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

Existing literature indicates that biofilms developed on anthropogenic litter accumulated on the streambed tend to be richer in antimicrobial resistance (AMR) and pathogens than natural stream substrata. The main objective of this PhD project is to improve our understanding of the role of anthropogenic litter in the formation and fate of antimicrobial resistance (AMR) and pathogen-rich biofilms in stream ecosystems. To achieve this goal, three specific objectives (SOs) will be addressed:
- The first (SO1) focuses on assessing the role of substrate type: anthropogenic litter (plastics and bioplastics) versus natural substrata, on biofilms enriched with AMR and pathogens;
- the second (SO2) will address the temporal and spatial dynamics of these biofilms;
- and the third (SO3) will focus on assessing the effectiveness of nature-based solutions (NBS) in reducing AMR and pathogens in stream ecosystems.
These specific objectives will be addressed through experimental and fieldwork. Thus, a field experiment will be carried out in an urban stream. In the field experiment, the different substrates will be colonised downstream of the confluence of a WWTP effluent input (SO1); and translocated further downstream to follow its dynamics (SO2). Differences between biofilms colonising different substrate types will be assessed by AMR analysis (using qPCR assays), together with analysis of a range of structural (microbial diversity analysis using metabarcoding); and functional (nutrient scavenging and virulence capacities) attributes. The same set of analyses will be carried out on biofilms growing on the different substrata along the study river at restored and non-restored reaches to assess the influence of the NBS implementation on the development and fate of (AMR) and pathogen-rich biofilms (SO1 and SO3).