Résumé
The aim of this thesis is to evaluate the fate of microbial contaminants carried by wastewater along the continuum: raw water, treated water, irrigation systems to irrigated soils. Trials were carried out on the Murviel-lès-Montpellier experimental water reuse platform, during the greenhouse cultivation of lettuces, as well as during field irrigation. Four different water qualities were used: water containing all organic matter, nutrients and anthropogenic bacteria (raw water: RWW), water containing little organic matter but nutrients and bacteria from the sewage system (outlet water from a forced-aeration reed bed plant: CWW), water containing little organic matter but nutrients and no bacteria (outlet water from a membrane bioreactor: MBW) and control water (tap water: TW). Analytical tools such as molecular biology (NGS sequencing, ddPCR and qPCR), coupled with microscopic observations (optical coherence tomography), have enabled us to characterize microbiomes in terms of their composition, richness and diversity. Other tools were used to quantify organic matter and the main ions (3DEEM fluorescence, ion chromatography, TOC, COD, etc.). These analyses concern the soil matrix and the various water matrices.Soil bacterial community structure showed a graded impact, with three differentiated groups: soils irrigated with drinking water on the one hand, soils irrigated with raw water on the other, and finally soils irrigated with both types of treated wastewater, indistinguishable from each other. In addition, the biomass response of functional bacteria linked to the nitrogen cycle was proportional to the quantity of nitrogen compounds supplied. At the same time, enteric bacteria concentrations could only be quantified and detected in soils irrigated with raw wastewater, not in soils irrigated with treated wastewater.The micro-irrigation network was studied on a full-scale for 4 months, sampling both drippers and pipes with drippers having different flow rates and flow regimes. Irrigation network efficiency was not impacted by different water qualities under the experimental conditions studied: uniformity was maintained throughout the irrigation network despite variability in hydrodynamic conditions. The position on the network (beginning, middle and end of line) had no significant impact on the level of clogging assessed by optical coherence tomography (OCT) (in drippers with optical access) and bacterial quantification.Finally, the last part of the thesis focused on the interactions between water in transit through the drip irrigation system and biofilm development, in order to assess whether the presence of biofilms modifies the microbiome of the water in transit and the concentrations of undesirable bacteria (enteric pathogens and opportunistic species). The results showed that the bacterial community structure of irrigation water could be influenced by biofilms, and that this was more likely to be the case after several months of irrigation. However, this modification did not lead to additional contamination of the irrigation water by opportunistic pathogens such as Legionella pneumophila or Aeromonas hydrophyla. On the other hand, the microbiological quality of the water could be degraded by Escherichia coli in the case of a more mature biofilm, where higher concentrations were found in the outlet water. The aim of this thesis work is to further our knowledge of the ecological, health and technical risks of field-scale reuse.