BACKGROUND

Global contamination of soil and aquatic ecosystems by pharmaceutical and microbiological pollutants (such as antimicrobial-resistant microorganisms and/or pathogens) raises severe concerns about impacts on ecosystem health and repercussions on humans and animals. Preserving ecosystems from adverse ecotoxicological effects of pharmaceuticals and their transformation products, and limiting the environmental spread of antimicrobial resistance and pathogens is imperative to reach several UN Sustainable Development Goals as well as the European Green Deal, Water Framework Directive and Biodiversity Strategy for 2030. In this context, the main scientific objective of Pharm-ERA is to develop and implement innovative concepts, methods and strategies to improve the monitoring and assessment of the environmental effects and risks of pharmaceuticals, their transformation products, antimicrobial resistances and pathogens from terrestrial to aquatic environments. The ultimate goal is to provide scientific evidence and expertise to contribute to reducing the environmental spread and impact of these chemical and microbiological contaminants and to preserve microbial diversity and functions across the soil-water-sediment continuum.

DESCRIPTION OF THE PhD PROJECT

The main goals of the project are 1/ to assess the resistance and resilience of riverbed native microbial communities exposed to mixed anthropogenic pressures leading to contamination by pharmaceuticals and exogenous soil bacteria; and 2/ to estimate the ability of exogenous soil bacteria including pathogens and antimicrobial-resistant bacteria to get established among native sediment bacterial communities exposed to pharmaceuticals.
To achieve these goals, laboratory microcosm experiments will be carried out for testing various exposure scenarios of sediment microbial communities to a panel of pharmaceuticals and exogenous soil microorganisms. Microbial responses of sediment communities will be assessed in terms of bacterial diversity, resistance and tolerance to selected pharmaceuticals, and other functional trait analyses. These will be achieved via the use of state-of-the art culture independent methods including high throughput sequencing of phylogenetic marker gene PCR amplicons (commonly termed “metabarcoding”), shotgun sequencing  and qPCR of antimicrobial resistance and pathogen  marker genes. Innovative pollution induced community tolerance (PICT) approaches will also be implemented. These microbial investigations will be combined with advanced chemical analyses to establish links between the observed microbial responses and the exposure scenarios. These, hand in hand with bioinformatics and biostatistics analyses, will make possible assessing correlations and the inference of associated causal relations.