In a changing environment, communities have to adapt continuously to survive. When microbial communities are chronically exposed to stress, adaptive mechanisms render them more tolerant. Yet a mechanistic understanding of differential adaptation processes to stress at a molecular level is lacking. Transcriptomics is a relevant methodology to tackle this challenge because it provides comprehensive functional information at molecular level. However, it was rarely applied for discriminating adaptive processes in communities differing in their exposure history and leading to community tolerance acquisition. Our study contributed to understanding acute stress responses of microbial communities differing in chronic pre-exposure to the photosynthesis inhibitor diuron, combining untargeted meta-transcriptomics (RNA-seq) and dose-response design. Freshwater microbial communities were incubated for 5-weeks in microcosms 1/ under constant exposure to 4μg/L diuron (stressed community) or 2/ without contamination (non-stressed community). Afterwards, both communities were exposed for 1 hour to a diuron concentration gradient to investigate differences in stress responses after chronic exposure. The meta-transcriptome analysis was handled by the DRomics R package, which provides a workflow dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of three replicates). This experimental design and the DRomics workflow enabled the determination of response trends as well as sensitivity thresholds for thousands of contigs and an accurate selection of responsive contigs within a dataset of more than three million contigs. Among the numerous responsive cellular processes, clear differences in gene expression and sensitivity were especially observed between both communities for photosynthesis-related processes. However, processes related to the carbon metabolism like fatty acid, lipid or glycolytic processes displayed impairment in both cases. In conclusion, meta-transcriptomics applied in a dose-response design provided key mechanistic insights for the understanding of adaptive processes and tolerance acquisition on environmental communities.