1887

Abstract

A Gram-reaction-positive, strictly aerobic, capsule-forming, motile and rod-shaped bacterium, designated strain XD80, was isolated from the soil of a native cave in Lichuan, Hubei province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XD80 was most closely related to CCTCC AB 2015183 (98.66 % sequence similarity), followed by DSM 25058(97.83 %), KCTC 33549 (97.70 %), CCTCC AB 2011121 (97.21 %) and DSM 28032 (96.96 %). Levels of DNA–DNA relatedness between strain XD80 and CCTCC AB 2015183, DSM 25058, KCTC 33549 and CCTCC AB 2011121 were 37.4 %, 53.8 %, 53.6 % and 52.7 %, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipid and two unknown phospholipids. The predominant fatty acids (>5 %) were iso-C (37.3 %), anteiso-C (10.8 %), C (10.4 %), iso-C (10.3 %), Cω11 (9.6 %) and anteiso-C (7.4 %). MK-6 (86.4 %) was the major respiratory quinone. The DNA G+C content was 46.4 mol%. The cell-wall peptidoglycan contained -diaminopimelic acid (type A1γ). Ribose and glucose were the major whole-cell sugars. In addition, strain XD80 showed differential physiological characteristics from most members of the genus , encompassing hydrolysis of starch, acid production from inositol and raffinose, and production of valine arylamidase. The results of this polyphasic study indicated that strain XD80 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is XD80(=CCTCC AB 2015053=KCTC 33636).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001080
2016-07-01
2020-08-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/7/2502.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001080&mimeType=html&fmt=ahah

References

  1. Brill J. A., Wiegel J.. 1997; Differentiation between spore-forming and asporogenic bacteria using a PCR and Southern hybridization based method. J of Microbiol Methods31:29–36[CrossRef]
    [Google Scholar]
  2. 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 Bacteriol48:459–470[CrossRef]
    [Google Scholar]
  3. Cowan S. T., Steel K. J.. 1965; Manual for the Identification of Medical Bacteria London: Cambridge University Press;
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–142[PubMed][CrossRef]
    [Google Scholar]
  5. Dong X. Z., Cai M. Y.. 2001; Determinative Manual for Routine Bacteriology Beijing: Scientific Press;
    [Google Scholar]
  6. Dussault H. P.. 1955; An improved technique for staining red halophilic bacteria. J Bacteriol70:484–485[PubMed]
    [Google Scholar]
  7. Fan H., Su C., Wang Y., Yao J., Zhao K., Wang Y., Wang G.. 2008; Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol105:529–539 [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376[PubMed][CrossRef]
    [Google Scholar]
  9. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791[CrossRef]
    [Google Scholar]
  10. Fitch W. M.. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zool20:406–416[CrossRef]
    [Google Scholar]
  11. Gyeong H. R., Baek K., Hwang C. Y., Park K. H., Kim H. M., Lee H. K., Lee Y. K.. 2015; Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus . Int J Syst Evol Microbiol
    [Google Scholar]
  12. 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. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  13. Kimura M.. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16:111–120[PubMed][CrossRef]
    [Google Scholar]
  14. 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 Chromatogr5:2359–2367[CrossRef]
    [Google Scholar]
  15. Kroppenstedt R. M.. 1985; Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series)vol. 20173–199 Edited by Goodfellow. M., Minnikin D. E.. New York: Academic Press;
    [Google Scholar]
  16. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. 2007; Clustal W and Clustal X version 2.0. Bioinformatics23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  17. 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 Microbiol59:2114–2121 [CrossRef][PubMed]
    [Google Scholar]
  18. Ryu E.. 1940; A simple method of differentiation between Gram-positive and Gram-negative organisms without staining. Kitasato Arch Exp Med17:58–63
    [Google Scholar]
  19. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  20. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark,DE: MIDI Inc;
    [Google Scholar]
  21. Schumann P.. 2011; Peptidoglycan structure. Methods Microbiol38:101–129[CrossRef]
    [Google Scholar]
  22. Seiler H., Wenning M., Scherer S.. 2013; Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. Int J Syst Evol Microbiol63:2054–2061 [CrossRef][PubMed]
    [Google Scholar]
  23. Sharma A., Dhar S. K., Prakash O., Vemuluri V. R., Thite V., Shouche Y. S.. 2014; Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus . Int J Syst Evol Microbiol64:3010–3015 [CrossRef][PubMed]
    [Google Scholar]
  24. Sonalkar V. V., Mawlankar R., Krishnamurthi S., Tang S. K., Dastager S. G.. 2014; Domibacillus enclensis sp. nov., isolated from marine sediment, and emended description of the genus Domibacillus . Int J Syst Evol Microbiol64:4098–4102 [CrossRef][PubMed]
    [Google Scholar]
  25. Sun Q.-L., Sun L.. 2015; Description of Domibacillus iocasae sp. nov., isolated from the deep sea sediment of Okinawa trough, and emended description of the genus Domibacillus . Int J Syst Evol Microbiol doi: 10.1099/ijsem.0.000823 [CrossRef]
    [Google Scholar]
  26. Tamaoka J., Komagata K.. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiology Letters25:125–128[CrossRef]
    [Google Scholar]
  27. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  28. Weeger W., Lièvremont D., Perret M., Lagarde F., Hubert J. C., Leroy M., Lett M. C.. 1999; Oxidation of arsenite to arsenate by a bacterium isolated from an aquatic environment. Biometals12:141–149[PubMed][CrossRef]
    [Google Scholar]
  29. Wilson K. H., Blitchington R. B., Greene R. C.. 1990; Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol28:1942–1946[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001080
Loading
/content/journal/ijsem/10.1099/ijsem.0.001080
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month 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