It's black mold spores and fungi spores. So, part of the reclamation filtration needs to filter down to 5 microns or less.
Yeah, I've noticed mold spores would form in the collection bucket when I was manually dumping it on a daily basis. However, in the previous fish room we had done the above re-circulation process with no faults (no copper coils, obviously..) and the black molds spores failed to formulate when the water was consistantly flowed through the collection bucket. Perhaps the standing water (from when the collection bucket would become full, and the unit would shut off.) is a more viable environment for the spores?
I am not nearly as scientifically versed as you, do you have any links so I can read up about 'microns'.. ?