||Sedimentary microbial lipids are widely used as sensitive indicators of environmental conditions in paleoenvironmental and biogeochemical studies. Nonetheless, systematic isotopic investigations of microbial lipids to constrain their sources, modes of production, and turnover remain fragmentary. In order to decipher the information encoded in sedimentary archaeal and bacterial lipids in different marine depositional environments, I conducted carbon isotopic analysis of marine environmental samples (Chapter III and IV) and laboratory-based stable isotope probing (SIP) experiments (Chapter V). Chapter III provides fundamental constraints on archaeal activity, sources of archaeal lipids, and preservation signatures in diverse marine sediments. This is, to my knowledge, the first systematic comparison of stable carbon isotopic compositions of archaeal core lipids (CLs) and intact polar lipids (IPLs). Results from lipid analysis are interpreted in the context of geochemical data in contrasting depositional regimes, including a transect from the Rhone River delta into the western Mediterranean Sea, the anoxic Black Sea, Marmara Sea, and sapropel layers in the Eastern Mediterranean Sea. Mass balance calculation along the transect of the Western Mediterranean Sea proved that terrestrial input of archaea into marine sediments can be substantial (up to 42%) and suggests caution when reconstructing such inputs based on existing molecular proxies, such as BIT (Branched isoprenoid tetraether index). Similar I 13C values of core and intact polar crenarchaeol strongly suggest that the alkyl moieties are not synthesized de novo, thus indicating that intact polar crenarchaeol is either a fossil relic from planktonic archaea or a product of lipid recycling by benthic archaea. By contrast, an average offset in I 13C values of 2.6a degree between core and intact polar caldarchaeol indicates active in-situ activity of benthic archaea. To further constrain the sources and turnover of sedimentary archaeal lipids, we compared the stable carbon isotopic compositions of archaeal IPLs and CLs through the oxic, suboxic and anoxic water column and in high resolution within an 8-m deep sediment core in the Black Sea (Chapter IV). The comparison between the water column and surface samples suggests that archaea residing in the lower suboxic zone are the main source of lipids found in surface sediments, including a large fraction of IPLs. The isotopic offset between core and intact caldarchaeol indicates sedimentary in-situ production by benthic archaea. Based on a two endmember mixing model, an average of 34% sedimentary intact polar caldarchaeol is likely produced by benthic archaea. Two independent isotope mass balance calculations suggested that on average 35% and 18% of CL-caldarchaeol are derived from IPL degradation in sediment. In addition to the analysis of environmental samples, laboratory-based SIP provides us another distinct perspective to understand the microbial-mediated processes in marine sediments, for example, anaerobic oxidation of methane (AOM). Their enrichment cultures have been increasingly purified but still contain additional community members, even after years of repeated dilution and inoculation. In order to investigate the potential heterotrophic activity of the microorganisms coexisting with AOM consortia, I performed an L-leucine-3-13C (13C-leu) labeling study on a mesophilic AOM enrichment culture (Chapter V). Our results showed that most 13C-Leu incorporation was observed in bacterial fatty acids, especially iso and anteiso-branched C15:0 and C17:0, but very limited in archaeal ether lipids. Interestingly, these incorporation patterns were independent of the addition of methane to the enrichments, suggesting the ancillary heterotopic bacteria (e.g. Anaerolineae and Spirochaetes) are the main producers of these 13C-labeled lipids rather than AOM consortia. These ancillary heterotopic bacteria probably thrive on the amino acids derived from AOM necromass and likely explain the common absence of AOM lipid signals in sedimentary records. This thesis highlights the presence of various archaeal lipid inputs from terrestrial, planktonic and sedimentary sources into marine sediments. New lipids are continuously produced and degraded by microorganisms in the active subseafloor biosphere. The incubation experiment suggests that heterotrophic bacteria may play a pivotal role in necromass turnover in marine sediments.