Type of samples collected from the different underwater springs and auxiliary sites, and of analyses preformed.

The northern system (springs 1–5), southern system (springs 10–12) and auxiliary sites are shaded in light and dark grey respectively. Community analysis refers to 454 pyrosequencing and Automated Ribosomal Intergenic Spacer Analysis (ARISA), pigment analysis was done by hyper-spectral imaging. Auja and Jericho 5 wells represent waters from the Lower Judea Group Aquifer (Mekorot Co., personal comm.), whereas Mitzpe Jericho 2 and Qilt springs represent waters originating from the marly sequences of the Upper Judea Group Aquifer (Mekorot Co., personal comm.). Qedem brine represents ascending water from the deep thermal aquifer south of the sampling area [10]. Pore water was sampled at a depth of 0.7 m below surface next to shore spring 3. The sample code field refers to the naming of the respective sample in subsequent analyses. W, S, B stand for water, sediment and biofilm respectively; w/g refers to white/green biofilms; SP# refers to the identification number of the spring.