Resumen
In order to decipher the ecology of hydrocarbon-degrading microbial communities, experimental ecology approaches were developed, maintaining crude-oil contaminated mudflat-sediments under conditions as close as possible to those prevailing in tidal environment. The omics analyses of the microbial communities facing the crude-oil contamination allowed an in-depth characterization of the petroleum influence on microbial communities at different biological organization levels.
First, we propose a scenario describing the dynamic of the microbial communities leading to the establishment of the hydrocarbon-degrading microbial community. Our results demonstrated that several yet unidentified genes were induced just after oil addition, before the induction of biodegradation genes and prior the restructuring of microbial communities. This adaptive stage, crucial for the organization of the microbial communities, was characterized by the expression of a specific integrase gene involved in adaptive mechanisms that occurred just before the modification of microbial community structures. After the adaptive stage, the microbial community structure was modified, concomitantly with the beginning of the degradation of hydrocarbon compounds, followed by a succession of bacterial community structures along the degradation process.
Secondly, submitting sediments to different oxygenation regimes in bioreactors showed the influence of the oxygenation on microbial assemblages and hydrocarbon degradation, which was favoured by oxygenation after a period of anoxia. The behaviour of specific functional groups, including hydrocarbon-degrading bacteria, sulfate-reducers and methanogens, highlights ecotypes able to cope with the oscillating conditions.
Finally, the metatranscriptome (RNA-seq) allowed the description of metabolic networks, emphasising the overexpression of genes involved in the anaerobic hydrocarbon-metabolism and in DNA repair processes.