Functional pathway microarray for monitoring potential for bioremediation of PAHs - feasibility study

There is a great need for estimating the potential for natural biodegradation of contaminants in the environment, and the feasibility of bioremediation technologies and inoculants. Functional genes responsible for the biocatalysis of organic pollutants can usually be found in degrader microorganisms at contaminated sites. Our approach has been to develop a pathway microarray based on the determination of biodegradation activity. Instead of spotting hundreds of genes on the microarray slide, we first evaluated the potential of this technology for bioremediation monitoring purposes. The developed method was based on direct hybridization of functional genes of the PAH pathway. The gene probes were designed to study the degradation potential of several genotypes in order to be able to determine the biodegradation potential with few probes in environmental samples. In addition, the sensitivity and quantitivity were improved in several ways by e.g. including internal standards and making the conditions more stringent and optimal. The feasibility of this assay was verified by comparing several methods such as quantitative PCR and biodegradation rate in an assay based on 14-labelled substrates. The methods were compared with artificially contaminated soil samples. In addition, the success of the inoculated microbes to enhance the rate of bioremediation was monitored by PCR-DGGE, including their functional genes.