ehh try some airstones maybe, that might help. the oxygen from the airstones will help with their breathing
what i do for the beneficial bacteria (though many people recomend against this) is put my airstone inside the actual filter part for a little while, this helps the anaerobic bacteria build up, but while it is in the filter, it wont clear the water up, it will have lots of small bubbes in it. after a day or two take it out.
also try changing your carbon (the black rocks)
glad i could help