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State Key Laboratory of Microbial Resources at the Institute of Microbiology, Chinese Academy of Sciences, Zhong-Guan-Cun, Haidian, Beijing 100080, PR China
Correspondence
Shuang-Jiang Liu
shuangjiang{at}hotmail.com
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ABSTRACT |
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). At present, the genus Planomicrobium includes the following species: Planomicrobium mcmeekinii (Junge et al., 1998), Planomicrobium okeanokoites (Nakagawa et al., 1996) and Planomicrobium koreense (Yoon et al., 2001). Two species belonging to the genus Planococcus, Planococcus psychrophilus (Reddy et al., 2002) and Planococcus alkanoclasticus (Engelhardt et al., 2001), may also be members of the genus Planomicrobium (Yoon et al., 2003). During an ecological survey of the microbial diversity of coastal sediments from the Eastern China Sea in Fujian Province, China, a nitrate-reducing isolate, strain DX3-12T, was obtained. Characterization and classification of this isolate is described.
Strain DX3-12T was isolated from coastal sediment of the Eastern China Sea. Samples (4–6 cm beneath surface) were diluted with 9 ml sterile saline solution and 10–3 and 10–4 dilutions (0·1 ml) were plated onto artificial sea water basal medium with 1 % peptone and 0·5 % yeast extract (Eguchi et al., 1996). Routine cultivation of strain DX3-12T was done at 30 °C in marine broth 2216 (MB; Difco). Observation of the morphology of strain DX3-12T was carried out with optical (Olympus BX51) and scanning electron (Hitachi S-570) microscopes. Physiological and biochemical tests, including catalase and oxidase activities, decomposition of gelatin and casein and hydrolysis of starch were determined by the methods of Cowan & Steel (1965). Nitrate reductase production was evaluated as described by Lanyi (1987). NaCl tolerance was investigated by supplementing MB with various NaCl concentrations. The temperature and pH ranges for growth were determined in MB.
Biomass for chemotaxonomic analysis was harvested from MB cultures on a rotary shaker (100 r.p.m., 30 °C). Preparation of cell walls and determination of peptidoglycan structure were carried out using the methods of Schleifer & Kandler (1972). Menaquinones were extracted and purified according to Collins (1985) and were analysed by HPLC (Wu et al., 1989) with Planomicrobium mcmeekinii as the reference. The fatty acid profile of whole cells was analysed by GC with a model HP6890 equipped with a hydrogen ionization detector (FID). Peaks were identified with pre-installed software, HPCHEM-STATION (version A5.01).
Genomic DNA of strain DX3-12T was extracted according to Marmur (1961) and G+C content (mol%) was determined by thermal denaturation, with Escherichia coli K-12 as the reference. The 16S rRNA gene of strain DX3-12T was amplified and sequenced as described previously (Zhang et al., 2003). Alignments of 16S rRNA gene sequences of strain DX3-12T and other type strains of the genera Planomicrobium and Planococcus were carried out with CLUSTAL X version 1.8 (Thompson et al., 1997). Evolutionary distance calculations were performed according to Kimura (1980). Phylogenetic trees were constructed according to the neighbour-joining (Saitou & Nei, 1987) and maximum-parsimony tree-making algorithms in the PHYLIP software package (Felsenstein, 1993). Positions 31–1431 (E. coli numbering) were used in all phylogenetic analyses. DNA relatedness was determined by the method of De Ley et al. (1970).
Cells of strain DX3-12T were cocci or short rods, 0·8x1·0 µm. Detailed phenotypic properties are given in the species description. Physiological and biochemical characteristics of this strain that enable it to be distinguished from other type strains of Planomicrobium species are listed in Table 1. The cell wall composition of strain DX3-12T was determined and contained L-lysine, L-aspartic acid, L-glutamic acid and alanine, but not L-ornithine; this is consistent with the A4
type (Schleifer & Kandler, 1972) cell wall of Planomicrobium. The major menaquinones were MK-8 and MK-7, with a peak area ratio of 55 : 8. Cells of strain DX3-12T grown in MB contained anteiso-C15 : 0 (49·7 %) as the major fatty acid and significant amounts of C16 : 1
7c alcohol (12·1 %). The genomic DNA G+C content was 34·8 mol%.
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)]. These species gathered and formed a cluster with moderate bootstrap support, as indicated by either neighbour-joining (Fig. 1) or maximum-parsimony (data not shown). Strain DX3-12T could be distinguished phenotypically from other Planomicrobium species (Table 1
). DNA relatedness to Planomicrobium mcmeekinii DSM 13963T, a phylogenetically related and phenotypically similar species, was 35·4 %. DNA–DNA hybridization to other species of Planomicrobium was not attempted because of the large differences in G+C content between these species and strain DX3-12T (11·5–12·2 %; Table 1). Based on the above characteristics, strain DX3-12T was identified as a representative of a novel species of Planomicrobium; the name Planomicrobium chinense sp. nov. is proposed.
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) showed that two members of the genus Planococcus, Planococcus psychrophilus and Planococcus alkanoclasticus, clustered with members of the genus Planomicrobium, rather than with members of the genus Planococcus. This clustering is consistently supported by different tree construction methods. When the 16S rRNA gene sequences were further examined, these two species were shown to have sequence signatures at positions 183 and 190 (E. coli numbering) indicative of Planomicrobium rather than Planococcus (Table 2). In addition, cells of these two species are rods, unlike members of the genus Planococcus, which have coccoid cells. Thus, these two species are here transferred to the genus Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. The very recently described species Planococcus stackebrandtii (Mayilraj et al., 2005) also clustered within the Planomicrobium group (Fig. 1) and had Planomicrobium signature nucleotides at positions 183 and 190; this species may possibly be a member of the genus Planomicrobium.
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Cells are coccoid or short rods, 0·8x1·0 µm. Gram-positive and non-spore-forming. Motile by polar flagella. Strictly aerobic. Colonies are smooth, circular, low-convex and yellow to orange in colour when cultivated on MA. Growth occurs at 10–45 °C; optimum growth at 30–35 °C and no growth above 46 °C. Optimal pH for growth is 6·0–7·0; no growth occurs below pH 5·0 or above pH 10·0. Growth occurs in 0–10 % NaCl. Gelatin is hydrolysed, but not casein, starch, Tween 80 or aesculin. Acid is produced from glucose, but not from sucrose, raffinose, lactose, arabinose, cellobiose, xylose, rhamnose, melibiose, mannose or mannitol. Citrate does not support growth. Nitrate is reduced. Cell wall is type A4. Cells contain MK-8 as major menaquinone. The cellular fatty acid profile is as follows: iso-C14 : 0 (10·4 %), anteiso-C15 : 0 (49·7 %), iso-C15 : 0 (3·8 %), C15 : 0 (4·9 %), C16 : 17c alcohol (12·1 %), iso-C16 : 0 (4·1 %), C16 : 111c (4·5 %), C16 : 0 (1·5 %), iso-C17 : 110c (1·7 %), iso-C17 : 1 I (4·4 %) and anteiso-C17 : 0 (2·8 %).
The type strain, DX3-12T (=AS 1.3454T=JCM 12466T), was isolated from coastal sediment from the Eastern China Sea in Fujian Province, China. The DNA G+C content of the type strain is 34·8 mol%.
Description of Planomicrobium psychrophilum comb. nov.
Planomicrobium psychrophilum (psy.chro.phi'lum. Gr. n. psychros cold; Gr. adj. philos loving; N.L. neut. adj. psychrophilum cold-loving).
Basonym: Planococcus psychrophilus Reddy et al. 2002.
The description is as given previously by Reddy et al. (2002). The type strain is DSM 14507T (=MTCC 3812T).
Description of Planomicrobium alkanoclasticum comb. nov.
Planomicrobium alkanoclasticum (al.kan.o.cla'sti.cum. N.L. n. alkanum alkane; Gr. adj. clastos broken; N.L. neut. adj. alkanoclasticum breaking alkanes).
Basonym: Planococcus alkanoclasticus Engelhardt et al. 2001.
The description is as given previously by Engelhardt et al. (2001). The type strain is NCIMB 13489T (=MAE2T=CIP 107718T).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTMAIN TEXTREFERENCES |
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Cowan, S. T. & Steel, K. J. (1965). Manual for the Identification of Medical Bacteria. London: Cambridge University Press.
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 143–153.[Medline]
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Engelhardt, M. A., Daly, K., Swannell, R. P. J. & Head, I. M. (2001). Isolation and characterization of a novel hydrocarbon-degrading, Gram-positive bacterium, isolated from intertidal sediment, and description of Planococcus alkanoclasticus sp. nov. J Appl Microbiol 90, 237–247.[CrossRef][Medline]
Felsenstein, J. (1993). PHYLIP (phylogenetic inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, WA, USA.
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Mayilraj, S., Prasad, G. S., Suresh, K., Saini, H. S., Shivaji, S. & Chakrabarti, T. (2005). Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol 55, 91–94.
Nakagawa, N., Sakane, T. & Yokota, A. (1996). Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. nov. Int J Syst Bacteriol 46, 866–870.[CrossRef][Medline]
Reddy, G. S. N., Prakash, J. S. S., Vairamani, M., Prabhakar, S., Matsumoto, G. I. & Shivaji, S. (2002). Planococcus antarcticus and Planococcus psychrophilus spp. nov. isolated from cyanobacterial mat samples collected from ponds in Antarctica. Extremophiles 6, 253–261.[CrossRef][Medline]
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. & Kandler, O. (1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477.
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.
Wu, C., Lu, X., Qin, M., Wang, Y. & Ruan, J. (1989). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology (English translation of Mikrobiologiya) 16, 176–178.
Yoon, J.-H., Kang, S.-S., Lee, K.-C., Lee, E.-S., Kho, Y. H., Kang, K. E. & Park, Y.-H. (2001). Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol 51, 1511–1520.[Abstract]
Yoon, J.-H., Weiss, N., Kang, K.-H., Oh, T.-K. & Park, Y.-H. (2003). Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. Int J Syst Evol Microbiol 53, 2013–2017.
Zhang, D., Yang, H., Zhang, W., Huang, Z. & Liu, S.-J. (2003). Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant. Int J Syst Evol Microbiol 53, 1111–1114.
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