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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 5

sp. nov., a species of the family ‘’ isolated from soil of a ginseng field Free

Abstract

A taxonomic study was carried out on Gsoil 085, a bacterial strain isolated from a soil sample from a ginseng field in Pocheon Province (South Korea). Comparative 16S rRNA gene sequence studies showed a clear affiliation of this bacterium to the family ‘’ and indicated that the closest relative was GPTSA100-15 (94.6 % sequence similarity). Lower sequence similarities (<83.0 %) were found with respect to all other recognized species of the family ‘’. Strain Gsoil 085 was found to be Gram-negative, strictly aerobic, non-motile and rod-shaped. It grew well on half-strength R2A medium but did not utilize a broad range of carbon sources. The G+C content of the genomic DNA was 40.5 mol%. The major fatty acids were summed feature 4 (iso-C 2-OH and/or C 7, 45.4 %), iso-C (13.9 %), C 5 (8.6 %) and C (8.2 %). On the basis of evidence from the polyphasic study, strain Gsoil 085 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Gsoil 085 (=KCTC 12588 =LMG 23396).

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2008-05-01
2024-05-01
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References

  1. Atlas, R. M.(1993).Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  2. Bowman, J. P., Nichols, C. M. & Gibson, J. A. E.(2003).Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 53, 1343–1355.[CrossRef] [Google Scholar]
  3. Brettar, I., Christen, R. & Höfle, M. G.(2004).Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54, 2335–2341.[CrossRef] [Google Scholar]
  4. Buck, J. D.(1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993. [Google Scholar]
  5. Cappuccino, J. G. & Sherman, N.(2002).Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
  6. Felsenstein, J.(1985). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  7. Glöckner, F. O., Fuchs, B. M. & Amann, R.(1999). Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65, 3721–3726. [Google Scholar]
  8. Hall, T. A.(1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98. [Google Scholar]
  9. Höfle, M. G.(1982). Glucose uptake of Cytophaga johnsonae studied in batch and chemostat culture. Arch Microbiol 133, 289–294.[CrossRef] [Google Scholar]
  10. Im, W.-T., Jung, H.-M., Cui, Y.-S., Liu, Q.-M., Zhang, S.-L. & Lee, S.-T.(2005). Cultivation of the three hundreds of bacterial species from soil of a ginseng field and mining the novel lineage bacteria. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract A035, p. 169. Seoul: Federation of Korean Microbiological Societies.
  11. Ivanova, E. P., Alexeeva, Y. V., Flavier, S., Wright, J. P., Zhukova, N. V., Gorshkova, N. M., Mikhailov, V. V., Nicolau, D. V. & Christen, R.(2004).Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 54, 705–711.[CrossRef] [Google Scholar]
  12. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T.(2005).Sphingopyxis granuli sp. nov., a β-glucosidase producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152–157. [Google Scholar]
  13. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  14. Kouker, G. & Jaeger, K.-E.(1987). Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53, 211–213. [Google Scholar]
  15. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  16. Lau, K. W. K., Ng, C. Y. M., Ren, J., Lau, S. C. L., Qian, P.-Y., Wong, P.-K., Lau, T. C. & Wu, M.(2005).Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’. Int J Syst Evol Microbiol 55, 1051–1057.[CrossRef] [Google Scholar]
  17. Liu, Q.-M., Im, W.-T., Lee, M., Yang, D.-C. & Lee, S.-T.(2006).Dyadobacter ginsengisoli sp. nov. isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 56, 1939–1944.[CrossRef] [Google Scholar]
  18. Ludwig, W. & Klenk, H.-P.(2001). Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 49–65. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  19. 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.[CrossRef] [Google Scholar]
  20. Moore, D. D. & Dowhan, D.(1995). Preparation and analysis of DNA. In Current Protocols in Molecular Biology, pp. 2–11. Edited by F. W. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
  21. Nedashkovskaya, O. I., Kim, S. B., Han, S. K., Rhee, M. S., Lysenko, A. M., Falsen, E., Frolova, G. M., Mikhailov, V. V. & Bae, K. S.(2004).Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 54, 119–123.[CrossRef] [Google Scholar]
  22. Nedashkovskaya, O. I., Kim, S. B., Lysenko, A. M., Frolova, G. M., Mikhailov, V. V., Lee, K. H. & Bae, K. S.(2005). Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov. Int J Syst Evol Microbiol 55, 225–229.[CrossRef] [Google Scholar]
  23. Nikitin, D. I., Strömpl, C., Oranskaya, M. S. & Abraham, W.-R.(2004). Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp. nov. (ex Nikitin et al. 1994), from a freshwater neuston biofilm. Int J Syst Evol Microbiol 54, 681–684.[CrossRef] [Google Scholar]
  24. O'Sullivan, L. A., Rinna, J., Humphreys, G., Weightman, A. J. & Fry, J. C.(2005).Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum ‘Bacteroidetes’. Int J Syst Evol Microbiol 55, 2189–2194.[CrossRef] [Google Scholar]
  25. O'Sullivan, L. A., Rinna, J., Humphreys, G., Weightman, A. J. & Fry, J. C.(2006). Culturable phylogenetic diversity of the phylum ‘Bacteroidetes’ from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int J Syst Evol Microbiol 56, 169–180.[CrossRef] [Google Scholar]
  26. Pinhassi, J., Azam, F., Hemphälä, J., Long, R. A., Martinez, J., Zweifel, U. L. & Hagström, Å.(1999). Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation. Aquat Microb Ecol 17, 13–26.[CrossRef] [Google Scholar]
  27. Reasoner, D. J. & Geldreich, E. E.(1985). A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49, 1–7. [Google Scholar]
  28. Reichenbach, H.(1989). The order Cytophagales Leadbetter 1974, 99AL. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 2011–2073. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. C. Holt. Baltimore: Williams & Wilkins.
  29. Rickard, A. H., Stead, A. T., O'May, G. A., Lindsay, S., Banner, M., Handley, P. S. & Gilbert, P.(2005).Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm. Int J Syst Evol Microbiol 55, 821–829.[CrossRef] [Google Scholar]
  30. Saha, P. & Chakrabarti, T.(2006).Emticicia oligotrophica gen. nov., sp. nov., a new member of the family ‘Flexibacteraceae’, phylum Bacteroidetes. Int J Syst Evol Microbiol 56, 991–995.[CrossRef] [Google Scholar]
  31. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  32. Sasser, M.(1990).Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  33. Sohn, J. H., Lee, J.-H., Yi, H., Chun, J., Bae, K. S., Ahn, T.-Y. & Kim, S.-J.(2004).Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide. Int J Syst Evol Microbiol 54, 675–680.[CrossRef] [Google Scholar]
  34. 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]
  35. Ten, L. N., Im, W.-T., Kim, M.-K., Kang, M.-S. & Lee, S.-T.(2004). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56, 375–382.[CrossRef] [Google Scholar]
  36. 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.[CrossRef] [Google Scholar]
  37. Tschech, A. & Pfennig, N.(1984). Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 137, 163–167.[CrossRef] [Google Scholar]
  38. Van Trappen, S., Vandecandelaere, I., Mergaert, J. & Swings, J.(2004).Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol 54, 445–448.[CrossRef] [Google Scholar]
  39. Widdel, F. & Bak, F.(1992). Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes, 2nd edn, pp. 3352–3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  40. Widdel, F., Kohring, G. & Mayer, F.(1983). Studies in dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134, 286–294.[CrossRef] [Google Scholar]
  41. Yi, H. & Chun, J.(2004).Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 157–162.[CrossRef] [Google Scholar]
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Emticicia ginsengisoli sp. nov., a species of the family ‘Flexibacteraceae’ isolated from soil of a ginseng field
Int J Syst Evol Microbiol 58, 1100 (2008); https://doi.org/10.1099/ijs.0.65386-0
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