1887
  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 66, Issue 5
  5. Article

f sp. nov. and sp. nov. isolated from a ginseng-cultivating field

HTML
55.08 Kb
PDF
197.61 Kb
  • Authors: Hye-Yeon Lee1 ,  Qingmei Liu1,2 ,  Myung-Suk Kang3 ,  Soo-Ki Kim4 ,  Soon-Youl Lee1 , Wan-Taek Im1,2
    • VIEW AFFILIATIONS
    • 1 1Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea 2 2Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea 3 3Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-708, Republic of Korea 4 4Department of Animal Science and Technology, Konkuk University, Seoul 05029, Republic of Korea
  • Wan-Taek Im [email protected]
  • First Published Online: 01 May 2016, International Journal of Systematic and Evolutionary Microbiology 66: 1996-2001, doi: 10.1099/ijsem.0.000977
  • Subject: NEW TAXA - Actinobacteria
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

sp. nov. and sp. nov. isolated from a ginseng-cultivating field, Page 1 of 1

| /docserver/preview/fulltext/ijsem/66/5/1996_ijsem000977-1.gif

  • Two novel actinobacteria, designated strains Gsoil 097 and Gsoil 818, isolated from soil of a ginseng field, South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. They were Gram-reaction-positive, aerobic, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus and were related most closely to KIS18-7 (99.1 and 98.3 % similarity, respectively), JOS5-1 (97.9 and 97.9 %), Sco-D01 (97.8 and 97.1 %) and SST-45 (97.5 and 97.0 %). The G+C content of the genomic DNA was 68.8 and 70.0 mol%, respectively. Both strains were characterized chemotaxonomically as having -2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H) as the predominant menaquinone and Cω6, Cω9, C 10-methyl and iso-C as major fatty acids. These chemotaxonomic data supported the affiliation of both strains to the genus . However, levels of DNA–DNA relatedness between the two strains and closely related type strains of species were less than 30 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 097 and Gsoil 818 from other species with validly published names. Therefore, the two isolates represent two novel species, for which the names sp. nov. (type strain Gsoil 097 = KACC 14267 = DSM 22772) and sp. nov. (type strain Gsoil 818 = KACC 14275 = DSM 22773) are proposed.

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains Gsoil 097 and Gsoil 818 are GQ339892 and GQ339906, respectively.

  • Two supplementary tables and three supplementary figures are available with the online Supplementary Material.

© 2016 IUMS | Published by the Microbiology Society

  • Atlas R. M.. ( 1993;). Handbook of Microbiological Media. Edited by Parks L. C. Boca Raton, FL: CRC Press;.
     [Google Scholar]
  • Buck J. D.. ( 1982;). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44: 992––993 [PubMed].
     [Google Scholar]
  • Cappuccino J.G, Sherman N.. ( 2002;). Microbiology: A Laboratory Manual, 6th edn.., Benjamin Cummings, CA: Pearson Education;.
     [Google Scholar]
  • Dastager S. G., Lee J. C., Ju Y. J., Park D. J., Kim C. J.. ( 2008;). Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae. Int J Syst Evol Microbiol 58: 1060––1063 [CrossRef] [PubMed].
     [Google Scholar]
  • de Menezes C. B., Tonin M. F., Silva L. J., de Souza W. R., Parma M., de Melo I. S., Zucchi T. D., Destéfano S. A., Fantinatti-Garboggini F.. ( 2015;). Marmoricola aquaticus sp. nov., an actinomycete isolated from a marine sponge. Int J Syst Evol Microbiol 65: 2286––2291 [CrossRef] [PubMed].
     [Google Scholar]
  • Ezaki T., Hashimoto Y., Yabuuchi E.. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39: 224––229 [CrossRef].
     [Google Scholar]
  • Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368––376 [CrossRef] [PubMed].
     [Google Scholar]
  • Felsenstein J.. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39: 783––791 [CrossRef].
     [Google Scholar]
  • Fitch W. M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406––416 [CrossRef].
     [Google Scholar]
  • 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]
  • Hiraishi A., Ueda Y., Ishihara J., Mori T.. ( 1996;). Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42: 457––469 [CrossRef].
     [Google Scholar]
  • Kim O. S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716––721 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim J. K., Kang M. S., Park S. C., Kim K. M., Choi K., Yoon M. H., Im W. T.. ( 2015a;). Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 53: 435––441 [CrossRef] [PubMed].
     [Google Scholar]
  • Kim S. J., Lim J. M., Hamada M., Ahn J. H., Weon H. Y., Suzuki K., Ahn T. Y., Kwon S. W.. ( 2015b;). Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola. Int J Syst Evol Microbiol 65: 1825––1830 [CrossRef] [PubMed].
     [Google Scholar]
  • Kimura M.. ( 1983;). The Neutral Theory of Molecular Evolution Cambridge:: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  • Komagata K., Suzuki K.. ( 1988;). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19: 161––207 [CrossRef].
     [Google Scholar]
  • Lee S. D.. ( 2007;). Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 57: 1391––1395 [CrossRef] [PubMed].
     [Google Scholar]
  • Lee D. W., Lee S. D.. ( 2010;). Marmoricola scoriae sp. nov., isolated from volcanic ash. Int J Syst Evol Microbiol 60: 2135––2139 [CrossRef] [PubMed].
     [Google Scholar]
  • Lee S. D., Lee D. W., Ko Y. H.. ( 2011;). Marmoricola korecus sp. nov. Int J Syst Evol Microbiol 61: 1628––1631 [CrossRef] [PubMed].
     [Google Scholar]
  • 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]
  • Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2: 233––241 [CrossRef].
     [Google Scholar]
  • Moore D. D., Dowhan D.. ( 1995;). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 2––11. Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K.. New York: Wiley;.
     [Google Scholar]
  • Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406––425 [PubMed].
     [Google Scholar]
  • Sasser M.. ( 1990;). Identification of bacteria through fatty acid analysis. . In Methods in Phytobacteriology, pp. 199––204. Edited by Klement Z., Rudolph K., Sands D. C.. Budapest: Akademiai Kaido;.
     [Google Scholar]
  • Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0.. Mol Biol Evol 30: 2725––2729 [CrossRef] [PubMed].
     [Google Scholar]
  • 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] [PubMed].
     [Google Scholar]
  • 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] [PubMed].
     [Google Scholar]
  • Urzig C., Salamone P., Schumann P., Stackebrandt E.. ( 2000;). Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50: 529––536 [CrossRef] [PubMed].
     [Google Scholar]
  • 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]
http://sgm.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000977
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000977
2016-05-01
2019-02-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/5/1996.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000977&mimeType=html&fmt=ahah

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error