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1 Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26–32, D-35392 Giessen, Germany
2 Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
3 Biofrontera Discovery GmbH, D-69123 Heidelberg, Germany
4 Institut für Mikrobiologie und Genetik, Universität Wien, A-1030 Wien, Austria
Correspondence
Peter Kämpfer
peter.kaempfer{at}agrar.uni-giessen.de
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-cycl); major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unknown glycolipid and an unknown phospholipid; major fatty acids: C16 : 0, C18 : 19c and 10 methyl C16 : 0] and the presence of mycolic acids supported the affiliation of strain GW39-1573T to the genus Nocardia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW39-1573T from those related species that showed 16S rRNA gene sequence similarity values of greater than 97 %. Strain GW39-1573T merits species status, and the name Nocardia tenerifensis is proposed with the type strain GW39-1573T (=DSM 44704T=CIP 107929T).
The EMBL accession number for the 16S rRNA gene sequence of Nocardia tenerifensis GW39-1573T is AJ556157.
Details of the major fatty acids of N. tenerifensis GW39-1573T and phylogenetic trees showing the relationship of N. tenerifensis with members of the genus Nocardia are available in IJSEM Online.
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; Zhang et al., 2003; Yassin et al., 2003). A comprehensive treatise of the history of the genus has been given by Goodfellow et al. (1999). During the characterization of organisms isolated from different soils, strain GW39-1573T was recovered from 1 g of a soil sample (heated for 100 °C) originating from the Spanish island of Tenerife, after a 2 h extraction in 10 ml of a 0·1 % (v/v) Tween 80 solution containing 5 mg ampicillin and dilution on mannitol/rifampicin agar [containing l-1: mannitol, 10 g; yeast extract, 7 g; Casamino acids, 2 g; peptone (Bacto), 1 g; NaCl, 1 g; CaCO3, 0·2 g; nystatin, 100 mg; rifampicin, 5 mg] with incubation for 6 weeks at 27 °C. The strain was maintained on medium 65 (DSMZ; http://www.dsmz.de/media/med065.htm) at 25 °C and showed on this medium an orange-coloured substrate mycelium that fragmented easily into irregular, rod-shaped cells. Orange–white aerial hyphae were formed.
The strain stained Gram-positive using the method of Gerhardt et al. (1994). Cell morphology was observed under a Zeiss light microscope at x1000, with cells grown for 3 days at 25 °C on medium 65. The 16S rRNA gene of the strain was analysed as described by Kämpfer et al. (2003). Phylogenetic analysis was performed using the ARB software package (Strunk et al., 2000) and the MEGA (Molecular Evolutionary Genetics Analysis) software package version 2.1 (Kumar et al., 2001) after multiple alignment of sequences by CLUSTAL_X (Thompson et al., 1997). Distances (distance options according to Kimura's two-parameter model) were calculated and clustering of the sequences was determined with the neighbour-joining method and maximum parsimony; bootstrap values were determined based on 1000 replications (results are available in IJSEM Online). The 16S rRNA gene sequence of strain GW39-1573T was a continuous stretch of 1481 nt. Sequence similarity calculations after a neighbour joining analysis indicated that the closest relatives of strain GW39-1573T were Nocardia brasiliensis (EMBL accession no.) X80608 (98·0 %), Nocardia beijingensis AF154129 (97·3 %), Nocardia transvalensis X80609 (97·5 %), Nocardia asteroides X84850 (97·2 %), Nocardia farcinica X80610 (97·0 %) and N. puris AJ508748 (96·9 %). Lower sequence similarities (<97·0 %) were found with all other validly described species of the genus Nocardia.
Results of chemotaxonomic analyses are given in the species description. The following analytical procedures were performed as described: menaquinones (Tindall, 1990); polar lipids (Ventosa et al., 1993); mycolic acids were extracted and analysed by one-dimensional TLC and developed in petroleum benzene/acetone (95 : 5, v/v) (Minnikin et al., 1980); fatty acids (Kämpfer & Kroppenstedt, 1996). The quinone system with the predominant compound (99 %) MK-8(H4, -cycl) supports affiliation of strain GW39-1573T to the genus Nocardia, where all species have MK-8(H4, -cycl) as the major quinone (Goodfellow et al., 1999). The polar lipid profile of strain GW39-1573T was similar to those reported for other nocardiae but the presence of significant amounts of phosphatidylglycerol has been reported only for N. asteroides ATCC 19247T and N. brasiliensis ATCC 19296T (Minnikin et al., 1977). The mycolic acid of strain GW39-1573T showed a chromatographic behaviour which was similar to that of N. brasiliensis DSM 43009, which was analysed in parallel. The fatty acid profile of strain GW39-1573T (available in IJSEM Online) was very similar to those of the other closely related species and was congruent with the fatty acid profiles reported for other Nocardia species.
Detailed results of the physiological characterization of strain GW39-1573T are given in the species description, with methods as described previously (Kämpfer et al., 1991). Degradation of polymeric substances was performed using standard procedures (Williams et al., 1983) and results were read after 7 days incubation at 28 °C. Results of DNA–DNA hybridization experiments between strain GW39-1573T and the type strains were: N. brasiliensis DSM 43758T, 29·3/26·2 %; N. beijingensis DSM 44636T, 25·4/16·8 %; N. transvalensis DSM 43405T, 16·2/23·6 %; N. farcinica DSM 43665T, 15·8/15·2 % (first value, performed with labelled DNA from strain GW39-1573T; second value, performed with labelled DNA from the type strain; all values are mean values of two analyses). The method of Ziemke et al. (1998) was used, except that for nick translation, and 2 µg of DNA was labelled during a 3 h incubation at 15 °C.
Description of Nocardia tenerifensis sp. nov.
Nocardia tenerifensis (te.ne.ri'fen.sis. N.L. fem. adj. tenerifensis named after Tenerife, from where the organism was isolated).
Forms an orange-coloured vegetative mycelium that fragments very easily into irregular, rod-shaped elements. Aerial mycelium is yellowish-white. Gram-positive, oxidase-positive, showing an oxidative metabolism. Good growth occurs on nutrient agar and medium 65 at 25–30 °C. Major fatty acids are C16 : 0, C18 : 19c and 10 methyl C16 : 0. Carbon source utilization and hydrolysis of chromogenic substrates (including differentiating characters) are indicated in Table 1. Urea and allantoin are hydrolysed. Tyrosine, casein, starch (weak) and hypoxanthine are degraded, but adenine, xylan and xanthine are not.
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REFERENCES |
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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.
Goodfellow, M., Isik, K. & Yates, E. (1999). Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold 312, 47–82.
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 characterisation 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.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.
Minnikin, D. E., Patel, P. V., Alshamaony, L. & Goodfellow, M. (1977). Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27, 104–117.
Minnikin, D. E., Iwona, G., Hutchinson, G. & Caldicott, A. B. (1980). Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188, 221–233.[CrossRef]
Strunk, O., Gross, O., Reichel, B. & 10 other authors (2000). ARB: a software environment for sequence data (http://www.mikro.biologie.tu-muenchen.de). Department of Microbiology, Technische Universität München, Munich, Germany.
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.
Tindall, B. J. (1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199–202.
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.[CrossRef][Medline]
Williams, S. T., Goodfellow, M., Alderson, G., Wellington, E. M. H., Sneath, P. H. A. & Sackin, M. J. (1983). Numerical classification of Streptomyces and related genera. J Gen Microbiol 129, 1743–1813.[Medline]
Yassin, A. F., Sträubler, B., Schumann, P. & Schaal, K. P. (2003). Nocardia puris sp. nov. Int J Syst Evol Microbiol 53, 1595–1599.
Zhang, J., Liu, Z. & Goodfellow, M. (2003). Nocardia caishijiensis sp. nov., a novel soil actinomycete. Int J Syst Evol Microbiol 53, 999–1004.
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-glucuronide. All strains were also positive for assimilation of D-glucose, acetate*, propionate and oxoglutarate. All strains were negative for assimilation of L-arabinose, p-arbutin, D-cellobiose, gluconate, D-mannose, D-maltose, 
-D-melibiose, sucrose, salicin, D-xylose*, maltitol, 4-aminobutyrate, ornithine*, L-phenylalanine and L-tryptophan.