Low gap between tires and rear fender
 

So I have 18" rims with low profile tires and a really heavy sub in the trunk. There is barely any gap between the tires and the rear fender and I can hear a noise when there is someone sitting in the back or when I go over a pothole. Is this bad? what's the best thing to do? I'm considering taking out the sub to see if that helps, what do you think? And is it bad for your suspensions if you have a heavy sub (300 pounds) in the trunk?
Thanks a lot guys