Metagenomic investigations on the effects of uranium and copper on sediment microbial communities

Freshwater systems are a reservoir of biodiversity and a hot spot for the biogeochemical processes underpinning global nutrient cycles. Microbial communities are a key component of these systems, forming the base of food webs and providing ecological services on which all higher trophic levels depend. Freshwater sediment microbial communities are particularly vulnerable to exposure to anthropogenic pollutants. This is due, in part, to the binding of pollutants to sediment particulates, and the intimate associations microorganisms form with sediments. To date relatively few studies have investigated the effect of metal contamination on freshwater sediment microbial communities and their function. This work explores the effect of uranium (U) and copper (Cu) on freshwater sediment microbial communities. Concentration gradients of each metal were created by spiking the sediments in the laboratory before deploying them in situ. This novel approach allowed sediments with known metal concentration gradients to be exposed to natural environmental fluctuations and biotic colonisation. Metagenomic sequencing techniques were then employed to investigate compositional shifts in microbial communities along these gradients. This work represents the first metagenomic data of sediment microbial communities along U and Cu concentration gradients in natural settings. The study demonstrates that these communities are responsive to elevated concentrations of U and Cu, and that taxonomic shifts cause functional changes. The study identifies taxa which are sensitive to elevated metal concentrations, as well as those which appear to be specialists in these environments. The ecophysiological profiles of six novel genomes, obtained from the metagenome of sediments spiked with 4 g kg-1 of uranium, were used to explore the life-strategies of taxa thriving under these challenging conditions. Additionally, the profiling of sediment fungal communities represents the first metagenomic survey of these taxa in freshwater sediments, and demonstrated considerable taxonomic novelty. The findings of this study provide insights into sediment microbial communities, their complexity and the structure-function relationships underpinning this complexity. Along with their contribution to our understanding of microbial ecology, findings from this study have broad ecotoxicological implications for the monitoring of contaminated freshwater environments, and are of relevance to ecotoxicologists, regulatory bodies and policy makers.