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Background  The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.    Results  The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes.  Methanosaeta  was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation.    Conclusions  This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-016-0652-5) contains supplementary material, which is available to authorized users.

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion