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Groundwater ecosystems host diverse and complex microbial communities that play important roles in the biogeochemical processing of organic matter and in the maintenance of drinking water quality. Here we investigated the microbial community in suspended particulate matter (SPM) of biogeochemically distinct groundwaters (Hainich Critical Zone Exploratory) by analyzing branched and isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) from bacteria and archaea, respectively. The contributions of those lipids derived from dead and living organisms were determined by analyses of the core lipid distributions of core and intact polar GDGTs. We compared the groundwater GDGT distributions to the ones from soils of potential recharge areas and with archaeal 16S rRNA-gene based community reconstructions to estimate their origin in these terrestrial subsurface environments and thus their potential use for …