1887

Abstract

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated HKS-05, was isolated from ginseng field soil. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. HKS-05 grew at 10–37 °C and at pH 6.0–8.0 on R2A agar. On the basis of 16S rRNA gene sequence similarity, HKS-05 was shown to represent a member of the family Caulobacteraceae and to be related to Phenylobacterium lituiforme FaiI3 (98.1 % sequence similarity), ‘ Phenylobacterium zucineum ’ HLK1 (97.9 %), Phenylobacterium muchangponense A8 (97.7 %), Phenylobacterium composti 4T-6 (97.2 %) and Phenylobacterium immobile E (97.1 %). The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, unidentified glycolipids and unidentified polar lipids. The G+C content of the genomic DNA was 70.4 mol%. DNA–DNA relatedness values between HKS-05 and its closest phylogenetically neighbours were low. HKS-05 could be differentiated genotypically and phenotypically from the species of the genus Phenylobacterium with validly published names. The isolate therefore represents a novel species, for which the name Phenylobacterium hankyongense sp. nov. is proposed, with the type strain HKS-05 (=KACC 18628=LMG 30081)

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2017-11-08
2019-10-16
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References

  1. Lingens F, Blecher R, Blecher H, Blobel F, Eberspacher J et al. Phenylobacterium immobile gen. nov., sp. nov., a Gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 1985; 35: 26– 39 [CrossRef]
    [Google Scholar]
  2. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 1997; 47: 590– 592 [CrossRef] [PubMed]
    [Google Scholar]
  3. Farh ME, Kim YJ, Singh P, Hoang VA, Yang DC. Phenylobacterium panacis sp. nov., isolated from the rhizosphere of rusty mountain ginseng. Int J Syst Evol Microbiol 2016; 66: 2691– 2696 [CrossRef] [PubMed]
    [Google Scholar]
  4. Jo JH, Choi GM, Lee SY, Im WT. Phenylobacterium aquaticum sp. nov., isolated from the reservoir of a water purifier. Int J Syst Evol Microbiol 2016; 66: 3519– 3523 [CrossRef] [PubMed]
    [Google Scholar]
  5. Chu C, Yuan C, Liu X, Yao L, Zhu J et al. Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 2015; 65: 325– 330 [CrossRef] [PubMed]
    [Google Scholar]
  6. Weon HY, Kim BY, Kwon SW, Go SJ, Koo BS et al. Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea. Int J Syst Evol Microbiol 2008; 58: 2301– 2304 [CrossRef] [PubMed]
    [Google Scholar]
  7. Zhang K, Han W, Zhang R, Xu X, Pan Q et al. Phenylobacterium zucineum sp. nov., a facultative intracellular bacterium isolated from a human erythroleukemia cell line K562. Syst Appl Microbiol 2007; 30: 207– 212 [CrossRef] [PubMed]
    [Google Scholar]
  8. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  9. Kim JK, Kang MS, Park SC, Kim KM, Choi K et al. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2015; 53: 435– 441 [CrossRef] [PubMed]
    [Google Scholar]
  10. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole-genome assemblies. Int J Syst Evol Microbiol 2017; (in press) doi: [CrossRef] [PubMed]
    [Google Scholar]
  11. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876– 4882 [CrossRef] [PubMed]
    [Google Scholar]
  12. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41: 95– 98
    [Google Scholar]
  13. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983; [Crossref]
    [Google Scholar]
  14. 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]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  18. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44: 992– 993 [PubMed]
    [Google Scholar]
  19. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th ed. CA: Pearson Education, Inc. Benjamin Cummings; 2002
    [Google Scholar]
  20. Atlas RM, Parks LC. Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  21. Ten LN, Im WT, Kim MK, Kang MS, Lee ST. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 2004; 56: 375– 382 [CrossRef] [PubMed]
    [Google Scholar]
  22. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York, NY: Wiley; 1995; pp. 2– 11
    [Google Scholar]
  23. 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]
  24. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990; pp. 199– 204
    [Google Scholar]
  25. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42: 457– 469 [CrossRef]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2: 233– 241 [CrossRef]
    [Google Scholar]
  27. 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]
  28. Abraham WR, Macedo AJ, Lünsdorf H, Fischer R, Pawelczyk S et al. Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium. Int J Syst Evol Microbiol 2008; 58: 1939– 1949 [CrossRef] [PubMed]
    [Google Scholar]
  29. Oh YS, Roh DH. Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2012; 62: 977– 983 [CrossRef] [PubMed]
    [Google Scholar]
  30. 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 approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37: 463– 464 [Crossref]
    [Google Scholar]
  31. Kanso S, Patel BK. Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2004; 54: 2141– 2146 [CrossRef] [PubMed]
    [Google Scholar]
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