Probably not... If we were seeded by aliens, then the message would have had to have been in a very primitive form, so it would necessarily be seen in all living things, including prokaryotes. Unfortunately bacterial genomes are much, much, smaller than humans, so there isn't much room to waste for hidden alien messages. Additionally, presumably, these messages wouldn't be functional, so they would be under any sort of evolutionary pressure. This means that they would likely be mutated or lost to natural selection.

That's not to say that we weren't seeded, just that if we were, any message would likely have been lost. Unless... maybe they seeded mitochondria intact, which are in all (ok, most) eukaryotes. Maybe that might work... :)

Unfortunately, chrM is pretty small too... so no hidden messages there either :(