Skip to main content

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

Antonie van Leeuwenhoek volume 107, pages 165–172 (2015)Cite this article

Abstract

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.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1

References

  • 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 56:2071–2078

    CAS  PubMed  Article  Google Scholar 

  • Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122

    CAS  Article  Google Scholar 

  • 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 64:2113–2118

    CAS  PubMed  Article  Google Scholar 

  • 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 50:1095–1102

    CAS  PubMed  Article  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diaminobutyric acid. Appl Bacteriol 48:459–470

    CAS  Article  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  PubMed  Article  Google Scholar 

  • 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 39:224–229

    Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  PubMed  Article  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715

    CAS  PubMed  Article  Google Scholar 

  • 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 105:971–978

    CAS  PubMed  Article  Google Scholar 

  • 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 55:1939–1944

    CAS  PubMed  Article  Google Scholar 

  • 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 21:374–383

    CAS  PubMed  Article  Google Scholar 

  • 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 62:716–721

    CAS  PubMed  Article  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Article  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704

    CAS  PubMed  Article  Google Scholar 

  • 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 5:2359–2387

    CAS  Article  Google Scholar 

  • Leifson E (1960) Atlas of Bacterial Flagellation. Academic Press, London

    Google Scholar 

  • 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 57:1424–1428

    PubMed  Article  Google Scholar 

  • 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 39:159–167

    CAS  Article  Google Scholar 

  • 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 47:87–95

    CAS  Article  Google Scholar 

  • Parte AC (2014) LPSN – list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • 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 44:846–849

    CAS  Article  Google Scholar 

  • 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 64:2108–2112

    CAS  PubMed  Article  Google Scholar 

  • 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 28:2731–2739

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 25:4876–4882

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • 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 55:1149–1153

    CAS  PubMed  Article  Google Scholar 

  • 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 57:1752–1756

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

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).

Author information

Affiliations

  1. Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    Lan Liu, En-Min Zhou, Jian-Yu Jiao, Deene Manikprabhu, Hong Ming & Wen-Jun Li

  2. State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    En-Min Zhou, Deene Manikprabhu, Wen-Sheng Shu & Wen-Jun Li

  3. Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, People’s Republic Of China

    Jian-Yu Jiao

  4. Department of Agriculture and Biological Sciences, Dali University, Dali, 671003, People’s Republic of China

    Wei-Hong Liu

  5. Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia

    Wael N. Hozzein

Authors
  1. Lan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. En-Min Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jian-Yu Jiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Deene Manikprabhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hong Ming
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei-Hong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wael N. Hozzein
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Wen-Sheng Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wen-Jun Li.

Additional information

Lan Liu and En-Min Zhou have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 803 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Liu, L., Zhou, EM., Jiao, JY. et al. Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment. Antonie van Leeuwenhoek 107, 165–172 (2015). https://doi.org/10.1007/s10482-014-0314-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0314-1

Keywords

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