1887

Abstract

A Gram-stain-negative, short-rod, aerobic, non-motile, red to pink-pigmented bacterium, designated Fur1, was isolated from the dry spikelet clusters of a plant called near Dongguk University. Phylogenetic analysis conducted based on 16S rRNA gene sequences indicated that strain Fur1 belonged to the genus of the family . The 16S rRNA gene of Fur1 showed highest sequence similarity to those of KACC 17381 (97.5 %) and KACC 19042 (97.1 %). Growth occurred at 4–37 °C (optimum, 25–28 °C), up to 1.0 % NaCl (optimum, 0 %) and pH 5.5–9.0 (optimum, pH 6.0–7.5). The major fatty acids of strain Fur1 were identified as iso-C, C ω5, anteiso-C, summed feature 3 (comprising C ω7 and/or C ω6) and summed feature 4 (comprising anteiso-CB and/or iso-CI) as the major cellular fatty acids. The predominant respiratory quinone was identified as MK-7. The polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, two unidentified phospholipids, one unidentified glycolipid and one unidentified polar lipid. The genomic DNA G+C content based on the draft genome sequence was 58.7 mol%. DNA–DNA relatedness between strain Fur1 and its closest relative was below 70 %. Characterization based on phylogenetic, chemotaxonomic and phenotypic analyses clearly indicated that strain Fur1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Fur1 (=KACC 19903=NBRC=113691).

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2020-05-18
2020-06-04
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References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Buczolits S, Denner EBM, Vybiral D, Wieser M, Kämpfer P et al. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 2002; 52:445–456 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Han L, Wu S-J, Qin C-Y, Zhu Y-H, Lu Z-Q et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie Van Leeuwenhoek 2014; 105:971–978 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Fan X, Wang Q, Zheng S, Shi K, Wang G. Hymenobacter monticola sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2016; 66:812–816 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Subhash Y, Sasikala C, Ramana CV. Hymenobacter roseus sp. nov., isolated from sand. Int J Syst Evol Microbiol 2014; 64:4129–4133 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Zhu H-Z, Yang L, Muhadesi J-B, Wang B-J, Liu S-J. Hymenobacter cavernae sp. nov., isolated from a karst cave. Int J Syst Evol Microbiol 2017; 67:4825–4829 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Sheu S-Y, Hsieh T-Y, Kwon S-W, Chen W-M. Hymenobacter rivuli sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018; 68:1220–1226 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z et al. Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. Int J Syst Evol Microbiol 2017; 67:856–861 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Kang H, Kim H, Joung Y, Kim K-J, Joh K. Hymenobacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2016; 66:2212–2217 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Chen W-M, Chen Z-H, Young C-C, Sheu S-Y. Hymenobacter paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 2016; 66:1546–1553 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Collins MD, Hutson RA, Grant IR, Patterson MF. Phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of Hymenobacter actinosclerus sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 2:731–734 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Chung AP, Lopes A, Nobre MF, Morais PV. Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system. Syst Appl Microbiol 2010; 33:436–443 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Lee J-J, Srinivasan S, Lim S, Joe M, Lee SH et al. Hymenobacter swuensis sp. nov., a gamma-radiation-resistant bacteria isolated from mountain soil. Curr Microbiol 2014; 68:305 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Waldeck W, Heidenreich E, Mueller G, Wiessler M, Tóth K et al. Ros-Mediated killing efficiency with visible light of bacteria carrying different red fluorochrome proteins. J Photochem Photobiol B 2012; 109:28–33 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Chhetri G, Yang D, Choi J, Kim H, Seo T. Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie Van Leeuwenhoek 2018; 111:2385–2392 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Winnepenninckx B, Backeljau T, De Wachter R. Extraction of high molecular weight DNA from molluscs. Trends Genet 1993; 9:407 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. Chhetri G, Kim J, Kim I, Seo T. Edaphorhabdus rosea gen. nov., sp. nov., isolated from garden soil. Antonie van Leeuwenhoek 2019; 112:1245–1252
    [Google Scholar]
  20. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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][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][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][PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  24. 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][PubMed]
    [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. Melis JPM, van Steeg H, Luijten M. Oxidative DNA damage and nucleotide excision repair. Antioxid Redox Signal 2013; 18:2409–2419 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Na S-I, Kim YO, Yoon S-H, Ha S-M, 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][PubMed][PubMed]
    [Google Scholar]
  29. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  30. Gillis M, De Ley J, De Cleene M. The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 1970; 12:143–153 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  31. Kim I, Choi J, Chhetri G, Seo T. Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea. Antonie Van Leeuwenhoek 2019; 112:1253 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Loveland-Curtze J, Miteva VI, Brenchley JE, Vanya IM, Jean EB. Evaluation of a new fluorimetric DNA-DNA hybridization method. Can J Microbiol 2011; 57:250–255 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  33. 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][PubMed][PubMed]
    [Google Scholar]
  34. Kim J, Chhetri G, Kim I et al. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 2020; 959:966
    [Google Scholar]
  35. 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
    [Google Scholar]
  36. Buck JD, Nonstaining BJD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed][PubMed]
    [Google Scholar]
  37. 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]
  38. Chhetri G, Kim J, Kim I, Seo T. Lysobacter caseinilyticus, sp. nov., a casein hydrolyzing bacterium isolated from sea water. Antonie van Leeuwenhoek 2019; 112:01267–7 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  39. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361
    [Google Scholar]
  40. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed][PubMed]
    [Google Scholar]
  41. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–205
    [Google Scholar]
  42. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91
    [Google Scholar]
  43. Minnikin DE, O'Donnell AG, Goodfellow M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241
    [Google Scholar]
  44. Chhetri G, Kim J, Kim H, Kim I, Seo T. Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie Van Leeuwenhoek 2019; 112:112 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  45. Hoang V-A, Kim Y-J, Nguyen NL, Yang D-C. Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2013; 63:661–666 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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