PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites

Hendrickx, Barbara, Dejonghe, Winnie, Faber, Folkert, Boënne, Wesley, Bastiaens, Leen, Verstraete, Willy, Top, Eva M. and Springael, Dirk (2006) PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbiology Ecology, 55 2: 262-273. doi:10.1111/j.1574-6941.2005.00018.x


Author Hendrickx, Barbara
Dejonghe, Winnie
Faber, Folkert
Boënne, Wesley
Bastiaens, Leen
Verstraete, Willy
Top, Eva M.
Springael, Dirk
Title PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites
Journal name FEMS Microbiology Ecology   Check publisher's open access policy
ISSN 0168-6496
1574-6941
Publication date 2006
Sub-type Article (original research)
DOI 10.1111/j.1574-6941.2005.00018.x
Volume 55
Issue 2
Start page 262
End page 273
Total pages 12
Place of publication Oxford, England
Publisher Blackwell
Language eng
Subject 050204 Environmental Impact Assessment
0605 Microbiology
Abstract tmoA and related genes encode the a-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent monooxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoAanalogues in the environment is larger than suggested from described TmoAanalogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence
Keyword BTEX biodegradation
catabolic gene
tmoA
PCR detection
DGGE analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Advanced Water Management Centre Publications
 
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