Promoteur: Monsieur Ruddy WATTIEZ

Résumé de la dissertation:

Metal contamination poses biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystems. The use of metals and metalloids as raw materials, in industries and technologies drastically increased from the industrial revolution and urbanization of the XVIIIth century. For 100 years (1893-2003), the MetalEurop foundry released zinc, copper, cadmium and lead directly into the river “la Deûle”, resulting in up to 30-fold increase in metal concentrations in downstream sediments. We used an integrative approach coupling in-situ 16Sr RNA sequencing from both DNA and RNA extracts, microcosm supervision and Horizontal Gene Transfer (HGT) monitoring in order to fully understand the mechanisms driving community resilience to metal pollution. We applied the ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the in-situ sediment communities through characterization of microbial strategists, revealing differences in diversity and composition. Furthermore, in-vitro microcosm analysis with upstream nonpolluted sediments challenged with metals and daily supplied of fresh river water, allowed to monitor the short-term impact of metal pollution on the microbial community over 6 months, in controlled conditions. We used qPCR and 16S rRNA gene amplicon sequencing with the ecological concept of Time Response Groups (TRGs). Both in-situ and microcosm studies reinforced the notion that mechanisms are taking place at the community level to face the metal pollution, such as facilitation processes and microbial community coalescence leading to an unexpectly high microbial diversity. However, if in-situ results suggest HGT as a key process in the long-term resilience of the community, the monitoring of IncP plasmid by qPCR in microcosms revealed a negative effect of metals on the short-term in comparison with control microcosms. Deeper HGT analysis using qPCR revealed the presence of an enriched native pool of conjugative IncP plasmids in the MetalEurop polluted sediments, confirming their importance for long-term adaptation of the community facing metal contamination. Besides, in-vitro conjugation assays coupled to Fluorescence Activated Cell Sorting (FACS) allowed to assess the plasmid transfer rate and permissiveness in Férin and MetalEurop communities showing sediments as hotspot for plasmid transfer. To understand the direct metal-impact on plasmid persistence in a microbial community, we used a consortium conjugative assay to monitor the dispersion efficiency of the plasmid in the recipient strain population by flow-cytometry and link it to the metaproteomic profile of the consortium by SWATH quantitative proteomics.