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1 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
2 Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
Correspondence
Wen-Jun Li
wjli{at}ynu.edu.cn
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ABSTRACT |
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and at present the genus comprises only five species with validly published names (Ventosa et al., 1990, 1992; Zhang et al., 2002; Franca et al., 2006; Aslam et al., 2007). Members of the genus Salinicoccus are moderately halophilic, aerobic Gram-positive cocci, which are chemotaxonomically characterized by having menaquinone-6 (MK-6) as the predominant isoprenoid quinone, a cell-wall peptidoglycan type based on L-Lys–Gly5 and a DNA G+C content of 46–51 mol% (Ventosa et al., 1992). In this paper, we present our studies on a new isolate affiliated to the genus Salinicoccus. Strain YIM 70202T was isolated from a desert soil sample collected from Wadi Sannur by using the dilution plating method on marine agar (Difco 2216; MA), supplemented with 15 % NaCl (w/v). Wadi Sannur is one of the most famous wadis in the Eastern Desert of Egypt where the mean monthly air temperature ranges from 12.2 °C during January to 29.1 °C during July. The pH value of the medium was adjusted to 8.0 using Na2CO3/NaHCO3 buffer. The strain was maintained on MA slants containing 10 % NaCl at 4 °C and as 20 % (w/v) glycerol suspensions at –20 °C. Biomass for chemical and molecular studies was obtained by cultivation in shaken flasks (about 150 r.p.m.) using marine broth (Difco 2216; MB) supplemented with 10 % NaCl (w/v) at pH 8.0 and 30 °C for 1 week.
Gram staining and the KOH lysis test were carried out according to Gram (1884) and Cerny (1978), respectively. Morphology and motility were examined by light microscopy (model BH 2; Olympus) and electron microscopy (JEM-1010) using cells from exponentially growing cultures. For transmission electron microscopy (TEM) observation, cells were negatively stained with 1 % (w/v) phosphotungstic acid after air-drying. Colony morphology was observed on MA or ISP5 medium (Shirling & Gottlieb, 1966) containing 10 % NaCl and trypticase soy agar (TSA) containing 10 % NaCl after incubation at 30 °C for 2 days. The colony colour was determined with the ISCC-NBS colour charts (Kelly, 1964). The growth temperature was tested at 4, 10, 28, 30, 37, 40, 45 and 55 °C using MB supplemented with 10 % NaCl. The ability of the strain to grow at different NaCl concentrations was examined on TSA and MA. To determine the optimum pH for growth, the following buffer solutions were used (with intervals of 0.5 pH units): pH 5.0–8.5: NaOH/KH2PO4; pH 9.0–9.5: borax/boric acid; pH 10.0–10.5: borax/NaOH; pH 11.0–11.5: Na2HPO4/NaOH; pH 12.0–13.0: KCl/NaOH. Metabolic properties were determined using API ID 32E, API Coryne and API ZYM test kits (bioMérieux) according to the manufacturer's instructions, except that the cell suspension to inoculate the systems was prepared by using sterilized artificial seawater supplemented with 10 % (w/v) NaCl. Most metabolic properties (listed in Table 1) were also checked as described by Shirling & Gottlieb (1966).
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and in the species description.
A purified cell-wall preparation was obtained after disruption of cells by shaking with glass beads and subsequent trypsin digestion by the method of Schleifer (1985). Amino acids and peptides in cell-wall hydrolysates were analysed by two-dimensional ascending TLC on cellulose plates using the solvent systems of Schleifer & Kandler (1972). Respiratory quinones were isolated according to the method of Collins et al. (1977) and analysed by HPLC (Groth et al., 1997). Polar lipids were extracted, examined by two-dimensional TLC and identified using previously published procedures (Minnikin et al., 1979; Collins & Jones, 1980). Analysis of the whole-cell fatty acid pattern followed the instructions of the MIDI system (Kroppenstedt, 1985) by using exponential phase cultures.
The cell-wall peptidoglycan structure of strain YIM 70202T was L-Lys–Gly5. The predominant respiratory quinone was MK-6 and minor amounts of MK-7 were also detected. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major cellular fatty acids were i-C15 : 0 (34.2 %) and ai-C15 : 0 (30.6 %).
Extraction of genomic DNA and PCR amplification of the 16S rRNA gene were performed as described by Xu et al. (2003). Multiple alignments with sequences of the most closely related moderately halophilic species and calculations of levels of sequence similarity were carried out using CLUSTAL_X (Thompson et al., 1997). A phylogenetic tree was constructed using the neighbour-joining method of Saitou & Nei (1987) from Knuc values (Kimura, 1980) using MEGA version 2.1 (Kumar et al., 2001). The topology of the phylogenetic tree was evaluated by the bootstrap resampling method of Felsenstein (1985) with 1000 replicates.
The DNA base composition of strain YIM 70202T was determined by reverse-phase HPLC of nucleosides according to Mesbah et al. (1989). DNA–DNA hybridizations were carried out between strain YIM 70202T and Salinicoccus roseus CCM 3516T applying the optical renaturation method (De Ley et al., 1970; Huß et al., 1983; Jahnke, 1992).
The nearly complete 16S rRNA gene (1507 bp) was sequenced for strain YIM 70202T. 16S rRNA gene sequence comparative analysis with sequences available from the NCBI online databases revealed that strain YIM 70202T was much closer to species of the genus Salinicoccus (94.5–96.8 % 16S rRNA gene sequence similarity) than to other moderately halophilic species. The closest neighbour of strain YIM 70202T was S. roseus CCM 3516T, showing 96.8 % gene sequence similarity. The phylogenetic tree (Fig. 1) depicts the phylogenetic position of strain YIM 70202T within the radiation of type strains of all recognized species of the genus Salinicoccus.
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) within the genus Salinicoccus. The chemotaxonomic characteristics of strain YIM70202T, containing MK-6 as the predominant respiratory quinone, L-Lys–Gly5 as the cell-wall peptidoglycan, i-C15 : 0 (34.2 %) and ai-C15 : 0 (30.6 %) as the predominant fatty acids and a DNA G+C content of 49.7 mol%, are all consistent with those of the genus Salinicoccus (Ventosa et al., 1990, 1992). Comparative analysis of the 16S rRNA gene sequence of strain YIM 70202T with all recognized species of the genus Salinicoccus were lower than 97.0 % suggesting that strain YIM 70202T represents a novel species (Stackebrandt & Goebel, 1994). Phenotypic characteristics (see Table 1) also differentiate strain YIM 70202T from all of the recognized species of the genus Salinicoccus. Furthermore, the DNA–DNA relatedness value of 12.7 % between strain YIM 70202T and S. roseus CCM 3516T is far lower than 70 %, which is considered to be the threshold value for the delineation of genomic species (Wayne et al., 1987). Thus, we propose that strain YIM 70202T be classified in the genus Salinicoccus as representing the type strain of a novel species, Salinicoccus luteus sp. nov.
Description of Salinicoccus luteus sp. nov.
Salinicoccus luteus (lu.te'us. L. masc. adj. luteus orange-coloured).
Aerobic, Gram-positive, non-spore-forming, non-motile cocci with a diameter of about 0.9 µm. The colony colour on most media tested is orange. Colonies are circular, opaque and approximately 1.0 mm in diameter after 48 h at 30 °C. The optimum concentration of NaCl, optimum pH and temperature for growth are 10 % (w/v), 8.0–9.0 and 30 °C, respectively. The concentration range of NaCl and pH and temperature ranges for growth are 1–25 % (w/v), 7.0–11.0, and 4–45 °C, respectively. Gives a positive reaction in tests for catalase, oxidase, ornithine decarboxylase, arginine dihydrolase, lysine decarboxylase, lipase, 
-glucosidase, nitrate reduction and Tween 20 hydrolysis, but is negative in tests for N-acetylglucosaminidase, -glucuronidase, -galactosidase, 
-galactosidase, gelatin liquefaction, indole and ammonia production, methyl red and Voges–Proskauer tests, milk peptonization and coagulation, growth on cellulose, H2S and melanin production, casein, starch, and Tween 80 hydrolysis. The following substrates are utilized: maltose, mannitol, glucose, adonitol, arabinose, arabitol, mannose, inositol, sorbitol, fructose, cellobiose, salicin, acetamide, galactose, xylose and dextrin, while rhamnose and starch are not utilized. Acid is produced from maltose, D-glucose, sucrose, malonate and N-acetylglucosamine. The cell-wall peptidoglycan structure is L-Lys–Gly5. The predominant respiratory quinone is MK-6. Polar lipids include phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major fatty acids are i-C15 : 0 and ai-C15 : 0. The DNA G+C content is 49.7 mol% (HPLC method).
The type strain, YIM 70202T (=CGMCC 1.6511T=KCTC 3941T), was isolated from a desert soil sample collected from Egypt.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Cerny, G. (1978). Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5, 113–122.[CrossRef]
Collins, M. D. & Jones, D. (1980). Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. J Appl Bacteriol 48, 452–470.
Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.
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]
Franca, L., Rainey, F. A., Nobre, M. F. & Costa, M. S. (2006). Salinicoccus salsiraiae sp. nov.: a new moderately halophilic gram-positive bacterium isolated from salted skate. Extremophiles 10, 531–536.[CrossRef][Medline]
Gram, H. C. (1884). Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten. Fortschr Med 2, 185–189 (in German).
Groth, I., Schumann, P., Rainey, F. A., Martin, K., Schuetze, B. & Augsten, K. (1997). Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47, 1129–1133.
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 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61–73.[CrossRef]
Kelly, K. L. (1964). Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC: US Government Printing Office.
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]
Kroppenstedt, R. M. (1985). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics, pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
Minnikin, D. E., Collins, M. D. & Goodfellow, M. (1979). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47, 87–95.[CrossRef]
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Schleifer, K. H. (1985). Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18, 123–156.
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]
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.
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.
Ventosa, A., Marquez, M. C., Ruiz-Berraquero, F. & Kocur, M. (1990). Salinicoccus roseus gen. nov., sp. nov., a new moderately halophilic Gram-positive coccus. Syst Appl Microbiol 13, 29–33.
Ventosa, A., Marquez, M. C., Weiss, N. & Tindall, B. J. (1992). Transfer of Marinococcus hispanicus to the genus Salinicoccus as Salinicoccus hispanicus comb. nov. Syst Appl Microbiol 15, 530–534.
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & 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.
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).
Zhang, W., Xue, Y., Ma, Y., Zhou, P., Ventosa, A. & Grant, W. D. (2002). Salinicoccus alkaliphilus sp. nov., a novel alkaliphile and moderate halophile from Baer Soda Lake in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 52, 789–793.[Abstract]
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