Recent studies suggest that freshwater ecosystems are the primary source of atmospheric methane which is 25-times more effective than carbon dioxide as a greenhouse gas. This estimation, however, could be biased because methane emission from tropical and subtropical lakes is still unknown. Methane oxidizing bacteria (MOB) which assimilate dissolved methane aerobically or anaerobically have great impacts on methane cycling in lake ecosystems. Methanotrophic food webs (MFWs), in which methane-derived carbon is trophically transferred through the MOB and embedded within a food web, serve as a carbon recycling unit in lake ecosystems. The understanding of controlling mechanisms for the MFWs therefore will help us to estimate global methane flux with accuracy. In boreal and temperate lakes, ecology, physiology and phylogeny of the MOB are well studied, whereas there is limited knowledge on those in sub-tropical and tropical lakes. Here we introduce our international research collaboration to conduct the long-term monitoring for MFWs in Fei-Tsui Reservoir (FTR), Taipei, which is characteristic of both sub-tropical and tropical lakes, depending on climate condition.