Diatoms and Sandbed

I have about a 2.5 inch sand bed, and the other day when i was cleaning my tank I thought I would really try to clean my sand bed out good. so for the past two water changes i have put my vacuum all the way to the bottom of the sand bed and adjusted the siphoning so that it was pulling a lot of the dirt and leaving the sand... Since I have started doing this i have had big Diatom outbreaks in my sand bed. I am guessing its directly related to the new vacuuming method. My question is should I just really only skim over the top layer of the sandbed when cleaning or should i keep going all the way to the bottom ?



Any suggestions would be nice.



Thanks!