1887

Abstract

A Gram-stain-negative, strictly aerobic bacterial strain, designated R29, was isolated from orchard soil in Hwasun, South Korea. Cells were non-motile rods with catalase and oxidase activities. Growth was observed at 15–40 °C (optimum, 30 °C) and pH 7.0–9.0. Ubiquinone-8 was identified as the predominant isoprenoid quinone. Major polar lipids consisted of phosphatidylethanolamine, six phospholipids, an unidentified aminolipid and two unidentified polar lipids. Strain R29 contained iso-C, iso-C and summed feature 9 (comprising iso-C 9/10-methyl-C) as major cellular fatty acids. The G+C content of the genomic DNA calculated from the whole-genome sequence was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that R29 was most closely related to T7-07 and CC-JY-1 with sequence similarities of 98.0 and 96.9 %, respectively The average nucleotide identity and DNA–DNA hybridization values between R29 and the type strains of and were 87.0 % and 31.6 % and 83.4 % and 26.1 %, respectively. On the basis of the phenotypic, chemotaxonomic and molecular features, strain R29 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is R29 (=KACC 19896=JCM 33216).

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2019-10-23
2019-11-19
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References

  1. Kwon SW, Kim BY, Weon HY, Baek YK, Go SJ. Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 2007;57: 954– 958 [CrossRef]
    [Google Scholar]
  2. Zhu J, Wang HM, Zhang Q, Dong WW, Kong DL et al. Arenimonas alkanexedens sp. nov., isolated from a frozen soil sample. Antonie van Leeuwenhoek 2017;110: 1027– 1034 [CrossRef]
    [Google Scholar]
  3. Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D et al. Arenimonas halophila sp. nov., isolated from soil. Int J Syst Evol Microbiol 2018;68: 2188– 2193 [CrossRef]
    [Google Scholar]
  4. Young CC, Kämpfer P, Ho MJ, Busse HJ, Huber BE et al. Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site. Int J Syst Evol Microbiol 2007;57: 2790– 2793 [CrossRef]
    [Google Scholar]
  5. Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ et al. Arenimonas soli sp. nov., isolated from saline–alkaline soil. Int J Syst Evol Microbiol 2017;67: 2829– 2833 [CrossRef]
    [Google Scholar]
  6. Jin L, Kim KK, Im WT, Yang HC, Lee ST. Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae. Int J Syst Evol Microbiol 2007;57: 1876– 1880 [CrossRef]
    [Google Scholar]
  7. Jin L, Kim KK, An KG, Oh HM, Lee ST. Arenimonas daejeonensis sp. nov., isolated from compost. Int J Syst Evol Microbiol 2012;62: 1674– 1678 [CrossRef]
    [Google Scholar]
  8. Aslam Z, Park JH, Kim SW, Jeon CO, Chung YR. Arenimonas oryziterrae sp. nov., isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime, and reclassification of Aspromonas composti as Arenimonas composti comb. nov. Int J Syst Evol Microbiol 2009;59: 8 2967– 2972 [CrossRef]
    [Google Scholar]
  9. Zhang S-Y, Xiao W, Xia YS, Wang YX, Cui XL et al. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China. Antonie van Leeuwenhoek 2015;107: 1181– 1187 [CrossRef]
    [Google Scholar]
  10. Kim AR, Lee S, Han K, Ahn TY. Arenimonas aquaticum [corrected] sp. nov., a member of the gammaproteobacterium, isolated from a freshwater reservoir. J Microbiol 2012;50: 354– 358 [CrossRef]
    [Google Scholar]
  11. Huy H, Jin L, Lee YK, Lee KC, Lee JS et al. Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2013;63: 484– 489 [CrossRef]
    [Google Scholar]
  12. Yuan X, Nogi Y, Tan X, Zhang RG, Lv J. Arenimonas maotaiensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2014;64: 3994– 4000 [CrossRef]
    [Google Scholar]
  13. Makk J, Nemes-Barnás K, Márialigeti K, Homonnay ZG, Kéki Z et al. Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas. Int J Syst Evol Microbiol 2015;65: 1915– 1921 [CrossRef]
    [Google Scholar]
  14. Jeong HI, Jin HM, Jeon CO. Arenimonas aestuarii sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2016;66: 1527– 1532 [CrossRef]
    [Google Scholar]
  15. Lee Y, Jeon CO. Solitalea longa sp. nov., isolated from freshwater and emended description of the genus Solitalea. Int J Syst Evol Microbiol 2018;68: 2826– 2831 [CrossRef]
    [Google Scholar]
  16. 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;67: 1613– 1617 [CrossRef]
    [Google Scholar]
  17. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73: 5261– 5267 [CrossRef]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef]
    [Google Scholar]
  19. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
    [Google Scholar]
  20. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1: 18 [CrossRef]
    [Google Scholar]
  21. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13: e1005595 [CrossRef]
    [Google Scholar]
  22. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56: 280– 285 [CrossRef]
    [Google Scholar]
  23. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66: 1100– 1103 [CrossRef]
    [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  25. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002;52: 1043– 1047 [CrossRef]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef]
    [Google Scholar]
  27. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955;1: 138– 146
    [Google Scholar]
  28. Smibert RM, Krieg NR. Phenotypic characterization In Gerhardt P. editor Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp 607– 654
    [Google Scholar]
  29. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987;19: 1– 67
    [Google Scholar]
  30. 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]
  31. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988;19: 161– 207
    [Google Scholar]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  33. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27: 104– 117 [CrossRef]
    [Google Scholar]
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