Advances in monitoring of catabolic genes during bioremediation

Abstract

Biodegradation of xenobiotic compounds by microbes is exploited in the clean up of contaminated environments by bioremediation. Catabolic (or functional) genes encode for specifi c enzymes in catabolic pathways such as key enzymes in xenobiotic degradation pathways. By assessing the abundance or the expression of key genes in environmental samples one can get a potential measure of the degradation activity. One way of assessing the abundance and expression of specifi c catabolic genes is by analyzing the metagenomic DNA and RNA from environmental samples. Three major challenges in the detection and quantifi cation of catabolic genes in bioremediation studies are 1) the accurate and sensitive quantifi cation from environmental samples 2) the coverage of the enzymatic potential by the targeted genes 3) the validation of the correlation with actual observed degradation activities in fi eld cases. New advances in realtime PCR, functional gene arrays and meta-transcriptomics have improved the applicability of catabolic gene assessment during bioremediation.

Dynamics of the Linuron HydrolaselibAGene Pool Size in Response to Linuron Application and Environmental Perturbations in Agricultural Soil and On-Farm Biopurification Systems

“…Alternative qPCR techniques, such as a TaqMan-based approach, do not result in a lower detection limit (3). Examples of catabolic functional gene detection in environmental samples by PCR are manifold (13,16,29,30), but qPCR approaches have only been reported for a few of them (2,3,11,15,27). The target genes are often involved in the degradation of aromatic hydrocarbons.…”

“…Moreover, horizontal gene transfer of linuron catabolic genes from indigenous degraders to organisms better suited to proliferate under the imposed enrichment conditions can occur (26). Monitoring genes associated with the catabolism of pollutants has been proposed as a better molecular approach to assess pollutant degradation potential (11). Previously, tfdA and tfdB, involved in 2,4-dichlorophenoxyacetic acid (2,4-D) degradation, and atzA, atzB, and atzC, involved in atrazine catabolism, have been reported as molecular markers to assess, respectively, the 2,4-D (9) and atrazine (14) degradation potential in natural communities.…”

Molecular Analyses of Microbial Activities Involved in Bioremediation

“…Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries provided information about specifi c phylotypes of bacteria that were associated with the degradation of each PAH (Ní Chadhain et al 2006 ) . Jorgensen ( 2008 ) in his review has shown that Real-time PCR in actual bioremediation studies have been concerned with naphthalene (Debruyn et al . 2007 ) , nitro aromatics (Indest et al .…”