Functional metagenomics constitute a powerful tool for the discovery of novel enzymes of biotechnological interest. Novel biocatalysts identified via functional metagenomics could find use in environmental protection, human health and agriculture. We have set up a high-throughput pipeline of functional metagenomics, based on an automatic liquid handler, for the isolation of novel hydrolases from polluted soil and other environmental samples (i.e. on-farm biodepuration systems like biobeds). Our hypothesis is that in such heavily exposed environments microorganisms are expected to evolve new biodegradation capacities which could be exploited via functional metagenomics.

Synthetic microbial ecology is the merge of synthetic biology with microbial ecology.  We have designed and established SynComs to (i) for optimized biodegradation of organic pollutants (i.e. pesticides) and (b) for ecological relevant ecotoxicity testing.  We have developed SynComs that through nutritional interdependencies are able to degrade recalcitrant organic pollutants like the fungicide thiabendazole in a more efficient way. In addition, we have developed several nitrifiers SynComs (NiSynComs) composed of ammonia oxidizing microorganisms and nitrite oxidizing bacteria that offer a more ecologically relevant tool to test the microbial toxicity or efficiency of agrochemicals instead of single species tests.