Can bacteria be reservoirs for animal viruses?
The Answer is No

There are no examples of animal viruses infecting bacteria or incorporating themselves into bacterial genomes. Nor is it a theoretical possibility, given our knowledge of bacteria, eukaryotes, eukaryotic viruses and bacteriophages.

Why is it not a possibility?

As the questioner admits, the replication, transcription and translational systems of eukaryotes and prokaryotes are quite different. None of the known viral genomes could replicate and their genes be expressed in cells of the other kingdom. Why, the questioner may ask, could not a virus evolve to have signals recognized in both types of cell — at least in theory. Perhaps it could, but there is another factor to be considered, and this is the question of how viruses interact with the cells they infect. This is relevant to how other species can harbour human viruses and why there would be nothing driving a virus to acquire the means to replicated and be expressed in both system.

Receptors for Viruses on Host Cells

The point the question fails to take into account is that entry of both eukaryotic and bacterial viruses is a specific process involving interaction between protein or carbohydrate components of the virus and those in the membrane of the host cell. The host components are called virus receptors, and generally differ for different viruses. There are many reviews of this topic in the literature, so I cite a couple of examples freely available on the internet: Grove and Marsh on animal viruses and Rakhuba et al. on bacteriophages.

Viruses evolve to exploit one particular host species, and tend to be specific to that species because, although there may be a functionally similar protein in other species, differences in amino acids in the proteins (or sugars in carbohydrates) preclude recognition. When viruses cross the species barrier, this is due to mutations that allow recognition of the receptor protein in another species. If the change still permits recognition of the receptor in the original species then even if the virus is eliminated from the second (e.g. human species) it will still be present in the original species. Subsequent contact between humans and the species can therefore lead to a reappearance of the virus in humans.

This is how the original species acts as a reservoir. There is no question of a virus ‘hiding’ in bats by some sort of evolutionary pressure to allow it to return later to humans. Understanding this you will see that:


The differences between the membranes of bacteria and humans are so great that there is little likelihood of an animal virus finding a receptor on a bacterial cell. 
Even if it managed to do so, it would not be able to replicate in the bacterium.
There is no evolutionary pressure that would select for the series of mutations that could convey the ability for such replication.


Footnote: ‘Dormant’ Viruses

There is another quite different phenomenon in which certain bacterial or animal viruses ‘hide’ within the species they normally cause a lytic infection. This involves incorporation in the genome and later release. In bacteriophages it is called lysogeny and in animal viruses examples include retroviruses and herpes viruses. This has no relevance to the question.