IJSEM Track the topics, authors and articles important to you
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Supplementary Table
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.
Agricola
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.
Int J Syst Evol Microbiol 56 (2006), 271-275; DOI  10.1099/ijs.0.63993-0
© 2006 International Union of Microbiological Societies

Nocardioides lentus sp. nov., isolated from an alkaline soil

Jung-Hoon Yoon, Choong-Hwan Lee and Tae-Kwang Oh

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 TEXT
 REFERENCES
 
Gram-positive, rod- or coccoid-shaped bacterial strains KSL-17T, KSL-18 and KSL-19 were isolated from an alkaline soil in Korea. They were subjected to analysis using polyphasic taxonomy. Strains KSL-17T, KSL-18 and KSL-19 grew optimally at pH 8·0 and 28 °C and in the presence of 0·5 % (w/v) NaCl. They were characterized chemotaxonomically as having LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. Their DNA G+C contents were in the range 74·6–74·8 mol%. Strains KSL-17T, KSL-18 and KSL-19 were identical in terms of their 16S rRNA gene sequences and exhibited a mean level of DNA–DNA relatedness of 85–90 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-17T, KSL-18 and KSL-19 formed a distinct phylogenetic lineage within the genus Nocardioides. The levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species were in the range 92·6–95·2 %. On the basis of phenotypic, genetic and phylogenetic data, strains KSL-17T (=KCTC 19039T=DSM 16315T), KSL-18 and KSL-19 should be classified as members of a novel species of the genus Nocardioides, for which the name Nocardioides lentus sp. nov. is proposed.

Published online ahead of print on 23 September 2005 as DOI 10.1099/ijs.0.63993-0.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains KSL-17T, KSL-18 and KSL-19 are DQ121389, DQ121390 and DQ121391, respectively.

A table giving the cellular fatty acid content of strains KSL-17T, KSL-18 and KSL-19 is available as supplementary material in IJSEM Online.


   MAIN TEXT
TOP
 ABSTRACT
 MAIN TEXT
REFERENCES
 
The genus Nocardioides was proposed by Prauser (1976)Go, and, at the time of writing, the genus comprises 15 recognized species, including the recently described species Nocardioides alkalitolerans (Yoon et al., 2005aGo), Nocardioides kribbensis (Yoon et al., 2005bGo), Nocardioides oleivorans (Schippers et al., 2005Go) and Nocardioides dubius (Yoon et al., 2005cGo). In this study, we report the taxonomic characterization of three Nocardioides-like strains, KSL-17T, KSL-18 and KSL-19, which were isolated from an alkaline soil (approximately pH 9·0–10·0) collected in Kwangchun, Korea.

Strains KSL-17T, KSL-18 and KSL-19 were isolated by using the standard dilution plating technique at 30 °C on 10x diluted nutrient agar (Difco) with the pH adjusted to 9·0 using Na2CO3. To investigate their morphological, physiological and biochemical characteristics, strains KSL-17T, KSL-18 and KSL-19 were routinely cultivated at 28 °C on 2x diluted nutrient agar with the pH adjusted to 8·0. Morphological, physiological, cultural and biochemical properties were examined as described by Yoon et al. (2005a)Go. Growth in the absence of NaCl was investigated in trypticase soy broth prepared according to the formula of the Difco medium except that no NaCl was used. Growth at various NaCl concentrations (0·5 %, w/v, and 1·0–7·0 %, w/v, at intervals of 1·0 %) was investigated in trypticase soy broth (Difco). The pH range for growth was determined in 2x diluted nutrient broth (Difco) that was adjusted to various pH values (initial pH 4·5–10·5 at intervals of 0·5 pH units). The pH was adjusted, prior to sterilization, to various levels by the addition of HCl or Na2CO3. Cell biomass for DNA extraction and for the analyses of cell-wall and isoprenoid quinones was obtained by cultivation at 28 °C in 2x diluted nutrient broth (pH 8·0). Chemotaxonomic and molecular systematic studies were performed as described by Yoon et al. (2005a)Go. 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)Go. For fatty acid methyl ester analysis, cell mass from the three strains was harvested from 2x diluted nutrient agar (pH 8·0) after incubation for 10 days at 28 °C.

The morphological, cultural, physiological and biochemical characteristics of strains KSL-17T, KSL-18 and KSL-19 are given in the species description (see later) or are shown in Table 1Go. The 16S rRNA gene sequences of strains KSL-17T, KSL-18 and KSL-19 were identical and each comprised 1491 nt, representing approximately 96 % of the Escherichia coli 16S rRNA gene sequence. Comparative 16S rRNA gene sequence analyses showed that the three strains were phylogenetically affiliated to the genus Nocardioides (Fig. 1Go). In the phylogenetic trees based on the neighbour-joining, maximum-parsimony and maximum-likelihood algorithms, strains KSL-17T, KSL-18 and KSL-19 formed a distinct phylogenetic lineage within the radiation of the cluster comprising Nocardioides species (Fig. 1Go). Similarity values between the 16S rRNA gene sequences of the three strains and those of recognized Nocardioides species ranged from 92·6 % (Nocardioides albus KCTC 9186T) to 95·2 % (N. kribbensis KSL-2T). Values for sequence similarity to other species included in the phylogenetic analysis were below 93·3 %.


View this table:
[in this window]
[in a new window]
  		Table 1. Differential phenotypic characteristics of Nocardioides lentus sp. nov. and related Nocardioides species

Species: 1, Nocardioides lentus sp. nov.; 2, Nocardioides albus; 3, Nocardioides luteus; 4, Nocardioides simplex; 5, Nocardioides plantarum; 6, Nocardioides pyridinolyticus; 7, Nocardioides nitrophenolicus; 8, Nocardioides aquaticus; 9, Nocardioides aquiterrae; 10, Nocardioides ganghwensis; 11, Nocardioides aestuarii; 12, Nocardioides alkalitolerans; 13, Nocardioides kribbensis; 14, Nocardioides oleivorans. Data are from Collins et al. (1989Go, 1994)Go, Lawson et al. (2000)Go, Prauser (1976Go, 1984Go, 1989)Go, Suzuki & Komagata (1983)Go, Yoon et al. (1997Go, 1999Go, 2004Go, 2005aGo, b)Go, Yi & Chun (2004aGo, b)Go and Schippers et al. (2005)Go. +, Positive reaction; –, negative reaction; ND, not determined; W, weakly positive reaction; V, variable reaction. Data for the type strain are shown in parentheses. All species are positive for Gram stain, catalase and esterase lipase (C8) (not determined for N. oleivorans). All species are negative for {beta}-glucuronidase, N-acetyl-{beta}-glucosaminidase and {alpha}-fucosidase (not determined for N. oleivorans).

 


View larger version (55K):
[in this window]
[in a new window]
  		Fig. 1. Neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the positions of strain KSL-17T and some other related taxa. Bootstrap values (expressed as percentages of 1000 replications) greater than 50 % are shown atbranch points. Bar, 0·01 substitutions per nucleotide position.

 
Strains KSL-17T, KSL-18 and KSL-19 contained LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan, the predominant menaquinone was MK-8(H4) and the fatty acid profiles comprised mainly iso-C16 : 0 (60·9–80·9 %), with smaller amounts of C17 : 1{omega}8c (0·5–6·6 %), 10-methyl C17 : 0 (1·5–5·8 %), iso-C14 : 0 (2·3–6·5 %) and so on (see the supplementary table in IJSEM Online). The chemotaxonomic characteristics were consistent with the affiliation of the strains to the genus Nocardioides (Yoon et al., 1997Go, 2004Go, 2005aGo, bGo; Lawson et al., 2000Go; Urzì et al., 2000Go; Yi & Chun, 2004aGo, bGo; Schippers et al., 2005Go). The DNA G+C contents of strains KSL-17T, KSL-18 and KSL-19 were 74·8, 74·7 and 74·6 mol%, respectively.

Phylogenetic analyses based on 16S rRNA gene sequences and chemotaxonomic data revealed that the three strains can be assigned to the genus Nocardioides (Miller et al., 1991Go; Tamura & Yokota, 1994Go; Park et al., 1999Go; Urzì et al., 2000Go; Wang et al., 2001Go). The mean DNA–DNA relatedness levels between strains KSL-17T, KSL-18 and KSL-19 were 85–90 %, indicating that the three strains represent the same genomic species (Wayne et al., 1987Go). They also shared almost identical phenotypic properties. The levels of 16S rRNA gene sequence similarity are low enough to exclude the possibility of assigning the three strains to a previously described Nocardioides species (Stackebrandt & Goebel, 1994Go). The three strains were distinguishable from the other Nocardioides species on the basis of some phenotypic properties, as shown in Table 1Go. Therefore, on the basis of the data presented, strains KSL-17T, KSL-18 and KSL-19 should be classified in the genus Nocardioides as members of a novel species, for which the name Nocardioides lentus sp. nov. is proposed.

Description of Nocardioides lentus sp. nov.
Nocardioides lentus (len'tus. L. masc. adj. lentus slow, delayed, referring to slow growth).

Cells are aerobic, non-endospore-forming rods (0·4–0·7x1·0–4·5 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, convex, smooth, glistening, yellow in colour and 0·5–1·0 mm in diameter after 10 days incubation on 2x diluted nutrient agar at 28 °C. Neither substrate mycelium nor aerial mycelium is formed. Growth occurs at 4 and 34 °C, but not at 35 °C. The optimal pH for growth is 8·0; growth occurs at pH 6·5 and 9·5, but not at pH 6·0 or 10·0. Growth occurs in the presence of 0–5 % (w/v) NaCl, with an optimum at 0·5 % (w/v) NaCl. Weakly positive for oxidase activity. Tweens 20, 40 and 60 are hydrolysed. D-Sorbitol is utilized, but adonitol is not. The cell-wall peptidoglycan contains LL-2,6-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone is MK-8(H4). The major fatty acid is iso-C16 : 0; 10-methyl fatty acids are present. The DNA G+C content is 74·6–74·8 mol% (determined by HPLC). Other phenotypic characteristics are given in Table 1Go.

The type strain, KSL-17T (=KCTC 19039T=DSM 16315T), was isolated from an alkaline soil in Kwangchun, Korea. Reference strains are KSL-18 and KSL-19.


   ACKNOWLEDGEMENTS
 
This work was supported by the 21C Frontier program of Microbial Genomics and Applications (grant MG05-0401-2-0) from the Ministry of Science and Technology (MOST) of the Republic of Korea.


   REFERENCES
TOP
 ABSTRACT
 MAIN TEXT
 REFERENCES
 
Collins, M. D., Dorsch, M. & Stackebrandt, E. (1989). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39, 1–6.

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.[Abstract/Free Full Text]

Komagata, K. & Suzuki, K. (1987). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–203.

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]

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.[Abstract/Free Full Text]

Park, Y.-H., Yoon, J.-H., Shin, Y. K., Suzuki, K.-I., 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.[Abstract/Free Full Text]

Prauser, H. (1976). Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.[Abstract/Free Full Text]

Prauser, H. (1984). Nocardioides luteus spec. nov. Z Allg Microbiol 24, 647–648.

Prauser, H. (1989). Genus Nocardioides Prauser 1976Go. 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.

Schippers, A., Schumann, P. & Spröer, C. (2005). Nocardioides oleivorans sp. nov., a novel crude oil-degrading bacterium. Int J Syst Evol Microbiol 55, 1501–1504.[Abstract/Free Full Text]

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.[Abstract/Free Full Text]

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.

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.[Abstract/Free Full Text]

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.[Free Full Text]

Yi, H. & Chun, J. (2004a). Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 1295–1299.[Abstract/Free Full Text]

Yi, H. & Chun, J. (2004b). Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 2151–2154.[Abstract/Free Full Text]

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.[Abstract/Free Full Text]

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.[Abstract/Free Full Text]

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.[Abstract/Free Full Text]

Yoon, J.-H., Kim, I.-G., Lee, M.-H., Lee, C.-H. & Oh, T.-K. (2005a). Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55, 809–814.[Abstract/Free Full Text]

Yoon, J.-H., Kim, I.-G., Lee, M.-H. & Oh, T.-K. (2005b). Nocardioides kribbensis sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 55, 1611–1614.[Abstract/Free Full Text]

Yoon, J.-H., Lee, C.-H. & Oh, T.-K. (2005c). Nocardioides dubius sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 55, 2209–2212.[Abstract/Free Full Text]




This article has been cited by other articles:


Home page
 Int. J. Syst. Evol. Microbiol.Home page
J.-Y. Zhang, X.-Y. Liu, and S.-J. Liu
Nocardioides terrae sp. nov., isolated from forest soil
Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2444 - 2448.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
S. C. Park, K. S. Baik, M. S. Kim, J. Chun, and C. N. Seong
Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment
Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2619 - 2623.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
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]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
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]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
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]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
D. W. Lee, C.-G. Hyun, and S. D. Lee
Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand
Int J Syst Evol Microbiol, December 1, 2007; 57(12): 2960 - 2963.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
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]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
D.-S. An, W.-T. Im, S.-T. Lee, and M.-H. Yoon
Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field
Int J Syst Evol Microbiol, September 1, 2007; 57(9): 2143 - 2146.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
D. H. Choi, H. M. Kim, J.-H. Noh, and B. C. Cho
Nocardioides marinus sp. nov.
Int J Syst Evol Microbiol, April 1, 2007; 57(4): 775 - 779.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
S. D. Lee
Nocardioides furvisabuli sp. nov., isolated from black sand
Int J Syst Evol Microbiol, January 1, 2007; 57(1): 35 - 39.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
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]

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Supplementary Table
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.
Agricola
Right arrow Articles by Yoon, J.-H.
Right arrow Articles by Oh, T.-K.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
INT J SYST EVOL MICROBIOL MICROBIOLOGY J GEN VIROL
J MED MICROBIOL ALL SGM JOURNALS