1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 9

Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment Free

Abstract

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming bacterial strain, designated DK6-66, was isolated from subsurface sandstone sediment located in the Qilian Mountains in Qinghai Province, Northwest China. Strain DK6-66 was found to grow optimally at pH 7.0 and 22 °C. The 16S rRNA gene sequence analysis indicated that strain DK6-66 belonged to the genus Hymenobacter and clustered with the type strain of Hymenobacter arcticus , with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. The DNA G+C content was 60.4 mol%. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, anteiso-C17 : 1 B and/or iso-C17 : 1 I, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω5c. On the basis of phylogenetic and phenotypic data, strain DK6-66 was classified in the genus Hymenobacter as a member of a novel species, for which the name Hymenobacter bucti sp. nov. is proposed. The type strain is DK6-66 (=CGMCC 1.15795=KCTC 52629).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Hymenobacter , novel species , polyphasic approach and Qilian Mountains
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002866
2018-07-31
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/9/2749.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002866&mimeType=html&fmt=ahah

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 [View Article][PubMed]
     [Google Scholar]
  2. Buczolits S, Denner EB, Kämpfer P, Busse HJ. Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2071–2078 [View Article][PubMed]
     [Google Scholar]
  3. Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ 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 [View Article][PubMed]
     [Google Scholar]
  4. Han J, Ten LN, Lee DH, Kang IK, Jung HY. Hymenobacter agri sp. nov., a novel bacterium isolated from soil. Antonie van Leeuwenhoek 2018 [View Article][PubMed]
     [Google Scholar]
  5. Sheu SY, Hsieh TY, Kwon SW, Chen WM. Hymenobacter rivuli sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018; 68:1220–1226 [View Article][PubMed]
     [Google Scholar]
  6. Sun J, Xing M, Wang W, Dai F, Liu J et al. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947–950 [View Article][PubMed]
     [Google Scholar]
  7. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article][PubMed]
     [Google Scholar]
  8. Kang JW, Choi S, Choe HN, Seong CN. Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2018; 68:277–282 [View Article][PubMed]
     [Google Scholar]
  9. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Hymenobacter frigidus sp. nov., isolated from a glacier ice core. Int J Syst Evol Microbiol 2017; 67:4121–4125 [View Article][PubMed]
     [Google Scholar]
  10. Baik KS, Seong CN, Moon EY, Park YD, Yi H et al. Hymenobacter rigui sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2006; 56:2189–2192 [View Article][PubMed]
     [Google Scholar]
  11. Kim KH, Im WT, Lee ST. Hymenobacter soli sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 2008; 58:941–945 [View Article][PubMed]
     [Google Scholar]
  12. Buczolits S, Denner EB, 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 [View Article][PubMed]
     [Google Scholar]
  13. Huang F, Zhang Y, Zhu Y, Wang P, Lu J et al. Flavobacterium qiangtangensis sp. nov., isolated from Qiangtang basin in Qinghai-Tibetan Plateau, China. Curr Microbiol 2014; 69:234–239 [View Article][PubMed]
     [Google Scholar]
  14. Wang YX, Huang FQ, Nogi Y, Pang SJ, Wang PK et al. Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment. Int J Syst Evol Microbiol 2015; 65:2048–2055 [View Article][PubMed]
     [Google Scholar]
  15. Feng XM, Mo YX, Han L, Nogi Y, Zhu YH et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015; 65:3658–3665 [View Article][PubMed]
     [Google Scholar]
  16. Jia L, Feng X, Zheng Z, Han L, Hou X et al. Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter. Int J Syst Evol Microbiol 2015; 65:3920–3925 [View Article][PubMed]
     [Google Scholar]
  17. Jia L, Zheng Z, Feng X, Nogi Y, Yang A et al. Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China. Antonie van Leeuwenhoek 2015; 108:1341–1347 [View Article][PubMed]
     [Google Scholar]
  18. Piao AL, Feng XM, Nogi Y, Han L, Li Y et al. Sphingomonas qilianensis sp. nov., isolated from surface soil in the permafrost region of Qilian Mountains, China. Curr Microbiol 2016; 72:363–369 [View Article][PubMed]
     [Google Scholar]
  19. Zhang RG, Tan X, Liang Y, Meng TY, Liang HZ et al. Description of Chishuiella changwenlii gen. nov., sp. nov., isolated from freshwater, and transfer of Wautersiella falsenii to the genus Empedobacter as Empedobacter falsenii comb. nov. Int J Syst Evol Microbiol 2014; 64:2723–2728 [View Article][PubMed]
     [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; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  21. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  22. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  25. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 1989; 29:170–179 [View Article][PubMed]
     [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  27. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  28. 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]
  29. 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]
  30. Moreira AP, Pereira N, Thompson FL. Usefulness of a real-time PCR platform for G+C content and DNA–DNA hybridization estimations in vibrios. Int J Syst Evol Microbiol 2011; 61:2379–2383 [View Article][PubMed]
     [Google Scholar]
  31. Feng Q, Gao Y, Nogi Y, Tan X, Han L et al. Flavobacterium maotaiense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2015; 65:171–176 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. Krieg NR, Padgett PJ. Phenotypic and physiological characterization methods. Methods Microbiol 2011; 38:15–60
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty acids, MIDI Technical Note 101. Newark: MIDI Inc; 1990
     [Google Scholar]
  35. 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]
  36. da C, Albuquerque L, Nobre M, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 2011; 38:197–206
     [Google Scholar]
  37. Collins MD, Goodfellow M, Minnikin DE. Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J Gen Microbiol 1980; 118:29–37 [View Article][PubMed]
     [Google Scholar]
  38. Reddy GS, Garcia-Pichel F. Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. Antonie van Leeuwenhoek 2013; 103:441–442 [View Article][PubMed]
     [Google Scholar]
  39. Klassen JL, Foght JM. Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl Environ Microbiol 2008; 74:2016–2022 [View Article][PubMed]
     [Google Scholar]
  40. Chang X, Zheng J, Jiang F, Liu P, Kan W et al. Hymenobacter arcticus sp. nov., isolated from glacial till. Int J Syst Evol Microbiol 2014; 64:2113–2118 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002866
Loading
Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment
Int J Syst Evol Microbiol 68, 2749 (2018); https://doi.org/10.1099/ijsem.0.002866
/content/journal/ijsem/10.1099/ijsem.0.002866
/content/journal/ijsem/10.1099/ijsem.0.002866
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error