Airline Baggage Regulation for Bikes:
http://www.ibike.org/encouragement/travel/bagregs.htm
Yes, there will be an additional fee ... and what they say on the website may or may not be the amount they actually charge you. It depends on the airline, the airport, who your airline actually uses to make the flight to Berlin (they could be in partnership with a different airline for flights across the Atlantic), and most importantly, the person behind the counter when you are checking in.

On my flight to Europe this past summer, I was charged $50 on the way out by a very apologetic and sympathetic lady, and quite a bit more on the way back by one who didn't care ... she was following the rules to the letter.

Where are you planning to use the train? Amtrak in California? Your bicycle should be fine in a cardboard box ... in fact they were very courteous and helpful with me and my bicycle.