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1 Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea
2 School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea
3 Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Suwon 441-707, Korea
4 Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
Correspondence
Soon-Wo Kwon
swkwon{at}rda.go.kr
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D-Asp and the main cellular fatty acid was i-C16 : 0. DNA–DNA hybridization experiments resulted in relatedness values of 37 % between 6T19T and U. thermosphaericus DSM 10633T and 41 % between 6T19T and U. terrenus DSM 12654T. Based on the polyphasic data, strains 6T19T and 6T29 can be described as members of a novel species of the genus Ureibacillus, for which the name Ureibacillus suwonenesis sp. nov. is proposed. The type strain is 6T19T (=KACC 11287T=DSM 16752T).
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 6T19T and 6T29 are AY850379 and AY850380.
Supplementary figure showing the morphological shapes of strain 6T19T and a supplementary table showing the cellular fatty-acid content of Ureibacillus suwonensis and other Ureibacillus species are available in IJSEM Online.
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and it comprises two ureolytic thermophilic bacilli species, Ureibacillus thermosphaericus and Ureibacillus terrenus. In Korea, composted cotton wastes are frequently used as medium for cultivation of oyster mushroom, Pleurotus ostreatus. During the sterilization and composting of cotton wastes, the temperature of composts is raised gradually from room temperature to 65 °C. Two bacterial strains were obtained from the cotton wastes during the composting process.
These strains were isolated from trypticase soy agar (TSA) at pH 7·0 incubated at 50 °C and maintained in TSA medium. Colonies were not detected as single entities because of the smeared growth on both TSA and nutrient agar (Oxoid). Gram staining was done by using a Gram stain kit (Difco) according to the manufacturer's recommended protocol. KOH test and L-alanine aminopeptidase assay were also used (Gregersen, 1978). The presence of flagella was sought according to Heimbrook et al. (1989). Cell morphology was observed in a phase-contrast microscope after incubation for 2 days on CASO agar (DSMZ medium no. 220; http://www.dsmz.de/media/media.htm) supplemented with 10 mg MnSO4 l–1. Cells grown on TSA for 24 h were examined by scanning electron microscopy. An agar block was cut from the plate, fixed in 1 % osmium tetroxide and observed under a scanning electron microscope (Hitachi S-2460N).
The following physiological tests were carried out according to Gordon et al. (1973) and Claus & Berkeley (1986): catalase test, anaerobic growth, Voges–Proskauer (VP) test, temperature range for growth (5–70 °C, increments of 5 °C), egg-yolk reaction, resistance to lysozyme, growth in the presence of NaCl (0, 2, 5, 7 and 10 %), growth at pH 5·7, acids from carbohydrates (D-glucose, L-arabinose, D-xylose and D-mannitol), formation of gas from glucose, hydrolysis of starch, utilization of citrate and propionate, nitrate reduction, production of indole, deamination of phenylalanine, decomposition of casein and tyrosine and liquefaction of gelatin. Oxidase test and hydrolysis of aesculin were conducted according to Smibert & Krieg (1994). Motility test was performed on 1/10 CESP agar (1·5 g casitone, 0·5 g yeast extract, 0·3 g soytone, 0·2 g peptone, 0·015 g MgSO4, 0·007 g FeCl2, 0·002 g MnCl2, made up to 1 l with distilled water, pH 7·2) (Fortina et al., 2001).
The 16S rRNA gene sequences were determined by PCR amplification (Kwon et al., 2003) and direct sequencing (Hiraishi, 1992). The 16S rRNA gene sequences were aligned by using the MEGALIGN program of DNASTAR. An evolutionary distance matrix was generated as described by Jukes & Cantor (1969). The evolutionary tree for the datasets was inferred from the neighbour-joining method of Saitou & Nei (1987) by using MEGA version 2.1 (Kumar et al., 2001). The stability of relationships was assessed by performing bootstrap analyses of the neighbour-joining data based on 1000 resamplings.
DNA–DNA hybridization was carried out as a filter-hybridization method described by Seldin & Dubnau (1985). Probe labelling was conducted by using the non-radioactive DIG-High prime system (Roche) and hybridized DNA was visualized by using the DIG luminescent detection kit (Roche). DNA–DNA relatedness was quantified by using a densitometer (Bio-Rad). The DNA G+C content (mol%) was determined by HPLC analysis of deoxyribonucleosides as described by Mesbah et al. (1989) using a reverse-phase column (Supelcosil LC-18-S; Supelco).
Peptidoglycan structure, menaquinones and polar lipids were analysed according to Fortina et al. (2001). After growth of cells on TSA for 24 h at 50 °C, fatty acid methyl esters were extracted and prepared by the standard protocol of the Microbial Identification system (MIDI; Microbial ID).
Supplementary Fig. S1 showing the morphological shapes of strain 6T19T is available in IJSEM Online. Comparisons of phenotypic properties among Ureibacillus species are presented in Table 1. In the report of the novel genus Ureibacillus, Fortina et al. (2001) characterized the genus as ureolytic, aerobic bacilli. For the urease test of the Ureibacillus species, Fortina et al. (2001) used the method by Atlas (1993), which relies on the demonstration of alkalinity. However, alkalinity can be produced from the use of peptone or other proteins in the medium, showing false-positive results (MacFaddin, 2000). In our tests, based on two different media, the medium used by Fortina et al. (2001) changed from yellow to pink–red colour, indicating a positive reaction. However, both control media inoculated with and without urea also showed a colour change to pink, indicating it to be an inappropriate test for urease of Ureibacillus strains. On the other hand, the cultures which were inoculated in Rustigian and Stuart's urea broth showed no colour change, indicating a negative reaction in all the strains tested. The phenotypic comparison among Ureibacillus species is shown in Table 1.
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). Strains 6T19T and 6T29 fell within the radiation of cluster comprising the two Ureibacillus species and Bacillus thermocloacae DSM 5250T (Fig. 1). The 16S rRNA gene sequence similarity between strains 6T19T and 6T29 was 99·8 %. The closest relatives of strain 6T19T were U. terrenus (97·5 %) and U. thermosphaericus (96·9 %). On the other hand, strain 6T19T was very distinct from species classified in other genera (<92 % sequence similarity).
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). The DNA–DNA reassociation values of 6T19T with U. thermosphaericus DSM 10633T and U. terrenus DSM 12654T proved to be 37 and 41 %, respectively. The DNA G+C content of strain 6T19T was 41·5 mol%.
Strains 6T19T and 6T29 contained L-lysD-Asp type (variation A4
) (A11.31) as the diagnostic diamino acid in the cell-wall peptidoglycan. The isoprenoid quinone composition of 6T19T was MK-9, MK-8, MK-7, MK-10 and MK-6 (45 : 27 : 18 : 5 : 4 %), and 6T29 contained MK-9, MK-8, MK-7, MK-6 and MK-10 (36 : 30 : 27 : 5 : 2 %). Strains 6T19T and 6T29 contained straight-chain and terminally saturated fatty acids with a composition of 5–6 and 76–85 %, respectively (Supplementary Table S1 available in IJSEM Online). No significant differences in fatty-acid profiles were found with other Ureibacillus species, except that strains 6T19T and 6T29 produced a higher proportion of ai-C17 : 0 and lower proportions of C16 : 0, i-C15 : 0 and i-C17 : 0 than the type strains of the two Ureibacillus species. Polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition.
On the basis of the polyphasic data, strains 6T19T and 6T29 can be described as members of a novel species of the genus Ureibacillus, for which the name Ureibacillus suwonensis sp. nov. is proposed.
Description of Ureibacillus suwonensis sp. nov.
Ureibacillus suwonensis (su.won.en'sis. N.L. masc. adj. suwonensis referring to Suwon Region in Korea, where the bacteria were first found).
Cells are Gram-negative, spore-forming rods, 0·5–0·7x1·5–2·0 µm in size, single or in chains. Cells form spherical or oval spores, occurring subterminally or terminally in swollen sporangia. Cells are peritrichously flagellated and motile. Clear colonies are not formed. Colonies grow smeared. Growth occurs at temperatures ranging from 35 to 60 °C and in the presence of 5 % NaCl. Positive for catalase, oxidase and arginine dihydrolase. Weak reaction for phenylalanine deamination. Negative for anaerobic growth, formation of indole and dihydroxyacetone, VP test, nitrate reduction, acid production from D-glucose, L-arabinose, D-xylose and D-mannitol and hydrolysis of aesculin, starch, gelatin, casein and urea. The cross-linkage of peptidoglycan is L-lysD-Asp type (variation A4). The major cellular fatty acid is i-C16 : 0. The major isoprenoid quinones are MK-9, MK-8 and MK-7. The DNA G+C content of the type strain 6T19T is 41·5 mol%.
The type strain, 6T19T (=KACC 11287T=DSM 16752T), was isolated from cotton composts in Suwon, Korea.
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
|---|
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.
Claus, D. & Berkeley, R. C. W. (1986). Genus Bacillus Cohn 1872. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1105–1140. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Fortina, M. G., Pukall, R., Schumann, P., Mora, D., Parini, C., Manachini, P. L. & Stackebrandt, E. (2001). Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Anderson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov. Int J Syst Evol Microbiol 51, 447–455.[Abstract]
Gordon, R. E., Haynes, W. C. & Pang, C. H.-N. (1973). The Genus Bacillus. Agriculture Handbook no. 427. Washington, DC: US Department of Agriculture.
Gregersen, T. (1978). Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5, 123–127.[CrossRef]
Heimbrook, M. E., Wang, W. L. L. & Campbell, G. (1989). Staining bacterial flagella easily. J Clin Microbiol 27, 2612–2615.
Hiraishi, A. (1992). Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15, 210–213.[Medline]
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.
Kwon, S. W., Kim, J. S., Park, I. C., Yoon, S. H., Park, D. H., Lim, C. K. & Go, S. J. (2003). Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int J Syst Evol Microbiol 53, 21–27.
MacFaddin, J. F. (2000). Urease test. In Biochemical Tests for Identification of Medical Bacteria, 3rd edn, pp. 424–438. Baltimore: Lippincott Williams & Wilkins.
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.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Seldin, L. & Dubnau, D. (1985). Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. Int J Syst Bacteriol 35, 151–154.
Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
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