Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half‐life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half‐life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.
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