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Eradicate protozoa from the soil? Not really. But once they're through this outbreak, they should be resistant to whatever strains are in your soil for their whole lives, so you likely won't have this problem again with them. It's more a matter of making them strong so they can resist it...

I would definitely treat for cocci right away. It's good that they're still active; that just means that they shouldn't have too hard a time getting through this.