Aquatic foodwebs can be fueled by photosynthetically produced organic matter (terrestrial or aquatic), or by chemo-autotrophic or methane (CH4)-based metabolic pathways. While CH4 production is generally much lower in estuarine and coastal systems than in freshwater sediments, the opposite holds for chemo-autotrophic pathways. While both the production and consumption of methane are known to be important to consumers in specific environments, their role in more ‘egular’benthic (= sedimentary) habitats remains largely unexplored, in particular for small but very abundant invertebrate communities. We speculate they are more ubiquitous than previously considered and will quantify their contribution to benthic foodwebs across tropical aquatic habitats in the Lake Edward region (Uganda) and the Gazi Bay area (Kenya), using a two-track approach: (a) we will use natural stable isotopes as chemical tracers of CH4 and CO2 into invertebrate consumers, and (b) we will perform specific tracer incubation experiments to quantify the importance of the different C flows in foodwebs. Finally, we will explore possible symbiotic relationships with microbiomes in meiofauna using state-of-the-art approaches (NanoSIMS and deep-sequencing).