1887

Abstract

A Gram-stain-positive, strictly aerobic, rod-shaped, motile and endospore-forming bacterial strain, designated TEGR-3, was isolated from the roots of collected from the Qinling Mountains in Shaanxi Province, China. Strain TEGR-3 produced siderophores and hydrolysed aesculin, starch and CM-cellulose. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TEGR-3 was a member of the genus , exhibiting the highest sequence similarity to LMG 27297 (97.3 %) and DSM 19417 (97.3 %). MK-7 was the only menaquinone detected and anteiso-C and C were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and an unidentified lipid. The cell-wall peptidoglycan contained -diaminopimelic acid as the diagnostic diamino acid. The DNA G+C content was 45.2 mol%. DNA–DNA relatedness values for strain TEGR-3 with respect to its closest phylogenetic relatives LMG 27297 and DSM 19417 were lower than 40 %. Based on the phenotypic, phylogenetic and genotypic data, strain TEGR-3 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TEGR-3 (=CCTCC AB 2016047=KCTC 33807).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001458
2016-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/4993.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001458&mimeType=html&fmt=ahah

References

  1. Ash C., Priest F. G., Collins M. D. 1993; Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus . Antonie van Leeuwenhoek 64:253–260[PubMed] [CrossRef]
    [Google Scholar]
  2. Ash C., Priest F. G., Collins M. D. 1994; Paenibacillus gen. nov. in validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 51. Int J Syst Bacteriol 44:852 [CrossRef]
    [Google Scholar]
  3. Carro L., Flores-Félix J. D., Cerda-Castillo E., Ramírez-Bahena M. H., Igual J. M., Tejedor C., Velázquez E., Peix A. 2013; Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum . Int J Syst Evol Microbiol 63:4433–4438 [View Article][PubMed]
    [Google Scholar]
  4. Claus D., Berkeley R. C. W. 1986; Genus Bacillus Cohn 1872, 174AL . In Bergey’s Manual of Systematic Bacteriology vol. 2 pp. 1105–1139 Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  5. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. 2002; Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52:1551–1558 [View Article][PubMed]
    [Google Scholar]
  6. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology pp. 21–33 Edited by Gerdhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  7. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; 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 39:224–229 [View Article]
    [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  10. Gao J. L., Yuan M., Wang X. M., Qiu T. L., Lv F. Y., Yang M. M., Sun J. G. 2015; Paenibacillus radicis sp. nov., a endophytic bacterium isolated from maize root in China. Int J Syst Evol Microbiol 66:807–811 [View Article]
    [Google Scholar]
  11. 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]
  12. Kim B.-C., Poo H., Lee K. H., Kim M. N., Kwon O.-Y., Shin K.-S. 2012a; Mucilaginibacter angelicae sp. nov., isolated from the rhizosphere of Angelica polymorpha Maxim. Int J Syst Evol Microbiol 62:55–60 [View Article][PubMed]
    [Google Scholar]
  13. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012b; 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]
  14. Lane D. J. 1991; 16S-23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 125–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  15. 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]
  16. Liu W., Yin D., Liu J., Li N. 2014; Genetic diversity and structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China. PLoS One 9:e110500 [View Article][PubMed]
    [Google Scholar]
  17. Liu W., Liu J., Yin D., Zhao X. 2015; Influence of ecological factors on the production of active substances in the anti-cancer plant Sinopodophyllum hexandrum (Royle) T.S. Ying. PLoS One 10:e0122981 [View Article][PubMed]
    [Google Scholar]
  18. Logan N. A., Berge O., Bishop A. H., Busse H.-J., De Vos P., Fritze D., Heyndrickx M., Kämpfer P., Rabinovitch L. et al. 2009; Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. Priest F. G. 2009; Genus I. Paenibacillus . In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2 pp. 269–296 Edited by De Vos P., Garrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K. H., Whitman W. B. New York: Springer;
    [Google Scholar]
  21. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  22. 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]
  23. Schwyn B., Neilands J. B. 1987; Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56 [View Article][PubMed]
    [Google Scholar]
  24. Shida O., Takagi H., Kadowaki K., Nakamura L. K., Komagata K. 1997; Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus . Int J Syst Bacteriol 47:289–298 [View Article][PubMed]
    [Google Scholar]
  25. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  26. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231[PubMed]
    [Google 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 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  30. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  31. Valverde A., Peix A., Rivas R., Velázquez E., Salazar S., Santa-Regina I., Rodríguez-Barrueco C., Igual J. M. 2008; Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller. Int J Syst Evol Microbiol 58:2560–2564 [View Article][PubMed]
    [Google Scholar]
  32. Valverde A., Fterich A., Mahdhi M., Ramírez-Bahena M. H., Caviedes M. A., Mars M., Velázquez E., Rodriguez-Llorente I. D. 2010; Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta . Int J Syst Evol Microbiol 60:2182–2186 [View Article][PubMed]
    [Google Scholar]
  33. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  34. Wilson K. 1987; Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology pp. 241–245 Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Greene Publishing and Wiley Interscience;
    [Google Scholar]
  35. Xie C. H., Yokota A. 2003; Phylogenetic analysis of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349 [View Article][PubMed]
    [Google Scholar]
  36. 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]
  37. Ying T. S. 1994; An analysis of the flora of Qinling Mountain range: its nature, characteristics and origins. Acta Phytotax Sin 32:389–410
    [Google Scholar]
  38. Zhang J., Wang Z. T., Yu H. M., Ma Y. 2013a; Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa . Int J Syst Evol Microbiol 63:1776–1781 [View Article][PubMed]
    [Google Scholar]
  39. Zhang L., Wang Y., Wei L., Wang Y., Shen X., Li S. 2013b; Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus . Int J Syst Evol Microbiol 63:3769–3776 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001458
Loading
/content/journal/ijsem/10.1099/ijsem.0.001458
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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