1887

Abstract

A novel biosurfactant-producing strain, designated YW1, was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1 was a member of the genus , and showed highest sequence similarities to LMG 2370 (98.5 %), LMG 3475 (97.7 %) and LMG 1253 (97.7 %). Furthermore, DNA–DNA hybridization experiments against these three strains gave results that were clearly lower than 70 % DNA–DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus . The major respiratory quinone was ubiquinone-8. The major fatty acids (>5 %) were C (30.1 %), summed feature 3 (Cω6 and/or Cω7; 25.4 %), summed feature 8 (Cω6 and/or Cω7; 15.3 %), C cyclo (7.4 %) and C (5.8 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1 was clearly distinguishable from all species of the genus with validly published names and should be classified as a representative of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YW1 ( = CCTCC AB 2012033 = KACC 16697).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31200087)
  • Natural Science Foundation of Jiangsu Province (Award BK2011066)
  • Fundamental Research Funds for the Central Universities (Award KYZ201122)
  • Grand Science and Technology Special Project of the Chinese Academy of Tropical Agricultural Sciences (Award 2010hzsZDZX001)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.045716-0
2013-06-01
2021-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/6/2168.html?itemId=/content/journal/ijsem/10.1099/ijs.0.045716-0&mimeType=html&fmt=ahah

References

  1. Breznak J. A., Costilow R. N. ( 1994 ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  2. Buck J. D. ( 1982 ). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. . Appl Environ Microbiol 44, 992993.[PubMed]
    [Google Scholar]
  3. Burgos-Díaz C., Pons R., Espuny M. J., Aranda F. J., Teruel J. A., Manresa A., Ortiz A., Marqués A. M. ( 2011 ). Isolation and partial characterization of a biosurfactant mixture produced by Sphingobacterium sp. isolated from soil. . J Colloid Interface Sci 361, 195204. [View Article] [PubMed]
    [Google Scholar]
  4. Chang Y. H., Han J. I., Chun J., Lee K. C., Rhee M. S., Kim Y. B., Bae K. S. ( 2002 ). Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo, Korea. . Int J Syst Evol Microbiol 52, 377381.[PubMed]
    [Google Scholar]
  5. Chou J.-H., Sheu S.-Y., Lin K.-Y., Chen W.-M., Arun A. B., Young C.-C. ( 2007 ). Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus . . Int J Syst Evol Microbiol 57, 887891. [View Article] [PubMed]
    [Google Scholar]
  6. 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, 459470. [View Article]
    [Google Scholar]
  7. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230. [View Article] [PubMed]
    [Google Scholar]
  8. Cowan S. T., Steel K. J. ( 1965 ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  9. Davis G. H. G., Park R. W. A. ( 1962 ). A taxonomic study of certain bacteria currently classified as Vibrio species. . J Gen Microbiol 27, 101119. [View Article] [PubMed]
    [Google Scholar]
  10. De Vos P., Kersters K., Falsen E., Pot B., Gillis M., Segers P., De Ley J. ( 1985 ). Comamonas Davis and Park 1962, gen. nov., nom. rev. emend., and Comamonas terrigena Hugh 1962, sp. nov., nom. rev. . Int J Syst Bacteriol 35, 443453. [View Article]
    [Google Scholar]
  11. Eck R. V., Dayhoff M. O. ( 1966 ). Atlas of Protein Sequence and Structure. Silver Springs, MD:: National Biomedical Research Foundation;.
    [Google Scholar]
  12. Etchebehere C., Errazquin M. I., Dabert P., Moletta R., Muxí L. ( 2001 ). Comamonas nitrativorans sp. nov., a novel denitrifier isolated from a denitrifying reactor treating landfill leachate. . Int J Syst Evol Microbiol 51, 977983. [View Article] [PubMed]
    [Google Scholar]
  13. 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, 224229. [View Article]
    [Google Scholar]
  14. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  15. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  16. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  17. Gumaelius L., Magnusson G., Pettersson B., Dalhammar G. ( 2001 ). Comamonas denitrificans sp. nov., an efficient denitrifying bacterium isolated from activated sludge. . Int J Syst Evol Microbiol 51, 9991006. [View Article] [PubMed]
    [Google Scholar]
  18. Hugh R., Leifson E. ( 1953 ). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. . J Bacteriol 66, 2426.[PubMed]
    [Google Scholar]
  19. Kim K. H., Ten L. N., Liu Q. M., Im W. T., Lee S. T. ( 2008 ). Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant. . J Microbiol 46, 390395. [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. et al. ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [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, 111120. [View Article] [PubMed]
    [Google Scholar]
  22. Lane D. L. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E. R., Goodfellow M. . Chichester, United Kingdom:: Wiley;.
    [Google Scholar]
  23. Mandel M., Marmur J. ( 1968 ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12B, 195206. [View Article]
    [Google Scholar]
  24. McCarthy A. J., Cross T. ( 1984 ). A taxonomic study of Thermomonospora and other monosporic actinomycetes. . J Gen Microbiol 130, 525.
    [Google Scholar]
  25. 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 Microbiol 47, 8795. [View Article]
    [Google Scholar]
  26. Narayan K. D., Pandey S. K., Das S. K. ( 2010 ). Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti . . Curr Microbiol 61, 248253. [View Article] [PubMed]
    [Google Scholar]
  27. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  28. Sambrook J., Russell D. W. ( 2001 ). Molecular Cloning: a Laboratory Manual, , 3rd Edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  29. Sasser, M. (1997). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  30. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  31. Suzuki T., Yamasato K. ( 1994 ). Phylogeny of spore-forming lactic acid bacteria based on 16S rRNA gene sequences. . FEMS Microbiol Lett 115, 1317. [View Article] [PubMed]
    [Google Scholar]
  32. Suzuki M., Nakagawa Y., Harayama S., Yamamoto S. ( 2001 ). Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. . Int J Syst Evol Microbiol 51, 16391652. [View Article] [PubMed]
    [Google Scholar]
  33. Tago Y., Yokota A. ( 2004 ). Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge. . J Gen Appl Microbiol 50, 243248. [View Article] [PubMed]
    [Google Scholar]
  34. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. ( 1983 ). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. . J Appl Bacteriol 54, 3136. [View Article]
    [Google Scholar]
  35. Tamaoka J., Ha D. M., Komagata K. ( 1987 ). Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an emended description of the genus Comamonas . . Int J Syst Bacteriol 37, 5259. [View Article]
    [Google Scholar]
  36. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  37. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  38. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249266. [View Article] [PubMed]
    [Google Scholar]
  39. Wauters G., De Baere T., Willems A., Falsen E., Vaneechoutte M. ( 2003 ). Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigena . . Int J Syst Evol Microbiol 53, 859862. [View Article] [PubMed]
    [Google Scholar]
  40. 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, 463464. [View Article]
    [Google Scholar]
  41. Wen A., Fegan M., Hayward C., Chakraborty S., Sly L. I. ( 1999 ). Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov. . Int J Syst Bacteriol 49, 567576. [View Article] [PubMed]
    [Google Scholar]
  42. Young C.-C., Chou J.-H., Arun A. B., Yen W.-S., Sheu S.-Y., Shen F.-T., Lai W.-A., Rekha P. D., Chen W.-M. ( 2008 ). Comamonas composti sp. nov., isolated from food waste compost. . Int J Syst Evol Microbiol 58, 251256. [View Article] [PubMed]
    [Google Scholar]
  43. Yu X. Y., Li Y. F., Zheng J. W., Li Y., Li L., He J., Li S. P. ( 2011 ). Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil. . Int J Syst Evol Microbiol 61, 255258. [View Article] [PubMed]
    [Google Scholar]
  44. Zhang J., Wang Y. Q., Zhou S. G., Wu C. Y., He J., Li F. B. ( 2013 ). Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment and emended description of the genus Comamonas . . Int J Syst Evol Microbiol 63, 809814. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.045716-0
Loading
/content/journal/ijsem/10.1099/ijs.0.045716-0
Loading

Data & Media loading...

Supplements

Supplementary material 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