| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
Correspondence
Jung-Hoon Yoon
jhyoon{at}kribb.re.kr
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
9c and C17 : 16c. The DNA G+C contents were 72·4–73·6 mol%. The four strains exhibited 16S rRNA gene sequence similarity levels of 94·0–96·3 % to the type strains of Nocardioides species with validly published names. DNA–DNA relatedness levels between the four strains were 85–91 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genotypic relatedness, strains KSL-1T, KSL-9, KSL-10 and KSL-12 were classified in the genus Nocardioides as members of a novel species, Nocardioides alkalitolerans sp. nov. The type strain is strain KSL-1T (=KCTC 19037T=DSM 16699T).
The GenBank/EMBL/DDBJ numbers for the 16S rRNA gene sequences of strains KSL-1T, KSL-9, KSL-10 and KSL-12 are AY633969–AY633972, respectively.
A full table of fatty acid compositions is available as supplementary data in IJSEM Online.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
with a single species, Nocardioides albus, and at present it comprises 11 species with validly published names. Nocardioides species have been isolated from a variety of habitats, including soils (Prauser, 1976, 1984; O'Donnell et al., 1982; Suzuki & Komagata, 1983), herbage (Collins et al., 1994), an oil shale column (Yoon et al., 1997), industrial wastewater (Yoon et al., 1999), water from hyper-saline lakes (Lawson et al., 2000), groundwater (Yoon et al., 2004) and tidal flats (Yi & Chun, 2004a, b). N. albus, Nocardioides luteus, Nocardioides simplex and Nocardioides jensenii were isolated from a variety of soils from different parts of the world (Prauser, 1976, 1984; O'Donnell et al., 1982; Suzuki & Komagata, 1983). Recently, in the course of screening micro-organisms from an alkaline serpentinite soil (approximate pH 9·0–10·0) in Korea, many bacterial strains were isolated and characterized taxonomically. Of these isolates, four Nocardioides-like strains, KSL-1T, KSL-9, KSL-10 and KSL-12, are described in this paper. Accordingly, the aim of the present work was to determine the exact taxonomic positions of the four strains by a polyphasic taxonomic characterization.
Strains KSL-1T, KSL-9, KSL-10 and KSL-12 were isolated by the standard dilution plating technique at 30 °C on tenfold-diluted nutrient agar (NA; Difco) with pH adjusted to 10·0. To investigate their morphological, physiological and biochemical characteristics, the four strains were routinely cultivated at 30 °C on twofold-diluted NA with pH adjusted to 9·0. Cell morphology was examined by light microscopy (Nikon E600) and transmission electron microscopy (TEM). Presence of flagella was examined by TEM using cells from exponentially growing cultures. The Gram reaction was determined by using the bioMérieux Gram stain kit according to the manufacturer's instructions. The pH range for growth was determined in twofold-diluted nutrient broth (NB; Difco) which had been adjusted to various pH values (initial pH 4·0–12·0 at intervals of 0·5 pH units). Prior to sterilization the pH of twofold-diluted NB was adjusted to various levels by the addition of Na2CO3 (below pH 10·5) or KOH (above pH 10·5). Growth at various temperatures (4–40 °C) was measured on twofold-diluted NA (pH 9·0). Growth at various NaCl concentrations was investigated in trypticase soy broth (Difco) lacking NaCl and in trypticase soy broth. Growth under anaerobic conditions was determined after incubation in an anaerobic chamber with twofold-diluted NA (pH 9·0) that had been prepared anaerobically using nitrogen. Catalase and oxidase activities and hydrolysis of casein, gelatin, hypoxanthine, starch, Tweens 20, 40, 60 and 80, tyrosine, urea and xanthine were determined as described by Cowan & Steel (1965). Hydrolysis of aesculin and nitrate reduction were studied as described previously (Lanyi, 1987). Enzyme activity was determined by using the API ZYM system (bioMérieux). Utilization of various substrates as sole carbon and energy sources was determined as described by Shirling & Gottlieb (1966).
Cell biomass for cell-wall and isoprenoid quinone analyses and for DNA extraction was obtained from cultivation in twofold-diluted NB (pH 9·0) at 30 °C. Isoprenoid quinones were analysed as described by Komagata & Suzuki (1987) using reversed-phase HPLC. Chromosomal DNA isolation and purification were performed according to the method described by Yoon et al. (1996), with the exception that RNase T1 was used together with RNase A to minimize contamination with RNA. For fatty acid methyl ester (FAME) analysis, cell mass of the four strains was harvested from agar plates after incubation for 7 days on twofold-diluted NA (pH 9·0) at 30 °C. FAMEs were extracted and prepared according to the standard protocol of the MIDI/Hewlett Packard Microbial Identification System (Sasser, 1990). The DNA G+C content was determined by the method of Tamaoka & Komagata (1984) with the modification that DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC. The 16S rRNA gene was amplified by PCR using two universal primers as described previously (Yoon et al., 1998). Sequencing of the amplified 16S rRNA gene and phylogenetic analysis were performed as described by Yoon et al. (2004). DNA–DNA 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 replicates for each sample. The highest and lowest values obtained in each sample were excluded, and DNA relatedness values quoted are the means of the remaining three values.
Strains KSL-1T, KSL-9, KSL-10 and KSL-12 grew optimally at 25–30 °C and pH 7·0–9·0; they grew relatively well at pH 11·0, and weakly at pH 12·0. The four strains were similar in most phenotypic characteristics. Gelatin was hydrolysed by strains KSL-1T, KSL-10 and KSL-12, but not by strain KSL-9. Strains KSL-9 and KSL-12 grew at pH 5·0, but the other two strains did not. Other phenotypic characteristics are shown in Table 1 or given in the species description.
|
. The four strains contained a tetrahydrogenated menaquinone with eight isoprene units [MK-8(H4)] as the predominant isoprenoid quinone. The four strains had similar fatty acid profiles that contained large amounts of branched, unsaturated, straight-chain and 10-methyl fatty acids; the major fatty acids were iso-C16 : 0, 10-methyl-C18 : 0, C18 : 19c and C17 : 16c (see supplementary table in IJSEM Online). These fatty acid profiles were generally similar to those of Nocardioides species described previously (Yoon et al., 1997, 2004; Lawson et al., 2000; Yi & Chun, 2004a). However, there were some differences in the contents of some fatty acids, particularly iso-C16 : 0 and 10-methyl-C18 : 0, between the four strains and Nocardioides species, which may be caused by different cultivation conditions (Yoon et al., 1997, 2004; Lawson et al., 2000; Yi & Chun, 2004a, b). The DNA G+C contents of strains KSL-1T, KSL-9, KSL-10 and KSL-12 were 72·4, 73·6, 73·2 and 73·2 mol%, respectively.
The 16S rRNA gene sequences of strains KSL-1T, KSL-9, KSL-10 and KSL-12 determined in this study comprised 1473 nucleotides, respectively, representing approximately 96 % of the Escherichia coli 16S rRNA gene sequence. The 16S rRNA gene sequences of the four strains were identical. As shown in the phylogenetic tree based on the neighbour-joining algorithm, the four strains formed a distinct evolutionary lineage within the radiation of the cluster comprising Nocardioides species (Fig. 1). Similar tree topology was found in the tree generated with the maximum-likelihood algorithm (data not shown). Levels of 16S rRNA gene sequence similarity between the four strains and the type strains of all Nocardioides species with validly published names ranged from 94·0 % (with Nocardioides plantarum) to 96·3 % (with N. jensenii). Sequence similarities to all other taxa included in the phylogenetic analysis were <94·4 % (with Marmoricola aurantiacus DSM 12652T) (Fig. 1). DNA–DNA relatedness levels between strains KSL-1T, KSL-9, KSL-10 and KSL-12 were 85–91 %, indicating that the four strains are members of the same genomic species (Wayne et al., 1987).
|
; Tamura & Yokota, 1994; Park et al., 1999; Urzì et al., 2000; Wang et al., 2001). The four strains are similar phylogenetically and genetically as well as phenotypically. The levels of 16S rRNA gene sequence similarity are low enough to exclude the possibility of assigning the four strains to a previously described Nocardioides species (Stackebrandt & Goebel, 1994). The four strains are distinguishable from the other Nocardioides species by some phenotypic properties as shown in Table 1
. Therefore, on the basis of phenotypic and chemotaxonomic data and phylogenetic distinctiveness, strains KSL-1T, KSL-9, KSL-10 and KSL-12 should be placed in the genus Nocardioides as members of a novel species, for which the name Nocardioides alkalitolerans sp. nov. is proposed.
Description of Nocardioides alkalitolerans sp. nov.
Nocardioides alkalitolerans (al.ka.li.to'le.rans. Arabic article al the; Arabic n. qaliy ashes of saltwort; L. part. adj. tolerans tolerating; N.L. masc. part. adj. alkalitolerans referring to the ability to tolerate high pH).
Cells are aerobic, non-spore-forming rods (0·8–1·0 µmx1·5–2·0 µm) in the exponential phase of growth. Cells show rod-to-coccus morphogenesis from the early exponential phase to the stationary phase. Gram-positive but Gram-variable in old cultures. Colonies are circular, smooth, glistening, convex, milky-white in colour and 0·7–1·0 mm in diameter after 7 days incubation on twofold-diluted NA (pH 9·0). Neither substrate nor aerial mycelia are formed. Optimal temperature for growth is 25–30 °C; grows at 4 and 34 °C, but not above 35 °C. Optimal pH for growth is 7·0–9·0; grows at pH 5·5 and 12·0, but growth at pH 5·0 is variable (no growth for type strain). Grows in the presence of 0–5 % (w/v) NaCl. Oxidase-positive. Tweens 20, 40 and 60 are hydrolysed. Adonitol and D-sorbitol are not utilized. Cell-wall peptidoglycan contains LL-diaminopimelic acid as the diagnostic diamino acid. Predominant menaquinone is MK-8(H4). Major fatty acids are iso-C16 : 0, 10-methyl-C18 : 0, C18 : 19c and C17 : 16c. DNA G+C content is 72·4–73·6 mol% (72·4 mol% for type strain) (determined by HPLC). Other phenotypic characteristics are given in Table 1.
The type strain, KSL-1T (=KCTC 19037T=DSM 16699T), was isolated from an alkaline serpentinite soil in Korea. Reference strains are KSL-9, KSL-10 and KSL-12.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Collins, M. D., Cockcroft, S. & Wallbanks, S. (1994). Phylogenetic analysis of a new LL-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov. Int J Syst Bacteriol 44, 523–526.
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, 224–229.
Komagata, K. & Suzuki, K. (1987). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–203.
Lanyi, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67.
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, 219–229.[Medline]
Lechevalier, M. P. & Lechevalier, H. A. (1970). A critical evaluation of the genera of aerobic actinomycetes. In The Actinomycetales, pp. 393–405. Edited by H. Prauser. Jena: Gustav Fischer Verlag.
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, 363–368.
O'Donnell, A. G., Goodfellow, M. & Minnikin, D. E. (1982). Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 133, 323–329.[CrossRef][Medline]
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, 743–752.
Prauser, H. (1976). Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.
Prauser, H. (1984). Nocardioides luteus spec. nov. Z Allg Microbiol 24, 647–648.
Prauser, H. (1989). Genus Nocardioides Prauser 1976. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2371–2375. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Sasser, M. (1990). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Newark, DE: MIDI.
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.
Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.
Suzuki, K. & Komagata, K. (1983). Pimelobacter gen. nov., a new genus of coryneform bacteria with LL-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29, 59–71.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.
Tamura, T. & Yokota, A. (1994). Transfer of Nocardioides fastidiosa Collins and Stackebrandt 1989 to the genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov. Int J Syst Bacteriol 44, 608–611.
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, 529–536.[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, 467–473.[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, 463–464.
Yi, H. & Chun, J. (2004a). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 1295–1299.
Yi, H. & Chun, J. (2004b). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 2151–2154.
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, 502–505.
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, 933–938.
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 rRNA gene sequences. Int J Syst Bacteriol 48, 187–194.
Yoon, J.-H., Cho, Y.-G., Lee, S. T., Suzuki, K.-I., Nakase, T. & Park, Y.-H. (1999). Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 49, 675–680.
Yoon, J.-H., Kim, I.-G., Kang, K. H., Oh, T.-K. & Park, Y.-H. (2004). Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int J Syst Evol Microbiol 54, 71–75.
This article has been cited by other articles:
|
|
 |
|
  H. M. Kim, D. H. Choi, C. Y. Hwang, and B. C. Cho Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2056 - 2064. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, M.-H. Lee, and T.-K. Oh Nocardioides hankookensis sp. nov., isolated from soil Int J Syst Evol Microbiol, February 1, 2008; 58(2): 434 - 437. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. Toth, Z. Keki, Z. G. Homonnay, A. K. Borsodi, K. Marialigeti, and P. Schumann Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera) Int J Syst Evol Microbiol, January 1, 2008; 58(1): 78 - 83. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, S.-Y. Lee, and T.-K. Oh Nocardioides terrigena sp. nov., isolated from soil Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2472 - 2475. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, C.-H. Lee, and T.-K. Oh Nocardioides insulae sp. nov., isolated from soil Int J Syst Evol Microbiol, January 1, 2007; 57(1): 136 - 140. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, J.-K. Lee, S.-Y. Jung, J.-A. Kim, H.-K. Kim, and T.-K. Oh Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1783 - 1787. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, C.-H. Lee, and T.-K. Oh Nocardioides lentus sp. nov., isolated from an alkaline soil Int J Syst Evol Microbiol, January 1, 2006; 56(1): 271 - 275. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, C.-H. Lee, and T.-K. Oh Nocardioides dubius sp. nov., isolated from an alkaline soil Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2209 - 2212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, I.-G. Kim, M.-H. Lee, and T.-K. Oh Nocardioides kribbensis sp. nov., isolated from an alkaline soil Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1611 - 1614. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
-glucuronidase, N-acetyl-
-fucosidase.