The potential of 16S rRNA gene and catabolic gene based molecular methods in monitoring field-scale bioremediation of oil contaminated soil

In bioremediation, knowledge regarding the relationship between the activity of contaminant degrading microbial populations and the efficiency of decontamination is relevant when more efficient decontamination strategies are designed. In recent studies, molecular biological methods based on the analysis of 16S rRNA genes in environmental DNA extracts have provided promising results in understanding the microbial community dynamics during remediation trials. With these methods, however, it is often difficult to demonstrate the relationship between specific species and the desired degradation activity. Catabolic genes, in contrast, can serve as a direct indication of degradation potential of specific compounds. Even though the presence of catabolic genes has been shown to describe the degradation potential of polluted environments, the application of these methods in monitoring field-scale bioremediation processes has been scarce. Herein we applied both 16S rRNA gene and functional gene based analysis methods to investigate the microbial community dynamics during field-scale bioremediation of contaminated soil. The oil-contaminated soil was excavated from an old bus depot and treated under controlled conditions to enhance the contaminant degradation activities. During treatment the community profiles were determined by PCR-DGGE analysis of 16S rRNA genes. Contaminant-degrading bacterial populations were targeted using PCR amplification of catabolic genes involved in the metabolism of aliphatic and aromatic hydrocarbons. With both methods changes in community composition in response to the decontamination treatment were successfully detected. However, screening with the catabolic marker genes enabled specific detection of bacteria with the capacity to degrade aliphatic hydrocarbons that were to be removed from the contaminated soil.