1887

Abstract

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated strain CR164, was isolated from the rhizosphere soil of a ginseng field at Geumsan in Korea. CR164 grew at between 15 and 37 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0–1.0 % (w/v) NaCl, growing optimally in the absence of NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that CR164 represents a member of the genus Rhodanobacter , showing the highest sequence similarity to Rhodanobacter caeni MJ01 (98.5 %), Rhodanobacter ginsenosidimutans Gsoil 3054 (98.4 %), Rhodanobacter thiooxydans LCS2 (98.3 %), Rhodanobacter lindaniclasticus RP5557 (98.1 %), Rhodanobacter denitrificans 2APBS1 (98.0 %), Rhodanobacter fulvus Jip2 (97.6 %), Rhodanobacter soli DCY45 (97.3 %) and ‘ Rhodanobacter xiangquanii’ BJQ-6 (97.0 %). The major fatty acids were iso-C17 : 1ω9c (21.8 %), iso-C15 : 0 (12.1 %), iso-C11 : 0 (11.9 %) and iso-C16 : 0 (11.1 %). The predominant ubiquinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the genomic DNA was 62.3 mol%. DNA–DNA relatedness between CR164 and the type strains of eight other species of the genus ranged from 51 to 9 %. On the basis of the polyphasic analysis, CR164 represents a novel species of the genus Rhodanobacter , for which the name Rhodanobacter rhizosphaerae sp. nov. is proposed. The type strain is CR164 (=KACC 18699=NBRC 111845).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001825
2017-05-30
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/5/1387.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001825&mimeType=html&fmt=ahah

References

  1. Nalin R, Simonet P, Vogel TM, Normand P. Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 1999;49:19–23 [CrossRef][PubMed]
    [Google Scholar]
  2. Parte AC. 2016; List of prokaryotic names with standing in nomenclature. www.bacterio.net
  3. Zhang J, Zheng JW, Hang BJ, Ni YY, He J et al. Rhodanobacter xiangquanii sp. nov., a novel anilofos-degrading bacterium isolated from a wastewater treating system. Curr Microbiol 2011;62:645–649 [CrossRef][PubMed]
    [Google Scholar]
  4. Weon HY, Kim BY, Hong SB, Jeon YA, Kwon SW et al. Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2007;57:2810–2813 [CrossRef][PubMed]
    [Google Scholar]
  5. An DS, Lee HG, Lee ST, Im WT. Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2009;59:691–694 [CrossRef][PubMed]
    [Google Scholar]
  6. Bui TP, Kim YJ, Kim H, Yang DC. Rhodanobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010;60:2935–2939 [CrossRef][PubMed]
    [Google Scholar]
  7. Wang L, An DS, Kim SG, Jin FX, Lee ST et al. Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2011;61:3028–3032 [CrossRef][PubMed]
    [Google Scholar]
  8. Kim YS, Kim SJ, Anandham R, Weon HY, Kwon SW. Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field. J Microbiol 2013;51:258–261 [CrossRef][PubMed]
    [Google Scholar]
  9. Murray RGE, Doetsch RN, Robinow F. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.21–41
    [Google Scholar]
  10. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  11. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987;19:1–67[CrossRef]
    [Google Scholar]
  12. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  13. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963;85:1183–1184[PubMed]
    [Google Scholar]
  14. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009;59:2114–2121 [CrossRef][PubMed]
    [Google Scholar]
  15. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  16. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992;89:5685–5689 [CrossRef][PubMed]
    [Google Scholar]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 2007;23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  24. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  25. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963;72:619–629 [CrossRef][PubMed]
    [Google Scholar]
  26. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  27. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  28. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464[CrossRef]
    [Google Scholar]
  29. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  30. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas. Microbiol Immunol 1999;43:339–349 [CrossRef][PubMed]
    [Google Scholar]
  31. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990;34:99–119[PubMed][CrossRef]
    [Google Scholar]
  32. Im WT, Lee ST, Yokota A. Rhodanobacter fulvus sp. nov., a β-galactosidase-producing gammaproteobacterium. J Gen Appl Microbiol 2004;50:143–147 [CrossRef][PubMed]
    [Google Scholar]
  33. Woo SG, Srinivasan S, Kim MK, Lee M. Rhodanobacter caeni sp. nov., a denitrifying bacterium isolated from sludge in a sewage disposal plant. Int J Syst Evol Microbiol 2012;62:2815–2821[CrossRef]
    [Google Scholar]
  34. Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A et al. Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 2012;62:2457–2462 [CrossRef][PubMed]
    [Google Scholar]
  35. Lee CS, Kim KK, Aslam Z, Lee ST. Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process. Int J Syst Evol Microbiol 2007;57:1775–1779 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001825
Loading
/content/journal/ijsem/10.1099/ijsem.0.001825
Loading

Data & Media loading...

Supplements

Supplementary File 1

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