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1 Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
2 National Research Laboratory of Molecular Ecosystematics, Institute of Probionic, Probionic Corporation, Bio-venture Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
3 Department of Food and Life Science, Sungkyunkwan University, Chunchun-dong 300, Jangan-gu, Suwon, Korea
Correspondence
Yong-Ha Park
yhpark{at}kribb.re.kr
| ABSTRACT |
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Published online ahead of print on 8 August 2003 as DOI 10.1099/ijs.0.02585-0.
The GenBank accession number for the 16S rDNA sequence of strain GW-9T is AF529063.
| MAIN TEXT |
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In this study, an LL-2,6-diaminopimelic acid (DAP)-containing actinomycete, GW-9T, isolated from groundwater in Korea, is described. This isolate was considered to be a Nocardioides-like strain from 16S rDNA sequence comparisons, as well as the presence of LL-DAP. Accordingly, the aim of the present study was to determine the exact taxonomic status of strain GW-9T using a combination of phenotypic properties, detailed phylogenetic analysis based on 16S rDNA sequence and genomic relatedness. On the basis of the data presented below, it is proposed that strain GW-9T represents a novel species in the genus Nocardioides, for which the name Nocardioides aquiterrae sp. nov. is proposed.
Strain GW-9T was isolated by the usual dilution plating technique on nutrient agar (NA; Difco) at 30 °C. Type strains of Nocardioides species used as reference organisms for DNADNA hybridization were obtained from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) and KCTC (Korean Collection for Type Cultures). Strain GW-9T was cultivated on NA and in nutrient broth (NB; Difco) at 30 °C to investigate its morphological and physiological characteristics. Cell mass of strain GW-9T for analyses of the cell wall and menaquinones was obtained from NB culture at 30 °C. Cell mass of strain GW-9T and reference strains for DNA extraction was produced in NB. For fatty acid methyl ester analysis, cell mass of strain GW-9T was obtained from agar plates after 6 days cultivation at 30 °C on NA. Cell morphology was examined by light microscopy (Nikon E600) and TEM. The presence or absence of flagella was determined using TEM with cells from exponentially growing cultures. For TEM observation, cells were negatively stained with 1 % (w/v) phosphotungstic acid and, after air drying, the grids were examined with a model CM-20 TEM (Philips). Oxidase activity was determined by oxidation of 1 % (w/v) p-aminodimethylaniline oxalate. Catalase activity was determined by bubble production in a 3 % (v/v) hydrogen peroxide solution. Hydrolysis of aesculin and nitrate reduction were determined as described previously (Lanyi, 1987
). Hydrolysis of casein, gelatin, hypoxanthine, starch, Tween 80, tyrosine and xanthine and urease activity were determined as described by Cowan & Steel (1965)
. Utilization of various substrates as sole carbon and energy sources was determined as described by Shirling & Gottlieb (1966)
. Growth under anaerobic conditions was determined after incubation in an anaerobic chamber with NA that had been prepared anaerobically. Growth at various temperatures (455 °C) was determined on NA.
The isomer type of the diamino acid in the cell-wall peptidoglycan was analysed using TLC according to the method described by Komagata & Suzuki (1987)
. Menaquinones were analysed as described previously (Komagata & Suzuki, 1987
) using reversed-phase HPLC. For quantitative analysis of the cellular fatty acid content, a loopful of cell mass was harvested and fatty acid methyl esters were prepared and identified according to the instructions of the Microbial Identification System (MIDI). Chromosomal DNA was isolated and purified according to Yoon et al. (1996)
, with the exception that ribonuclease T1 was used together with ribonuclease A. The G+C content was determined by the method of Tamaoka & Komagata (1984)
. DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC.
16S rDNA was amplified by PCR using two universal primers as described previously (Yoon et al., 1998
). The PCR product was purified with a QIAquick PCR purification kit (Qiagen). Sequencing of the purified 16S rDNA was performed using an ABI PRISM BigDye Terminator cycle sequencing ready reaction kit (Applied Biosystems) as recommended by the manufacturer. Purified sequencing reaction mixtures were electrophoresed automatically using an Applied Biosystems model 377 automatic DNA sequencer. Alignment of sequences was carried out with CLUSTAL W software (Thompson et al., 1994
). Gaps at the 5' and 3' ends of the alignment were omitted from further analysis. Phylogenetic trees were inferred using three tree-making algorithms, the neighbour-joining (Saitou & Nei, 1987
), maximum-likelihood (Felsenstein, 1981
) and maximum-parsimony (Kluge & Farris, 1969
) methods in the PHYLIP package (Felsenstein, 1993
). Evolutionary distance matrices for the neighbour-joining method were calculated using the algorithm of Jukes & Cantor (1969)
with the program DNADIST. The stability of relationships was assessed by bootstrap analysis based on 1000 resamplings of the neighbour-joining dataset using the programs SEQBOOT, DNADIST, NEIGHBOR and CONSENSE of the PHYLIP package. DNADNA hybridization was performed fluorometrically by the method of Ezaki et al. (1989)
using photobiotin-labelled DNA probes and microdilution wells. Hybridization was performed with five replications for each sample. Of the values obtained, the highest and lowest values in each sample were excluded and the means of the remaining three values were taken as DNA relatedness values.
Physiological and biochemical characteristics of strain GW-9T are given in the species description below and are compared with those of N. pyridinolyticus in Table 1
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Description of Nocardioides aquiterrae sp. nov.
Nocardioides aquiterrae (a.qui.ter'rae. L. n. aqua water; L. gen. fem. n. terrae of earth or ground; N.L. gen. fem. n. aquiterrae from/of groundwater).
Cells are aerobic, non-spore-forming, non-acid-fast rods, 0·81·0x1·72·0 µm in the exponential phase of growth after approximately 7 days incubation at 30 °C on NA. Motile by means of a single lateral flagellum. Cells show rod-to-coccus morphogenesis from the early exponential phase to the stationary phase. Gram-positive (Gram-variable in old cultures). Colonies are smooth, circular, convex, cream-coloured and 0·51·0 mm in diameter after 7 days incubation on NA. Neither substrate nor primary mycelium is formed. Optimal temperature for growth is 30 °C; grows at 15 and 42 °C, but not at 10 °C or temperatures above 43 °C. Optimal pH for growth is 6·07·0; no growth at pH 5·0. Oxidase-positive. Urease-negative. Casein and Tween 80 are hydrolysed. Hypoxanthine, starch, tyrosine and xanthine are not hydrolysed. The cell-wall peptidoglycan contains LL-DAP as the diagnostic diamino acid. The predominant menaquinone is MK-8(H4). The cellular fatty acids consist of straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid is iso-C16 : 0. The DNA G+C content of the type strain is 73 mol% (determined by HPLC). Other characteristics are given in Table 1
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The type strain, strain GW-9T (=KCCM 41647T=JCM 11813T), was isolated from groundwater in Korea.
| ACKNOWLEDGEMENTS |
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| REFERENCES |
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|
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Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224229.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368376.[CrossRef][Medline]
Felsenstein, J. (1993). PHYLIP (phylogenetic inference package), version 3.5. Distributed by the author. Department of Genetics, University of Washington, Seattle, USA.
Iizuka, H. & Komagata, K. (1964). Microbiological studies on petroleum and natural gas. I. Determination of hydrocarbon-utilizing bacteria. J Gen Appl Microbiol 10, 207221.[CrossRef]
Jensen, H. L. (1934). Studies on saprophytic mycobacteria and corynebacteria. Proc Linn Soc N S W 59, 1961.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by H. N. Munro. New York: Academic Press.
Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 132.
Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161206.
Lanyi, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 167.
Lawson, P. A., Collins, M. D., Schumann, P., Tindall, B. J., Hirsch, P. & Labrenz, M. (2000). New LL-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella lacustris sp. nov. Syst Appl Microbiol 23, 219229.[Medline]
Lechevalier, M. P. & Lechevalier, H. A. (1970). A critical evaluation of the genera of aerobic actinomycetes. In The Actinomycetales, pp. 393405. Edited by H. Prauser. Jena: Gustav Fischer.
Miller, E. S., Woese, C. R. & Brenner, S. (1991). Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov. Int J Syst Bacteriol 41, 363368.
Park, Y.-H., Yoon, J.-H., Shin, Y. K., Suzuki, K., Kudo, T., Seino, A., Kim, H.-J., Lee, J.-S. & Lee, S. T. (1999). Classification of Nocardioides fulvus IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49, 743752.
Prauser, H. (1976). Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 5865.
Prauser, H. (1989). Genus Nocardioides Prauser 1976
. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 23712375. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406425.[Abstract]
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313340.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125128.
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 46734680.
Urzì, C., Salamone, P., Schumann, P. & Stackebrandt, E. (2000). Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50, 529536.[Abstract]
Wang, Y. M., Zhang, Z. S., Xu, X. L., Ruan, J. S. & Wang, Y. (2001). Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51, 467473.[Abstract]
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463464.
Yoon, J.-H., Kim, H., Kim, S.-B., Kim, H.-J., Kim, W. Y., Lee, S. T., Goodfellow, M. & Park, Y.-H. (1996). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46, 502505.
Yoon, J.-H., Rhee, S.-K., Lee, J.-S., Park, Y.-H. & Lee, S. T. (1997). Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int J Syst Bacteriol 47, 933938.
Yoon, J.-H., Lee, S. T. & Park, Y.-H. (1998). Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48, 187194.
Yoon, J.-H., Cho, Y.-G., Lee, S. T., Suzuki, K., Nakase, T. & Park, Y.-H. (1999). Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 49, 675680.
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