about a year ago, I had black tongue. It was pretty much all over the tongue. I went to see a doctor, he prescribed a culture. It came back as yeast infection. The doc told me that when you have systemic Candida Infection , you tend to have localized yeast infections: bladder, throat, etc.
I am not a worshipper of allopathic doctors, but you could have a test done to find out if it's a yeast infection. Or are the bugs coming out the woodwork because of your treatment?