The investigation of microbial ecosystems in permafrost sediments is an important approach to understand the role of microbial organic matter transformation in permafrost sediments for past and future climate changes, and is of high relevance in today’s geoscience research (Wagner, 2008) due to the current debate on the temperature vulnerability of permafrost deposits. Especially, the interplay between the organic substrate and the distribution of the living and past microbial communities in Late Pleistocene (Yedoma) and Holocene permafrost deposits, as well as the substrate potential of the organic matter stored in potentially thawing permafrost deposits are in the focus of the current study. Our investigation is part of the BMBF CarboPerm project an interdisciplinary Russian-German cooperation on the formation, turnover and release of carbon from Siberian permafrost landscapes. Sample material derived from terrestrial permafrost cores drilled at the coast of Bour Khaya in the North-Eastern Siberian Arctic. The gathered core material comprises Late Pleistocene to early Holocene deposits separated by an ice wedge. The microbial life markers (intact phospholipids, PLs) prove the presence of currently living microorganisms in the entire permafrost sequence and show the highest concentration in the uppermost sample indicating an abundant microbial life in the active layer. In comparison, the PL profile is strongly decreased in the underlying permafrost deposits. Nevertheless, the inventory of the Phospholipid fatty acids (PLFAs) suggests that the cell membrane temperature adaptation to cold environmental conditions is mainly regulated via the ratio between iso- and anteiso-fatty acids (FAs) as well as the ratio between saturated and unsaturated FAs. The surface samples show higher proportions of anteiso and unsaturated FAs (adaptation to cooler conditions), which might derive from the fact that surface layers are more affected from the harsh Siberian winter conditions than the deeper constantly cold permafrost deposits, where the above-ground temperature extremes are buffered due to the overlying deposits. Indeed within the deeper permafrost sequence the variations of the ratios are rather small, indicating adaptation to similar constantly cold temperature conditions. Other microbial markers (GDGTs), already partly degraded and, therefore, not indicating microbial life, reveal similarities with the TOC content and an increase especially in Late Pleistocene deposits. This suggests increased microbial life during intervals in the Late Pleistocene presumably caused by periods of moisture and temperature increased environments. Pore water analysis reveals the presence of low molecular weight organic acids (LMWOA) such as acetate, being excellent substrates for microbial metabolism. In the Late Pleistocene deposits below the ice wedge the substrate depth profiles show significant similarities to the TOC content. These points to a link between the organic matter and the LMWOA concentrations solved in the pore water and to the potential of those permafrost layers to provide substrates for microbial greenhouse gas production. In contrast, in the active layer the LMWOA concentrations are low, reflecting an active microbial turnover in the surface layers. Ester cleavage experiments on the residual organic matter resulted in the release of ester linked LMWOAs forming a potential substrate pool when released in future. These bound LMWOA profiles are even better correlated to the TOC content suggesting that the deeper permafrost deposits (older organic material)are not significantly different from those in the surface sediment (fresh organic material). Overall this indicates that the organic matter stored in the permafrost deposits and, therefore, removed from the surface carbon cycle is not much different in terms of organic matter quality than the fresh surface organic material. Considering the discussed increase of permafrost thawing, this might imply a strong impact on the generation of greenhouse gases from permafrost areas in future with its feedback on climate evolution. In a second and ongoing study, four terrestrial permafrost cores spanning from the Eemian interglacial into the Holocene form Bol’shoy Lyakhovsky Island are investigated with the focus on the differences and potential of the organic matter by comparing Eemian, Late Pleistocene and Holocene deposits. First results already reveal similar relations between the living and dead microbial communities with respect to the availability of free substrates, and the quality and amount of the total organic carbon. The results on the future potential of these deposits will also be presented.