1887

Abstract

An exopolysaccharide-producing bacterium, designated strain DRP 35, was isolated from the rhizosphere soil of a medicinal herb, at Geumsan in Korea. Cells were Gram-staining-negative, non-motile, catalase-positive and oxidase-negative short rods. The isolate grew aerobically from 15 to 45 °C (optimum 30 °C), pH 3.5–7.0 (optimum pH 5.0) and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain DRP 35 belongs to the genus in the phylum with a sequence similarity of 97.2 % and 97.0 % to SP1PR4 and KBS63, respectively. The genomic DNA G+C content was 62.1 mol%. DNA–DNA relatedness between strain DRP 35 and the type strains of the other species of the genus SP1PR4 and KBS63, were 24.6 and 17.2 %, respectively. The predominant menaquinone was MK-8. Major fatty acids were iso-C, Cω7 and C. The polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and unknown phospholipids. On the basis of polyphasic analysis from this study, strain DRP 35 represents a novel species of the genus for which the name Terriglobus sp. nov. is proposed. The type strain is DRP 35 ( = KACC 16474 = NBRC 109677).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.053769-0
2014-02-01
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/2/431.html?itemId=/content/journal/ijsem/10.1099/ijs.0.053769-0&mimeType=html&fmt=ahah

References

  1. Coates J. D., Ellis D. J., Gaw C. V., Lovley D. R.. ( 1999;). Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. . Int J Syst Bacteriol 49:, 1615–1622. [CrossRef][PubMed]
    [Google Scholar]
  2. Collins M. D., Jones D.. ( 1981;). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45:, 316–354.[PubMed]
    [Google Scholar]
  3. Dedysh S. N., Kulichevskaya I. S., Serkebaeva Y. M., Mityaeva M. A., Sorokin V. V., Suzina N. E., Rijpstra W. I. C., Damsté J. S.. ( 2012;). Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. . Int J Syst Evol Microbiol 62:, 654–664. [CrossRef][PubMed]
    [Google Scholar]
  4. DeLong E. F.. ( 1992;). Archaea in coastal marine environments. . Proc Natl Acad Sci U S A 89:, 5685–5689. [CrossRef][PubMed]
    [Google Scholar]
  5. Eichorst S. A., Breznak J. A., Schmidt T. M.. ( 2007;). Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. . Appl Environ Microbiol 73:, 2708–2717. [CrossRef][PubMed]
    [Google Scholar]
  6. 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]
  7. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J.. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. 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]
  10. Fukunaga Y., Kurahashi M., Yanagi K., Yokota A., Harayama S.. ( 2008;). Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum ‘Acidobacteria’. . Int J Syst Evol Microbiol 58:, 2597–2601. [CrossRef][PubMed]
    [Google Scholar]
  11. Janssen P. H.. ( 2006;). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. . Appl Environ Microbiol 72:, 1719–1728. [CrossRef][PubMed]
    [Google Scholar]
  12. 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]
  13. Kimura M.. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef][PubMed]
    [Google Scholar]
  14. Kishimoto N., Kosako Y., Tano T.. ( 1991;). Acidobacteria capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. . Curr Microbiol 22:, 1–7. [CrossRef]
    [Google Scholar]
  15. Koch I. H., Gich F., Dunfield P. F., Overmann J.. ( 2008;). Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. . Int J Syst Evol Microbiol 58:, 1114–1122. [CrossRef][PubMed]
    [Google Scholar]
  16. Kulichevskaya I. S., Suzina N. E., Liesack W., Dedysh S. N.. ( 2010;). Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. . Int J Syst Evol Microbiol 60:, 301–306. [CrossRef][PubMed]
    [Google Scholar]
  17. Kulichevskaya I. S., Kostina L. A., Valášková V., Rijpstra W. I. C., Damsté J. S. S., Boer W., Dedysh S. N.. ( 2012;). Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.. [CrossRef][PubMed]
    [Google Scholar]
  18. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A.. & other authors ( 2007;). clustal w and clustal x version 2.0. . Bioinformatics 23:, 2947–2948. [CrossRef][PubMed]
    [Google Scholar]
  19. Liesack W., Bak F., Kreft J. U., Stackebrandt E.. ( 1994;). Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. . Arch Microbiol 162:, 85–90. [CrossRef][PubMed]
    [Google Scholar]
  20. Losey N. A., Stevenson B. S., Busse H. J., Damsté J. S., Rijpstra W. I. C., Rudd S., Lawson P. A.. ( 2013;). Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring. . Int J Syst Evol Microbiol 63:, 4149–4157. [CrossRef][PubMed]
    [Google Scholar]
  21. Männistö M. K., Rawat S., Starovoytov V., Häggblom M. M.. ( 2011;). Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. . Int J Syst Evol Microbiol 61:, 1823–1828. [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Murray R. G. E., Doetsch R. N., Robinow F.. ( 1994;). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 21–41. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  25. Pankratov T. A., Dedysh S. N.. ( 2010;). Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella. rosea sp. nov., novel acidophilic, polymer-degrading Acidobacteria from Sphagnum peat bogs. . Int J Syst Evol Microbiol 60:, 2951–2959. [CrossRef][PubMed]
    [Google Scholar]
  26. Pankratov T. A., Kirsanova L. A., Kaparullina E. N., Kevbrin V. V., Dedysh S. N.. ( 2012;). Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. . Int J Syst Evol Microbiol 62:, 430–437. [CrossRef][PubMed]
    [Google Scholar]
  27. Parte A. C.. ( 2013;). List of prokaryotic names with standing in nomenclature. . http://www.bacterio.net/ [Last full update 23 October 2013].
  28. Rosselló-Mora R., Amann R.. ( 2001;). The species concept for prokaryotes. . FEMS Microbiol Rev 25:, 39–67. [CrossRef][PubMed]
    [Google Scholar]
  29. Saito H., Miura K. I.. ( 1963;). Preparation of transforming deoxyribonucleic acid by phenol treatment. . Biochim Biophys Acta 72:, 619–629. [CrossRef][PubMed]
    [Google Scholar]
  30. 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]
  31. Sinninghe Damsté J. S., Rijpstra W. I. C., Hopmans E. C., Weijers J. W. H., Foesel B. U., Overmann J., Dedysh S. N.. ( 2011;). 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. . Appl Environ Microbiol 77:, 4147–4154. [CrossRef][PubMed]
    [Google Scholar]
  32. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  33. Stackebrandt E., Ebers J.. ( 2006;). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33:, 152–155.
    [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. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J.. & other authors ( 2002;). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52:, 1043–1047. [CrossRef][PubMed]
    [Google Scholar]
  36. Tamaoka J., Komagata K.. ( 1984;). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25:, 125–128. [CrossRef]
    [Google Scholar]
  37. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.053769-0
Loading
/content/journal/ijsem/10.1099/ijs.0.053769-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error