Conclusions
Here we have shown that eRNA shotgun sequencing is a useful tool to study the biodiversity of benthic microeukaryotes. The latest sequencing technology yields tens of million sequences per sample and this makes it possible to investigate the biodiversity of multiple communities. In our study we focused on three microeukaryotic groups (nematodes, forams, and ciliates). We were able to detect a decrease in biodiversity for nematodes and forams in sediments with higher OC, when compared to low OC sediments. Moreover, we detected differences in beta diversity for all three groups between the stations along the OC gradient, as well as in the functional ecology of nematodes (i.e. feeding type). Considering that future sequencing technologies are likely to develop and decrease in cost, shotgun sequencing of eRNA to assess biodiversity of alive benthic microeukaryotes could be a useful method in recurring monitoring programmes. Taken together, eRNA shotgun sequencing and new bioinformatic tools give the opportunity to study a large diversity of microeukaryotes from bulk sediment samples within a reasonable time frame that was previously not possible.