The present paper is the result of a workshop sponsored by the DFG Research Center/Cluster of Excellence MARUM "The Ocean in the Earth System", the International Graduate College EUROPROX, and the Alfred Wegener Institute for Polar and Marine Research. The workshop brought together specialists on organic matter degradation and on proxy-based environmental reconstruction. The paper deals with the main theme of the workshop, understanding the impact of selective degradation/preservation of organic matter (OM) in marine sediments on the interpretation of the fossil record. Special attention is paid to (A) the influence of the molecular composition of OM in relation to the biological and physical depositional environment, including new methods for determining complex organic biomolecules, (B) the impact of selective OM preservation on the interpretation of proxies for marine palaeoceanographic and palaeoclimatic reconstruction, and (C) past marine productivity and selective preservation in sediments. It appears that most of the factors influencing OM preservation have been identified, but many of the mechanisms by which they operate are partly, or even fragmentarily, understood. Some factors have not even been taken carefully into consideration. This incomplete understanding of OM breakdown hampers proper assessment of the present and past carbon cycle as well as the interpretation of OM based proxies and proxies affected by OM breakdown. To arrive at better proxy-based reconstructions "deformation functions" are needed, taking into account the transport and diagenesis-related molecular and atomic modifications following proxy formation. Some emerging proxies for OM degradation may shed light on such deformation functions. The use of palynomorph concentrations and selective changes in assemblage composition as models for production and preservation of OM may correct for bias due to selective degradation. Such quantitative assessment of OM degradation may lead to more accurate reconstruction of past productivity and bottom water oxygenation. Given the cost and effort associated with programs to recover sediment cores for paleoclimatological studies, as well as with generating proxy records, it would seem wise to develop a detailed sedimentological and diagenetic context for interpretation of these records. With respect to the latter, parallel acquisition of data that inform on the fidelity of the proxy signatures and reveal potential diagenetic biases would be of clear value.

Particulate organic matter collected during a 2‐year period, as part of an ongoing sediment trap study, and a high‐resolution sediment record from 1850 to 1987 A.D. from the Santa Barbara Basin were analyzed for TEX₈₆, a temperature proxy based on marine crenarchaeotal membrane lipids. Highest fluxes of crenarchaeotal lipids in the water column were found in May–June 1996 and from October 1996 to January 1997 and, in general, showed a good correlation with mass fluxes. TEX₈₆ reconstructed temperatures from the sediment trap series ranged from 8 to 11°C and were usually substantially lower than sea surface temperatures (SST), indicating that unlike in previous studies, the TEX₈₆ corresponds to subsurface temperatures, likely between 100 and 150 m. TEX₈₆ temperature variations observed in trap samples were not coupled to changes in SST or deep‐water temperatures and only to some degree with crenarchaeotal lipid fluxes. This suggests that a complex combination of different depth origins and seasonal growth periods of Crenarchaeota contributed to the variations in TEX₈₆ signal during the annual cycle. TEX₈₆ temperatures in the two sediment cores studied (8–13°C) were also substantially lower than those of instrumental SST records (14–17.5°C) confirming that TEX₈₆ records a subsurface temperature signal in the Santa Barbara Basin. This result highlights the importance of performing calibration studies using sediment traps and core tops before applying the TEX₈₆ temperature proxy in a given study area.