Lacustrine sediments are excellent archives of past environments while sheltering active microbial populations. However, up to now, microbiological studies in lakes have been confined to surficial sediments with a poor characterization of the evolution of the hosted populations. Microbial biogeochemical cycles can nevertheless induce specific diagenetic changes on primary environmental signals. Determining microbial interactions in these lacustrine sediments is fundamental to clarify the diagenetic impact of microbes in both the sedimentary organic matter and the mineral fraction. The multidisciplinary approach developed in this thesis clearly indicates a link between initial environmental conditions and the degree of sediment colonization. Biogeochemistry of methane and fatty acids provided evidence of a microbial imprint on organic proxies in the most colonized intervals as methanogenic populations appear to be stratified in Holocene sediments. The substantial role of microbes could also be demonstrated by the formation of phosphate concretions within Glacial sediments.