Thesis defense // Angélique DOMINGUEZ LAGE

THESIS

Dynamics of bacterial community mixtures within a mixed-use peri-urban watershed: coalescence and impact on health and ecological conditions

Abstract

Human activities release chemical contaminants (nutrients, micropollutants) and biological contaminants (bacteria, viruses, parasites) that accumulate on the surface and subsurface of urban, agricultural, and forested areas, as well as in sewage and storm drainage systems. During rainfall events, these diffuse and point sources are remobilized and discharged into receiving watercourses. These inputs alter the ecological and sanitary quality of hydrosystems: chemical pollutants influence the structure of microbial communities through their toxicity or as metabolic resources, while exogenous microorganisms can merge with endogenous aquatic communities according to the concept of microbial coalescence. These processes, which have yet to be studied extensively in anthropized watersheds, can reorganize metabolic networks and promote the establishment of pathogenic species, with implications for human health, livestock, and wildlife. In this context, the thesis was organized into two parts: (i) specifying the phenomena of remobilization of microorganisms accumulated on urban surfaces and in forest and agricultural sub-basins, which are likely to seed watercourses (two chapters); (ii) evaluating the contributions of these sources to surface water microbial communities and periphytic biofilms as a function of pollution levels and rainfall events (three chapters). This work was carried out in the Yzeron basin (Ratier and Mercier watercourses) within the urban hydrology field observatory. In (i), approaches combining qPCR, 16S rRNA gene and tpm metabarcoding, functional inferences, and Microbial Source Tracking (qMST) revealed multiple fecal contaminations, the presence of pathogenic species (including Aeromonas caviae and Pseudomonas aeruginosa), and a significant transfer (>50%) of communities to drainage networks. qMST analyses showed that occurrences of A. caviae were correlated with Bacteroides associated with wastewater and runoff, while P. aeruginosa showed no particular association. These results demonstrated the major impact of wastewater and grazing areas on the microbiological quality of streams. In (ii), a clay bead-based substrate (CBAS), initially used in aquifers, was adapted and validated for monitoring periphyton and studying microbial coalescence phenomena. Incubated for 10 weeks, CBAS made it possible to link community evolution (metabarcoding) to levels of chemical (UHPLC-MS/MS) and microbial (qMST) contamination. They proved to be suitable for the joint assessment of health and ecological status. A multi-site device was then used to compare community structure according to pollution gradients, showing that CBAS periphytic assemblages integrate exogenous pressures and are good indicators of the impact of contamination on microbial functioning. This thesis thus highlighted the central role of rainfall events in the recomposition of bacterial communities in watershed headwaters. It showed that microbial coalescence, induced by exogenous inputs, can lead to a reorganization of surface water and biofilm assemblages, modifying their functioning and promoting the establishment of exogenous species that are sometimes pathogenic. The integrated approach developed, combining source and pollutant monitoring with genetic analyses of periphytic communities and water, has made it possible to robustly characterize the health and ecological impacts of microbial contamination in peri-urban context.

Thesis directors

Benoit Cournoyer (UMR LEM - BPOE)