1887

Abstract

A strictly aerobic, Gram-stain-negative, rod-shaped, yellow, non-spore-forming bacterial strain, designated P-25, was isolated from soil collected in Yantai, Shandong Province, PR China. The temperature, pH and NaCl concentration ranges for the growth of strain P-25 were 10–37 °C (optimum, 28–30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and 0–4 % (w/v) (optimum, 1 % w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P-25 was most closely related to S27 (98.1 % 16S rRNA gene sequence similarity), followed by CM134L-2 (97.2 %) and THG-T11 (97.1 %). The genomic DNA G+C content of strain P-25 based on its draft genome sequence was 38.1 %. MK-7 was the major respiratory quinone, and iso-C, Cω7 and/or Cω6 (summed feature 3) and iso-C 3-OH were the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified lipids, five unidentified aminolipids and two unidentified glycolipids. Average nucleotide identity values for the draft genomes between strain P-25 and strains S27, CM134L-2 and THG-T11 were 81.8, 77.6 and 81.2 %, respectively, and the digital DNA–DNA hybridization (dDDH) values were 30.0, 19.2 and 27.6 %, respectively. Based on their phylogenetic and phenotypic characteristics, chemotaxonomic data, and dDDH results, strain P-25 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed; the type strain is strain P-25 (KCTC 62821=CCTCC AB 2018185).

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/content/journal/ijsem/10.1099/ijsem.0.003684
2019-08-29
2019-10-16
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References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998;48:165–177 [CrossRef]
    [Google Scholar]
  2. Yang DJ, Hong JK. Pedobacter solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017;67:4814–4819 [CrossRef][PubMed]
    [Google Scholar]
  3. Gallego V, García MT, Ventosa A. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006;56:1853–1858 [CrossRef][PubMed]
    [Google Scholar]
  4. Baik KS, Park YD, Kim MS, Park SC, Moon EY et al. Pedobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007;57:2079–2083 [CrossRef][PubMed]
    [Google Scholar]
  5. Asker D, Beppu T, Ueda K. Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater. Int J Syst Evol Microbiol 2008;58:601–606 [CrossRef][PubMed]
    [Google Scholar]
  6. Urios L, Intertaglia L, Magot M. Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer. Int J Syst Evol Microbiol 2013;63:303–308 [CrossRef][PubMed]
    [Google Scholar]
  7. Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ et al. Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 2007;57:480–484 [CrossRef][PubMed]
    [Google Scholar]
  8. Kwon SW, Son JA, Kim SJ, Kim YS, Park IC et al. Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 2011;61:2874–2879 [CrossRef][PubMed]
    [Google Scholar]
  9. An DS, Kim SG, Ten LN, Cho CH. Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int J Syst Evol Microbiol 2009;59:69–72 [CrossRef][PubMed]
    [Google Scholar]
  10. Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL et al. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 2009;59:1720–1726 [CrossRef][PubMed]
    [Google Scholar]
  11. Vanparys B, Heylen K, Lebbe L, de Vos P. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 2005;55:1315–1318 [CrossRef][PubMed]
    [Google Scholar]
  12. Shivaji S, Chaturvedi P, Reddy GS, Suresh K. Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 2005;55:1083–1088 [CrossRef][PubMed]
    [Google Scholar]
  13. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014;64:2431–2436 [CrossRef][PubMed]
    [Google Scholar]
  14. Park S, Jung YT, Park JM, Won SM, Yoon JH. Pedobacter silvilitoris sp. nov., isolated from wood falls. Int J Syst Evol Microbiol 2015;65:1284–1289 [CrossRef][PubMed]
    [Google Scholar]
  15. Park S, Park JM, Jung YT, Won SM, Yoon JH. Pedobacter lignilitoris sp. nov., isolated from wood falls. Int J Syst Evol Microbiol 2015;65:3481–3486 [CrossRef][PubMed]
    [Google Scholar]
  16. Kook M, Park Y, Yi TH, Th Y. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2014;64:1789–1794 [CrossRef][PubMed]
    [Google Scholar]
  17. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012;62:1963–1969 [CrossRef][PubMed]
    [Google Scholar]
  18. Ausubel FM, Brent R, Kingston RE. Short Protocols in Molecular Biology: Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley (; 1995
    [Google Scholar]
  19. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991; pp.115–175
    [Google Scholar]
  20. Yoon SH, Ha SM, 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: [CrossRef][PubMed]
    [Google Scholar]
  21. 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]
  22. 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][PubMed]
    [Google Scholar]
  23. 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]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  26. Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014;64:3683–3689 [CrossRef][PubMed]
    [Google Scholar]
  27. Zhang LL, Gan LZ, Xu ZB, Yang F, Li Y et al. Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue. Int J Syst Evol Microbiol 2018;68:3713–3719 [CrossRef][PubMed]
    [Google Scholar]
  28. Ngo HT, Kook M, Yi TH, Htt N, Th Y. Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil. Int J Syst Evol Microbiol 2015;65:1008–1014 [CrossRef][PubMed]
    [Google Scholar]
  29. Beveridge TJ, Lawrence JR, Murray RGE. et al. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder RL. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007
    [Google Scholar]
  30. Breznak JA, Costilow RN. Physicochemical factors in growth. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.137–154
    [Google Scholar]
  31. Zhang H, Cheng MG, Sun B, Guo SH, Song M et al. Flavobacterium suzhouense sp. nov., isolated from farmland river sludge. Int J Syst Evol Microbiol 2015;65:370–374 [CrossRef][PubMed]
    [Google Scholar]
  32. Bernardet JF, Nakagawa Y, Holmes B..Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef][PubMed]
    [Google Scholar]
  33. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.611–651
    [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  36. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  37. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef][PubMed]
    [Google Scholar]
  38. 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][PubMed]
    [Google Scholar]
  39. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  40. 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][PubMed]
    [Google Scholar]
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