*2.1. Sample Collection*

All samples were taken during the research expedition of the Joint Danube Survey 2013 (JDS3). The survey was organized by the International Commission for the Protection of the Danube River (ICPDR), Vienna. The water samples were taken between 12 August and 26 September 2013, from 68 sampling sites along the River Danube, starting at Böfinger Halde (Germany) downstream to the delta (Romania). At each sampling site, samples were collected at three sampling points (left, middle, right), in sterile 1 L glass flasks from 30 cm below the river surface. From each flask, duplicate volumes of 45 mL of river water were filled into sterile non-toxic 50 mL plastic vials (Techno Plastic Products AG, TPP, Trasadingen, Switzerland), containing 5 mL of glycerine (final conc. 10% v/v). The vials were completely mixed by hand and immediately stored at −20 ◦C on board of the cruise ship until analysis in the laboratory. After transfer to the laboratory (beginning in October 2013), the samples were stored at −80 ◦C. Fourteen sampling sites, four of them downstream of megacities (Vienna, Budapest, Belgrade and Bucharest), two at the beginning as well as two at the delta, four rural sampling sites, and two after confluence of two biggest tributaries (Drave, Tisa) were chosen for investigation (Table 1).


**Table 1.** JDS3 sampling sites chosen for isolation and their assignment to the upper-, middle-, or downstream stretches (SP = sampling point; us = upstream; ds = downstream). Country codes: Germany: DE; Austria: AT; Hungary: HU; Croatia: HR; Serbia: RS; Romania: RO; Bulgaria: BG.
