The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4+ pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4+ had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic–anoxic boundary layer regardless of NH4+ addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.