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 objective of the PhD project is to elucidate the pathogens and antimicrobial resistance (AMR) flows between terrestrial and freshwater ecosystems in agri-urban catchments focusing on soil and periphytic microbial communities. This will be achieved through the following specific sub-objectives:
1- Study the AMR and pathogens spread from soils to freshwater ecosystem communities as a consequence of manure application in agriculture;
2- Investigate the AMR and pathogen spread from urban waste water treatment plants (WWTPs) to freshwater communities;
3- Evaluate the AMR and pathogen occurrence in surface waters used for irrigation purposes and in reclaimed water obtained from wastewater to assess its potential role in AMR spread from water to soils.
To this end, a multi-scale approach, combining a long-term field study and 2 laboratory experiments in mesocosms, will be used. A wide range of methodologies will be employed to fulfill the main and specific objectives of the project combining classical microbiology cultivation methods with state-of-the-art molecular ecology/biology tools. These will include generation of datasets from qPCR/ddPCR assays which can enable a tracking of exogenous taxa such as those emitted by animals or contaminating organic wastes (e. g. the microbial source tracking (MST) qPCR assays, those enabling pathogen-specific trackings), and the production of DNA sequence libraries from PCR amplicons through DNA meta-barcoding analytical schemes, and global approaches such as metagenomics. These large datasets will imply using bioinformatics/biostatistics approaches to test the hypotheses of AMR and exogenous bacterial transfers among the 3 main microbial compartments considered in this thesis: the soils, benthic and planktonic communities. Briefly, the field study will be carried out in a nearby agri-urban catchment and will be focused on understanding the relative contribution of punctual and diffuse sources of pollution (urban WWTPs and manure application in agriculture) to the resistome and pathogens occurrences in river compartments.
The two experiments planned will be dedicated to investigating:
1- the role of runoff from agricultural soils fertilized with animal manure (and derived organic amendments) as a potential source of AMR and pathogens to freshwaters ecosystems;
2- if reclaimed wastewater can be safer than surface water (for irrigation) in terms of AMR and pathogens risk spread from water to soil, depending on treatment technologies applied in WWTP regeneration plants and river catchment/s considered.