Recent advances in the application of molecular genetic approaches have emphasized our potentially huge underestimate of microbial diversity in a range of natural environments(1). These approaches, however, give no direct information about the biogeochemical processes in which microorganisms are active(2). Here we describe an approach to directly link specific environmental microbial processes with the organisms involved, based on the stable-carbon-isotope labelling of individual lipid biomarkers. We demonstrate this approach in aquatic sediments and provide evidence for the identity of the bacteria involved in two important biogeochemical processes : sulphate reduction coupled to acetate oxidation in estuarine and brackish sediments(3,4), and methane oxidation in a freshwater sediment(5). Our results suggest that acetate added in a C-13-labelled form was predominantly consumed by sulphate-reducing bacteria similar to the Gram-positive Desulfotomaculum acetoxidans and not by a population of the more widely studied Gram-negative Desulfobacter spp. Furthermore, C-13-methane labelling experiments suggest that type I methanotrophic bacteria dominate methane oxidation at the freshwater site.