It depends on what sort of communication you are thinking of. Each PDM vault has its own separate SQL database, recording the history of each file, metadata, user information, etc. From a software perspective, each vault is a completely separate entity.
If you have different departments both needing PDM, and they're never ever going to share information, then you could have separate vaults.
Otherwise you can have one vault, but with multiple sections, and different sets of permissions applied to each section.
Hope this makes sense.
As an example of what Prasad said. We had two completely separate groups, one was on the East Coast and made hospital EKG machines, the other is on the west coast and makes consumer level difibulators. They never talked to each other or shared designs so they had separate vaults.
Then one day out of the blue the East coast group was shut down and the West coast one took over all their designs. Now the West coast group has two vaults with no capability to link the two or migrate one into the other.
If you know that the groups will share data in any way make one vault with multiple workflows/permission schemes.