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.