Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation

To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA‐genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture‐dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture‐dependent approach. The molecular analysis also revealed the frequent occurrence of nifH‐genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen‐fixation potential. Nitrogen fertilization is long known to enhance microbial oil‐bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil‐pollution was more effective in oil‐removal in the desert soil than in seawater microcosms. Bacterial communities in oily environmental samples were analyzed molecularly by sequencing of the constituent 16S rRNA‐genes in the total genomic extracts. By consulting the literature for hydrocarbonoclastic bacterial taxa, it was concluded that this approach revealed much greater hydrocarbonoclastic communities than the culture‐dependent method. This approach showed also the dynamics of those communities during oil‐bioremediation in the studied samples.