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Volume 67, Issue 5

gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring Free

Abstract

Two closely related thermophilic bacterial strains, designated YIM 73013 and YIM 73008, were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. The taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-stain-negative, aerobic, short-rod-shaped and motile by means of a polar flagellum. They were oxidase- and catalase-positive and were able to grow at 30–55 °C (optimum, 37–45 °C), at pH 6.0–8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013 and YIM 73008 formed a distinct lineage with respect to closely related genera in the family and shared highest 16S rRNA gene sequences similarities with R-24608 (96.3 and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were Cω6, C and summed feature 3 (Cω7 and/or Cω). The genomic DNA G+C contents of strains YIM 73013 and YIM 73008 were 68.7 and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates represent a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is YIM 73013 (=DSM 101684=KCTC 42873).

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Keyword(s): family Comamonadaceae and Tibeticola sediminis gen. nov., sp. nov.,
© 2017 IUMS
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2017-05-01
2024-04-18
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References

  1. Willems A, de Ley J, Gillis M, Kersters K. NOTES: comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Bacteriol 1991; 41:445–450 [View Article]
     [Google Scholar]
  2. Dubinina GA, Grabovich MY. Isolation, cultivation, and characteristics of Macromonas bipunctata. Microbiology 1984; 53:610–617
     [Google Scholar]
  3. Hiraishi A, Sugiyama J, Shin YK. Brachymonas denitrificans gen. nov., sp. nov., an aerobic chemoorganotrophic bacterium which contains rhodoquinones, and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes. J Gen Appl Microbiol 1995; 41:99–117 [View Article]
     [Google Scholar]
  4. Grabovich M, Gavrish E, Kuever J, Lysenko AM, Podkopaeva D et al. Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol 2006; 56:569–576 [View Article][PubMed]
     [Google Scholar]
  5. Heylen K, Lebbe L, de Vos P, De, Vos P. Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge. Int J Syst Evol Microbiol 2008; 58:73–77 [View Article][PubMed]
     [Google Scholar]
  6. Spring S, Wagner M, Schumann P, Kämpfer P. Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov. Int J Syst Evol Microbiol 2005; 55:621–629 [View Article][PubMed]
     [Google Scholar]
  7. Yu XY, Li YF, Zheng JW, Li Y, Li L et al. Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil. Int J Syst Evol Microbiol 2011; 61:255–258 [View Article][PubMed]
     [Google Scholar]
  8. Zhang WY, Fang MX, Zhang WW, Xiao C, Zhang XQ et al. Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae. Int J Syst Evol Microbiol 2013; 63:2062–2068 [View Article][PubMed]
     [Google Scholar]
  9. Rouvière PE, Chen MW. Isolation of Brachymonas petroleovorans CHX, a novel cyclohexane-degrading beta-proteobacterium. FEMS Microbiol Lett 2003; 227:101–106[PubMed] [CrossRef]
     [Google Scholar]
  10. Juretschko S, Loy A, Lehner A, Wagner M. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 2002; 25:84–99 [View Article][PubMed]
     [Google Scholar]
  11. Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 2000; 66:5368–5382 [View Article][PubMed]
     [Google Scholar]
  12. Blackall LL, Crocetti GR, Saunders AM, Bond PL. A review and update of the microbiology of enhanced biological phosphorus removal in wastewater treatment plants. Antonie Van Leeuwenhoek 2002; 81:681–691[PubMed] [CrossRef]
     [Google Scholar]
  13. Lee N, Nielsen PH, Aspegren H, Henze M, Schleifer KH et al. Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal. Syst Appl Microbiol 2003; 26:211–227 [View Article][PubMed]
     [Google Scholar]
  14. Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J et al. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl Environ Microbiol 2004; 70:588–596 [View Article][PubMed]
     [Google Scholar]
  15. Bruland N, Bathe S, Willems A, Steinbüchel A. Pseudorhodoferax soli gen. nov., sp. nov. and Pseudorhodoferax caeni sp. nov., two members of the class β-proteobacteria belonging to the family Comamonadaceae. Int J Syst Evol Microbiol 2009; 59:2702–2707 [View Article][PubMed]
     [Google Scholar]
  16. Weber N, Klein E, Vosmann K. Dialkyl 3,3'-thiodipropionate and dialkyl 2,2'-thiodiacetate antioxidants by lipase-catalyzed esterification and transesterification. J Agric Food Chem 2006; 54:2957–2963 [View Article][PubMed]
     [Google Scholar]
  17. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  18. Cerny G. Studies on the aminopeptidase test for the distinction of gram-negative from gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:113–122 [View Article]
     [Google Scholar]
  19. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
     [Google Scholar]
  20. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
     [Google Scholar]
  21. MacFaddin RM. Biochemical Tests for Identification of Medical Bacteria Philadelphia: Williams & Wilkins Co.; 1976
     [Google Scholar]
  22. 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]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  24. 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]
  25. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  26. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  27. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  28. 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]
  29. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  34. 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]
  35. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  37. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 2000; 50:1095–1102 [View Article][PubMed]
     [Google Scholar]
  38. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  39. Ding L, Yokota A. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol 2004; 54:2223–2230 [View Article][PubMed]
     [Google Scholar]
  40. Chen WM, Lin YS, Young CC, Sheu SY. Pseudorhodoferax aquiterrae sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2013; 63:169–174 [View Article][PubMed]
     [Google Scholar]
  41. Ryu SH, Lee DS, Park M, Wang Q, Jang HH et al. Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:1064–1068 [View Article][PubMed]
     [Google Scholar]
  42. Choi JH, Kim MS, Roh SW, Bae JW. Acidovorax soli sp. nov., isolated from landfill soil. Int J Syst Evol Microbiol 2010; 60:2715–2718 [View Article][PubMed]
     [Google Scholar]
  43. Gardan L, Dauga C, Prior P, Gillis M, Saddler GS. Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium. Int J Syst Evol Microbiol 2000; 50:235–246 [View Article][PubMed]
     [Google Scholar]
  44. Gardan L, Stead DE, Dauga C, Gillis M. Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr]. Int J Syst Evol Microbiol 2003; 53:795–800 [View Article][PubMed]
     [Google Scholar]
  45. Li D, Rothballer M, Schmid M, Esperschütz J, Hartmann A. Acidovorax radicis sp. nov., a wheat-root-colonizing bacterium. Int J Syst Evol Microbiol 2011; 61:2589–2594 [View Article][PubMed]
     [Google Scholar]
  46. Mechichi T, Stackebrandt E, Fuchs G. Alicycliphilus denitrificans gen. nov., sp. nov., a cyclohexanol-degrading, nitrate-reducing β-proteobacterium. Int J Syst Evol Microbiol 2003; 53:147–152 [View Article][PubMed]
     [Google Scholar]
  47. Willems A, Falsen E, Pot B, Jantzen E, Hoste B et al. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Bacteriol 1990; 40:384–398 [View Article][PubMed]
     [Google Scholar]
  48. Willems A, Goor M, Thielemans S, Gillis M, Kersters K et al. Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int J Syst Bacteriol 1992; 42:107–119 [View Article][PubMed]
     [Google Scholar]
  49. Kämpfer P, Thummes K, Chu H I, Tan CC, Arun AB et al. Pseudacidovorax intermedius gen. nov., sp. nov., a novel nitrogen-fixing β- proteobacterium isolated from soil. Int J Syst Evol Microbiol 2008; 5:491–495 [CrossRef]
     [Google Scholar]
  50. Madigan MT, Jung DO, Woese CR, Achenbach LA. Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat. Arch Microbiol 2000; 173:269–277 [View Article][PubMed]
     [Google Scholar]
  51. Hiraishi A, Hoshino Y, Satoh T. Rhodoferax fermentans gen. nov., sp. nov., a phototrophic purple nonsulfur bacterium previously referred to as the ‘‘Rhodocyclus gelatinosus-like’’ group. Arch Microbiol 1991; 155:330–336 [View Article]
     [Google Scholar]
  52. Finneran KT, Johnsen CV, Lovley DR. Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). Int J Syst Evol Microbiol 2003; 53:669–673 [View Article][PubMed]
     [Google Scholar]
  53. Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J et al. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2010; 60:1358–1365 [View Article][PubMed]
     [Google Scholar]
  54. Ramana CV, Sasikala C. Albidoferax, a new genus of Comamonadaceae and reclassification of Rhodoferax ferrireducens (Finneran et al., 2003) as Albidoferax ferrireducens comb. nov. J Gen Appl Microbiol 2009; 55:301–304 [View Article][PubMed]
     [Google Scholar]
  55. Ding L, Yokota A. Curvibacter fontana sp. nov., a microaerobic bacteria isolated from well water. J Gen Appl Microbiol 2010; 56:267–271 [View Article][PubMed]
     [Google Scholar]
  56. Spring S, Jäckel U, Wagner M, Kämpfer P. Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54:99–106 [View Article][PubMed]
     [Google Scholar]
  57. Heulin T, Barakat M, Christen R, Lesourd M, Sutra L et al. Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing acteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 2003; 53:589–594 [View Article][PubMed]
     [Google Scholar]
  58. Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J. Description of Roseateles aquatilis sp. nov. and Roseateles terrae sp. nov., in the class Betaproteobacteria, and emended description of the genus Roseateles. Int J Syst Evol Microbiol 2008; 58:6–11 [View Article][PubMed]
     [Google Scholar]
  59. Tetsushi S, Toru S, Shinichi T, Yoshinobu NSF, Hiroyuki H et al. Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the β-subclass of the Proteobacteria. Int J Syst Evol Microbiol 1999; 49:449–457
     [Google Scholar]
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Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring
Int J Syst Evol Microbiol 67, 1133 (2017); https://doi.org/10.1099/ijsem.0.001777
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