Methane emissions from aquatic and terrestrial ecosystems play a crucial role in global warming, which is particularly affecting high-latitude ecosystems. As major contributors to methane emissions in natural environments, the microbial communities involved in methane production and oxidation deserve a special attention. Microbial diversity and activity are expected to be strongly affected by the already observed (and further predicted) temperature increase in high-latitude ecosystems, eventually resulting in disrupted feedback methane emissions. The METHANOBASE project has been designed to investigate the intricate relations between microbial diversity and methane emissions in Arctic, Subarctic and Subantarctic ecosystems, under natural (baseline) conditions and in response to simulated temperature increments. To achieve this highly challenging purpose, the METHANOBASE project relies on the use of state of the art molecular tools and on a pluridisciplinary team including experts from Europe (France, Belgium, Norway) and South America (Chile, Uruguay), as well as local partners in Siberia, Alaska and Patagonia for field expedition support.