1887

Abstract

Strain XMU 706, isolated from the rhizosphere soil of a herbaceous plant, L., collected from Xiamen City, China, was characterized using a polyphasic approach to clarify its taxonomic position. Strain XMU 706 shared the highest 16S rRNA gene sequence similarity with YIM 31530 (97.2 %), and formed a distinct branch in the subclade of the genus in the 16S rRNA gene phylogenetic tree. The genetic distances of gyrase subunit B gene () sequence between strain XMU 706 and other species of the genus ranged from 0.045 to 0.116, greater than the threshold value of 0.014 for species delineation of this genus. DNA–DNA hybridization experiments gave a DNA–DNA relatedness value of 34.82 ± 6.31 % between strain XMU 706 and YIM 31530. The chemotaxonomic properties further supported the assignment of strain XMU 706 to the genus . -Diaminopimelic acid was the diagnostic amino acid in the cell-wall peptidoglycan and cell hydrolysates contained ribose and glucose. The major menaquinone was MK-9(H). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and other unidentified phospholipids and lipids. The major fatty acids of the strain were anteiso-C and iso-C, and the G+C content of the genomic DNA was 67.3 mol%. Based on the results of phylogenetic analysis, phenotypic and genotypic characterization, strain XMU 706 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is XMU 706 ( = KCTC 29676 = MCCC 1K00429).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000393
2015-09-01
2019-09-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/9/3143.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000393&mimeType=html&fmt=ahah

References

  1. Carlsohn M.R., Groth I., Spröer C., Schütze B., Saluz H.P., Munder T., Stackebrandt E.. ( 2007;). Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57: 1943–1947 [CrossRef] [PubMed].
    [Google Scholar]
  2. Christensen H., Angen O., Mutters R., Olsen J.E., Bisgaard M.. ( 2000;). DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50: 1095–1102 [CrossRef] [PubMed].
    [Google Scholar]
  3. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E.. ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100: 221–230 [CrossRef] [PubMed].
    [Google Scholar]
  4. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 [CrossRef] [PubMed].
    [Google Scholar]
  5. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  6. Hasegawa T., Takizawa M., Tanida S.. ( 1983;). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29: 319–322 [CrossRef].
    [Google Scholar]
  7. Kelly K.L.. ( 1964;). Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, D.C: US Government Printing Office;.
    [Google Scholar]
  8. 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 [CrossRef] [PubMed].
    [Google Scholar]
  9. 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 [CrossRef] [PubMed].
    [Google Scholar]
  10. Kirby B.M., Everest G.J., Meyers P.R.. ( 2010;). Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella. Antonie van Leeuwenhoek 97: 131–142 [CrossRef] [PubMed].
    [Google Scholar]
  11. Kroppenstedt R.M.. ( 1985;). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics, pp. 173–179. Edited by Goodfellow M., Minnikin D. E.. London: Academic Press;.
    [Google Scholar]
  12. Lechevalier M.P., Lechevalier H.A.. ( 1970;). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20: 435–443 [CrossRef].
    [Google Scholar]
  13. Lechevalier M.P., De Bièvre C., Lechevalier H.A.. ( 1977;). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5: 249–260 [CrossRef].
    [Google Scholar]
  14. Li W.J., Wang D., Zhang Y.Q., Schumann P., Stackebrandt E., Xu L.H., Jiang C.L.. ( 2004;). Kribbella antibiotica sp. nov., a novel nocardioform actinomycete strain isolated from soil in Yunnan, China. Syst Appl Microbiol 27: 160–165 [CrossRef] [PubMed].
    [Google Scholar]
  15. 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 [CrossRef].
    [Google Scholar]
  16. 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 [CrossRef].
    [Google Scholar]
  17. Nesterenko O.A., Kvasnikov E.I., Nogina T.M.. ( 1985;). Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zhurnal 47: 3–12.
    [Google Scholar]
  18. Park Y.H., Yoon J.H., Shin Y.K., Suzuki K., Kudo T., Seino A., Kim H.J., Lee J.S., Lee S.T.. ( 1999;). Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp., ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49: 743–752 [CrossRef] [PubMed].
    [Google Scholar]
  19. Rainey F.A., Ward-Rainey N., Kroppenstedt R.M., Stackebrandt E.. ( 1996;). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46: 1088–1092 [CrossRef] [PubMed].
    [Google Scholar]
  20. 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]
  21. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20: 16.
    [Google Scholar]
  22. Shirling E.B., Gottlieb D.. ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16: 313–340 [CrossRef].
    [Google Scholar]
  23. 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, D.C: American Society for Microbiology;.
    [Google Scholar]
  24. Stackebrandt E.. ( 1988;). Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. Can J Microbiol 34: 552–556 [CrossRef] [PubMed].
    [Google Scholar]
  25. Takahashi K., Nei M.. ( 2000;). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17: 1251–1258 [CrossRef] [PubMed].
    [Google Scholar]
  26. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. ( 2013;). mega6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725–2729 [CrossRef] [PubMed].
    [Google Scholar]
  27. 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., other authors. ( 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]
  28. Wu Y., Lu C., Qian X., Huang Y., Shen Y.. ( 2009;). Diversities within genotypes, bioactivity and biosynthetic genes of endophytic actinomycetes isolated from three pharmaceutical plants. Curr Microbiol 59: 475–482 [CrossRef] [PubMed].
    [Google Scholar]
  29. 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 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000393
Loading
/content/journal/ijsem/10.1099/ijsem.0.000393
Loading

Data & Media loading...

Supplementary Data



PDF

Most Cited This Month

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