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 material
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 Li, W.-J.
Right arrow Articles by Jiang, C.-L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, W.-J.
Right arrow Articles by Jiang, C.-L.
Agricola
Right arrow Articles by Li, W.-J.
Right arrow Articles by Jiang, C.-L.
Int J Syst Evol Microbiol 55 (2005), 463-466; DOI  10.1099/ijs.0.63281-0
© 2005 International Union of Microbiological Societies

Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia

Wen-Jun Li1, Hua-Hong Chen1,2, Chang-Jin Kim3, Yu-Qin Zhang1, Dong-Jin Park3, Jae-Chan Lee3, Li-Hua Xu1 and Cheng-Lin Jiang1

1 The Key Laboratory for Microbial Resources of Ministry of Education, PR China, Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
2 Department of Chemistry, Chuxiong Normal College, Chuxiong, Yunnan 675000, PR China
3 Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea

Correspondence
Cheng-Lin Jiang
lihxu{at}ynu.edu.cn or
liact{at}hotmail.com


   ABSTRACT
TOP
 ABSTRACT
MAIN TEXT
 REFERENCES
 
Two novel actinobacteria isolates, designated YIM 70009T and YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009T and YIM 70081T were cocci, although only the latter were motile. The G+C contents of their DNAs were 64·0 and 64·5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genus Nesterenkonia. DNA–DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009T and YIM 70081T differed from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genus Nesterenkonia: Nesterenkonia sandarakina sp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) and Nesterenkonia lutea sp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains YIM 70009T and YIM 70081T are AY588277 and AY588278, respectively.

Electron micrographs of strains YIM 70009T and YIM 70081T are available as supplementary material in IJSEM Online.


   MAIN TEXT
TOP
 ABSTRACT
 MAIN TEXT
REFERENCES
 
The genus Nesterenkonia was first proposed by Stackebrandt et al. (1995)Go in the reclassification of Micrococcus halobius Onishi and Kamekura 1972 as Nesterenkonia halobia (Stackebrandt et al., 1995Go). At present, the genus comprises four valid species: N. halobia (Stackebrandt et al., 1995Go), Nesterenkonia lacusekhoensis (Collins et al., 2002Go), and Nesterenkonia halotolerans and Nesterenkonia xinjiangensis (Li et al., 2004Go). In this report, two novel species of the genus Nesterenkonia that were discovered during our taxonomic study of extremophilic actinomycetes are described.

Strain YIM 70009T was isolated from a soil sample collected from the eastern desert of Egypt using modified medium A (supplemented with 15 % NaCl, w/v, pH 10·0–10·5), as described previously (Hozzein et al., 2004Go). Strain YIM 70081T was isolated from a saline soil sample from China using a modified glycerol/asparagine agar medium (ISP 5) (Shirling & Gottlieb, 1966Go) supplemented with 15 % (w/v) MgCl2.6H2O. Isolation plates were incubated at 28 °C for 2 weeks. The purified strains were cultivated and maintained on modified TSA medium containing 5–10 % NaCl (w/v), pH 8·0–9·0 for strain YIM 70009T or 5–10 % MgCl2.6H2O (w/v), pH 7·0–8·0 for strain YIM 70081T. Biomass for chemical and molecular systematic studies was grown in shaken flasks (about 150 r.p.m.) at 28 °C for 1 week using the same media as above without agar. Morphological properties were examined by light microscopy (Olympus microscope BH-2) and electron microscopy (JEOL JEM-1010).

The G+C contents of isolates YIM 70009T and YIM 70081T, determined using the thermal denaturation method of Marmur & Doty (1962)Go, were 64·0 and 64·5 mol%, respectively. 16S rRNA genes were analysed as described previously (Li et al., 2004Go). Phylogenetic analysis was performed using the software packages PHYLIP (Felsenstein, 1993Go) and MEGA (Molecular Evolutionary Genetics Analysis) version 2.1 (Kumar et al., 2001Go) after multiple alignment of data by CLUSTAL_X (Thompson et al., 1997Go). Distances were calculated using distance options according to the Kimura two-parameter model (Kimura, 1980Go, 1983Go) and clustering was performed using the neighbour-joining method (Saitou & Nei, 1987Go). Bootstrap analysis was used to evaluate tree topology of the neighbour-joining data by performing 1000 resamplings (Felsenstein, 1985Go). The neighbour-joining tree (Fig. 1Go) indicated that strains YIM 70009T and YIM 70081T were highly related to each other (99·4 % sequence similarity) and to N. halotolerans YIM 70084T (99·8 and 99·4 % sequence similarity, respectively), forming a distinct branch with this species. Sequence similarities between strains YIM 70009T and YIM 70081T and other members of the genus Nesterenkonia were no more than 97·2 %.



View larger version (21K):
[in this window]
[in a new window]
  		Fig. 1. Phylogenetic dendrogram, obtained by distance matrix analysis of 16S rRNA gene sequences, showing the position of strains YIM 70009T and YIM 70081T among phylogenetic neighbours. Numbers on branch nodes are bootstrap values (1000 resamplings). The sequence of Streptomyces megasporus DSM 41476T (GenBank/EMBL/DDBJ accession no. Z68100) was used as a root. Bar, 1 % sequence divergence.

 
Growth at various pH values and salt concentrations was tested as reported by Tang et al. (2003)Go, except that TSA medium was used as the basic medium. Strains were grown on TSA medium containing 0, 1, 3, 5, 10, 15, 20, 25 or 30 % (w/v) total salts (NaCl, KCl or MgSO4.6H2O) and at initial pH values of 4·0, 5·0, 6·0, 7·0, 8·0, 9·0, 10·0, 11·0,12·0 and 13·0 for 30 days at 28 °C. Cell morphology and motility, physiological and biochemical test results, and chemotaxonomic properties, determined using previously described methods (Li et al., 2004Go), are given in detail in Table 1Go and the species description.


View this table:
[in this window]
[in a new window]
  		Table 1. Phenotypic characteristics of strains YIM 70009T, YIM 70081T and N. halotolerans YIM 70084T

Strains: 1, YIM 70009T; 2, YIM 70081T; 3, N. halotolerans YIM 70084T. All three strains are Gram-positive, non-spore-forming coccoid cells. All are positive for catalase, milk coagulation, melanin production, growth in cellulose, and lysine decarboxylase, {beta}-glucosidase, {beta}-galactosidase and {alpha}-maltosidase activities. All are negative for oxidase, H2S and indole production, decomposition of Tween 20 and Tween 80, casein and starch, and ornithine decarboxylase, arginine dihydrolase and N-acetylglucosaminidase activities. Maltose, sucrose, mannose, mannitol, fructose, salicin and galactose are utilized by the three strains as sole carbon sources for growth; rhamnose, acetamide, inositol, adonitol and sorbitol are not utilized. +, Positive; –, negative; W, weak reaction.

 
DNA–DNA relatedness tests were performed between YIM 70009T, YIM 70081T and N. halotolerans YIM 70084T using the optical renaturation method (De Ley et al., 1970Go; Huß et al., 1983Go; Jahnke, 1992Go). DNA–DNA reassociation values of N. halotolerans YIM 70084T with strains YIM 70009T and YIM 70081T were 43·3 and 39·1 %, respectively, and DNA–DNA hybridization between the two isolates was 45·2 % (repeated twice). DNA–DNA relatedness data provide decisive evidence that isolates YIM 70009T and YIM 70081T, and the related type strain N. halotolerans YIM 70084T, are members of different genomic species (Wayne et al., 1987Go). Genomic distinctness was also revealed by differences in a number of phenotypic characteristics (Table 1Go). It is therefore proposed that strains YIM 70009T and YIM 70081T should be classified as representatives of two novel Nesterenkonia species, Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., respectively.

Emended description of the genus Nesterenkonia Stackebrandt et al. 1995Go emend. Collins et al. 2002Go
The description of the genus Nesterenkonia is as given previously (Stackebrandt et al., 1995Go; Collins et al., 2002Go), but with the following amendments. Moderately halophilic or halotolerant. Some species are alkaliphilic or alkalitolerant. Peptidoglycan is of the A4{alpha} type, L-lys–gly–L-Glu, L-lys–L-glu or lys–gly–D-Asp. The G+C content of the DNA is 64–72 mol%.

Description of Nesterenkonia sandarakina sp. nov.
Nesterenkonia sandarakina [san.da.ra'ki.na. N.L. fem. adj. sandarakina (from Gr. fem. adj. sandarakinê) of orange colour].

Cells are Gram-positive, non-spore-forming cocci (see electron micrograph available as supplementary material in IJSEM Online). Colony colour on most tested media is orange–yellow. Colonies are circular, opaque and approximately 0·5–1·0 mm in diameter after 24 h at 28 °C. Growth occurs at 1–15 % (w/v) NaCl (optimum at 5 %, w/v) and pH 5·0–12·0 (optimum at 8·0–9·0). Results of some physiological and biochemical characteristics, and metabolic and enzymic properties are indicated in Table 1Go. Peptidoglycan type is A4{alpha}, Lys–Gly–D-Asp. Cell wall sugars are ribose, xylose and arabinose. Main polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Predominant menaquinones are MK-7 and MK-8. Cellular fatty acids are C16 : 0 (33·11 %), aiC15 : 0 (27·63 %), aiC17 : 0 (20·68 %), C14 : 0 (0·81 %), C15 : 0 (0·81 %), C17 : 0 (1·46 %), C18 : 0 (2·18 %), iC16 : 0 (6·33 %), iC17 : :0 (0·47 %), A-aiC15 : 1 (4·81 %), G-iC16 : 1 (0·82 %) and A-aiC17 : 1 (0·88 %).

The type strain is YIM 70009T (=CCTCC AA 203007T=DSM 15664T=KCTC 19011T), isolated from a soil sample collected from the eastern desert of Egypt. The DNA G+C content of the type strain is 64·0 mol%.

Description of Nesterenkonia lutea sp. nov.
Nesterenkonia lutea (lu'te.a. L. fem. adj. lutea gold–yellow).

Cells are Gram-positive, non-spore-forming, motile cocci with flagella (see electron micrograph available as supplementary material in IJSEM Online). Colony colour on most tested media is light yellow to primrose yellow. Colonies are circular, opaque, somewhat convex and approximately 0·5–1·0 mm in diameter after 24 h at 28 °C. Growth occurs at 0–20 % (w/v) MgCl2.6H2O (optimum at 5–10 %, w/v) and pH 6·5–10·0 (optimum at 7·0–8·0). Results of some physiological and biochemical characteristics, and metabolic and enzymic properties are indicated in Table 1Go. Peptidoglycan type is A4{alpha}, Lys–Gly–D-Asp. Cell wall sugars are ribose, xylose, arabinose and glucose. Predominant menaquinones are MK-8 and MK-7. Main polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Cellular fatty acids are aiC15 : 0 (10·27 %), iC16 : 0 (31·40 %), aiC17 : 0 (15·27 %), A-aiC15 : 1 (15·12 %), G-iC16 : 1 (11·09 %), G-iC15 : 1 (0·84 %), C14 : 0 (0·34 %), 2-OH C14 : 0 (0·24 %), C16 : 0 (5·75 %), iC14 : 0 (0·99 %), iC15 : 0 (0·57 %), iC17 : 0 (0·96 %), C17 : 1{omega}6c (0·36 %), A-aiC17 : 1 (3·21 %), iC18 : 0 (1·55 %), C18 : 1{omega}7c (1·64 %) and summed feature 3 (C16 : 1{omega}7c and/or 2-OH i-C15 : 0; 0·40 %).

The type strain is YIM 70081T (=CCTCC AA 203010T=DSM 15666T=KCTC 19013T), isolated from a saline soil sample from the Xinjiang Province, China. The DNA G+C content of the type strain is 64·5 mol%.


   ACKNOWLEDGEMENTS
 
The authors are grateful to Dr Peter Schumann for help with peptidoglycan analysis and Dr Jean Euzéby and Professor Dr Hans G. Trüper for support with nomenclature. This research was supported by the National Basic Research Program of China (2004CB719600), the National Natural Science Foundation of China (30270004), Yunnan Provincial Natural Science Foundation (2004C0002Q), Yunnan Education Commission Foundation (02QJ077) and the 21C Frontier Microbial Genomics and Application Center Program, Ministry of Science & Technology (MG02-0101-002-1-0-0) and the International Cooperation R&D Program, Ministry of Science & Technology (M6-0203-00-0002), Korea.


   REFERENCES
TOP
 ABSTRACT
 MAIN TEXT
 REFERENCES
 
Collins, M. D., Lawson, P. A., Labrenz, M., Tindall, B. J., Weiss, N. & Hirsch, P. (2002). Nesterenkonia lacusekhoensis sp. nov., isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol 52, 1145–1150.[Abstract]

De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[Medline]

Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]

Felsenstein, J. (1993). PHYLIP (phylogenetic inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, WA, USA.

Hozzein, W. N., Li, W.-J., Ali, M. I. A., Hammouda, O., Mousa, A. S., Xu, L.-H. & Jiang, C.-L. (2004). Nocardiopsis alkaliphila sp. nov., a novel alkaliphilic actinomycete isolated from desert soil in Egypt. Int J Syst Evol Microbiol 54, 247–252.[Abstract/Free Full Text]

Huß, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.

Jahnke, K. D. (1992). Basic computer program for evaluation of spectroscopic DNA renaturation data from GILFORD System 2600 spectrometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61–73.

Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef][Medline]

Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.

Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[Abstract/Free Full Text]

Li, W.-J., Chen, H.-H., Zhang, Y.-Q., Schumann, P., Stackebrandt, E., Xu, L.-H. & Jiang, C.-L. (2004). Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China. Int J Syst Evol Microbiol 54, 837–841.[Abstract/Free Full Text]

Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[Medline]

Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]

Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]

Stackebrandt, E., Koch, C., Gvozdiak, O. & Schumann, P. (1995). Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 45, 682–692.[CrossRef][Medline]

Tang, S. K., Li, W. J., Wang, D., Zhang, Y. G., Xu, L. H. & Jiang, C. L. (2003). Studies of the biological characteristics of some halophilic and halotolerant actinomycetes isolated from saline and alkaline soils. Actinomycetology 17, 6–10.

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.[Abstract/Free Full Text]

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.[CrossRef]




This article has been cited by other articles:


Home page
 Int. J. Syst. Evol. Microbiol.Home page
W.-J. Li, Y.-Q. Zhang, P. Schumann, H.-Y. Liu, L.-Y. Yu, Y.-Q. Zhang, E. Stackebrandt, L.-H. Xu, and C.-L. Jiang
Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil
Int J Syst Evol Microbiol, June 1, 2008; 58(6): 1359 - 1363.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
Y.-Q. Zhang, P. Schumann, L.-Y. Yu, H.-Y. Liu, Y.-Q. Zhang, L.-H. Xu, E. Stackebrandt, C.-L. Jiang, and W.-J. Li
Zhihengliuella halotolerans gen. nov., sp. nov., a novel member of the family Micrococcaceae
Int J Syst Evol Microbiol, May 1, 2007; 57(5): 1018 - 1023.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, S.-Y. Jung, W. Kim, S.-W. Nam, and T.-K. Oh
Nesterenkonia jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.
Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2587 - 2592.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
O. Delgado, J. Quillaguaman, S. Bakhtiar, B. Mattiasson, A. Gessesse, and R. Hatti-Kaul
Nesterenkonia aethiopica sp. nov., an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake
Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1229 - 1232.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
W.-J. Li, P. Schumann, Y.-Q. Zhang, P. Xu, G.-Z. Chen, L.-H. Xu, E. Stackebrandt, and C.-L. Jiang
Proposal of Yaniaceae fam. nov. and Yania flava sp. nov. and emended description of the genus Yania
Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1933 - 1938.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Supplementary material
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 Li, W.-J.
Right arrow Articles by Jiang, C.-L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, W.-J.
Right arrow Articles by Jiang, C.-L.
Agricola
Right arrow Articles by Li, W.-J.
Right arrow Articles by Jiang, C.-L.

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