Changes in the (micro-)biome structure and function of two forest sites in the Alps at different elevations and seasons using metatranscriptomics

Forest soils in the Alps play a crucial role in global carbon cycling. Soil (micro-)organisms drive carbon cycling in soils through biogeochemical transformations and predator-prey interactions. These relations are dynamic and depend on environmental factors such as elevation and season. Here we present a quantitative metatranscriptomic study on forest ecosystems, comparing 24 metatranscriptomes of a submontane and a subalpine site in Italy with different vegetation covers (deciduous and coniferous) and seasons (spring and autumn). By parallel analysis of ribosomal RNA and transcribed mRNA, we conducted community composition analysis and linked the putative contribution of different taxonomic groups (rRNA) to different functional processes (mRNA) mainly focusing on carbon-cycling. We studied the presence of bacteria, microeukaryotes and viruses. A seasonal influence on the functional profile (mRNA) was observed showing a change in cellular activity. Among the transcripts encoding decomposition enzymes, the transcripts of Terrabacteria were most abundant and Alveolata and Amoebozoa were detected as potential cellulose and lignin biodegradation contributors. Taxonomic profiles showed only site-specific signatures, with no clear seasonal change. The biggest difference was found within Acidobacteriota which were more abundant at higher elevation whereas predatory protists and predatory bacteria were more abundant at lower elevation. • Quantitative metatranscriptomics reveals structural and functional changes. • Community structure driven by site rather than season • Seasonal changes more pronounced on functional than taxonomic level • Protists' abundance decreases at the higher elevated site and may partake in biodegradation.