Soil Metatranscriptomes Reveal Microbial Responses to Warming

A total of 16 soil metatranscriptomes, originating from the LTW and the MTW grassland sites sampled in July 2016 [6 (link), 11 (link), 17 (link)], were analysed to test for significant differences in relative community-level rRNA operon copy numbers between non-warmed control soils (A_T) and warmed soils (E_T). Subsamples of 200 000 SSU rRNA reads have been taxonomically classified previously using CREST3 [21 (link)] and a lowest common ancestor approach [6 (link)]. Bacterial reads, which accounted for >99% of all prokaryotic reads, were extracted and further analysed. Mean rRNA operon copy numbers were obtained from the ribosomal RNA operon database (rrnDB) v5.8 (ref. [22 (link)]). For each bacterial read, the lowest assigned taxonomic level with a match in the rrnDB was selected, and copy-number corrected relative abundances were calculated by dividing relative rRNA read abundances of bacterial taxa by their mean rRNA operon copy numbers. Two-sided t-tests were used to test for significant differences in copy-number corrected relative abundances between LTW-A_T and LTW-E_T as well as MTW-A_T and MTW-E_T. Whereas higher copy number corrected relative abundances are indicative for lower relative community-level rRNA operon copy numbers. Subsequently, we estimated community mean rRNA operon copy numbers and tested for significant differences between LTW-A_T and LTW-E_T as well as MTW-A_T and MTW-E_T. Furthermore, the functionally annotated mRNA reads, assigned to metabolic pathways and functional complexes defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology database, of the 16 soil metatranscriptomes [17 (link)] were re-analysed to investigate transcriptional investment in carbohydrate metabolisms and ribosomes.