Microorganisms support complex ecosystems sustainably using sunlight, water, air and minerals through myriad functions as hydrogen oxidation and production, carbon dioxide and nitrogen fixation, methanogenesis and methanotrophy, photosynthesis and more. Recent global changes suggest that Earth has now entered another distinct geological era, the Anthropocene, where we can identify profound impact of humans on the Earth, including the atmosphere, oceans and land. Although freshwaters constitute only about 2,5% of the total Earth water, lakes and other inland waters, aside of being the principal drinking water resources are disproportionally important for the global carbon budget and sensitive indicators for global and regional environmental change. Lakes emit significant amounts of greenhouse gases, in particular methane, a greenhouse gas more that twenty times more potent than carbon dioxide. Total freshwater greenhouse gas emissions are estimated to make up around 22 % of total global methane emissions and around three quarters of all natural emissions. In Croatia, lakes are very vulnerable and subjected to strong environmental and anthropogenic influence. Using the state-of-the-art technologies in the MALENA project we want to understand the microbial significance in methane cycling in the investigated lakes. The results of this multiphasic project will give significant answers for the lake functioning as well the identification of the most significant players in the methane cycling. Finally, we aim to form a group of scientists in microbial ecology of global change, because evidently, solutions to environmental problems and our future require a holistic approach to decision taking, indisputably including knowledge of the role of microorganisms.