The two in situ control mesocosms were labeled C1 and C2, while the two mesocosms in which terrestrial runoff was simulated were labeled B1 and B2.

Cytometry analysis:

• For viruses, 1.5 mL samples fixed with glutaraldehyde Grade I (final concentration 2%) were stained with SYBR Green I (final concentration 0.25%) and analyzed using a FACSCanto2 flow cytometer (Becton–Dickinson). Virus-like particles were identified and enumerated based on green fluorescence and side scatter (SSC) signals, following Brussaard (2004) 
• For bacteria, 1.5 mL samples fixed with glutaraldehyde Grade I (final concentration 4%) were also stained with SYBR Green I (0.25%) and analyzed using a FACSCanto2 flow cytometer. One bacterial population was identified and quantified based on the SSC and green fluorescence, according to Marie et al. (1997).
• For phytoplankton, 1.5 mL samples fixed with glutaraldehyde Grade I (final concentration 4%) were analyzed using a CytoFLEX flow cytometer (Beckman Coulter), operated at high speed for 3 minutes. Populations were identified and enumerated based on forward scatter (FSC), side scatter (SSC), and natural pigment fluorescence (chlorophyll-a, phycoerythrin). This allowed the discrimination of cyanobacteria (Cyano), picophytoplankton (Pico), and two groups of nanophytoplankton (Nano1 and Nano2).
• For heterotrophic nanoflagellates (HNF), 4 mL samples were fixed with glutaraldehyde Grade I (final concentration 4%), stained with SYBR Green I (0.25%), and analyzed using a FACSCanto2 flow cytometer, following Christaki et al. (2011). One HNF population was identified and counted based on SSC and green fluorescence signals.

Microscopy analysis:

• For larger phytoplankton organisms (>10 µm), 100 mL samples were fixed with formaldehyde (final concentration 4%) and analyzed using an inverted microscope Olympus IX70). Specifically, samples collected on days 1, 2, 6, 9, 12, 16, and 18 were settled for 24 hours in Utermöhl chambers prior to analysis. Organisms were identified and counted according to the following taxonomic groups: Diatoms, Cryptophytes, Chlorophytes, Prymnesiophytes, Autotrophic inoflagellates, Pyramimonadophytes, Chrysophytes, and Euglenoids (Kraberg et al., 2010).
• For protozooplankton, 220 mL samples were fixed with acidic Lugol solution (final concentration 1.8%) and also analyzed using an inverted microscope (Olympus IX70). Samples from days 1, 2, 6, 9, 12, 16 and 18 were settled in Utermöhl chambers, and organisms were identified and counted into the following groups: Tintinnids, Naked ciliates, Heterotrophic dinoflagellates, and Mixotrophic dinoflagellates.
• For metazooplankton, 20 L samples were collected using a Niskin bottle and filtered through a 20 µm mesh net (Hydrobios), then fixed with formaldehyde (final concentration 4%). Organisms were identified and counted using a macroscope (Leica Z16 APO) and classified into the following taxonomic categories: Eggs, Appendicularians, Echinoderms, Worms and polychaete larvae, Rotifers, Molluscs, Copepod nauplii, and Adult copepods (Tregouboff and Rose, 1957a; Tregouboff and Rose 1957b).

High Performance Liquid Chromatography:

For the Chlorophyll-a (Chl-a) concentration, samples of 0.5 to 1L were filtered over glass-fibre filters (Whatman GF/F, 0.7 µm, 25mm diameter) in a light-reduced room using a low vacuum pump. The filters were then fast frozen in liquid nitrogen and kept at -80°C until analysis. Chl-a concentration was then determined by high-performance liquid chromatography  (HPLC, Shimadzu) following the method of Zapata et al. (2000) and the protocol of Vidussi et al. (2011).