Shifts in the structure and function of the microbial community in response to metal pollution of fresh water sediments in Finland

Abstract

Mining is a common source of metals in aquatic ecosystems. Metal loading in the environment is thought to be a selective pressure that induces compositional and functional changes within the affected microbial community in the sediment. This study aims to explore shifts in the diversity, structure, and functional gene abundance of microbial communities in the sediment of the copper mining-induced contaminated lakes in Finland. The sediment microbial community structures and abundance of the functional groups involved in carbon/nitrogen/sulfur cycling in four lakes located downstream from metal mines (Kirkkoselka (KS), Junttiselka (JS), Laakajarvi (LJ), and Sysmajarvi (SJ)) and one reference lake (Parkkimanjarvi (PJ)) in Finland were compared using high throughput sequencing and quantitative PCR. Compared to the PJ reference lake sediment, the relative abundances were higher for Bacteroidetes, Gemmatimonadetes, Acidobacteria, and Nitrospirae but lower for Firmicutes and Alphaproteobacteria in the mine-contaminated sediment samples. The number of copies of copper-resistant genes (copA) in the two copper-contaminated sediments (5.34 × 106 and 4.95 × 106 copies ng−1 DNA for KS and JS, respectively) was significantly higher than that in the PJ sediment (1.33 × 106 copies ng−1 DNA). Methanogens (mcrA gene) accounted for 5.09–11.5% of the total archaea (16S rRNA) in these lake sediments. In addition, ammonia-oxidizing archaea (amoA gene) in the LJ sediment accounted for 36.0% of the total archaea but only 0.83–1.63% in the sediment of other lakes. The abundance of eight investigated functional groups accounted for 28.8% of the total bacteria in the PJ sediment but less than 1.3% in the metal-contaminated sediments. The canonical correspondence analysis showed that the microbial community structure of Lake LJ was scattered far from the other lakes and was significantly correlated with nitrate; the community structural change in the JS and KS sediments was positively correlated with copper or negatively correlated with nitrate concentration. These results indicate that the sedimentary indigenous microbial community may shift its composition and structure as well as its function to increase its adaptability and/or resistance to metal-contaminated freshwater sediments.