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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 5

sp. nov., a novel betaproteobacterium isolated from lysimeter soil Free

Abstract

A Gram-negative, strictly aerobic bacterium, designated strain byr23-80, was isolated from lysimeter soil by using a high-throughput cultivation technique. Cells of strain byr23-80 were found to be short rods that multiplied by binary fission and were motile by means of a single polar flagellum. Occasionally, two to three polar or lateral flagella were observed. The optimum growth temperature was 15 °C and the pH optimum was 7.0–7.5. The predominant cellular fatty acids were C 7 (54.7 %) and C (21.4 %). In addition, the diagnostic fatty acids C 3-OH and C 2-OH were detected. Q-8 was the predominant respiratory quinone. The isolate was physiologically very versatile, using a wide range of sugars, organic acids and amino acids as single carbon and energy sources for growth. The G+C content of the genomic DNA was 65.3 mol%. Phylogenetic analyses supported the assignment of strain byr23-80 to the genus within the family of the class . Within the genus, strain byr23-80 was most closely related to DSM 18055, with a 16S rRNA gene sequence similarity of 98.3 %. However, DNA–DNA hybridization revealed a pairwise similarity for the genomic DNA of only 20.1 % between strain byr23-80 and strain DSM 18055. The novel isolate could be distinguished from the existing species , , , , and by its significantly lower temperature optimum for growth and by the absence of gelatinase, -galactosidase and -galactosidase activities. On the basis of these characteristics, strain byr23-80 constitutes a novel species of the genus , for which the name sp. nov. is proposed. The type strain is byr23-80 (=DSM 18925=ATCC BAA-1465).

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Keyword(s): TEM, transmission electron microscopy
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2008-05-01
2024-04-25
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References

  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Angle, J. S., McGrath, S. P. & Chaney, R. L.(1991). New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution. Appl Environ Microbiol 57, 3674–3676. [Google Scholar]
  3. Bodour, A. A., Wang, J. M., Brusseau, M. L. & Maier, R. M.(2003). Temporal changes in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environ Microbiol 5, 888–895.[CrossRef] [Google Scholar]
  4. Bruns, A., Hoffelner, H. & Overmann, J.(2003). A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol Ecol 45, 161–171.[CrossRef] [Google Scholar]
  5. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M.(1977). A rapid method for base ratio determination of bacterial DNA. Anal Biochem 81, 461–466.[CrossRef] [Google Scholar]
  6. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  7. Ederer, G. M., Chu, J. H. & Blazevic, D. J.(1971). Rapid test for urease and phenylalanine deaminase production. Appl Microbiol 21, 545 [Google Scholar]
  8. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  9. Gallego, V., Sánchez-Porro, C., García, M. T. & Ventosa, A.(2006).Massilia aurea sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 56, 2449–2453.[CrossRef] [Google Scholar]
  10. Gich, F. & Overmann, J.(2006).Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. Int J Syst Evol Microbiol 56, 847–854.[CrossRef] [Google Scholar]
  11. Gich, F., Schubert, K., Bruns, A., Hoffelner, H. & Overmann, J.(2005). Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl Environ Microbiol 71, 5908–5919.[CrossRef] [Google Scholar]
  12. 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.[CrossRef] [Google Scholar]
  13. Khammar, N., Malhautier, L., Degrange, V., Lensi, R., Godon, J.-J. & Fanlo, J.-L.(2005). Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters. J Appl Microbiol 98, 476–490.[CrossRef] [Google Scholar]
  14. Kuykendall, L. D., Roy, M. A., O'Neill, J. J. & Devine, T. E.(1988). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38, 358–361.[CrossRef] [Google Scholar]
  15. La Scola, B., Birtles, R. J., Mallet, M.-N. & Raoult, D.(1998).Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 36, 2847–2852. [Google Scholar]
  16. Lane, D. J.(1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  17. Lányí, B.(1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67. [Google Scholar]
  18. Lindquist, D., Murrill, D., Burran, W. P., Winans, G., Janda, J. M. & Probert, W.(2003). Characteristics of Massilia timonae and Massilia timonae-like isolates from human patients, with an emended description of the species. J Clin Microbiol 41, 192–196.[CrossRef] [Google Scholar]
  19. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors(2004).arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef] [Google Scholar]
  20. Mandel, M., Igambi, L., Bergendahl, J., Dodson, M. L. & Scheltgen, E.(1970). Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 101, 333–338. [Google Scholar]
  21. Marmur, J.(1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef] [Google Scholar]
  22. Miller, L. T.(1982). A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 16, 584–586. [Google Scholar]
  23. Øvreas, L., Daae, F. L., Torsvik, V. & Rodríguez-Valera, F.(2003). Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 46, 291–301.[CrossRef] [Google Scholar]
  24. Padmanabhan, P., Padmanabhan, S., DeRito, C., Gray, A., Gannon, D., Snape, J. R., Tsai, C. S., Park, W., Jeon, C. & Madsen, E. L.(2003). Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Appl Environ Microbiol 69, 1614–1622.[CrossRef] [Google Scholar]
  25. Skerman, V. B. D.(1967).A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore: Williams & Wilkins.
  26. Spurr, A. R.(1969). A low-viscosity epoxy resin embedding medium for electron microscopy. J Ultrastruct Res 26, 31–43.[CrossRef] [Google Scholar]
  27. 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.[CrossRef] [Google Scholar]
  28. Tindall, B. J.(1990a). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128–130.[CrossRef] [Google Scholar]
  29. Tindall, B. J.(1990b). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199–202.[CrossRef] [Google Scholar]
  30. 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.[CrossRef] [Google Scholar]
  31. Zhang, Y.-Q., Li, W.-J., Zhang, K.-Y., Tian, X.-P., Jiang, Y., Xu, L.-H., Jiang, C.-L. & Lai, R.(2006).Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China. Int J Syst Evol Microbiol 56, 459–463.[CrossRef] [Google Scholar]
  32. Zul, D., Denzel, S. & Overmann, J.(2007). Effects of plant biomass, plant diversity and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity. Appl Environ Microbiol 73, 6916–6929.[CrossRef] [Google Scholar]
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Massilia brevitalea sp. nov., a novel betaproteobacterium isolated from lysimeter soil
Int J Syst Evol Microbiol 58, 1245 (2008); https://doi.org/10.1099/ijs.0.65473-0
/content/journal/ijsem/10.1099/ijs.0.65473-0
/content/journal/ijsem/10.1099/ijs.0.65473-0
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