1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_11

sp. nov., isolated from a karst cave soil sample Free

Abstract

A novel Gram-stain-negative, non-motile, rod-shaped and watermelon-red-pigmented aerobic bacterial strain, designated YIM 77969, was isolated from a soil sample of Jiuxiang cave, a tourism cave located in Yiliang county, Yunnan province, south-west China. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77969 belongs to the genus , and was closely related to XTM003 (96.58 %), Txg1 (96.02 %) and X2-1g (95.80 %). Growth of strain YIM 77969 occurred at 5–35 °C, at pH 5.0–9.0 and in the presence of 0–1 % (w/v) NaCl. The predominant menaquinone was MK-7. The major fatty acids were iso-C, Cω5 and summed feature 3 (Cω7 and/or Cω6). The polar lipid profiles consisted of the major compound phosphatidylethanolamine, two unknown aminolipids, three unknown aminophospholipids, one glycolipid and one unknown polar lipid. Pigment analysis showed that the pigment belonged to the plectaniaxanthin series of carotenoid pigments. The genomic DNA G+C content was 55.2 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM 77969 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM 77969 ( = KCTC 32567 = DSM 28041).

  • Published Online:
Funding
This study was supported by the:
  • ‘Scholarship Award for Excellent Doctoral Student’ granted by Yunnan province (Award 2014)
  • Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000550
2015-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/11/4121.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000550&mimeType=html&fmt=ahah

References

  1. Baik K.S., Seong C.N., Moon E.Y., Park Y.D., Yi H., Chun J. ( 2006;). Hymenobacter rigui sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 56 2189–2192 [View Article] [PubMed].
     [Google Scholar]
  2. Bou G., Cerveró G., Domínguez M.A., Quereda C., Martínez-Beltrán J., PCR-based D.N.A. ( 2000;). PCR-based DNA fingerprinting (REP-PCR, AP-PCR) and pulsed-field gel electrophoresis characterization of a nosocomial outbreak caused by imipenem- and meropenem-resistant Acinetobacter baumannii . Clin Microbiol Infect 6 635–643 [View Article] [PubMed].
     [Google Scholar]
  3. Brosius J., Palmer M.L., Kennedy P.J., Noller H.F. ( 1978;). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 75 4801–4805 [View Article] [PubMed].
     [Google Scholar]
  4. Buczolits S., Denner E.B.M., Kämpfer P., Busse H.J. ( 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 [View Article] [PubMed].
     [Google Scholar]
  5. Cerny G. ( 1978;). Studies on the aminopeptidase test for the distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5 113–122 [View Article].
     [Google Scholar]
  6. Chung A.P., Lopes A., Nobre M.F., Morais P.V. ( 2010;). Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system. Syst Appl Microbiol 33 436–443 [View Article] [PubMed].
     [Google Scholar]
  7. Collins M.D., Jones D. ( 1980;). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48 459–470 [View Article].
     [Google Scholar]
  8. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E. ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria . J Gen Microbiol 100 221–230 [View Article] [PubMed].
     [Google Scholar]
  9. Dai J., Wang Y., Zhang L., Tang Y., Luo X., An H., Fang C. ( 2009;). Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai-Tibet plateau. Syst Appl Microbiol 32 543–548 [View Article] [PubMed].
     [Google Scholar]
  10. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368–376 [View Article] [PubMed].
     [Google Scholar]
  11. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783–791 [View Article].
     [Google Scholar]
  12. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406–416 [View Article].
     [Google Scholar]
  13. 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 [View Article] [PubMed].
     [Google Scholar]
  14. Hall T.A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 95–98.
     [Google Scholar]
  15. Han L., Wu S.J., Qin C.Y., Zhu Y.H., Lu Z.Q., Xie B., Lv J. ( 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 [View Article] [PubMed].
     [Google Scholar]
  16. Hirsch P., Ludwig W., Hethke C., Sittig M., Hoffmann B., Gallikowski C.A. ( 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 [View Article] [PubMed].
     [Google Scholar]
  17. Hoang V.A., Kim Y.J., Nguyen N.L., Yang D.C. ( 2013;). Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 63 661–666 [View Article] [PubMed].
     [Google Scholar]
  18. Jin L., Lee H.G., Kim S.G., Lee K.C., Ahn C.Y., Oh H.M. ( 2014;). Hymenobacter ruber sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 64 979–983 [View Article] [PubMed].
     [Google Scholar]
  19. Kim K.H., Im W.T., Lee S.T. ( 2008;). Hymenobacter soli sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 58 941–945 [View Article] [PubMed].
     [Google Scholar]
  20. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H. & other authors ( 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 [View Article] [PubMed].
     [Google Scholar]
  21. 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 [View Article] [PubMed].
     [Google Scholar]
  22. Klassen J.L., Foght J.M. ( 2008;). Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl Environ Microbiol 74 2016–2022 [View Article] [PubMed].
     [Google Scholar]
  23. Kovacs N. ( 1956;). Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178 703–704 [View Article] [PubMed].
     [Google Scholar]
  24. Kroppenstedt R.M. ( 1982;). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5 2359–2367 [View Article].
     [Google Scholar]
  25. Lee J.J., Srinivasan S., Lim S., Joe M., Lee S.H., Kwon S.A., Kwon Y.J., Lee J., Choi J.J. & other authors ( 2014;). Hymenobacter swuensis sp. nov., a gamma-radiation-resistant bacteria isolated from mountain soil. Curr Microbiol 68 305–310 [View Article] [PubMed].
     [Google Scholar]
  26. Li W.J., Xu P., Schumann P., Zhang Y.Q., Pukall R., Xu L.H., Stackebrandt E., Jiang C.L. ( 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 [View Article] [PubMed].
     [Google Scholar]
  27. Liu L., Zhou E.M., Jiao J.Y., Manikprabhu D., Ming H., Liu W.H., Hozzein W.N., Shu W.S., Li W.J. ( 2015;). Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment. Antonie van Leeuwenhoek 107 165–172 [View Article] [PubMed].
     [Google Scholar]
  28. Mesbah M., Premachandran U., Whitman W.B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159–167 [View Article].
     [Google Scholar]
  29. Minnikin D.E., Collins M.D., Goodfellow M. ( 1979;). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47 87–95 [View Article].
     [Google Scholar]
  30. Mishra R.K., Pandey B.K., Pathak N., Zeeshan M. ( 2015;). BOX-PCR- and ERIC-PCR-based genotyping and phylogenetic correlation among Fusarium oxysporum isolates associated with wilt disease in Psidium guajava L. Biocatalysis and Agricultural Biotechnology 4 25–32 [View Article].
     [Google Scholar]
  31. Parte A.C. ( 2014;). LPSN–List of Prokaryotic Names with Standing in Nomenclature. Nucleic Acids Res 42 (D1), D613–D616 [View Article] [PubMed].
     [Google Scholar]
  32. Reddy G.S. ( 2013;). Phylogenetic analyses of the genus Hymenobacter and description of Siccationidurans gen. nov., and Parahymenobacter gen. nov. J Phylogen Evolution Biol 1 122 [View Article].
     [Google Scholar]
  33. Reddy G.S., Garcia-Pichel F. ( 2005;). Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. Int J Syst Evol Microbiol 55 1295–1299 [View Article] [PubMed].
     [Google Scholar]
  34. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406–425 [PubMed].
     [Google Scholar]
  35. Srinivasan S., Joo E.S., Lee J.J., Kim M.K. ( 2015;). Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 107 1411–1419 [View Article] [PubMed].
     [Google Scholar]
  36. Su S., Chen M., Teng C., Jiang S., Zhang C., Lin M., Zhang W. ( 2014;). Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium. Int J Syst Evol Microbiol 64 2108–2112 [View Article] [PubMed].
     [Google Scholar]
  37. 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 [View Article] [PubMed].
     [Google Scholar]
  38. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 4876–4882 [View Article] [PubMed].
     [Google Scholar]
  39. Xu P., Li W.J., Tang S.K., Zhang Y.Q., Chen G.Z., Chen H.H., Xu L.H., Jiang C.L. ( 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 [View Article] [PubMed].
     [Google Scholar]
  40. Zhang Q., Liu C., Tang Y., Zhou G., Shen P., Fang C., 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 [View Article] [PubMed].
     [Google Scholar]
  41. Zhang L., Dai J., Tang Y., Luo X., Wang Y., An H., Fang C., Zhang C. ( 2009;). Hymenobacter deserti sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 59 77–82 [View Article] [PubMed].
     [Google Scholar]
  42. Zhang D.C., Busse H.J., Liu H.C., Zhou Y.G., Schinner F., Margesin R. ( 2011;). Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 61 859–863 [View Article] [PubMed].
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000550
Loading
Hymenobacter mucosus sp. nov., isolated from a karst cave soil sample
Int J Syst Evol Microbiol 65, 4121 (2015); https://doi.org/10.1099/ijsem.0.000550
/content/journal/ijsem/10.1099/ijsem.0.000550
/content/journal/ijsem/10.1099/ijsem.0.000550
Loading

Data & Media loading...

Supplements

Supplementary Data

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