Application of Metagenomics to Bioremediation

George, Isabelle [UCL] Stenuit, Benoît [UCL] Agathos, Spiros N. [UCL]

In this chapter, we discuss the potential of metagenomics to boost the development of improved strategies for monitoring the impact of pollutants on ecosystems and for cleaning up contaminated environments. Increased understanding of how microbial communities cope with pollutants could help to assess the potential of contaminated sites to recover from pollution and increase the chances of bioaugmentation or biostimulation trials to succeed. Moreover, by providing direct access to the pool of environmental genomes without the bias of cultivation, metagenomics offers the possibility to explore the vast diversity of degradation pathways of environmental microorganisms, which remain to a large extent poorly characterized (if not totally unknown). This could lead, among others, to the design of more efficient customized strains/consortia for targeted use in bioremediation applications. Finally, we provide an overview of the obstacles encountered in the implementation of metagenomic-based knowledge into field applications and propose solutions to facilitate such a technology transfer.