Forget AUTO!!!!
If you want to learn shooting with the D90 (or any D-SLR) get out of AUTO-Mode.
Learn about the relation between ISO, shutter speeds and aperture. Once you master those 3 things you'll be a much happier person.
First: Increasing ISO to the highest possible is not recommended IMHO as you will create more noise than necessary BUT that depends on what you shoot!
For example if you shoot a skyline at night there is no need whatsoever to shoot at 1600 ISO. Leave it 200 but reduce shutter speeds to maybe 1 or 2 seconds. Shutter speeds and aperture settings depend on the overall light which is in your scene.
Second: Different aperture does interesting things when shooting lights. It can create great effects when using f22 instead of f5.6.
However, you will get much shorter exposure times if you shoot with f5.6 in case you need to capture walking people. Those would be recognizable as people but blurry. If you use f22 in the same sceen with people walking by, your shutter speeds would be so slow that you couldn't even tell that somebody walked through the frame.
This is a learning curve. Play with the settings and write them down to compare the results later.
In AUTO mode the camera does the thinking for you and adjust the settings,, well AUTOmatically. Like I said, shooting at night should be done manually to get best results and you're not going to learn anything when shooting in AUTO.