| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, P. R. China
2 Research Centre of Industrial Microbiology, School of Biotechnology, Southern Yangtze University, Wuxi, 214036, China
3 New Drug R & D, North China Pharmaceutic Corp., Shijiazhuang, 050015, P. R. China
Correspondence
Cheng-Lin Jiang
wjli{at}ynu.edu.cn or
lihxu{at}ynu.edu.cn
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
region of the 16S rRNA gene. It could be differentiated by phenotypic and genotypic analysis from all the Streptomyces species whose names have been validly published. On the basis of polyphasic evidence, Streptomyces sodiiphilus sp. nov. is proposed. The type strain is YIM 80305T (=CCTCC AA 203015T=CIP 107975T).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain YIM 80305T is AY236339.
These authors contributed equally to the work. 
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
; Jones et al., 1998; Duckworth et al., 1998). Mikami et al. (1982) first reported alkaliphilic actinomycetes, and some taxonomic data and applications for alkaliphilic actinomycetes were reported subsequently (Groth et al., 1997; Duckworth et al., 1998). Alkaliphilic actinomycetes can produce many alkaline enzymes (Horikoshi, 1999) and bioactive substances, such as antibiotics (Tsujibo et al., 1988, 1990) and enzyme inhibitors (Bahn et al., 1998), and they also have typical metabolites and wide exploitation in industries.
Alkaliphilic actinomycetes that thrive in alkaline environments have typical nutrient requirements, cultural conditions and physiological properties. Up to now, there have been several reports on the physiology and energetics of alkaliphilic bacteria (Krulwich et al., 2001; Yumoto, 2002), while there are few reports on alkaliphilic actinomycetes. Thus, studies on the physiology of alkaliphilic actinomycetes are urgently required to exploit this microbial resource of great potential.
The effect of Na2CO3, which is usually used to regulate pH when cultivating alkaliphilic actinomycete strains, NaOH, KOH and K2CO3 on the growth of some alkaliphilic actinomycete isolates, including strain YIM 80305T, was determined. The results showed that strain YIM 80305T had special physiological characteristics; thus it was classified further using a polyphasic approach.
Strain YIM 80305T was isolated from a muddy saline–alkaline soil sample collected near Chaka salt lake, Qinghai Province, China, using soil-extract agar (pH 10·0). The isolate was cultivated on yeast extract/malt extract agar (ISP medium 2, pH 9·0) at 28 °C. Modified ISP medium 2 was used as basic medium for pH and other physiological tests; the pH was regulated to pH 9·0 by using autoclaved Na2CO3 and the cultivation temperature was 28 °C unless stated otherwise. The following buffers were used: pH 6·0, 7·0 and 8·0–0·1 M KH2PO4/0·1 M NaOH; pH 9·0 and 10·0–0·1 M NaHCO3/0·1 M Na2CO3; pH 11·0–0·05 M Na2HPO4/0·1 M NaOH; and pH 12·0–0·2 M KCl/0·2 M NaOH. Strain YIM 80305T was incubated in liquid ISP medium 2 for 2–3 weeks. After the basic medium was sterilized, the pH was regulated to pH 6·0, 7·0, 8·0, 9·0, 10·0, 11·0 or 12·0 using autoclaved KOH, K2CO3, NaOH or Na2CO3 before pouring the medium onto plates. A further test was carried out by adding 1·0, 2·0 or 3·0 % (w/v) NaCl to the basic medium and the pH was regulated by using autoclaved KOH or K2CO3. The inoculated plates were cultivated for 2–3 weeks.
Morphological features were observed on ISP medium 2 under different conditions (pH 7·0, pH 9·0 and pH 9·0 with 3 % NaCl) for 3–4 weeks with an Olympus BH-2 microscope and by scanning electron microscopy (JSM-5600LV; JEOL). Media and procedures used for cultural characteristics, physiological and biochemical features and carbon source utilization were those described by Shirling & Gottlieb (1966) and Locci (1989), except that pH was regulated to pH 9·0 using autoclaved Na2CO3. Growth temperature range of strain YIM 80305T was determined on modified ISP medium 2 (pH 9·0) and inoculated plates were incubated at 4, 10, 20, 28, 37, 45, 55 or 65 °C for 1–2 weeks. NaCl tolerance of strain YIM 80305T was determined by adding 0, 3, 5, 7, 10 or 15 % (w/v) NaCl to the basic medium, followed by incubation for 3–4 weeks.
Cell-wall amino acids were purified and analysed by the methods of Jiang et al. (2001). The procedure of Lechevalier & Lechevalier (1980) was used for analysis of whole-cell sugar hydrolysates. Polar lipids were extracted, examined by two-dimensional TLC and identified using published procedures (Minnikin et al., 1984). Menaquinones were determined using the procedures of Collins (1985) and separated by HPLC (Kroppenstedt, 1982). Cellular fatty acid analysis was performed as described by Sasser (1990).
The genomic DNA of strain YIM 80305T was extracted and purified by using the method of Marmur (1961). The DNA G+C content of strain YIM 80305T was measured using the thermal denaturation method (Marmur & Doty, 1962).
Extraction of genomic DNA, amplification of the 16S rRNA gene and sequencing were done as described by Cui et al. (2001). Reference strains were chosen from BLAST (Altschul et al., 1997) search results. Phylogenetic analysis was performed using the software package MEGA (Molecular Evolutionary Genetics Analysis) version 2.1 (Kumar et al., 2001) after multiple alignment of data by CLUSTAL_X (Thompson et al., 1997). A phylogenetic tree 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 using the bootstrap resampling method of Felsenstein (1985) with 1000 replicates.
Morphological observation of a 21-day culture of strain YIM 80305T grown on yeast extract/malt extract agar (ISP medium 2) (pH 9·0 or pH 9·0 with 3 % NaCl) revealed that strain YIM 80305T had typical characteristics of the genus Streptomyces. Aerial mycelium and substrate mycelium were well-developed and not fragmented. Long or short chains of spores were straight to flexuous and spores were non-motile (Fig. 1). The control for strain YIM 80305T grown on ISP medium 2 at pH 7·0 produced very little aerial mycelium (data not shown). For cultural characteristics, strain YIM 80305T developed well on most media including Czapek's agar medium, oatmeal agar (ISP medium 3), glycerol/asparagine agar (ISP medium 5) and yeast extract/malt extract (ISP medium 2). It showed poor growth on nutrient agar. No growth was observed on inorganic salt/starch agar (ISP medium 4). No diffusible pigments were produced except on nutrient agar medium (pale orange–yellow).
|
, b). The whole-cell hydrolysates mainly contained galactose and glucose but no diagnostic sugars. The predominant menaquinones were MK-9(H4) (13 %), MK-9(H6) (68 %) and MK-9(H8) (19 %), and the diagnostic phospholipid was phosphatidylethanolamine. The major fatty acid components were ai-C15 : 0 (16·47 %), ai-C17 : 0 (13·30 %) and i-C16 : 0 (31·32 %). Thus, chemotaxonomic and phenotypic data showed that strain YIM 80305T should be assigned to the genus Streptomyces.
Strain YIM 80305T could grow between pH 7·0 and 12·0, and its optimal pH was 9·0–10·0. KOH, K2CO3, NaOH and Na2CO3 had different effects on its growth (Table 1). KOH and K2CO3 showed obvious inhibition of the growth of strain YIM 80305T, and it only grew at pH 7·0–8·0 with them, while NaOH and Na2CO3 showed no obvious effect on growth. However, when 1, 2 or 3 % NaCl was added to the basic medium using KOH and K2CO3 to regulate pH, the pH range for the growth of YIM 80305T was increased: it grew at pH 7·0–11·0 when using KOH and at pH 7·0–9·0 with K2CO3. Small amounts of NaCl could promote the growth of YIM 80305T. It was interesting that strain YIM 80305T showed a wider pH range for growth on the basic medium using KOH than that using K2CO3 when adding 1·0, 2·0 or 3·0 % NaCl. All the results showed that YIM 80305T was obligately dependent on Na+, especially in highly alkaline media, but that it showed sensitivity to K+ in highly alkaline media. The optimum growth temperature and NaCl concentration are 28 °C and 3 % (w/v), respectively.
|
). Phylogenetic analyses based on a dataset consisting of 1452 unambiguous nucleotides at positions 45 to 1496 (Escherichia coli numbering; Brosius et al., 1978) showed that the novel isolate falls into one distinct subclade with two other species, Streptomyces albus subsp. albus (GenBank/EMBL/DDBJ accession no. AJ621602) (97·6 % sequence similarity) and Streptomyces armeniacus (GenBank/EMBL/DDBJ accession no. AB018094) (96·0 % sequence similarity). The phylogenetic tree based on the 16S rRNA gene sequences of strain YIM 80305T and the most closely related type strains of the genus Streptomyces is shown in Fig. 2.
|
region sequences (positions 158 to 277) of the 16S rRNA gene from 452 known Streptomyces species obtained from the DDBJ databases and from strain YIM 80305T were aligned. Analysis of region sequences showed that strain YIM 80305T was grouped into a branch with strains of recognized Streptomyces species, including Streptomyces rimosus ISP 5260T, Streptomyces ochraceiscleroticus ISP 5594T, Streptomyces olivaceus JCM 4066, Streptomyces violens ISP 5597T, Streptomyces purpurogeneiscleroticus ISP 5271T and Streptomyces niger ISP 5302T. Although strain YIM 80305T had almost the same sequence of the variable region as those strains, it had broad phenotypic differences (Table 2). The renaturation rates of genomic fragments from pairs of strains were determined spectrophotometrically with a model 1601 UV spectrophotometer equipped with a Thermoelectric Cell Temperature Controller (Shimadzu) according to the previously described methods (De Ley et al., 1970; Huss et al., 1983), and the low DNA–DNA relatedness (all below 40 %) between strain YIM 80305T and the related type strains also confirmed that they are different genomic species.
|
Description of Streptomyces sodiiphilus sp. nov.
Streptomyces sodiiphilus (so.di.i'phi.lus. N.L. n. sodium -i; Gr. adj. philos loving; N.L. adj. sodiiphilus sodium ion-loving, referring to the characteristic of Na+-dependent growth).
Aerobic and Gram-positive. Both vegetative and aerial hyphae are well-developed and not fragmented. Long or short chains of spores are straight to flexuous and spores are non-motile. No diffusible pigments are produced except on nutrient agar medium (pale orange–yellow). Sodium acetate and rhamnose can be used as sole carbon sources for growth, but not most other carbon sources, such as lactose, maltose, fructose, xylose, ribose, arabinose, sucrose, glucose, galactose, sodium citrate, cellobiose, cellubinose, raffinose, mannitol, sorbitol, glycerol and starch. Positive for gelatin liquefaction and nitrate reduction, but negative for urease, melanin production, starch hydrolysis, H2S production, milk coagulation and milk peptonization. Cell wall contains LL-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contain galactose and glucose and no diagnostic sugars. Predominant menaquinones are MK-9(H4) (13 %), MK-9(H6) (68 %) and MK-9(H8) (19 %), and the diagnostic phospholipid is phosphatidylethanolamine. Major fatty acid components are ai-C15 : 0 (16·47 %), ai-C17 : 0 (13·30 %) and i-C16 : 0 (31·32 %). Grows optimally at 28 °C and in ISP medium 2 with 3 % NaCl and pH 9·0–10·0. DNA G+C content is 70·5 mol%.
The type strain, YIM 80305T (=CCTCC AA 203015T=CIP 107975T), was isolated from a soil sample collected from Chaka salt lake, Qinghai Province, China.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Bahn, Y. S., Park, J. M., Bai, D. H., Takase, S. & Yu, J. H. (1998). YUA001, a novel aldose reductase inhibitor isolated from alkalophilic Corynebacterium sp. YUA25. I. Taxonomy, fermentation, isolation and characterization. J Antibiot (Tokyo) 51, 902–907.[Medline]
Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75, 4801–4805.
Collins, M. D. (1985). Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
Cui, X.-L., Mao, P.-H., Zeng, M., Li, W.-J., Zhang, L.-P., Xu, L.-H. & Jiang, C.-L. (2001). Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51, 357–363.[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]
Duckworth, A. W., Grant, S., Grant, W. D., Jones, B. E. & Meijer, D. (1998). Dietzia natronolimnaios sp. nov., a new member of the genus Dietzia isolated from an East African soda lake. Extremophiles 2, 359–366.[CrossRef][Medline]
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Groth, I., Schumann, P., Rainey, F. A., Martin, K., Schuetze, B. & Augsten, K. (1997). Bogoriella caseilytica gen. nov., sp. nov., a new alkaliphilic actinomycete from a soda lake in Africa. Int J Syst Bacteriol 47, 788–794.
Horikoshi, K. (1999). Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63, 735–750.
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.
Jiang, L.-Y., Li, M.-G., Li, W.-J., Cui, X.-L., Xu, L.-H. & Jiang, C.-L. (2001). Study on the application of quantitative analysis of cell-wall amino acids in actinomycetes classification. Wei Sheng Wu Xue Bao 41, 270–277 (in Chinese).[Medline]
Jones, B. E., Grant, W. D., Duckworth, A. W. & Owenson, G. G. (1998). Microbial diversity of soda lakes. Extremophiles 2, 191–200.[CrossRef][Medline]
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.
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 Liquid Chromatogr 5, 2359–2387.[CrossRef]
Krulwich, T. A., Ito, M. & Guffanti, A. A. (2001). The Na+-dependence of alkaliphily in Bacillus. Biochim Biophys Acta 1505, 158–168.[Medline]
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.
Lechevalier, H. A. & Lechevalier, M. P. A. (1970a). Critical evaluation of the genera of aerobic actinomycetes. In The Actinomycetes, pp. 393–405. Edited by H. Prauser. Jena: Gustav Fischer Verlag.
Lechevalier, M. P. & Lechevalier, H. A. (1970b). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20, 435–443.
Lechevalier, M. P. & Lechevalier, H. A. (1980). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, pp. 22–291. Edited by A. Dietz & D. W. Thayer. Arlington, VA: Society for Industrial Microbiology.
Locci, R. (1989). Streptomycetes and related genera. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2451–2508. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.
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]
Mikami, Y., Miyashita, K. & Arai, T. (1982). Diaminopimelic acid profiles of alkalophilic and alkaline-resistant strains of actinomycetes. J Gen Microbiol 128, 1709–1712.
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 quinines and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16.
Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.
Shirling, E. B. & Gottlieb, D. (1968). Cooperative description of type cultures of Streptomyces. II. Species descriptions from the first study. Int J Syst Bacteriol 18, 69–189.
Shirling, E. B. & Gottlieb, D. (1969). Cooperative description of type cultures of Streptomyces. IV. Species descriptions from the second, third and fourth studies. Int J Syst Bacteriol 19, 391–512.
Shirling, E. B. & Gottlieb, D. (1972). Cooperative description of type cultures of Streptomyces. V. Additional descriptions. Int J Syst Bacteriol 22, 265–394.
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.
Tsujibo, H., Sato, T., Inui, M., Yamamoto, H. & Inamori, Y. (1988). Intracellular accumulation of phenazine antibiotics produced by an alkalophilic actinomycete. I. Taxonomy, isolation and identification of the phenazine antibiotics. Agric Biol Chem 52, 301–306.
Tsujibo, H., Sakamoto, T., Miyamoto, K., Kusano, G., Ogura, M., Hasegawa, T. & Inamori, Y. (1990). Isolation of cytotoxic substance, kalafungin from an alkalophilic actinomycete, Nocardiopsis dassonvillei subsp. prasina. Chem Pharm Bull (Tokyo) 38, 2299–2300.[Medline]
Yumoto, I. (2002). Bioenergetics of alkaliphilic Bacillus spp. J Biosci Bioeng 93, 342–353.
This article has been cited by other articles:
|
|
 |
|
  M. le Roes-Hill and P. R. Meyers Streptomyces polyantibioticus sp. nov., isolated from the banks of a river Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1302 - 1309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X.-P. Tian, Y.-Q. Zhang, Q.-X. Li, X.-Y. Zhi, S.-K. Tang, S. Zhang, and W.-J. Li Streptomyces nanshensis sp. nov., isolated from the Nansha Islands in the South China Sea Int J Syst Evol Microbiol, April 1, 2009; 59(4): 745 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Xu, Y. Wang, S.-J. Xie, J. Xu, J. Xiao, and J.-S. Ruan Streptomyces xiamenensis sp. nov., isolated from mangrove sediment Int J Syst Evol Microbiol, March 1, 2009; 59(3): 472 - 476. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-G. Chen, X.-L. Cui, R. M. Kroppenstedt, E. Stackebrandt, M.-L. Wen, L.-H. Xu, and C.-L. Jiang Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China Int J Syst Evol Microbiol, March 1, 2008; 58(3): 699 - 705. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Jiang, S.-K. Tang, J. Wiese, L.-H. Xu, J. F. Imhoff, and C.-L. Jiang Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2694 - 2698. [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 | |
