sp. nov., isolated from the surface of a glacier in the Indian trans-Himalayas Free

Abstract

A novel bacterial strain, IHBB 10212, of the genus was isolated from a glacier near the Kunzum Pass located in the Lahaul-Spiti in the North-Western Himalayas of India. The cells were Gram-negative, aerobic, non-sporulating, single rods, lacked flagella, and formed yellow to orange pigmented colonies. The strain utilized maltose, trehalose, sucrose, gentibiose, glucose, mannose, fructose, mannitol, arabitol and salicin for growth. Flexirubin-type pigments were produced by strain IHBB 10212. The 16S rRNA gene sequence analysis showed relatedness of strain IHBB 10212 to DSM 26899 (97.43 %), CIP 110007 (97.29 %) and KCTC 12483 (96.80 %). Iso-C and summed feature 3 (Cω7/Cω6) constituted the major cellular fatty acids. The polar lipids present were six unidentified aminolipids, one unidentified phospholipid and three unidentified lipids. MK-6 was identified as the major quinone. The DNA G+C content was 34.08  mol%. Digital DNA–DNA hybridization of strain IHBB 10212 with and showed values far below the prescribed thresholds of 95 % for average nucleotide identity and 70 % for the Genome-to-Genome Distance Calculator for species delineation. Based on its differences from validly published species, strain IHBB 10212 is identified as a new species, for which the proposed name is sp. nov., with IHBB 10212 as the type strain (=MTCC 12457=JCM 31156=KACC 19170).

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2018-03-01
2024-03-28
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References

  1. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. New perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994; 44:827–831 [View Article]
    [Google Scholar]
  2. Yi H, Oh HM, Lee JH, Kim SJ, Chun J. Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic. Int J Syst Evol Microbiol 2005; 55:637–641 [View Article][PubMed]
    [Google Scholar]
  3. Chen XY, Zhao R, Chen ZL, Liu L, Li XD et al. Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium. Antonie van Leeuwenhoek 2015; 107:403–410 [View Article][PubMed]
    [Google Scholar]
  4. Loveland-Curtze J, Miteva V, Brenchley J. Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles 2010; 14:61–69 [View Article][PubMed]
    [Google Scholar]
  5. Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A et al. Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield. Int J Syst Evol Microbiol 2013; 63:2666–2671 [View Article][PubMed]
    [Google Scholar]
  6. Kim T, Kim M, Kang O, Jiang F, Chang X et al. Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense. Int J Syst Evol Microbiol 2016; 66:609–615 [View Article][PubMed]
    [Google Scholar]
  7. Park SC, Kim MS, Baik KS, Kim EM, Rhee MS et al. Chryseobacterium aquifrigidense sp. nov., isolated from a water-cooling system. Int J Syst Evol Microbiol 2008; 58:607–611 [View Article][PubMed]
    [Google Scholar]
  8. Zhao Q, Bai Y, Zhang G, Zhu S, Sheng H et al. Chryseobacterium xinjiangense sp. nov., isolated from alpine permafrost. Int J Syst Evol Microbiol 2011; 61:1397–1401 [View Article][PubMed]
    [Google Scholar]
  9. Skerman VBD. A guide to the identification of the genera of bacteria. In Skerman VBD. (editor) Abstracts of Microbiological Methods New York: Wiley; 1967 pp. 147
    [Google Scholar]
  10. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  11. Gulati A, Rahi P, Vyas P. Characterization of phosphate-solubilizing fluorescent pseudomonads from the rhizosphere of seabuckthorn growing in the cold deserts of Himalayas. Curr Microbiol 2008; 56:73–79 [View Article][PubMed]
    [Google Scholar]
  12. Chun J, Lee JH, Jung Y, Kim M, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Montero-Calasanz MC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense. Syst Appl Microbiol 2014; 37:342–350 [View Article][PubMed]
    [Google Scholar]
  16. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  17. Pal M, Swarnkar MK, Dhar H, Chhibber S, Gulati A. Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes. Genom Data 2017; 13:46–49 [View Article][PubMed]
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. 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 [View Article][PubMed]
    [Google Scholar]
  20. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  21. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  23. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article][PubMed]
    [Google Scholar]
  24. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  25. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  26. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  27. Kämpfer P, Trček J, Skok B, Šorgo A, Glaeser SP. Chryseobacterium limigenitum sp. nov., isolated from dehydrated sludge. Antonie van leeuwenhoek 2015; 107:1633–1638 [View Article][PubMed]
    [Google Scholar]
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