1887

Abstract

A Gram-reaction-positive, aerobic, non-spore-forming, rod- or coccoid-shaped, strain, CD40127, was isolated from a green biofilm covering the wall of the Domitilla Catacombs in Rome, Italy. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CD40127 belongs to the genus , closely related to DSM 43366 and DSM 43109 with 98.86 % and 98.01 % similarity values, respectively. Strain CD40127 exhibited 16S rRNA gene sequence similarity values below 96.29 % with the rest of the species of the genus . The G+C content of the genomic DNA was 69.7 mol%. The predominant fatty acid was iso-C and the major menaquinone was MK-8(H) in accordance with the phenotypes of other species of the genus . A polyphasic approach using physiological tests, fatty acid profiles, DNA base ratios and DNA–DNA hybridization showed that isolate CD40127 represents a novel species within the genus , for which the name is proposed. The type strain is CD40127 ( = DSM 25218 = CECT 8014).

Funding
This study was supported by the:
  • , Consolider project , (Award TCP CSD2007-00058)
  • , Fundação para a Ciência e a Tecnologia (FCT) , (Award SFRH/BPD/63836/2009)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.043885-0
2013-04-01
2020-07-08
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/4/1280.html?itemId=/content/journal/ijsem/10.1099/ijs.0.043885-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Dastager S. G., Lee J. C., Ju Y. J., Park D. J., Kim C. J. ( 2008 ). Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea. . Int J Syst Evol Microbiol 58, 22922296. [CrossRef] [PubMed]
    [Google Scholar]
  3. Dastager S. G., Lee J. C., Pandey A., Kim C. J. ( 2010 ). Nocardioides mesophilus sp. nov., isolated from soil. . Int J Syst Evol Microbiol 60, 22882292. [CrossRef] [PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [CrossRef] [PubMed]
    [Google Scholar]
  5. Edgar R. C. ( 2004 ). MUSCLE: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32, 17921797. [CrossRef] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  7. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [CrossRef]
    [Google Scholar]
  8. Groth I., Vettermann R., Schuetze B., Schumann P., Saiz-Jimenez C. ( 1999 ). Actinomycetes in Karstic caves of northern Spain (Altamira and Tito Bustillo). . J Microbiol Methods 36, 115122. [CrossRef] [PubMed]
    [Google Scholar]
  9. Groth I., Schumann P., Laiz L., Sanchez-Moral S., Cañaveras J. C., Saiz-Jimenez C. ( 2001 ). Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. . Geomicrobiol J 18, 241258. [CrossRef]
    [Google Scholar]
  10. Halebian S., Harris B., Finegold S. M., Rolfe R. D. ( 1981 ). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. . J Clin Microbiol 13, 444448.[PubMed]
    [Google Scholar]
  11. 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. [CrossRef] [PubMed]
    [Google Scholar]
  12. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics, vol. 20, pp. 173199. Edited by Goodfellow M., Minnikin D. E. . New York:: Academic Press;.
    [Google Scholar]
  13. Küster E., Williams S. T. ( 1964 ). Selection of media for isolation of streptomycetes. . Nature 202, 928929. [CrossRef] [PubMed]
    [Google Scholar]
  14. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol 3, 208218. [CrossRef]
    [Google Scholar]
  15. Prauser H. ( 1976 ). Nocardioides, a new genus of the order Actinomycetales . . Int J Syst Bacteriol 26, 5865. [CrossRef]
    [Google Scholar]
  16. Rosselló-Mora R., Amann R. ( 2001 ). The species concept for prokaryotes. . FEMS Microbiol Rev 25, 3967. [CrossRef] [PubMed]
    [Google Scholar]
  17. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  18. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. et al. ( 2002 ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52, 10431047. [CrossRef] [PubMed]
    [Google Scholar]
  19. 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. [CrossRef] [PubMed]
    [Google Scholar]
  20. Yoon J. H., Rhee S. K., Lee J. S., Park Y. H., Lee S. T. ( 1997 ). Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. . Int J Syst Bacteriol 47, 933938. [CrossRef] [PubMed]
    [Google Scholar]
  21. Yoon J. H., Kang S. J., Park S., Kim W., Oh T. K. ( 2009 ). Nocardioides caeni sp. nov., isolated from wastewater. . Int J Syst Evol Microbiol 59, 27942797. [CrossRef] [PubMed]
    [Google Scholar]
  22. Yoon J. H., Park S., Kang S. J., Lee J. S., Lee K. C., Oh T. K. ( 2010 ). Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil. . Int J Syst Evol Microbiol 60, 13341338. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.043885-0
Loading
/content/journal/ijsem/10.1099/ijs.0.043885-0
Loading

Data & Media loading...

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