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Abstract

A Gram-stain-negative, strictly aerobic, motile, ivory-coloured and rod-shaped bacterium (designated Gsoil 520) isolated from ginseng cultivation soil was characterized by using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 520 was observed to grow optimally at 30 °C and pH 7.0 on Reasoner's 2A agar medium. The results of phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that Gsoil 520 belongs to the genus of the family and was most closely related to E84 (98.0 %), Yak96B (97.7 %), J1 (97.7 %) and IPL18 (96.8 %). The complete genome of strain Gsoil 520 is a presumptive circular chromosome of 4 480 314 base pairs having G+C content of 63.7 mol%. A total of 4 354 genes, 4 303 CDS and 43 rRNA genes were assigned a putative function. The major isoprenoid quinone was Q-10. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids (AL1 and AL3). The predominant fatty acids of strain Gsoil 520 were Cω7 11-methyl, C and C ω7/C ω6 (summed feature 8) supporting the affiliation of strain Gsoil 520 to the genus . The low values of DNA–DNA hybridization distinguished strain Gsoil 520 from the recognized species of the genus . Thus, the novel isolate represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain Gsoil 520 (=KACC 19440=LMG 30329).

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2020-01-16
2020-02-28
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References

  1. Nakagawa Y, Sakane T, Yokota A. Transfer of "Pseudomonas riboflavina" (Foster 1944), a Gram-Negative, Motile Rod with Long-Chain 3-Hydroxy Fatty Acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 1996;46: 16– 22 [CrossRef]
    [Google Scholar]
  2. Parte AC. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42: D613– D616 [CrossRef]
    [Google Scholar]
  3. Yoon J-H, Kang S-J, Park S, Oh T-K. Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 2007;57: 1310– 1314 [CrossRef]
    [Google Scholar]
  4. Jia Y-Y, Sun C, Pan J, Zhang W-Y, Zhang X-Q et al. Devosia pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014;64: 2637– 2641 [CrossRef]
    [Google Scholar]
  5. Park S, Jung Y-T, Kim S, Yoon J-H. Devosia confluentis sp. nov., isolated from the junction between the ocean and a freshwater lake, and reclassification of two Vasilyevaea species as Devosia enhydra comb. nov. and Devosia mishustinii comb. nov. Int J Syst Evol Microbiol 2016;66: 3935– 3941 [CrossRef]
    [Google Scholar]
  6. Zhang L, Song M, Chen X-L, Xu R-J, Chen K et al. Devosia honganensis sp. nov., isolated from the soil of a chemical factory. Antonie van Leeuwenhoek 2015;108: 1301– 1307 [CrossRef]
    [Google Scholar]
  7. Muhammad NMN, Vikineswary S, Geok YAT. Devosia Elaeis sp. nov., isolated from oil palm rhizospheric soil. Int J Syst Evol Microbiol 2017;67: 851– 855
    [Google Scholar]
  8. Du J, Kook M, Akter S, Singh H, Won K et al. Devosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden. Int J Syst Evol Microbiol 2016;66: 341– 346 [CrossRef]
    [Google Scholar]
  9. Rivas R, Willems A, Subba-Rao NS, Mateos PF, Dazzo FB et al. Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst Appl Microbiol 2003;26: 47– 53 [CrossRef]
    [Google Scholar]
  10. Siddiqi MZ, Kim Y-J, Hoang V-A, Siddiqi MH, Huq MA et al. Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Arch Microbiol 2014;196: 863– 870 [CrossRef]
    [Google Scholar]
  11. Siddiqi MZ, Liu Q, Kang M-S, Kim MS, Im W-T. Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng. Int J Syst Evol Microbiol 2016a;66: 1125x– 1130 [CrossRef]
    [Google Scholar]
  12. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im W-T. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016b;66: 4039– 4045 [CrossRef]
    [Google Scholar]
  13. Siddiqi MZ, Im W-T. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016;66: 3449– 3455 [CrossRef]
    [Google Scholar]
  14. Siddiqi MZ, Lee SY, Choi KD, Im W-T. Aeromicrobium panacisoli sp. nov. Isolated from Soil of Ginseng Cultivating Field. Curr Microbiol 2018;75: 624– 629 [CrossRef]
    [Google Scholar]
  15. Siddiqi MZ, Shafi SM, Im W-T, Muhammad Shafi S, WT I. Complete genome sequencing of Arachidicoccus ginsenosidimutans sp. nov., and its application for production of minor ginsenosides by finding a novel ginsenoside-transforming β-glucosidase. RSC Adv 2017;7: 46745– 46759 [CrossRef]
    [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67: 1613– 1617 [CrossRef]
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999;41: 95– 98
    [Google Scholar]
  19. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge Universite Press; 1983
    [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]
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  23. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One 2014;9: e104984 [CrossRef]
    [Google Scholar]
  24. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019;47: W276– W282 [CrossRef]
    [Google Scholar]
  25. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44: 992– 993
    [Google Scholar]
  26. Weon H-Y, Kim B-Y, Joa J-H, Son J-A, Song M-H et al. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 2008;58: 93– 96 [CrossRef]
    [Google Scholar]
  27. Schädler S, Burkhardt C, Kappler A. Evaluation of electron microscopic sample preparation methods and imaging techniques for characterization of cell-mineral aggregates. Geomicrobiol J 2008;25: 228– 239 [CrossRef]
    [Google Scholar]
  28. Ten LN, Im W-T, Kim M-K, Kang MS, Lee S-T. 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]
    [Google Scholar]
  29. 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]
  30. Sasser M. Identification of bacteria through fatty acid analysis. Methods in Phytobacteriol 1990; 199– 204
    [Google Scholar]
  31. 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]
  32. 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]
  33. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  34. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68: 461– 466 [CrossRef]
    [Google Scholar]
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. 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
    [Google Scholar]
  36. Galatis H, Martin K, Kämpfer P, Glaeser SP. Devosia epidermidihirudinis sp. nov. isolated from the surface of a medical leech. Antonie van Leeuwenhoek 2013;103: 1165– 1171 [CrossRef]
    [Google Scholar]
  37. Bautista VV, Monsalud RG, Yokota A. Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi. Int J Syst Evol Microbiol 2010;60: 627– 632 [CrossRef]
    [Google Scholar]
  38. Kumar M, Verma M, Lal R. Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int J Syst Evol Microbiol 2008;58: 861– 865 [CrossRef]
    [Google Scholar]
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