Legacy and Emerging Pollutants in an Urban River Stretch and Effects on the Bacterioplankton Community

River contamination is due to a chemical mixture of point and diffuse pollution, which can compromise water quality. Polycyclic Aromatic Hydrocarbons (PAHs) and emerging compounds such as pharmaceuticals and antibiotics are frequently found in rivers flowing through big cities. This work evaluated the presence of fifteen priority PAHs, eight pharmaceuticals including the antibiotics ciprofloxacin (CIP) and sulfamethoxazole (SMX), together with their main antibiotic resistant genes (ARGs) and the structure of the natural bacterioplankton community, in an urbanized stretch of the river Danube. SMX and diclofenac were the most abundant chemicals found (up to 20 ng/L). ARGs were also found to be detected as ubiquitous contaminants. A principal component analysis of the overall microbiological and chemical data revealed which contaminants were correlated with the presence of certain bacterial groups. The highest concentrations of naphthalene were associated with Deltaproteobacteria and intI1 gene. Overall, the most contaminated site was inside the city and located immediately downstream of a wastewater treatment plant. However, both the sampling points before the river reached the city and in its southern suburban area were still affected by emerging and legacy contamination. The diffuse presence of antibiotics and ARGs causes particular concern because the river water is used for drinking purposes.