Adaptive strategies of sediment microbiomes towards long-term anthropogenic metal pollution: An integrative molecular approach

Metal contamination of sediments poses serious biotoxicity and bioaccumulation risks affecting ecosystem abiotic factors and biological activity. For a century, the MetalEurop foundry released zinc, copper, cadmium and lead directly into the French river 'la Deûle', resulting in a 30-fold increase in metal concentrations in downstream sediments. Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different, microbial communities dwelling in sediments upstream and downstream MetalEurop (Gillan et al., 2015), suggesting a potential involvement of conjugative plasmids in metal adaptation. In the present study, we applied an integrated molecular approach to decipher adaptive strategies in this ecosystem in response to long-term anthropogenic pollution. For that purpose, we combined taxonomic profiling of the complete (DNA) and the potentially active (cDNA) fraction of communities via 16S rRNA gene sequencing together with qPCR and in vitro conjugation assays. The ecological concept of Functional Response Groups (FRGs) was applied to highlight microbial sensitivity levels to the long-term pollution (Nunes et al., 2016), resulting in identification of six functional groups with distinct DNA/cDNA signatures characteristic to specific strategies and lifestyles. Higher microbial richness was observed in metal contaminated sediments without any noticeable consequence on the functional genetic diversity. The qPCR and in vitro sediment bacteria confrontation with a reporting conjugative plasmid, pKJK5, revealed a peculiar permissiveness potential of the microbiomes, as well as a native pool of IncP plasmids that were significantly enriched at the polluted site. Our results support the idea that conjugative plasmids and their related functions are crucial drivers of the bacterial community adaptation to metal stress, resulting in establishment of several strategies and lifestyles in these ecosystems.