Seasonal Aquatic Microbiome Sampling

Samples were collected monthly, from April 2011 to April 2013, in a pond (La Claye) and a brook (Ru Sainte Anne). These two semi-permanent small freshwater systems are located in the Natural Regional Park of the Haute Vallée de Chevreuse (France, South of Paris). See Simon et al. (2015a) (link) for more details on these sites and the sampling procedure. Briefly, surface water was systematically collected in the morning at ca. 10 a.m. using sterile bottles and processed immediately back in the laboratory (around 25 km away from the sampling site). The whole sampling processing, including nutrient measurements was completed within 4–5 h. Planktonic cells were collected onto 0.2 μm pore-size Nuclepore filters (Whatman) after a pre-filtration step through 5 μm pore-size Nuclepore membranes (Whatman). Filters were then stored frozen at -20°C until DNA extraction. During drought periods, when the freshwater systems underwent complete desiccation, samples were collected by directly scratching the surface of the dry sediment (top 1 cm) with 50 ml sterile Falcon tubes (Becton Dickinson, Biosciences), then transferred to 5 ml sterile cryotubes back to the laboratory and immediately frozen until DNA extraction.