Coping with Stress: Exploring the use of RNA-based approaches for the study of soil microbial communities

With the on growing use of RNA based sequencing techniques in molecular ecology, new concerns regarding the effects of different soil homogenization methods on the interpretation of results were raised, since soil bacteria transcriptional regulation is highly sensitive and indicative towards environmental changes. We present the first study addressing the effects of sieving to the structure of the potentially active soil bacterial community and respective gene expression patterns using 16S rRNA gene transcript amplicons and metatranscriptomics. The results show a significant change in the structure of the potential active soil microbial community after sieving. Two distinct microbial behavioral responses (Functional Response Groups or FRGs for short) were respectively characterized in both sieved and non-sieved conditions. FRG1 was dominating in the non-sieved controls and mostly constituted by typical oligotrophic members (K-strategists) such as Deltaproteobacteria, Acidobacteria and Verrucomicrobia. On the other hand, FRG2 was enriched after sieving and presented a significantly higher taxonomical relatedness between its constituent taxa suggesting the presence of active competing opportunists, like the fastgrowing copiotrophic (r-strategists) Actinobacteria, Firmicutes and Alphaproteobacteria, which might be benefiting from nutrient released by aggregate disruption. An astonishing 50% of the mRNA gene transcripts were found to be affiliated to functions significantly altered by sieving, indicating major changes in gene regulation and expression patterns. Sieving resulted in a significant down regulation of niche specific functions and sporulation, in parallel with an up regulation of photosynthesis, diverse carbohydrate metabolism and stress response related transcripts. The effect of sampling time affected approximately 10% of the obtained transcripts