| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
2 Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
Correspondence
Wen-Jun Li
wjli{at}ynu.edu.cn
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
7c, C16 : 0, C17 : 0 and C17 : 18c. L-Ornithine was detected in its peptidoglycan. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 007T showed 16S rRNA gene sequence similarity levels of 86.8–92.1 % to the other described Deinococcus species. Based on the high 16S rRNA gene sequence divergence and phenotypic differences, it is proposed that the unknown strain should be classified as a novel species in the genus Deinococcus with the name Deinococcus yunweiensis sp. nov. The type strain is YIM 007T (=KCTC 3962T=DSM 17005T).
Fatty acid profiles of strain YIM 007T and related strains are available as supplementary material in IJSEM Online.
These authors contributed equally to this work. 
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
; Moseley, 1983; Smith et al., 1992). The colony colour of most members of this genus is bright red, orange or light pink and the surface of the colonies is usually dry with pleats. At the time of writing, the genus Deinococcus comprises 20 species with validly published names (Suresh et al., 2004; Ferreira et al., 1997; Rainey et al., 1997; Brooks & Murray, 1981; de Groot et al., 2005; Rainey et al., 2005; Lai et al., 2006), including 11 recently named species, Deinococcus deserti, D. ficus, D. hohokamensis, D. navajonensis, D. hopiensis, D. apachensis, D. maricopensis, D. pimensis, D. yavapaiensis, D. papagonensis and D. sonorensis (de Groot et al., 2005; Rainey et al., 2005; Lai et al., 2006). Of these 20 species, which were isolated from a wide range of environments, Deinococcus radiodurans, the type species of this genus, has been studied most extensively to elucidate the mechanisms of radiation-resistance, and it has been determined that the radioresistance of this species is a direct result of its ability to repair efficiently the DNA damage generated during irradiation (Smith et al., 1992; Minton, 1994; Mattimore & Battista, 1996; Battista, 1997; Battista et al., 1999). In this paper, we report the results of a polyphasic study of another hitherto-unknown gamma- and UV-radiation-resistant strain, designated YIM 007T, which was found on a contaminated plate in our laboratory.
A red-pigmented contaminant was found on a yeast extract-malt extract agar plate [4.0 % yeast extract, 10.0 % malt extract, 4.0 % glucose, 2.0 % agar; ISP 2 medium (Shirling & Gottlieb, 1966)] with a bacterial culture at 28 °C for about 2 weeks. It was then picked and serially diluted on ISP 2 agar plates. The purified strain, designed YIM 007T, was maintained on ISP 2 agar slants at 4 °C and as a 20 % (w/v) glycerol suspension at –20 °C. Biomass for chemical and molecular studies was obtained by cultivation using ISP 2 broth or trypticase soy broth (Difco) (30 °C, 5 days, 150 r.p.m.).
Morphology and motility of cells grown for 12–48 h on ISP 2 agar medium were examined by light microscopy (model BH 2; Olympus) and using a Hitachi H-800 transmission electron microscope (TEM). For TEM observation, cells were negatively stained with 1 % (w/v) phosphotungstic acid after air-drying. Motility and flagella observation was performed using semi-solid agar and the staining method of Leifson (1960). Gram staining was carried out using the standard Gram reaction (Gram, 1884). Growth at different temperatures and pH was investigated as described by Xu et al. (2005), but using ISP 2 as the basic medium. Tolerance to NaCl (0.5, 1, 3, 7, 10, 13 and 15 %) was also tested using ISP 2 medium. Metabolic properties were determined using API ID 32 E and API 32 GN test kits (bioMérieux) according to the manufacturer's instructions. Other physiological and biochemical tests were performed as described previously (Li et al., 2004).
To determine the tolerance of the isolate to UV radiation, the cultures were grown in the appropriate liquid medium to the exponential phase. The cells were recovered by centrifugation, washed with 0.067 M potassium phosphate buffer at pH 7.0 and then diluted serially, and 0.1 ml was spread on ISP 2 agar plates (with their lids open) and then exposed to UV light at a distance of 30 cm from a UV source for the required dose and were then incubated at 30 °C for 14 days. For the gamma-radiation-resistance determination, cells were prepared as above and then exposed at room temperature to gamma radiation from a cobalt-60 source at doses of 1 and 8 kGy h–1. After exposure to 0.1, 3, 5, 9, 10 and 20 kGy, suspensions were diluted in triplicate on the appropriate solid medium. Growth after 15 days was scored as positive or negative in comparison to an unirradiated control. At the same time, D. radiodurans AS 1.633T and Escherichia coli DH5
(both from the China General Microbiological Culture Collection Center, Beijing) were tested as positive and negative controls. Relative survival was determined by comparing with unirradiated cultures.
Purified peptidoglycan was prepared and analysed by the method of Schleifer & Kandler (1972). The respiratory quinone was isolated using the methods of Minnikin et al. (1984) and separated by HPLC (Kroppenstedt, 1982). Analysis of the cellular fatty acid pattern followed described methods (Miller, 1982) using the MIDI system (Microbial ID, Inc.). Polar lipids were extracted and analysed by two-dimensional TLC according to Tindall (1990). The DNA base composition of strain YIM 007T was determined by using the thermal denaturation method (Marmur & Doty, 1962).
Extraction and amplification of genomic DNA for 16S rRNA gene sequence analysis were carried out as described by Xu et al. (2003). Multiple alignments with sequences of a broad selection of related species and calculations of levels of sequence similarity were carried out using CLUSTAL X (Thompson et al., 1997). A phylogenetic tree (Fig. 1) was reconstructed using the neighbour-joining method of Saitou & Nei (1987) from Knuc values (Kimura, 1980, 1983). The topology of the phylogenetic tree was evaluated by the bootstrap resampling method of Felsenstein (1985) with 1000 replicates.
|
; de Groot et al., 2005), whereas those of all other members of the genus are spherical (Rainey et al., 1997; Hirsch et al., 2004). As with cells of D. indicus, D. grandis and D. deserti, strain YIM 007T stained Gram-negative, whereas those of other Deinococcus species stain Gram-positive (Suresh et al., 2004; Hirsch et al., 2004). Colonies of strain YIM 007T were red, circular, shining and opaque on most agar media tested. The temperature range for growth was 10–50 °C, with optimum growth at 30 °C. The pH range for growth was 6.0–9.0, with optimum growth occurring between pH 7.0 and 7.5. The other physiological and biochemical properties of strain YIM 007T are listed in Table 1 or in the species description.
|
. There was no growth for E. coli DH5 at a dose of 3.0 kGy gamma radiation, whereas almost no decrease in survival was observed for strains D. radiodurans AS 1.633T and YIM 007T. At 16.0 kGy gamma radiation, there was still growth for D. radiodurans AS 1.633T and YIM 007T. As for UV radiation tolerance, the lethal dose of UV radiation for E. coli DH5 was 30 J m–2, whereas strains YIM 007T and D. radiodurans AS 1.633T could grow at the highest dose of 624 J m–2.
The peptidoglycan of strain YIM 007T contained L-ornithine. The predominant respiratory quinone was detected as MK-8. The major fatty acids were monounsaturated and straight-chain saturated fatty acids, such as C16 : 17c, C16 : 0, C17 : 0 and C17 : 18c, which were also predominant in most other Deinococcus species (see Supplementary Table S1 available in IJSEM Online). Specifically, for the new isolate YIM 007T, relative amounts of some straight-chain saturated components, such as C16 : 0, C17 : 0, C18 : 0, were higher than in any other described Deinococcus species (Supplementary Table S1).
The results of two-dimensional TLC analysis of polar lipids extracted from D. radiodurans AS 1.633T and strain YIM 007T are shown in Fig. 2. Based on their staining behaviour, the polar lipid profiles of the two strains consisted of various unknown phosphoglycolipids (three in total) and glycolipids (five in total), and an unknown phospholipid and an unknown aminophospholipid were also detected. Polar lipid profiles of both strains were dominated by phosphoglycolipids, which is consistent with previously reported results for some Deinococcus species (Thompson et al., 1980; Counsell & Murray, 1986; Embley et al., 1987). D. radiodurans AS 1.633T exhibited an unknown glycolipid component (GL5) and a relatively larger amount of unknown phosphoglycolipids PGL1 and PGL2, distinguishing it from YIM 007T. Strain YIM 007T showed an unknown phosphoglycolipid (PGL3) that was not detected in D. radiodurans AS 1.633T. The chromatographic behaviour of the polar lipids GL1–GL4, PGL1, PGL2 and PGL3 of strain YIM 007T was similar to the polar lipid spots GL1–GL4, PGL1, PGL2 and PGL4 reported for D. ficus (Lai et al., 2006) and the polar lipids reported for Deinococcus radiophilus D16 and Deinococcus radiopugnans D17 (Embley et al., 1987). The presence of these lipids in extracts of strain YIM 007T confirms its assignment to the genus Deinococcus.
|
. In the dendrogram, strain YIM 007T is encompassed by the major branch of the genus Deinococcus. The DNA G+C content was determined to be 64.1 mol%.
The results of 16S rRNA gene sequence comparison together with chemotaxonomic data clearly demonstrate that strain YIM 007T is a member of the genus Deinococcus. However, strain YIM 007T forms a separate lineage within the genus (Fig. 1). Additionally, strain YIM 007T differs from some other Deinococcus species with validly published names in some phenotypic characteristics (Table 1). Therefore, based on the above phenotypic and genotypic data, it is proposed that strain YIM 007T represents a novel species of the genus Deinococcus, for which the name Deinococcus yunweiensis sp. nov. is proposed.
Description of Deinococcus yunweiensis sp. nov.
Deinococcus yunweiensis (yun.wei.en'sis. N.L. masc. adj. yunweiensis pertaining to Yunwei, an abbreviation of the Chinese name of Yunnan Institute of Microbiology, China, where the type strain was isolated).
Aerobic, Gram-negative, non-spore-forming, non-motile rods. The colony colour on most tested media is reddish. Colonies are circular, opaque and approximately 1.5–2.8 mm in diameter after incubation on ISP 2 medium for 24 h at 30 °C. The optimum growth pH, NaCl concentration and temperature are respectively pH 7.0–7.5, 0–1 % and 30 °C. Resistant to gamma (>16 kGy) and UV (>624 J m–2) irradiation. Catalase and oxidase reactions are positive. Casein is decomposed, while starch and Tween 80 are not decomposed. Positive for urease, lipase, -maltosidase, 
-glucuronidase, -galactosidase, N-acetylglucosaminidase, -glucosidase, lysine decarboxylase, gelatin liquefaction, methyl red test and Tween 20 esterase, while negative for ornithine decarboxylase, arginine dihydrolase and nitrate reduction. Glucose, rhamnose, sucrose, maltose, malonate, mannitol, salicin, D-melibiose, sorbitol, L-arabinose and galacturonate can be utilized as sole carbon sources. The peptidoglycan contains L-ornithine. The predominant respiratory quinone is MK-8. The polar lipid profile consists mainly of various unknown phosphoglycolipids and glycolipids. The cellular fatty acids are C16 : 17c (27.7 %), C16 : 0 (26.0 %), C17 : 0 (13.4 %), C17 : 18c (9.4 %), C18 : 0 (5.0 %) and small amounts of i-C11 : 0 (0.5 %), C12 : 0 (0.6 %), i-C13 : 0 (1.0 %), C15 : 16c (0.4 %), C15 : 0 (1.8 %), C16 : 19c (0.8 %), i-C17 : 0 (1.4 %), C17 : 16c (1.4 %), i-C17 : 19c (1.4 %), C18 : 17c (2.8 %) and C18 : 19c (4.1 %). The DNA G+C content of the type strain is 64.1 mol%.
The type strain is strain YIM 007T (=DSM 17005T=KCTC 3962T).
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Battista, J. R., Earl, A. M. & Park, M. J. (1999). Why is Deinococcus radiodurans so resistant to ionizing radiation? Trends Microbiol 7, 362–365.[CrossRef][Medline]
Brooks, B. W. & Murray, R. G. E. (1981). Nomenclature for "Micrococcus radiodurans" and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Bacteriol 31, 353–360.
Counsell, T. J. & Murray, R. G. E. (1986). Polar lipid profiles of the genus Deinococcus. Int J Syst Bacteriol 36, 202–206.
de Groot, A., Chapon, V., Servant, P., Christen, R., Fischer-Le Saux, M., Sommer, S. & Heulin, T. (2005). Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 55, 2441–2446.
Embley, T. M., O'Donnell, A. G., Watt, R. & Rostron, J. (1987). Lipid and cell wall amino acid composition in the classification of members of the genus Deinococcus. Syst Appl Microbiol 10, 20–27.
Felsenstein, J. (1985). Conference limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–789.[CrossRef]
Ferreira, A. C., Nobre, M. F., Rainey, F. A., Silva, M. T., Wait, R., Burghardt, J., Chung, A. P. & da Costa, M. S. (1997). Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 47, 939–947.
Gram, H. C. (1884). Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten. Fortschr Med 2, 185–189 (in German).
Hirsch, P., Gallikowski, C. A., Siebert, J., Peissl, K., Kroppenstedt, R. M., Schumann, P., Stackebrandt, E. & Anderson, R. (2004). Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Syst Appl Microbiol 27, 636–645.[CrossRef][Medline]
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J Mol Evol 16, 111–120.[CrossRef][Medline]
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Kroppenstedt, R. M. (1982). Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5, 2359–2387.[CrossRef]
Lai, W. A., Kämpfer, P., Arun, A. B., Shen, F. T., Huber, B., Rekha, P. D. & Young, C. C. (2006). Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int J Syst Evol Microbiol 56, 787–791.
Leifson, E. (1960). Atlas of Bacterial Flagellation. London: Academic Press.
Li, W.-J., Zhang, Y.-Q., Park, D.-J., Li, C.-T., Xu, L.-H., Kim, C.-J. & Jiang, C.-L. (2004). Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil. Int J Syst Evol Microbiol 54, 1811–1814.
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]
Mattimore, V. & Battista, J. R. (1996). Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. J Bacteriol 178, 633–637.
Miller, L. T. (1982). Single derivatization method for routine analysis of bacterial whole-cell, fatty acids methyl esters, including hydroxy acids. J Clin Microbiol 16, 584–586.
Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Minton, K. W. (1994). DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans. Mol Microbiol 13, 9–15.[Medline]
Moseley, B. E. B. (1983). Photobiology and radiobiology of Micrococcus (Deinococcus) radiodurans. Photochem Photobiol Rev 7, 223–275.
Rainey, F. A., Nobre, M. F., Schumann, P., Stackebrandt, E. & da Costa, M. S. (1997). Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 47, 510–514.
Rainey, F. A., Ray, K., Ferreira, M., Gatz, B. Z., Nobre, M. F., Bagaley, D., Rash, B. A., Park, M.-J., Earl, A. M. & other authors (2005). Extensive diversity of ionizing-radiation-resistant bacteria recovered from a Sonoran Desert soil and the description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol 71, 5225–5235.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4, 406–425.[Abstract]
Schleifer, K. H. & Kandler, O. (1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[Medline]
Smith, M. D., Masters, C. I., & Moseley, B. E. B. (1992). Molecular biology of radiation resistant bacteria. In Molecular Biology and Biotechnology of Extremophiles, pp. 258–280. Edited by R. A. Herbert & R. J. Sharp. New York: Chapman & Hall.
Suresh, K., Reddy, G. S. N., Sengupta, S. & Shivaji, S. (2004). Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India. Int J Syst Evol Microbiol 54, 457–461.
Thompson, B. G., Anderson, R. & Murray, R. G. (1980). Unusual polar lipids of Micrococcus radiodurans strain Sark. Can J Microbiol 26, 1408–1411.[Medline]
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.
Xu, P., Li, W. J., Xu, L. H. & Jiang, C. L. (2003). A microwave-based method for genomic DNA extraction from actinomycetes. Microbiology (Beijing) 30, 82–84 (in Chinese).
Xu, P., Li, W.-J., Tang, S.-K., Zhang, Y.-Q., Chen, G.-Z., Chen, H.-H., Xu, L.-H. & Jiang, C.-L. (2005). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55, 1149–1153.
This article has been cited by other articles:
|
|
 |
|
  M. Yuan, W. Zhang, S. Dai, J. Wu, Y. Wang, T. Tao, M. Chen, and M. Lin Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1513 - 1517. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Asker, T. S. Awad, T. Beppu, and K. Ueda Deinococcus aquiradiocola sp. nov., isolated from a radioactive site in Japan Int J Syst Evol Microbiol, January 1, 2009; 59(1): 144 - 149. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kampfer, N. Lodders, B. Huber, E. Falsen, and H.-J. Busse Deinococcus aquatilis sp. nov., isolated from water Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2803 - 2806. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. P. Callegan, M. F. Nobre, P. M. McTernan, J. R. Battista, R. Navarro-Gonzalez, C. P. McKay, M. S. da Costa, and F. A. Rainey Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments Int J Syst Evol Microbiol, May 1, 2008; 58(5): 1252 - 1258. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. A. Rainey, M. Ferreira, M. F. Nobre, K. Ray, D. Bagaley, A. M. Earl, J. R. Battista, B. Gomez-Silva, C. P. McKay, and M. S. da Costa Deinococcus peraridilitoris sp. nov., isolated from a coastal desert Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1408 - 1412. [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 | |
