Membrane based catabolic gene array for monitoring bioremediation processes

Bioremediation is a cost-effective method for decontamination of polluted sites. For development of effective bioremediation processes, a good understanding of the microbial processes is necessary. Especially, there is growing interest to monitoring the bioremediation processes in situ. Molecular biological tools developed for environmental analysis provide interesting possibilities for analysing microbial degradation processes. The biodegradation of the contaminants can be monitored by analysing catabolic genes involved in the degradation. In many cases the pollution is caused by a mixture of contaminants, where effective biodegradation requires presence of microorganisms possessing different types of catabolic activities. Therefore, a possibility to analyse the activity or number of several catabolic genes simultaneously is preferential. A DNA-hybridisation based biosensor was developed for detection of several catabolic genes for monitoring of bioremediation processes. DNA probes for todC1 , xylA, xylE, nahA, nahH and nahE - genes encoding aromatic hydrocarbon degrading enzymes were generated by PCR and attached on the nylon membrane. The suitability of this macroarray for monitoring the biodegradation was evaluated in a study where 14C-labelled naphthalene and toluene were mineralised by the aromatic hydrocarbon degrading strains Pseudomonas putida Fl, P. putida mt-2 and P. putida G7. The macroarray was applied to determine proportional amount of catabolic genes in the course of the biodegradation. The proportional changes in the catabolic genotypes were in good agreement with the mineralisation data. According to these results, the macroarray is a promising tool for monitoring bioremediation processes.