I am not sure about Berlin but there is a big aerobiological group working in Münich, you can try getting into contact with either Jose Oteros or Jeroen T.M. Buters for more information about the german pollen monitoring network.
There was one in Berlin at the Naturkunde Museum (NMH), but I don't know if its still running. I have processed palyno samples in my own HF lab in Oslo for a PhD student in Berlin who I co-supervise. Maybe this is an option for you too.
He is working in the Freie Universität Berlin and as far as I know his work includes pollen analyses and climate reconstruction. May he can help you out.
I am a PhD in Berlin working on Mesozoic Palynology with Wolfram Kürschner and has he said already, there was one at the Natural History Museum which is closed at the moment (or better say not reopen yet after renovation - you might have heard how things go here, no one ever intended to open an airport ;) so I cannot tell when that one is going to reopen, but its planned.
As far as I hear there is one plans to built an HF lab in Pavel's lab (Freie Universität Berlin) (as mentioned above) (once he answers I am sure you'll hear more) but I don't know how far things have proceeded. There is also Eckhardt Schrank at the TU - Technische Universität who works with pollen who might be someone to ask.
Other wise the commercial organisations like the Pollen-informationsdienst also mentioned above are a possibility depending on your material, how old it is and what kind of treatment you intend (i.e. whether it needs to be an HF lab or not). So other labs (abroad to treat your material might be a good option - that's how I do it). Hope that helps!