Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART4, 2013, Pages 1342-1349

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

^a UNIVERSITY OF MUNICH   (Germany)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c UNIVERSITY OF VETERINARY MEDICINE   (Austria)

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

Author keywords

[No Author keywords available]

Indexed keywords

1,3 PROPANEDIAMINE; CARDIOLIPIN; CYTOSINE; FATTY ACID; FRESH WATER; GENOMIC DNA; GLYCOSPHINGOLIPID; GUANINE; LIPID; NUCLEOTIDE; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLDIMETHYLETHANOLAMINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLMETHYLETHANOLAMINE; PUTRESCINE; RNA 16S; SPERMIDINE; SPERMINE; UBIDECARENONE; UBIQUINONE; UBIQUINONE 9; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; GENE SEQUENCE; GERMANY; GRAM NEGATIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPHINGOMONADACEAE; SPHINGOPYXIS; SPHINGOPYXIS FLAVIMARIS; SPHINGOPYXIS LITORIS; SPHINGOPYXIS MARINA; SPHINGORHABDUS PLANKTONICA;

EID: 84876094810     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.043133-0     Document Type: Article

References (53)

1. Altschul, S. F., Madden, T. L., Schäffer, 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. Asker, D., Beppu, T. & Ueda, K. (2007). Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int J Syst Evol Microbiol 57, 1435-1441.
3. Balkwill, D. L., Frederickson, J. K. & Romine, M. F. (2006). Sphingomonas and related genera. Prokaryotes 7, 605-629.
4. 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.
5. Basta, T., Buerger, S. & Stolz, A. (2005). Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. Microbiology 151, 2025-2037.
6. 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 EnvironMicrobiol 68, 3978-3987.
7. Bruns, A., Nübel, U., Cypionka, H. & Overmann, J. (2003). Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 69, 1980-1989.
8. Busse, H.-J. & Auling, G. (1988). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8.
9. Busse, H.-J., Denner, E. B. M., Buczolits, S., Salkinoja-Salonen, M., Bennasar, A. & Kämpfer, P. (2003). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. andSphingomonas 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.
10. 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.
11. 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.
12. Choi, J.-H., Kim, M.-S., Jung, M.-J., Roh, S. W., Shin, K.-S. & Bae, J.-W. (2010). Sphingopyxis soli sp. nov., isolated from landfill soil. Int J Syst Evol Microbiol 60, 1682-1686.
13. 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.
14. Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (1994). Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
15. Gich, F. & Overmann, J. (2006). Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. Int J Syst Evol Microbiol 56, 847-854.
16. 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.
17. Glöckner, F. O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A. & Amann, R. (2000). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66, 5053-5065.
18. Godoy, F., Vancanneyt, M., Martínez, M., Steinbüchel, A., Swings, J. & Rehm, B. H. (2003). Sphingopyxis chilensis sp. nov., a chlorophenoldegrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 53, 473-477.
19. Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59, 307-321.
20. 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.
21. Jenkins, C. L., Andrewes, A. G., McQuade, T. J. & Starr, M. P. (1979). The pigment of Pseudomonas paucimobilis is a carotenoid (nostoxanthin) rather than a brominated aryl-polyene (xanthomonadin). Curr Microbiol 3, 1-4.
22. 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.
23. Kalnenieks, U. (2006). Physiology of Zymomonas mobilis: some unanswered questions. Adv Microb Physiol 51, 73-117.
24. Kämpfer, P., Arun, A. B., Young, C.-C., Busse, H.-J., Kassmannhuber, J., Rossello-Mora, R., Geueke, B., Rekha, P. D. & Chen, W.-M. (2012). Proposal of Sphingomicrobium lutaoense gen. nov. sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 62, 1326-1330.
25. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T. (2005). Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria. J Microbiol 43, 152-157.
26. Kim, M. K., Schubert, K., Im, W.-T., Kim, K.-H., Lee, S.-T. & Overmann, J. (2007). Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes. Int J Syst Evol Microbiol 57, 1527-1534.
27. Kim, B.-S., Lim, Y. W. & Chun, J. (2008). Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 58, 2415-2419.
28. 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, UK: Wiley.
29. Lee, M., Ten, L. N., Lee, H.-W., Oh, H. W., Im, W.-T. & Lee, S.-T. (2008). Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 58, 2342-2347.
30. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
31. 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.
32. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
33. 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.
34. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
35. Sharma, P., Verma, M., Bala, K., Nigam, A. & Lal, R. (2010). Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 60, 780-784.
36. Sikorski, J., Brambilla, E., Kroppenstedt, R. M. & Tindall, B. J. (2008). The temperature-adaptive fatty acid content in Bacillus simplex strains from 'Evolution Canyon', Israel. Microbiology 154, 2416-2426.
37. Srinivasan, S., Kim, M. K., Sathiyaraj, G., Veena, V., Mahalakshmi, M., Kalaiselvi, S., Kim, Y.-J. & Yang, D.-C. (2010). Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60, 2358-2363.
38. Stead, D. E., Sellwood, J. E., Wilson, J. & Viney, I. (1992). Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. J Appl Bacteriol 72, 315-321.
39. Stolz, A., Schmidt-Maag, C., Denner, E. B. M., Busse, H.-J., Egli, T. & Kämpfer, P. (2000). Description of Sphingomonas xenophaga sp. nov. for strains BN6T and N, N which degrade xenobiotic aromatic compounds. Int J Syst Evol Microbiol 50, 35-41.
40. Stolz, A., Busse, H.-J. & Kämpfer, P. (2007). Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57, 572-576.
41. Takeuchi, M., Kawai, F., Shimada, Y. & Yokota, A. (1993). Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the 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.
42. 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.
43. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
44. Tindall, B. J. (1990a). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
45. Tindall, B. J. (1990b). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128-130.
46. Vancanneyt, M., Schut, F., Snauwaert, C., Goris, J., Swings, J. & Gottschal, J. C. (2001). Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int J Syst Evol Microbiol 51, 73-79.
47. Wittich, R. M., Wilkes, H., Sinnwell, V., Francke, W. & Fortnagel, P. (1992). Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl Environ Microbiol 58, 1005-1010.
48. 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.
49. Yoon, J.-H. & Oh, T.-K. (2005). Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 369-373.
50. Yoon, J.-H., Lee, C.-H., Yeo, S.-H. & Oh, T.-K. (2005). Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 1223-1227.
51. Yurkov, V., Stackebrandt, E., Buss, O., Vermeglio, A., Gorlenko, V. & Beatty, J. T. (1997). Reorganization of the genus Erythromicrobium: description of 'Erythromicrobium sibiricum' as Sandaracinobacter sibiricus gen. nov., sp. nov., and of 'Erythromicrobium ursincola' as Erythromonas ursincola gen. nov., sp. nov. Int J Syst Bacteriol 47, 1172-1178.
52. Zhang, D.-C., Liu, H.-C., Xin, Y.-H., Zhou, Y.-G., Schinner, F. & Margesin, R. (2010). Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 60, 2618-2622.
53. Zwart, G., Crump, B. C., Kamst-Van Agterveld, M. P., Hagen, F. & Han, S. (2002). Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28, 141-155.