Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland)

► Vidy Bay (Lake Geneva) heavily contaminated with organic and inorganic pollutants. ► Microbial composition significantly different between polluted and non-polluted sediments. ► Microbial diversity affected by nutrients, organic matter and degree of pollution. ► Large proportion of clones from Vidy sediments related to Dechloromonas sp.