Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium

International Journal of Systematic and Evolutionary Microbiology

Volumn 58, Issue 8, 2008, Pages 1939-1949

  Abraham, Wolf Rainer ^a   Macedo, Alexandre J ^a,d   Lünsdorf, Heinrich ^a   Fischer, Roman ^a   Pawelczyk, Sonja ^a   Smit, John ^b   Vancanneyt, Marc ^c  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c GHENT UNIVERSITY   (Belgium)

^d FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; NUCLEOTIDE; RIBOSOME RNA; RNA 16S; BACTERIAL DNA; FATTY ACID; FRESH WATER;

ARTICLE; ASTICCACAULIS; BACTERIAL STRAIN; BACTERIUM ISOLATION; BLOOD SAMPLING; BREVUNDIMONAS; CAULOBACTER; CAULOBACTER FUSIFORMIS; CAULOBACTER HENRICII; CAULOBACTER MIRABILIS; CAULOBACTERALES; CHEMICAL ANALYSIS; CHEMOTAXONOMY; CONTROLLED STUDY; FRESHWATER SPECIES; GRAM NEGATIVE BACTERIUM; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENYLOBACTERIUM; PHENYLOBACTERIUM CONJUNCTUM; PHENYLOBACTERIUM HAEMATOPHILUM; PHENYLOBACTERIUM IMMOBILE; PHENYLOBACTERIUM KOREENSE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY; TYPE STRAIN; BACTERIUM IDENTIFICATION; BLOOD; CAULOBACTERACEAE; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOTYPE; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHENOTYPE; PHYSIOLOGY; SPECIES DIFFERENCE;

ASTICCACAULIS; BREVUNDIMONAS; CAULOBACTER; CAULOBACTER FUSIFORMIS; CAULOBACTER HENRICII; CAULOBACTERALES; MIRABILIS; NEGIBACTERIA; PHENYLOBACTERIUM; PHENYLOBACTERIUM IMMOBILE; PHENYLOBACTERIUM KOREENSE;

BACTERIAL TYPING TECHNIQUES; BLOOD; CAULOBACTER; CAULOBACTERACEAE; DNA, BACTERIAL; FATTY ACIDS; FRESH WATER; GENOTYPE; HUMANS; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 54749129005     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65567-0     Document Type: Article

References (32)

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., Strömpl, C., Meyer, H., Lindholst, S., Moore, E. R. B., Bennasar, A., Christ, R., Vancanneyt, M., Tindall, B. & other authors (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with M. 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. Albuquerque, L., Santos, J., Travassos, P., Nobre, M. F., Rainey, F. A., Wait, R., Empadinhas, N., Silva, M. T. & da Costa, M. S. (2002). Albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus Rhodovulum. Appl Environ Microbiol 68, 4266-4273.
4. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
5. Aslam, Z., Im, W.-T., Ten, L. N. & Lee, S.-T. (2005). Phenylobacterium koreense sp. nov., isolated from South Korea. Int J Syst Evol Microbiol 55, 2001-2005.
6. Bellmann, W. & Lingens, F. (1985). Structural studies on the core oligosaccharide of Phenylobacterium immobile strain K2 lipopolysaccharide. Chemical synthesis of 3-hydroxy-5c-dodecenoic acid. Biol Chem Hoppe Seyler 366, 567-575.
7. Bligh, E. G. & Dyer, W. J. (1959). A rapid method for total lipid extraction and purification. Can J Biochem Physiol 37, 911-917.
8. Henrici, A. T. & Johnson, D. E. (1935). Studies on fresh water bacteria. II. Stalked bacteria, a new order of schizomycetes. J Bacteriol 30, 61-93.
9. Kanso, S. & Patel, B. K. C. (2004). Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 54, 2141-2146.
10. 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.
11. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
12. Lingens, F., Blecher, R., Blecher, H., Blobel, F., Eberspächer, J., Fröhner, C., Görisch, H., Görisch, H. & Layh, G. (1985). Phenylobacterium immobile gen. nov., sp. nov., a Gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 35, 26-39.
13. Löffler, F. (1890). Weitere Untersuchungen über die Beizung und Färbung der Geisseln bei den Bakterien. Zentralbl Bakteriol Parasitenkd 7, 625-639 (in German).
14. 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.
15. Neefs, J.-M., Van de Peer, Y., De Rijk, P., Chapelle, S. & De Wachter, R. (1993). Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res 21, 3025-3049.
16. Poindexter, J. S. (1964). Biological properties and classification of the Caulobacter group. Bacteriol Rev 28, 231-295.
17. Poindexter, J. S. (1981). Oligotrophy. Fast and famine existence, pp. 63-89. In Microbial Ecology, vol. 5. Edited by M. Alexander. New York: Plenum Publishing Corp.
18. Poindexter, J. S. & Lewis, R. F. (1966). Recommendations for revision of the taxonomic treatment of stalked bacteria. Int J Syst Bacteriol 16, 377-382.
19. Rüger, H.-J. & Krambeck, H.-J. (1994). Evaluation of the BIOLOG substrate metabolism system for classification of marine bacteria. Syst Appl Microbiol 17, 281-288.
20. Segers, P., Vancanneyt, M., Pot, B., Torck, U., Hoste, B., Dewettinck, D., Falsen, E., Kersters, K. & De Vos, P. (1994). Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Büsing, Döll and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. Int J Syst Bacteriol 44, 499-510.
21. Spurr, A. R. (1969). A low viscosity epoxy resin embedding medium for electron microscopy. J Ultrastruct Res 26, 31-43.
22. Stahl, D. A., Key, R., Flesher, B. & Smit, J. (1992). The phylogeny of marine and freshwater Caulobacters reflects their habitat. J Bacteriol 174, 2193-2198.
23. Staley, J. T. (1968). Prosthecomicrobium and Acalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95, 1921-1942.
24. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
25. 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.
26. Tiago, I., Mendes, V., Pires, C., Morais, P. V. & Verssimo, A. (2005). Phenylobacterium falsum sp. nov., an alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium. Syst Appl Microbiol 28, 295-302.
27. Urakami, T., Oyanagi, H., Araki, H., Suzuki, K.-I. & Komagata, K. (1990). Recharacterization and emended description of the genus Mycoplana and description of two new species, Mycoplana ramosa and Mycoplana segnis. Int J Syst Bacteriol 40, 434-442.
28. Vancanneyt, M., Witt, S., Abraham, W.-R., Kersters, K. & Fredrickson, H. L. (1996). Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. Syst Appl Microbiol 19, 528-540.
29. Walker, S. G., Smith, S. S. & Smit, J. (1992). Isolation and comparison of the paracrystalline surface layer proteins of freshwater caulobacters. J Bacteriol 174, 1783-1792.
30. Wilson, K. (1987). Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology, pp. 2.4.1-2.4.5. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Green Publishing & Wiley-Interscience.
31. Yakimov, M. M., Golyshin, P. N., Lang, S., Moore, E. R. W., Abraham, W.-R., Lünsdorf, H. & Timmis, K. N. (1998). Alcanivorax borkumensis gen. nov., sp. nov., a new hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48, 339-348.
32. Zhang, K., Han, W., Zhang, R., Xu, X., Pan, Q. & Hu, X. (2007). Phenylobacterium zucineum sp. nov., a facultative intracellular bacterium isolated from a human erythroleukemia cell line K562. Syst Appl Microbiol 30, 207-212.