Synthetic microbial ecology, synthetic biology and functional metagenomics to optimize bioremediation processess

Functional metagenomics constitute a powerful molecular tool which has facilitated the isolation of novel enzymes of biotechnological interest. Novel pesticide biocatalysts identified via functional metagenomics could find use in environmental protection, human health and agriculture. Our group has applied functional metagenomics in environmental samples with heavy pesticide exposure, i.e. on-farm biodepuration systems like biobeds, in order to isolate novel pesticide hydrolyzing enzymes. Our hypothesis is that in such heavily exposed environments microorganisms are expected to evolve new biodegradation capacities which could be exploited via functional metagenomics. Fosmid libraries developed from the matrix of a biobed system resulted in the isolation of novel esterases whose activity against pyrethroids and phenyureas is on-going. In parallel known catabolic enzymes like PdmAB involved in the demethylation of phenylurea herbicides have been isolated through functional metagenomics and their substrate specificity is compared to native PdmAB isolated from soil bacteria. Our hypothesis is that amino acid polymorphisms in the metagenomics-derived PdmAB are associated with a relaxation of the substrate specificity of these enzyme.

In addition, we utilize synthetic microbial ecology approaches to optimize bioremediation and bioaugmentation efficiency. In this respect we work with wild type and synthetic microbial consortia with optimized biodegradation capacities. In this context we create synthetic microbial consortia composed of bacteria which exhibit nutritional (vitamins and amino acid auxotrophy-based) and pesticide metabolic interdependencies. Upon stabilization of the synthetic microbial consortia their degradation capacity is optimized

Synthetic biology and synthetic microbial ecology approaches are used as tools to optimize pesticide bioremediation strategies.


  1. IAPP Marie Curie project, Pesticides – Felicity or curse for the soil microbes (Acronym LOVE-TO-HATE). Funding: EC-FP7, Duration: 1/1/2013 – 31/12/2016, Website
  2. Research Infrastructure project, Title: The research infrastructure of Synthetic Biology in Agro-Nutrition. Funding Body: Ministry of Development, Finance and Tourism. Total Funding: 1,600,000 €. Duration 2017-2021


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- Dr Chiara Perruchon, Postodoctoral fellow

- Konstantina Rousidou, PhD Student