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1 Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26–32, D-35392 Giessen, Germany
2 DSMZ, D-38124 Braunschweig, Germany
Correspondence
Peter Kämpfer
peter.kaempfer{at}agrar.uni-giessen.de
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ABSTRACT |
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 TOP ABSTRACT MAIN TEXTREFERENCES |
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A table showing fatty acid compositions of species of the genus Pseudonocardia and a parsimony tree based on 16S rRNA gene sequences are available as supplementary material in IJSEM Online.
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MAIN TEXT |
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TOPABSTRACTMAIN TEXTREFERENCES |
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for mycolate-less, nocardioform actinomycetes with a type IV cell wall; on the basis of a detailed phylogenetic analysis, the genus presently comprises 21 species, most of which were listed by Lee et al. (2000, 2001, 2002) and Huang et al. (2002). During the characterization of organisms from soil that was contaminated by various chlorinated, aromatic compounds from Bitterfeld, Germany, strain B5T was recovered on a selective medium that contained 1,2,3,5-tetrachlorobenzene as the sole carbon source at 25 °C, showing a beige-coloured vegetative mycelium with a white aerial mycelium that fragmented into coccoid and rod-shaped elements. Subcultivation was done on R2A agar at 25 °C for 24 h.
Gram-staining was performed as described by Gerhardt et al. (1994). Cell morphology was observed under a Zeiss light microscope at x1000, using cells that had been grown for 3 days at 25 °C on R2A agar. The 16S rRNA gene was analysed as described previously (Kämpfer et al., 2003). Phylogenetic analysis was performed by using the ARB software package (Strunk et al., 2000) and also the software package MEGA (Molecular Evolutionary Genetics Analysis) version 2.1 (Kumar et al., 2001), after multiple alignment of data by CLUSTALX (Thompson et al., 1997). Distances (distance options according to the Kimura two-parameter model) and clustering with the neighbour-joining (Fig. 1) and maximum-parsimony (see Supplementary Figure, available in IJSEM Online) methods were performed by using bootstrap values based on 1000 replications. The 16S rRNA gene sequence of strain B5T was a continuous stretch of 1494 bp. Sequence similarity calculations after neighbour-joining analysis indicated that the closest relatives of strain B5T were Pseudonocardia sulfidoxydans (GenBank accession no. AF378364; 98·8 %) and Pseudonocardia hydrocarbonoxydans (GenBank accession no. AJ252826; 98·3 %). Lower sequence similarities (<97·0 %) were found with all other species of the genus Pseudonocardia with validly published names.
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); polar lipids (Lechevalier et al., 1977; Minnikin et al., 1984); fatty acids (Kämpfer & Kroppenstedt, 1996). The quinone system supports affiliation of strain B5T to the genus Pseudonocardia, where all species have MK-8(H4) as the major quinone (McVeigh et al., 1994; Warwick et al., 1994; Reichert et al., 1998; Huang et al., 2002). The polar lipid profile of strain B5T was similar to that reported for P. sulfidoxydans (Reichert et al., 1998) (data not shown). The fatty acid profile of strain B5T (available as supplementary material in IJSEM Online) was very similar to those of the closely related species P. sulfidoxydans and P. hydrocarbonoxydans and was congruent with the fatty acid profiles that were reported by Reichert et al. (1998).
Results of physiological characterization are given in the species description, using methods that were described previously (Kämpfer et al., 1991). DNA–DNA hybridization experiments were performed between strain B5T and the type strains of P. sulfidoxydans and P. hydrocarbonoxydans, using the method described by Ziemke et al. (1998), except that for nick translation, 2 µg DNA was labelled during 3 h incubation at 15 °C. Strain B5T showed relatively low DNA–DNA similarity to P. sulfidoxydans DSM 44248T (38 %, mean value of six hybridizations; SD, 16 %) and P. hydrocarbonoxydans DSM 43281T (23 %, mean value of two hybridizations; SD, 10 %).
Description of Pseudonocardia benzenivorans sp. nov.
Pseudonocardia benzenivorans (ben.ze.ni.vo'rans. N.L. n. benzenum benzene; L. v. vorare to devour; L. part. adj. vorans devouring, digesting; N.L. part. adj. benzenivorans digesting benzene).
Forms a pale vegetative mycelium that fragments very easily into rod-shaped and coccoid elements. Aerial mycelium is white. Gram-positive and oxidase-positive; shows an oxidative metabolism. Good growth occurs after 3 days incubation on R2A agar and nutrient agar at 25–30 °C; no growth is observed at 4, 10, 15, 20, 40, 45 or 55 °C. Main menaquinone of the type strain is MK-8(H4). Predominant polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol; phosphatidylcholine is missing. Major fatty acids are iso-branched hexadecanoate and hexadecanoate. Small amounts of methyl-branched fatty acids (C16 : 0 10-methyl and C17 : 0 10-methyl) are detected. Carbon source utilization and hydrolysis of chromogenic substrates (including differentiating characters) are indicated in Table 1.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Goodfellow, M. & Lechevalier, M. P. (1989). Genus Nocardia Trevisan 1889, 9AL. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2350–2361. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Henssen, A. (1957). Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26, 373–414 (in German).[CrossRef][Medline]
Huang, Y., Wang, L., Lu, Z., Hong, L., Liu, Z., Tan, G. Y. A. & Goodfellow, M. (2002). Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov. Int J Syst Evol Microbiol 52, 977–982.[Abstract]
Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.
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.
Kämpfer, P., Dreyer, U., Neef, A., Dott, W. & Busse, H.-J. (2003). Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 53, 93–97.
Kroppenstedt, R. M. (1985). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics, pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. New York: Academic Press.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetic analysis software. Bioinformatics 17, 1244–1245.
Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A. (1977). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249–260.[CrossRef]
Lee, S. D., Kim, E. S. & Hah, Y. C. (2000). Phylogenetic analysis of the genera Pseudonocardia and Actinobispora based on 16S ribosomal DNA sequences. FEMS Microbiol Lett 182, 125–129.[CrossRef][Medline]
Lee, S. D., Kim, E. S., Min, K.-L., Lee, W. Y., Kang, S.-O. & Hah, Y. C. (2001). Pseudonocardia kongjuensis sp. nov., isolated from a gold mine cave. Int J Syst Evol Microbiol 51, 1505–1510.[Abstract]
Lee, S. D., Kim, E. S., Kang, S.-O. & Hah, Y. C. (2002). Pseudonocardia spinosispora sp. nov., isolated from Korean soil. Int J Syst Evol Microbiol 52, 1603–1608.[Abstract]
McVeigh, H. P., Munro, J. & Embley, T. M. (1994). The phylogenetic position of Pseudoamycolata halophobica (Akimov et al. 1989) and a proposal to reclassify it as Pseudonocardia halophobica. Int J Syst Bacteriol 44, 300–302.[CrossRef][Medline]
Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, K. & Parlett, J. H. (1984). An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Reichert, K., Lipski, A., Pradella, S., Stackebrandt, E. & Altendorf, K. (1998). Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Bacteriol 48, 441–449.[CrossRef][Medline]
Strunk, O., Gross, O., Reichel, B. & 10 other authors (2000). ARB: a software environment for sequence data. Department of Microbiology, Technische Universität München, Munich, Germany (http://www.arb-home.de/).
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.
Warwick, S., Bowen, T., McVeigh, H. & Embley, T. M. (1994). A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44, 293–299.[CrossRef][Medline]
Ziemke, F., Höfle, M. G., Lalucat, J. & Rosselló-Mora, R. (1998). Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179–186.[CrossRef][Medline]
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-D-glucopyranoside, bis-p-nitrophenyl phosphate, L-alanine-p-nitroanilide and L-proline-p-nitroanilide. All strains were negative for hydrolysis of aesculin, p-nitrophenyl phosphorylcholine, 2-deoxythymidine-5'-p-nitrophenyl phosphate and L-glutamate-
-3-carboxy-p-nitroanilide. All strains were also positive for assimilation of D-fructose*, D-galactose*, D-glucose*, D-maltose, acetate, propionate, glutarate, DL-3-hydroxybutyrate, oxoglutarate, pyruvate, suberate, L-aspartate, L-leucine and phenylacetate. All strains were negative for assimilation of N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, L-arabinose*, L-rhamnose*, adonitol, D-sorbitol, cis-aconitate, trans-aconitate, 4-aminobutyrate, citrate, mesaconate, salicin, putrescine, L-histidine, ornithine, adipate,