Bacteriol 40, 175-188.
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. Yabuuchi, E. & Kosako, Y. (2005). Order IV Sphingomonadales Yabuuchi E., Kosako Y. In Bergey's Manual of Systematic Bacteriology. The Proteobacteria part C, 2nd edn, vol. 2, pp. 230-286. Edited by G. M. Garrity, D. J. Brenner, N. R. Krieg & J. R. Staley. New York: Springer.
37. Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T. & Yamamoto, H. (1990). Proposal 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.
38. Yabuuchi, E., Kosako, Y., Naka, T., Suzuki, S. & Yano, I. (1999). Proposal of Sphingomonas suberifaciens (Van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al., 1997) comb. nov., and emendation of the genus Sphingomonas. Microbiol Immunol 43, 339-349.
39. 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.