We hypothesized that soil history in terms of i) water management, ii) type of cultivation and iii) duration of flooding affects the microbial community composition, which requires an adaptation period in the response to new management practices. Laboratory approaches are useful to understand soil processes because the controlled conditions allow us to analyze responses that can otherwise be masked by the high level of heterogeneity and variability encountered in the field (Schaufler et al., 2010). However, soil storage and conditioning procedures may strongly affect results, through physico-chemical and microbiological changes. In order to reduce possible artifacts, soil microbial activity is usually determined in fresh samples . Nevertheless, air-drying is preferred for practical reasons allowing soil to be stable during storage with minimum cost and may significantly reduce variability among soil samples collected at different moisture content (Haney et al., 2004). Air drying and sieving can cause a temporary increase of mineralization of organic matter released from broken soil aggregates. Moreover, rewetting of air-dried soil causes slaking, i.e. increased breakdown of soil aggregates, which leads to a release of mineralizable organic matter. Thus, the comparison of different preparation methods for soil samples can provide specific information on processes affecting GHG emissions. To assess the influence of soil management on N2O and CH4 potential production, four soils with different history of water management were compared, using three different soil conditioning procedures. The objectives of this study were to i) assess the influence of water management history on GHG production potential and microbial community structure, ii) relate the microbial communities inhabiting the different soils to CH4 and N2O production and iii) determine the influence of different soil conditioning procedures on GHG production measurement. By means of ad hoc laboratory approach, the work aimed to present a comprehensive view of the interactions among GHG production, microorganisms involved and past management. The effect of past water management systems in rice paddies on the CH4 and N2O producers adaptation and consequent GHG production has rarely been addressed, as present literature mainly focuses on seasonal dynamics .