However, in general N2O emissions are very low in permanently flooded rice paddies due to inhibited nitrification and usage of ammonium rather than nitrate based fertilizers, whereas peaks occur during alternate wetting and drying or midseason drainage . The water management system under which rice is grown is therefore one of the most important factors affecting the respective magnitudes of CH4 and N2O emissions. Field drainage, while significantly reducing CH4, may actually increase N2O emissions under conditions promoting nitrification and denitrification . Therefore, effects of water management techniques on emissions need to be better understood for developing climate-friendly management techniques for rice production. For example, water management may strongly affect microbial communities present in the soil and thereby C and N cycling processes and their impact on field-scale GHG emissions. Moreover, in the case of rice paddies, previous land use may strongly affect GHG fluxes and the relative importance of CH4 with respect to other gases. Several authors reported delayed or minor CH4 emissions when paddy fields were previously managed under aerobic conditions. Even if methanogen communities can persist in soil during dry periods (Angel et al., 2011), a full development of methanogen communities appears to require a certain amount of time . However, as indicated by Watanabe et al. (2011) the ecology of methanogens in soil under non-flooded condition is still not fully understood. Even less is known about nitrifier/denitrifier communities in soils under different water regimes and crops cultivation. The present manuscript therefore intends to cover this knowledge gap by specifically focusing on the impact of past management on GHG production and soil microbial communities in anoxic environments. To our knowledge no other articles specifically approached this topic on rice paddies, even if legacy effects of past management have been regarded as important for mitigating GHG emissions in croplands (Ogle et al., 2014) and microbial community composition .