Final Activity Report Summary - CARBOCYC (Carbon cycling in lakes: Response to water column stratification) Particulate organic matter (POM) in the water columns was sampled during spring and fall from the oligotrophic Lake Brienz and the eutrophic Lake Lugano, which were both located in Switzerland. Six sampling depths were chosen based on the temperature, depth, oxygen content and turbidity profiles. Water samples were collected at the same locations and the same depths for water analyses. Sediment cores of approximately 60 cm in length were recovered from the lake floors below the water sampling sites. Sedimentation rates of between 0.70 and 0.82 cm/year at the sampling site of Lake Brienz and of 0.55 to 0.64 cm/year at the sampling location of Lake Lugano were derived from Pb-210 profiles by using Cs-137 peaks that originated from the nuclear weapon tests in 1963 and the Chernobyl fallout in spring 1986. Biomarker compositions of POM and sediment profiles were compared. Differences in primary productivity and water-column stratification were responsible for the anoxic bottom water in Lake Lugano and for the well-oxygenated bottom water of Lake Brienz, as well as for the higher total organic carbon and lipid contents in the sediments of Lake Lugano. An organic matter (OM) source from algae, zooplankton and bacteria along with generally minor contributions from land plants were indicated. The organic matter (OM) composition of sediments indicated changing contributions from land plants in both lakes. The Brienz sedimentary OM was characterised by low terrestrial input in the lower part and higher contributions in the upper parts of the profile. Enhanced bacterial activity during sediment deposition in Lake Lugano was suggested by the higher concentrations of branched-chain fatty acids, namely C15 and C17, hopanoic acids and triterpenoid alcohols, i.e. tetrahymanol and diplopterol. Inputs of OM from diatoms were reflected by highly-branched isoprenoid (HBI) alkenes and C28-sterols. High relative proportions of cholesterol in the autumn POM samples, most pronounced at Lake Lugano, were attributed to an increased input from zooplankton grazing in the water columns. The presence of archeol and hydroxyarcheol in very low concentrations in the Lake Lugano sediments argued for the activity of methanogens or anaerobic methanotrophs. The high relative abundances of diplopterol in the Lake Lugano sediments were consistent with the predominance of cyanobacteria. Differences in OM degradation processes and enhanced bacterial activity in the water column and the sediments of Lake Lugano were reflected by differences in lipid composition. The results argued for intensified bacterial activity and degradation of OM during autumn in both lakes. High relative contents of sterols close to the chemocline at Lake Lugano during spring were interpreted to reflect higher primary productivity in the photic zone and OM export into the deeper parts. The distributions of membrane tetraether lipids of archaea (GDGTs) in the water column and sediments confirmed previous observations about higher GDGT abundances during periods of reduced primary productivity. The increased input of soil OM or the improved preservation of branched GDGTs under anoxic conditions was reflected by higher branched and isoprenoid tetraether (BIT) indices below the chemocline. Calculated water temperatures reflected the relative differences in mean lake surface temperatures. They suggested that 30 to 65 % of archaeal lipids at greater water depths in Lake Brienz occurred from in situ production. In contrast, the data argued for a predominant export of archaeal lipids from surface water and for in situ production in Lake Lugano ranging between only 10 and 50 %. The results about GDGT concentrations in the sediment cores indicated that archaeal lipids in lacustrine sediments might be used to detect periods of eutrophication. Changes towards relatively higher contributions of euryarchaeota and increased inputs of soil OM during deposition of the upper part of the sedimentary succession in Lake Brienz were evidenced by changing crenarchaeol and caldarchaeol ratios. The comparison with records of mean annual temperature variations indicated that the GDGT-based temperature proxy might be used to reconstruct mean surface temperature variations from sediment core data.