Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems

摘要: Metatranscriptome analysis relates to the transcriptome of microbial communities directly sampled in environment. Accessing mRNA pool natural bacterial presents some technical challenges such as RNA extraction, rRNA depletion, and choice high-throughput sequencing technique. The lack details scientific articles is a major problem correctly obtained from community thus corresponding data. In our study, we present methodological procedure that was developed order access metatranscriptome during two cyanobacterial blooms successively occurring freshwater eutrophic lake. Each step detailed discussed with regard choices difficulties encountered recent literature. Finally, limits for metatranscriptomic approaches targeting environments were (i) removal increase putative reads number after sequencing, (ii) most living environments, reference genomes databases leads non-assignation numerous reads. Once these overcome, managed dominant species, i.e. cyanobacteria (from 6 72 % assigned), surrounding bacteria 1 5 % assigned).