Biodegradation of pharmaceuticals: Searching for bacteria and pathways

Abstract

[Introduction]: The elimination of organic pollutants by microbial degradation is a proven method for counteracting the contamination caused by these recalcitrant substances. The isolation, characterization and genetic improvement of bacterial strains capable of degrading such compounds, is a high priority for biotechnological development. There is much interest in using this approach for environmental protection both at a remedial (bio-recovery of contaminated sites) as well as at a preventive level (e.g. treatment of industrial water wastes). For many well-known contaminants such as aromatic compounds, many different bacterial strains have been isolated and characterised that can use them as carbon and energy source. However, there are many other molecules, such as pharmaceutical compounds (PhCs) that are increasingly appearing in water effluents and are considered emerging contaminants of public concern (Directive 2008/105/EC updated by Directive 2013/39/EU), whose biodegradation is not known. Among those, the long-term release and persistence of PhCs is of particular concern, because these compounds can be biologically active, even at the nM concentrations found in the environment, which may lead to chronic toxicity and subtle effects such as endocrine disruption, growth inhibition, disruption of microbial ecosystems, cytotoxicity, mutagenicity, teratogenicity, etc. In our laboratory, we have initiate studies in order to isolate and characterise bacterial strains, obtained from different environments, able to biodegrade selected emerging contaminants and identify and characterize genes from metagenomic libraries that confer to E.coli the capacity to biodegrade these PhCs. We have selected different PhCs, such as ibuprofen and norfloxacin, that are referred in the literature as toxic or potentially toxic compounds, detected in surface waters, or have been cited in Directives 2008/105/EC or 2013/39/EU. [Material and methods]: The starting materials to isolate bacterial strains capable to biodegrade PhCs were activated sludges obtained from domestic and hospital WWTPs, since these sludges are more exposed to PhCs excreted by the patients and may represent a good source of biodegrading strains. However, since all PhCs contain aromatic rings, biomass from other sources, such as soils contaminated with crude oil or alpechin (residue rich in phenolic compounds from olive oil manufacturing), and subjected to bioremediation, was also used as starting material in enrichment cultures. The biomass from different origins was used as inoculant to enrichment cultivation. Initial enrichment was performed in minimal liquid media containing the selected PhCs as the sole carbon and energy source. In the same way, in order to identify genes involved in the biodegradation of these compounds, clones of a metagenomic library were selected to growth on plates of minimal medium containing one of the PhCs as the sole carbon and energy source. [Results]: To date, we have isolated different strains able to biodegrade ibuprofen and one clone, from a metagenomic library of a petroleum-contaminated soil, which confers to E.coli the capacity to biodegrade naproxen. These isolated strains and clone are currently under study in our laboratory in order to characterise the biodegradation pathways. We are also performing new searches of strains and genes by using different PhCs and starting materials.