Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons

Leys, N., Ryngaert, A., Bastiaens, L., Verstraete, W., Top, E. M. and Springael, D. (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Applied and Environmental Microbiology, 70 4: 1944-1955. doi:10.1128/AEM.70.4.1944-1955.2004

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Author Leys, N.
Ryngaert, A.
Bastiaens, L.
Verstraete, W.
Top, E. M.
Springael, D.
Title Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons
Journal name Applied and Environmental Microbiology   Check publisher's open access policy
ISSN 0099-2240
1098-5336
Publication date 2004-04
Sub-type Article (original research)
DOI 10.1128/AEM.70.4.1944-1955.2004
Open Access Status File (Publisher version)
Volume 70
Issue 4
Start page 1944
End page 1955
Total pages 12
Place of publication Washington, D.C.
Publisher American Society for Microbiology
Language eng
Subject 050303 Soil Biology
100203 Bioremediation
Abstract Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil–1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Faculty of Engineering, Architecture and Information Technology Publications
Excellence in Research Australia (ERA) - Collection
 
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