I'm going to have to argue against your selected answer.
The problem is, just how are yon aliens going to get rid of the nitrogen? You referred to "converting so much nitrogen into nitrates" which suggests that this is what you had in mind. So the N2 molecules get converted to NO3 ions, right? Mmm, no. In fixing the nitrogen you deplete the atmosphere of much more oxygen than you do nitrogen, specifically 3 times as much. So, since the earth's atmosphere is (roughly) 80% nitrogen and 20% oxygen, when about 8.3% of the 80% has been converted to NO3, ALL of the oxygen will be used up.
The other alternative, ammonia, is much worse. Ammonia, NH4, takes 4 times as much hydrogen as nitrogen, and since the total free hydrogen in the atmosphere is only 55 parts per million (by volume, not weight) there's just not a lot of leverage you can get.
Of course, if the aliens are examples of Clarke's Law ("Any sufficiently advanced technology is indistinguishable from magic), They can get around this by transmuting about 3/8 of the nitrogen to oxygen, binding it to 1/8 of the nitrogen, and thereby nitrify 1/2 of the total nitrogen.
Is this a good idea? I'd suggest not. Let's ignore the energy release caused by converting oxygen to nitrogen - those aliens are really good at the "indistinguishable from magic" part. If we're not willing to overlook this, the surface of the earth turns into crispy critters, and this is generally considered to be A Bad Thing.
NO3 is the standard measure of nitrogen in fertilizers, and dumping this much nitrate into the soil would constitute (essentially) massive overfertilization and would quickly kill most plants. The NO3 produced accounts for about half of the total atmosphere, and atmospheric pressure is 15 lb/sq in, so the total NO3 will amount to about 7 pounds per square inch, which is far beyond anything we have experience with. For a somewhat specialized perspective, see http://www.growweedeasy.com/nitrogen-toxicity-cannabis. About 70% of this nitrate would be directly deposited in the oceans, and water runoff would contain extraordinarily high levels of nitrogen, and this would quickly produce algal blooms in the world's oceans which would deplete the oxygen levels and kill off all surface fish, followed more slowly by the deeper species as the oxygen depletion worked its way downwards. The local, surface version of this phenomenon is already seen in places like the Gulf of Mexico, where fertizer runoff from farms along the Mississippi River cause "dead zones". Of course, this assumes that the nitrate levels would not directly kill the existing algae (not a good assumption, IMO, but I'm not an expert in the field).
With all due respect, this is a good example of the principle that you should wait at least 24 hours before selecting an answer.