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Volume 68, Issue 4

sp. nov., isolated from grassland soil Free

Abstract

A Gram-stain-negative, rod-shaped, motile by gliding and strictly aerobic bacterial strain, named 1-32, was isolated from soil of the Ordos grassland in Inner Mongolia, PR China. Strain 1-32 showed highest 16S rRNA gene sequence similarities to N7d-4 (95.4 %), DSM 19973 (95.3 %), ‘' 12157 (95.2 %) and TF5-37.2-LB10 (95.1 %). Phylogenetic analyses clustered strain 1-32 with ‘' 12157 and TF5-37.2-LB10. The DNA G+C content was 43.4 mol%. Menaquinone 7 was the main respiratory quinone. The predominant fatty acids (>5 %) were iso-C, summed feature 3 (C 6 and/or C 7), iso-C 3-OH, iso-C 3-OH and C 5. The polar lipids of strain 1-32 comprised phosphatidylethanolamine, two unidentified polar lipids, one unidentified glycolipid and two unidentified phospholipids. Strain 1-32 could be distinguished from the other members of the genus based on its phylogenetic distance and physiological and biochemical characteristics such as being negative for the assimilation of rhamnose and the activity of -glucosidase. Therefore, strain 1-32 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 1-32 (=KCTC 52859=CCTCC AB 2017084).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , Pedobacter , Pedobacter mongoliensis and taxa
© 2018 IUMS
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2018-04-01
2024-04-19
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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 [View Article][PubMed]
     [Google Scholar]
  2. Kook M, Park Y, Yi TH. 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 [View Article][PubMed]
     [Google Scholar]
  3. Du J, Singh H, Ngo HT, Won KH, Kim KY et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article][PubMed]
     [Google Scholar]
  4. Luo X, Wang Z, Dai J, Zhang L, Li J et al. Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil. Int J Syst Evol Microbiol 2010; 60:229–233 [View Article][PubMed]
     [Google Scholar]
  5. Muurholm S, Cousin S, Päuker O, Brambilla E, Stackebrandt E. Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int J Syst Evol Microbiol 2007; 57:2221–2227 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  7. 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 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article][PubMed]
     [Google Scholar]
  9. 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 [View Article][PubMed]
     [Google Scholar]
  10. Lee HG, Kim SG, Im WT, Oh HM, Lee ST. Pedobacter composti sp. nov., isolated from compost. Int J Syst Evol Microbiol 2009; 59:345–349 [View Article][PubMed]
     [Google Scholar]
  11. 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 [View Article][PubMed]
     [Google Scholar]
  12. Derichs J, Kämpfer P, Lipski A. Pedobacter nutrimenti sp. nov., isolated from chilled food. Int J Syst Evol Microbiol 2014; 64:1310–1316 [View Article][PubMed]
     [Google Scholar]
  13. Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014; 64:3683–3689 [View Article][PubMed]
     [Google Scholar]
  14. 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 [View Article][PubMed]
     [Google Scholar]
  15. Margesin R, Zhang DC. Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2013; 63:339–344 [View Article][PubMed]
     [Google Scholar]
  16. 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 [View Article][PubMed]
     [Google Scholar]
  17. Oh HW, Kim BC, Park DS, Jeong WJ, Kim H et al. Pedobacter luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:1304–1310 [View Article][PubMed]
     [Google Scholar]
  18. Tang Y, Wang Y, Ji S, Zhang K, Dai J et al. Pedobacter xinjiangensis sp. nov., from desert, Xinjiang. J Microbiol Biotechnol 2010; 20:397–402[PubMed] [Crossref]
     [Google Scholar]
  19. Ngo HT, Kook M, Yi TH. Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:1008–1014 [View Article][PubMed]
     [Google Scholar]
  20. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article][PubMed]
     [Google Scholar]
  21. Marmur J, Schildkraut CL, Doty P. The reversible denaturation of DNA and its use in studies of nucleic acid homologies and the biological relatedness of microorganisms. Journal de Chimie Physique 1961; 58:945–955 [View Article]
     [Google Scholar]
  22. Fan H, Su C, Wang Y, Yao J, Zhao K et al. Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 2008; 105:529–539 [View Article][PubMed]
     [Google Scholar]
  23. Kim OS, Cho YJ, Lee K, Yoon SH, 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 [View Article][PubMed]
     [Google Scholar]
  24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  28. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  30. 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 [View Article][PubMed]
     [Google Scholar]
  31. Bernardet JF, Nakagawa Y, Holmes B. 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 [View Article][PubMed]
     [Google Scholar]
  32. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  33. Tarrand JJ, Gröschel DH. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982; 16:772–774[PubMed]
     [Google Scholar]
  34. Zimmermann JJ, Langer R, Cooney CL. Specific plate assay for bacterial heparinase. Appl Environ Microbiol 1990; 56:3593–3594[PubMed]
     [Google Scholar]
  35. Cowan ST, Steel KJ. Manual for the identification of medical bacteria. Q Rev Biol 1970; 17:680
     [Google Scholar]
  36. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  37. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26[PubMed]
     [Google Scholar]
  38. Prescott LM, Harley JP. The effects of chemical agents on bacteria II: antimicrobial agents (Kirby-Bauer Method). In Prescott LM, Harley JP. (editors) Laboratory Exercises in Microbiology, 5th ed. New York: McGraw-Hill; 2001 pp. 257–262
     [Google Scholar]
  39. 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 [View Article]
     [Google Scholar]
  40. 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 [View Article]
     [Google Scholar]
  41. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
     [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  43. Castegnaro M, Garren L, Gaucher I, Wild CP. Development of a new method for the analysis of sphinganine and sphingosine in urine and tissues. Nat Toxins 1996; 4:284–290 [View Article][PubMed]
     [Google Scholar]
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Pedobacter mongoliensis sp. nov., isolated from grassland soil
Int J Syst Evol Microbiol 68, 1112 (2018); https://doi.org/10.1099/ijsem.0.002637
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