| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
2 Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
3 Labor Grün-Wollny, D-35394 Giessen, Germany
Correspondence
Peter Kämpfer
peter.kaempfer{at}agrar.uni-giessen.de
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
-cycl) (99.5 %) and traces of MK-8 (H4), characteristic for the genus Nocardia. The polar lipid profile of strain GW4-1778T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, a unknown polar lipid and trace amounts of two unknown lipids and the major fatty acids were C15 : 0, C16 : 0, C17 : 18c and 10-methyl C17 : 0. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW4-1778T from related species with 16S rRNA gene similarities of >97.5 %. Therefore, strain GW4-1778T merits species status, for which the name Nocardia acidivorans sp. nov. is proposed, with the type strain GW4-1778T (=CCUG 53410T=CIP 109315T=DSM 45049T).
An extended neighbour-joining tree based on 16S rRNA gene sequences showing the positions of strain GW4-1778T and other Nocardia species is available as supplementary material with the online version of this paper.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
; Cui et al., 2005; Iida et al., 2006; Kageyama et al., 2004a, b, c, 2005; Kämpfer et al., 2004; Lee, 2006; Wang et al., 2004; Xu et al., 2005; Yamamura et al., 2005; Yassin & Brenner, 2005; Yassin et al., 2003; Zhang et al., 2003, 2004). A comprehensive summary of the taxonomy of the genus has been given by Goodfellow et al. (1999). During the characterization of organisms isolated from different soils, strain GW4-1778T was recovered from 1 g of a soil sample (heated for 10 s at 100 °C) that originated from the Italian island of Stromboli, after extraction for 2 h in 10 ml 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; and rifampicin, 5 mg] 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. Yellowish-white aerial hyphae were formed.
Cells of strain GW4-1778T were Gram-positive using the staining procedure described by 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 was analysed as described by Kämpfer et al. (2003). Phylogenetic analysis was performed using the software package MEGA (Molecular Evolutionary Genetics Analysis) version 2.1 (Kumar et al., 2001) after multiple alignment of data using CLUSTAL_X (Thompson et al., 1997). Distances (distance options according to the Kimura two-parameter model) and clustering with the neighbour-joining method and maximum-parsimony (data not shown) were performed by using bootstrap values based on 1000 replications. The sequenced length of the 16S rRNA gene of strain GW4-1778T was 1493 bp. Sequence similarity calculations (based on 1299 nt) after a neighbour-joining analysis (Fig. 1 and Supplementary Fig. S1 available in IJSEM Online) indicated that the closest relatives of strain GW4-1778T were Nocardia pseudobrasiliensis (GenBank accession no. DQ659914; 98.6 %), Nocardia nova (Z36930; 98.6 %), Nocardia niigatensis (AB092563; 98.4 %), Nocardia jiangxiensis (AY639902; 98.0 %), Nocardia uniformis (Z46752; 98.0 %) and Nocardia miyunensis (AY639901; 97.8 %). Lower sequence similarities (<97.5 %) were found with all other established species of the genus Nocardia.
|
and Altenburger et al. (1997) and that of polar lipids as described by Ventosa et al. (1993). Strain GW4-1778T exhibited a quinone system with the predominant compound MK-8 (H4, -cycl) (99.5 %) and traces of MK-8 (H4). This trait is characteristic of members of the genus Nocardia (Goodfellow et al., 1999). The polar lipid profile of strain GW4-1778T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, an unknown polar lipid and trace amounts of two unknown lipids. Traces of phosphatidylglycerol may be present, as assumed by the presence of a weak spot showing the chromatographic behaviour for this lipid, but could not be stained with molybdenum blue, which is used to indicate the presence of phosphate groups (data not shown). However, the lack or presence only of trace amounts of phosphatidylglycerol has been reported for several nocardiae (Minnikin et al. 1977). The presence of only one aminolipid, phosphatidylethanolamine, demonstrates that strain GW4-1778T exhibits phospholipid type II (Lechevalier et al., 1977) and thus this polar lipid profile is in accordance with the characteristics of the genus Nocardia.
Fatty acid analysis was performed according to Kämpfer & Kroppenstedt (1996). The fatty acid profile of strain GW4-1778T given in Table 1 was similar to those of the other closely related species, but also showed pronounced quantitative differences.
|
and the species description, using methods as described previously (Kämpfer et al., 1991). DNA–DNA hybridization experiments were performed using labelled DNA from strain GW4-1778T and type strains of other Nocardia species using the method described by Ziemke et al. (1998) except that, for nick translation, 2 µg of DNA was labelled during a 3 h incubation at 15 °C. The DNA–DNA hybridization values obtained were as follows: N. pseudobrasiliensis DSM 44290T (46.1 %), N. nova DSM 44481T (62.6 %), N. jiangxiensis DSM 17684T (50.9 %), N. miyunensis DSM 17685T (41.7 %), N. niigatensis DSM 44670T (11.0 %) and N. uniformis DSM 43136T (21.0 %).
|
Forms a light orange-coloured vegetative mycelium. Aerial mycelium is yellowish-white. Gram-positive and oxidase-positive, showing an oxidative metabolism. Good growth occurs on nutrient agar and Medium 65 at 25–30 °C. The menaquinone system contains predominantly MK-8 (H4, -cycl) and traces of MK-8 (H4). The polar lipid profile consists of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, an unknown polar lipid and trace amounts of two unknown lipids. Major fatty acids are C15 : 0, C16 : 0, C17 : 18c and 10-methyl C17 : 0. Carbon source utilization and hydrolysis of chromogenic substrates (including differential characteristics) are given in Table 2
.
The type strain, GW4-1778T (=CCUG 53410T=CIP 109315T=DSM 45049T), was isolated from soil of Stromboli, Italy.
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Altenburger, P., Kämpfer, P., Akimov, V. N., Lubitz, W. & Busse, H.-J. (1997). Polyamine distribution in actinomycetes with group B peptidoglycan and species of the genera Brevibacterium, Corynebacterium, and Tsukamurella. Int J Syst Bacteriol 47, 270–277.
Cui, Q., Wang, L., Huang, Y., Liu, Z. & Goodfellow, M. (2005). Nocardia jiangxiensis sp. nov. and Nocardia miyuensis sp. nov., isolated from acidic soils. Int J Syst Evol Microbiol 55, 1921–1925.
Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) (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 Leopoldina NF80 (312), 47–82.
Iida, S., Kageyama, A., Yazawa, K., Uchiyama, N., Toyohara, T., Chohnabayashi, N., Suzuki, S.-i., Nomura, F., Kroppenstedt, R. M. & Mikami, Y. (2006). Nocardia exalbida sp. nov., isolated from Japanese patients with nocardiosis. Int J Syst Evol Microbiol 56, 1193–1196.
Kageyama, A., Yazawa, K., Mukai, A., Kinoshita, M., Takata, N., Nishimura, K., Kroppenstedt, R. M. & Mikami, Y. (2004a). Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan. Int J Syst Evol Microbiol 54, 1927–1931.
Kageyama, A., Yazawa, K., Mukai, A., Kohara, T., Nishimura, K., Kroppenstedt, R. M. & Mikami, Y. (2004b). Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 54, 2025–2029.
Kageyama, A., Yazawa, K., Nishimura, K. & Mikami, Y. (2004c). Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 54, 563–569.
Kageyama, A., Yazawa, K., Taniguchi, H., Chibana, H., Nishimura, K., Kroppenstedt, R. M. & Mikami, Y. (2005). Nocardia concava sp. nov., isolated from Japanese patients. Int J Syst Evol Microbiol 55, 2081–2083.
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.[CrossRef]
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.
Kämpfer, P., Buczolits, S., Jäckel, U., Grün-Wollny, I. & Busse, H. J. (2004). Nocardia tenerifensis sp. nov. Int J Syst Evol Microbiol 54, 381–383.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244–1245.
Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. (1977). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249–260.[CrossRef]
Lee, S. D. (2006). Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea. Int J Syst Evol Microbiol 56, 559–562.
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.
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.[CrossRef]
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.
Wang, L., Zhang, Y., Huang, Y., Maldonado, L. A., Liu, Z. & Goodfellow, M. (2004). Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate. Int J Syst Evol Microbiol 54, 1683–1686.
Xu, P., Li, W.-J., Tang, S.-K., Jiang, Y., Chen, H.-H., Xu, L.-H. & Jiang, C.-L. (2005). Nocardia polyresistens sp. nov. Int J Syst Evol Microbiol 55, 1465–1470.
Yamamura, H., Hayakawa, M., Nakagawa, Y., Tamura, T., Kohno, T., Komatsu, F. & Iimura, Y. (2005). Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge. Int J Syst Evol Microbiol 55, 433–436.
Yassin, A. F. & Brenner, S. (2005). Nocardia elegans sp. nov., a member of the Nocardia vaccinii clade isolated from sputum. Int J Syst Evol Microbiol 55, 1505–1509.
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.
Zhang, Y., Liu, Z. & Goodfellow, M. (2004). Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 54, 2301–2305.
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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
-D-glucuronide, pNP phosphorylcholine, L-glutamate-
-3-carboxy pNA, L-proline pNA and utilization of gluconate, maltose, D-xylose, adonitol, trans-aconitate, adipate, itaconate, DL-lactate, mesaconate, oxoglutarate, suberate, L-aspartate, L-ornithine, L-phenylalanine, L-tryptophan, 3-hydroxybenzoate, 4-hydroxybenzoate and phenylacetate.