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Methane production is the terminal step in the degradation of organic matter in most anoxic lake sediments. It has been suggested that CH4 production in lake sediments is dominated by hydrogenotrophic methanogenesis, especially in deeper layers. We investigated the vertical sediment profile from the surface to 50 cm depth in the sediment of Bangong Co, an oligotrophic high altitude lake on the Tibetan plateau. We measured CH4 production, stable carbon isotopefractionation and the archaeal community structure. We found that the methane production rates, the acetate concentrations and the numbers of bacteria and archaea strongly decreased with sediment depth. The enrichment factor (epsilon) for hydrogenotrophic methanogenesis also decreased with depth, while delta C-13 of acetate stayed fairly constant. The contribution of hydrogenotrophic methanogenesis to total CH4 production increased with depth from similar to 36% to 100%. Analysis of terminal restriction fragment polymorphism (T-RFLP) of archaeal 16S rRNA genes showed that the relative abundance of aceticlastic (Methanosaetaceae) methanogens also decreased with depth disappearing completely at 50 cm depth. Our study firstly showed that the methanogenic pathway and the methanogenic archaeal community systematically changed with sediment depth in a high altitude lake, probably controlled by the availability of easily degradable organic matter. (C) 2016 Elsevier B.V. All rights reserved.