Dismantle the lens, lens cleaning solution and put it under a UV light for 24 hours to ensure the fungus is dead.
Unfortunately fungal spores are everywhere so you cannot avoid them but storing your gear in dry conditions is the best way to avoid it affecting your lenses. I always have a couple of sachets of silica gel in my camera bags just in case and I have yet to have had a lens suffer from fungal growth.
Last summer I actually dismantled a friends lens (well, removed the front element) to clean the beginning of fungus growth and last I asked there had been no return.
If the lens is valuable enough to you take it down to your local camera shop and ask their advice.