From short-lived to persistent: the significance of extracellular RNA in disinfected drinking water microbiomes

To assure the safe distribution of drinking water, it is critical to identify and limit adaptations that allow microorganisms to thrive in an oligotrophic system under disinfectant stress. Microbial adaptive responses are determined using RNA–based differential transcriptomics, which cannot be performed in environmental settings due to a lack of a baseline. This study introduces the concept of using extracellular RNA (eRNA) as a reference to determine important adaptive features in the disinfected drinking water microbiome. Using this method, we determined energy efficiency, dynamic membrane composition, oxidative stress response, and proper protein folding to be extremely important for survival in drinking water systems. Additionally, multiple antibiotic resistance genes are expressed and upregulated in the intracellular RNA fraction, indicating selection pressure. Non-coding RNA and transfer-messenger RNA found in eRNA suggest important regulatory functions. This study advances our understanding of eRNA in drinking water microbiomes and provides a framework for exploration in other environmental systems.