Why rhizomes are black?

The black layer, which is only a few millimeters thick on the outer surface of the wasabi
rhizome, is the result of an oxidation process that occurs over time and does not affect 
the overall quality of the freshly grated wasabi.

If the rhizome is not fresh, you will notice a white or gray color and an unpleasant 
odor. Therefore, if the wasabi rhizome does not produce an unpleasant odor, it means 
that the rhizome is safe to eat.

The black layer is simply a natural way to protect the rhizome - so it's a good sign! 
The black layer protects the rhizome from the effects of oxygen in the atmosphere.

You can eat a black layer, but you do not have to do it, because freshly grated wasabi
is much more pleasant to eat. The thin black layer can be easily removed with a knife, 
and then go to abrasion.