Next to carbon dioxide, methane is the most important greenhouse gas which predominantly is released from natural wetlands and rice paddies. Climate change predictions indicate enhanced methane emission from global ecosystems under elevated CO2 and temperature. However, the extent of this positive feedback is far from clear and depends on factors modulating microbial responses of microbes involved in methane cycling in various ecosystems. Nitrogen input by atmospheric deposition or fertilizer additions, is such a factor with a range of possible effects on microbial methane production and consumption. In this paper we discuss the crucial lacks in knowledge preventing a better understanding and predictions of climate change effects on global methane emissions.