How possible is it to annotate and taxonomically assign the RNA of an eukaryotic community?

Question

[a.mailli]

Our project explores the molecular structure and functional diversity of the sea benthos using metatranscriptomics. We have currently extracted the total RNA from our samples without having any prior knowledge of what our samples contain. Considering that most similar reseach has mostly looked at the total sediment community with an emphasis on the prokaryotic constituents, is it possible to annotate and taxonomically assign the whole eukaryotic portion of our samples? If so what workflow would you recommend? Thank you in advance.