Antonie van Leeuwenhoek

, Volume 107, Issue 1, pp 165–172 | Cite as

Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment

  • Lan Liu
  • En-Min Zhou
  • Jian-Yu Jiao
  • Deene Manikprabhu
  • Hong Ming
  • Wei-Hong Liu
  • Wael N. Hozzein
  • Wen-Sheng Shu
  • Wen-Jun LiEmail author
Original Paper


Two novel Gram-stain negative, non-motile, rod-shaped and aerobic bacterial strains, designated YIM 77920T and YIM 77921T, were isolated from freshwater sediment of Jiuxiang cave, a tourism cave located in Yiliang county, Yunnan province, south-west China. The 16S rRNA gene sequences of strains YIM 77920T and YIM 77921T exhibited sequence similarities of 96.59 and 96.66 % to Hymenobacter xinjiangensis X2-YT, respectively, and indicated that the two isolates belong to the genus Hymenobacter. The major fatty acids present in the two strains were identified as C16:1 ω5c, iso-C15:0 and Summed Feature 4 (C17:1 anteiso B/iso I). MK-7 was identified as the respiratory quinone component for both strains. The polar lipids profile of strain YIM 77920T was found to consist of phosphatidylethanolamine, four unidentified polar lipids, three unidentified aminophospholipids, two unidentified phospholipids and two unidentified aminolipids, while that of strain YIM 77921T consisted of phosphatidylethanolamine, four unidentified polar lipids, two unidentified aminolipids, one unidentified phospholipid and four unidentified aminophospholipids. The DNA G+C contents of strains YIM 77920T and YIM 77921T were determined to be 57.5 and 59.6 mol%, respectively. DNA–DNA hybridization between them had a low value (56.55 %). Based on the morphological and physiological properties, and phylogenetic analyses, strains YIM 77920T and YIM 77921T are considered to represent two novel species of the genus Hymenobacter, for which the names Hymenobacter latericoloratus sp. nov. (type strain YIM 77920T = JCM 30327T = CCTCC AB 2012949T) and Hymenobacter luteus sp. nov. (type strain YIM 77921T = JCM 30328T = CCTCC AB 2012947T) are proposed.


Hymenobacter latericoloratus sp. nov. Hymenobacter luteus sp. nov. 16S rRNA gene Polyphasic taxonomy Jiuxiang cave 



We are grateful to Prof. Dr. Takuji Kudo (JCM) for his kind providing reference type strain and Prof. Aharon Oren (The Hebrew University of Jerusalem, Israel) for his kind help with the Latin etymology for the new species. This work was supported by the National Natural Science Foundation of China (No. 81102806), the Deanship of Scientific Research at King Saud University for funding this work through the research group no RGP-205, the opening project of the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences (No. SKLMR-20100602), Yunnan Provincial Natural Science Foundation (2011FZ166, 2013FA004). W-J Li was also supported by Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014).

Supplementary material

10482_2014_314_MOESM1_ESM.docx (802 kb)
Supplementary material 1 (DOCX 803 kb)


  1. Buczolits S, Denner EBM, Kämpfer P, Busse HJ (2006) 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 56:2071–2078PubMedCrossRefGoogle Scholar
  2. Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122CrossRefGoogle Scholar
  3. Chang XL, Zheng JL, Jiang F, Liu P, Kan WJ, Qu ZH, Fang CX, Peng F (2014) Hymenobacter arcticus sp. nov., isolated from high arctic glacial till. Int J Syst Evol Microbiol 64:2113–2118PubMedCrossRefGoogle Scholar
  4. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (2000) DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102PubMedCrossRefGoogle Scholar
  5. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diaminobutyric acid. Appl Bacteriol 48:459–470CrossRefGoogle Scholar
  6. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230PubMedCrossRefGoogle Scholar
  7. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyriboribonucleic 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 39:224–229CrossRefGoogle Scholar
  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  11. Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715PubMedCrossRefGoogle Scholar
  12. Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, Xie B, Jie Lv (2014) 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 105:971–978PubMedCrossRefGoogle Scholar
  13. He L, Li W, Huang Y, Wang LM, Liu ZH, Lanoot BJ, Vancanneyt M, Swings J (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944PubMedCrossRefGoogle Scholar
  14. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B, Gallikowski CA (1998) Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctic soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 21:374–383PubMedCrossRefGoogle Scholar
  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721PubMedCrossRefGoogle Scholar
  16. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  17. Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704PubMedCrossRefGoogle Scholar
  18. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2387CrossRefGoogle Scholar
  19. Leifson E (1960) Atlas of Bacterial Flagellation. Academic Press, LondonGoogle Scholar
  20. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) 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 57:1424–1428PubMedCrossRefGoogle Scholar
  21. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  22. Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95CrossRefGoogle Scholar
  23. Parte AC (2014) LPSN – list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616PubMedCentralPubMedCrossRefGoogle Scholar
  24. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  25. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar
  26. Su SY, Chen M, Teng C, Jiang SJ, Zhang C, Lin M, Zhang W (2014) Hymenobacter kanuolensis sp. nov., a novel radiation-resistant 1 bacterium from the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 64:2108–2112PubMedCrossRefGoogle Scholar
  27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCentralPubMedCrossRefGoogle Scholar
  28. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCentralPubMedCrossRefGoogle Scholar
  29. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu H, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family Oxalobacteraceae isolated from China. Int J Syst Evol Microbiol 55:1149–1153PubMedCrossRefGoogle Scholar
  30. Zhang QJ, Liu C, Tang YL, Zhou GL, Shen P, Fang CX, Yokota A (2007) Hymenobacter xinjiangensis sp. nov., a radiation resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 57:1752–1756PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Lan Liu
    • 1
  • En-Min Zhou
    • 1
    • 2
  • Jian-Yu Jiao
    • 1
    • 3
  • Deene Manikprabhu
    • 1
    • 2
  • Hong Ming
    • 1
  • Wei-Hong Liu
    • 4
  • Wael N. Hozzein
    • 5
  • Wen-Sheng Shu
    • 2
  • Wen-Jun Li
    • 1
    • 2
    Email author
  1. 1.Yunnan Institute of MicrobiologyYunnan UniversityKunmingPeople’s Republic of China
  2. 2.State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and EvolutionSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  3. 3.Medical Faculty of Kunming University of Science and TechnologyKunming University of Science and TechnologyKunmingPeople’s Republic Of China
  4. 4.Department of Agriculture and Biological SciencesDali UniversityDaliPeople’s Republic of China
  5. 5.Bioproducts Research Chair (BRC), College of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia

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