Then, in that case, what separates pithovius from the prokaryotes?
Structure, from the sound of it, although mostly this is people committing various fallacies of reification and making false claims of "natural kinds".
Everything is a continuum. Humans divide the continuum up using acts of selective attention. The only infinitely sharp edge is the edge of our attention (because we scale the edge to match the scale we are attending to, so whatever scale we are attending to seems to have a sharp division between the things we are selecting out.)
"Species" do not have particularly crisp boundaries in the general case: they fade into each other, and we draw edges around them in more-or-less arbitrary ways. When we find new varieties we can either create new categories (by drawing new edges) or lump them into old categories (by moving old edges). Which move is to be preferred depends on the purposes of the knowing subject.