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All day I have been scrubbing, and looking for the source of the oder in my guest bathroom. Tonight I found that the water in the tank is dark, almost black and underneath the tank there is a black mold growing --about the area of a quarter that I can wipe off but I can see that it is moldy between the tank and the toilet. Any suggestions?

It sounds like the water is stagnant from the guest bath not being used. Just clean the visible mold and flush the toilet occasionally. I'm not a fan of those inside-the-tank chemicals but a small splash of liquid bleach added to the tank will keep the water fresher longer. I doubt if that is the source of the odor though. If the bath has been sitting unused then it is likely that the water has evaporated from the sink and or tub traps, letting in sewage gases. Run some water in both of those and let the room air out and see if that helps.

Spray with bleach or any bath cleaner with mold cleaner in it. Take a bottle brush to scrub between the space.
The reason for this is condensate on the tank. It gets wet during the times when the cold water enters into the tank and the warm are inside the house condenses on the walls. Dust that collects on the bottom of the tank then mold grows this dust. If you keep the tank clean, mold will not grow on the porcelain surface.
You can purchase chlorine tabs to use in the tank that should help the tank inside from getting black.