Metagenomics for bioremediation

Metagenomics, the culture-independent analysis of the collective genomes of microorganisms, is a powerful tool to access the genetic and metabolic diversity encoded in environmental microbes without the bias of cultivation. In particular, this technique is increasingly being applied to explore a great variety of microbial degradation pathways of pollutants, which remain to a large extent partly or totally uncharacterized. Based on a better knowledge of such pathways, more efficient customized strains/consortia could be designed for targeted use in bioremediation applications. Moreover, a better understanding of how microbial communities respond to environmental pollution is needed to predict the ability of contaminated sites to recover from pollution and to increase the chances of bioremediation strategies to succeed. We provide here an updated overview of past, present, and emerging applications of metagenomics to contaminated sites, discuss its limitations in the specific context of biodegradation, and report how such limitations are being overcome by methodological improvements.